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Advancing Disease Modeling in Animal-Based Research in Support of Precision Medicine: Proceedings of a...
Erin Hammers Forstag and Lida Anestidou, Rapporteurs
Roundtable on Science and Welfare in Laboratory Animal Use
Institute for Laboratory Animal Research
Division on Earth and Life Studies
Copyright National Academy of Sciences. All rights reserved.

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This project was supported by the American Veterinary Medical Association; Baylor
College of Medicine; Emory University; Genentech; GlaxoSmithKline; Indiana Uni-
versity; Johns Hopkins University; Johnson & Johnson; Massachusetts General Hos-
pital; Massachusetts Institute of Technology; Medical College of Wisconsin; Merck
and Co., Inc.; National Institutes of Health (Contract No. HHSN263201200074I;
Task Order HHSN26300122); National Primate Research Centers; Novartis; Uni-
versity of California, Davis; University of Miami; University of Michigan; University
of Pittsburgh; and Yale University. Funding for this conference was made pos-
sible, in part, by the U.S. Food and Drug Administration through grant 5 R13 FD
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2018. Advancing Disease Modeling in Animal-Based Research in Support of Preci-
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PLANNING COMMITTEE ON ADVANCING DISEASE

MODELING IN ANIMAL-BASED RESEARCH IN SUPPORT
OF PRECISION MEDICINE: A WORKSHOP
Members
Brian R. Berridge, GlaxoSmithKline (Co-Chair)
K.C. Kent Lloyd, University of California, Davis (Co-Chair)
Cory Brayton, Johns Hopkins University
Robert M. Califf, Duke University School of Medicine
Melissa Haendel, Oregon Health & Science University
John P.A. Ioannidis, Stanford University

ROUNDTABLE ON SCIENCE AND WELFARE

IN LABORATORY ANIMAL USE
Co-Chairs
Robert C. Dysko, University of Michigan Medical School
K.C. Kent Lloyd, University of California, Davis
Liaison to ILAR Council

Paul A. Locke, Johns Hopkins Bloomberg School of Public Health
Members
Jill Ascher, U.S. Food and Drug Administration
Szczepan Baran, Novartis Institutes for Biomedical Research, Inc.
Bonnie V. Beaver, Texas A&M University
Cindy Buckmaster, Baylor College of Medicine
Saverio (Buddy) Capuano III, University of Wisconsin–Madison
Carol Clarke, U.S. Department of Agriculture
Michael DuVall, Janssen Pharmaceuticals
James G. Fox, Massachusetts Institute of Technology
Alema Galijatovic-Idrizbegovic, Merck & Co., Inc.
Gail C. Golab, American Veterinary Medical Association
Debra L. Hickman, Indiana University School of Medicine
Michael Huerkamp, Emory University
Donna Matthews Jarrell, Massachusetts General Hospital
Bruce W. Kennedy, Chapman University
David M. Kurtz, National Institute of Environmental Health Sciences
Margaret S. Landi, GlaxoSmithKline
Joseph T. Newsome, University of Pittsburgh
Patricia Preisig, Yale University
Edda (Floh) Thiels, National Science Foundation
Joseph Thulin, Medical College of Wisconsin
Rhonda J. Wiler, Genentech
Axel Wolff, National Institutes of Health
Robert H. Wurtz, National Institutes of Health
Julia Zaias, University of Miami
vi

Staff
Lida Anestidou, Director, Roundtable on Science and Welfare in
Laboratory Animal Use
Angela Kolesnikova, Senior Program Assistant, Board on Life Sciences
Jenna Ogilvie, Research Associate, Board on Life Sciences (until
November 27, 2017)
Consultant
Erin Hammers Forstag, Writer
vii

INSTITUTE FOR LABORATORY ANIMAL RESEARCH
Members
Margaret S. Landi, Chief of Animal Welfare, Ethics and Strategy,
GlaxoSmithKline (Chair)
Karin Blumer, Scientific Affairs, Novartis International AG
Cory Brayton, Associate Professor of Molecular and Comparative
Pathobiology, Johns Hopkins University
Joseph J. DeGeorge, Global Head of Safety Assessment and Laboratory
Animal Resources, Merck Research Laboratories
Michael DuVall, Scientific Director, Head of Toxicology and Laboratory
Animal Medicine, Johnson and Johnson, Janssen Pharmaceuticals
Lewis B. Kinter, Independent Consultant
Paul A. Locke, Associate Professor, Department of Environmental Health
and Engineering Director, DrPH Program in Environmental Health
Sciences, Johns Hopkins Bloomberg School of Public Health
Daniel S. Marsman, Head, Safety and Regulatory Affairs, Procter &
Gamble Health Care
Melinda A. Novak, Professor of Psychology, University of Massachusetts
James A. Roth, Clarence Hartley Covault Distinguished Professor,
Director, Center for Food Security and Public Health, College of
Veterinary Medicine, Iowa State University
Lawrence B. Schook, Edward William and Jane Marr Gutsgell
Professor of Animal Sciences and Radiology, University of Illinois at
Urbana-Champaign
Robert S. Sikes, Professor of Biology, University of Arkansas at Little
Rock
Staff
Gregory Symmes, Interim Director (from November 1, 2017)
Dorothy Zolandz, Interim Director (until October 31, 2017)
Lida Anestidou, Senior Program Officer
viii

Acknowledgments
This Proceedings of a Workshop was reviewed in draft form by indi-

viduals chosen for their diverse perspectives and technical expertise. The
purpose of this independent review is to provide candid and critical com-
ments that will assist the National Academies of Sciences, Engineering, and
Medicine in making each published proceedings as sound as possible and
to ensure that it meets the institutional standards for quality, objectivity,
evidence, and responsiveness to the charge. The review comments and draft
manuscript remain confidential to protect the integrity of the process.
We thank the following individuals for their review of this proceedings:
Mary E. Dickinson, Baylor College of Medicine

Alema Galijatovic-Idrizbegovic, Merck & Co., Inc.
Charles L. Sawyers, Memorial Sloan Kettering Cancer Center
Joe V. Selby, Patient-Centered Outcomes Research Institute
Although the reviewers listed above provided many constructive com-

ments and suggestions, they were not asked to endorse the content of the
proceedings nor did they see the final draft before its release. The review
of this proceedings was overseen by Huda Akil, University of Michigan
Medical School. She was responsible for making certain that an indepen-
dent examination of this proceedings was carried out in accordance with
standards of the National Academies and that all review comments were
carefully considered. Responsibility for the final content rests entirely with
the rapporteurs and the National Academies.
ix

x ACKNOWLEDGMENTS
The support of the Roundtable on Science and Welfare in Laboratory

Animal Use was vital to the planning and conduct of the workshop on
Advancing Disease Modeling in Animal-Based Research in Support of Preci-
sion Medicine. Federal sponsors are the National Institutes of Health, the
National Science Foundation, and the U.S. Food and Drug Administration.
Nonfederal sponsorship was provided by the American Veterinary Medical
Association; Baylor College of Medicine; Emory University; Genentech;
GlaxoSmithKline; Indiana University; Johns Hopkins University; Johnson
& Johnson; Massachusetts General Hospital; Massachusetts Institute of
Technology; Medical College of Wisconsin; Merck and Co., Inc.; National
Primate Research Centers; Novartis; University of California, Davis;
University of Miami; University of Michigan; University of Pittsburgh; and
Yale University.
The Roundtable on Science and Welfare in Laboratory Animal Use
expresses deep gratitude to the members of the planning committee for de-
veloping an expansive and multifaceted workshop agenda and to the expert
speakers who took part in the workshop’s discussions.

Contents
1 INTRODUCTION TO PRECISION MEDICINE AND

ANIMAL MODELS 1
Introduction, 2
Organization of This Proceedings of a Workshop, 3
What Is Precision Medicine and How Did We Get Here?, 4
Regulation of Precision Medicine, 6
Ethical Considerations of Animal-Based Research, 9
Gene–Environment, 11
Gene–Lifestyle, 12
Longitudinal Data, 12
Bioethics, Public Opinion, and Community Advisory Boards, 12
2 EXISTING PRECISION MEDICINE INITIATIVES 16

United States: All of Us, 16
United Kingdom: 100,000 Genomes, 18
France: The French Plan for Genomic Medicine, 20
Japan: Initiative on Rare and Undiagnosed Diseases, 22
World Economic Forum: Center for the Fourth Industrial
Revolution, 23
3 THE PROMISE AND PERILS OF ANIMAL MODELS 26

Mouse Models, 27
Introduction to Model Organisms, 27
International Mouse Phenotyping Consortium, 29
xi

xii CONTENTS
Essential Genes, 30
Precision Mouse Models, 32
Unique Animal-Based Approaches, 36
Opossum, 36
Precision Pathology, 37
Mouse Hospital Co-Clinical Trials, 40
Pets with Naturally Occurring Tumors, 43
Challenges of Using Animal Models for Precision Medicine, 46
Big Data, 46
The Animal Rule and Appropriate Modeling, 48
4 REPRODUCIBILITY AND PREDICTIVITY 51

Translational Stroke Research: The “Worst Practices” of
Animal Research, 52
Systematic Reviews, 53
Reproducibility in Large Shared Datasets, 56
The Paradoxes of Precision Medicine, 58
5 IN VITRO ALTERNATIVES TO ANIMAL MODELS 61

iPSCs to Model Chemotherapy-Induced Cardiotoxicity, 61
In Vitro Cardiac Disease Models, 63
Human Microphysiological Systems, 64
Organ-on-a-Chip, 65
Organoids, 65
Quantitative Systems Pharmacology and Microphysiological
Systems, 66
Human Microphysiological Systems, 67
6 ASSESSING SAFETY AND TOXICOLOGY 69

Patient Susceptibilities in Preclinical Drug Safety Assessment, 69
Next-Generation Vivaria, 71
Alternative Models, 71
Co-expressed Gene Network Analysis as a Bridge for
Extrapolation Between Species, 71
Using Genetically Diverse Mice to Test Susceptibility to Toxins, 74
To Identify Specific Polymorphisms Associated with
Xenobiotic Toxicity, 75
To Evaluate Biomarker Performance Toward Assessing
Human Clinical Adverse Outcomes, 76
As a Tool for Population-Based Estimates of Chemical Potency
for Risk Assessment, 76
Integrating Evidence from Animal and Human Studies, 76

CONTENTS xiii
7 PATIENT PERSPECTIVES 82
Personalized Medicine Coalition, 82
Parkinson’s Disease, 84
8 REFLECTIONS ON THE WORKSHOP 87
REFERENCES 90
APPENDIXES
A AGENDA 95
B PLANNING COMMITTEE BIOGRAPHIES 103
C SPEAKER BIOGRAPHIES 108
BOX
1-1 Statement of Task, 3
FIGURES
1-1 Building a knowledge network, 5
3-1 Genetic background of mouse models, 34

3-2 Idealized mouse models, 35
3-3 Co-clinical mouse trials for cancer, 42
3-4 Comparative oncology with dogs, 44
6-1 Founder strains of Diversity Outbred mice, 75

6-2 Individual epidemiological study ratings, 78
6-3 Across study evaluations, 79
6-4 Table to summarize evidence synthesis and integration
judgments, 80


Introduction to Precision
Medicine and Animal Models
Key points:
• “The First Law of Technology says we invariably overestimate
the short-term impact of a truly transformational discovery,
while underestimating its longer-term effects.”
• Ultimately, all medicine is personalized—everyone has their
own disease. (Valle)
• It is important to talk about the ethical issues before a technol-
ogy is diffused, not after. (Heitman)
• The key to improving dialogue and engendering trust is com-
munity engagement. (Sharp)
o familiarize the audience with the concept of precision medi-

T
cine, the workshop began with the historical context and roots
of precision medicine, followed by an overview of the regulatory
framework as it relates to precision medicine. In both the opening
and penultimate sessions, ethical discourse regarding the use and
welfare of laboratory animals, public opinion, and involvement of
communities as precision medicine unfolds anchored the sessions.

2 ADVANCING DISEASE MODELING IN ANIMAL-BASED RESEARCH
INTRODUCTION
Precision medicine is focused on the individual and will require the
rapid and accurate identification and prioritization of causative factors
of disease, said Kent Lloyd, professor and director of the Mouse Biol-
ogy Program at University of California, Davis, and the co-chair of the
National Academies of Sciences, Engineering, and Medicine’s Institute for
Laboratory Animal Research (ILAR) Roundtable on Science and Welfare
in Laboratory Animal Use. To move forward and accelerate the delivery of
the anticipated benefits of precision medicine, he said, developing predict-
able, reproducible, and reliable animal models will be essential. In order
to explore the topic of animal-based research and its relevance to precision
medicine, the Roundtable on Science and Welfare in Laboratory Animal
Use, with support from the Office of Research Infrastructure Programs at
the National Institutes of Health, convened a 2-day workshop on October
5 and 6, 2017.
The idea for the workshop, Lloyd said, stemmed from an editorial that
he, Peter Robinson, and Calum MacRae wrote in Science Translational
Medicine in 2016 (Lloyd et al., 2016). The editorial, “Animal-based studies
will be essential for precision medicine,” included four principles of animal
modeling and precision medicine:
• Animal models must reflect -omic variation in patients in order

to define downstream functional consequences and discriminate
causal from correlative factors at relative efficiency.
• Animal models can effectively link -omic data with environmental,
behavioral, and lifestyle information to identify actionable findings.
• Animal models can provide quick and accurate assessment of the sci-
entific validity and clinical utility of gene–environment correlations.
• The incorporation of computational reasoning and semantic map-
ping efforts will be critical for enabling cross-species phenotype
comparisons and maximizing the potential of patient data.
Expanding on these four ideas, this workshop was designed to focus

on the development, implementation, and interpretation of model organ-
isms to advance and accelerate the field of precision medicine. In particu-
lar, the workshop looked at the extent to which next-generation animal
models, designed using patient data and phenotyping platforms targeted to
reveal and inform disease mechanisms, will be essential to the successful
implementation of precision medicine. The full Statement of Task for the
workshop is in Box 1-1.
This workshop was organized under the auspices of the Roundtable
on Science and Welfare in Laboratory Animal Use. The purpose of the

INTRODUCTION TO PRECISION MEDICINE AND ANIMAL MODELS 3
Box 1-1: Statement of Task
An ad hoc planning committee will plan and conduct a public workshop to

explore the potential of ongoing and future research in animal models with implica-
tions for precision medicine. This workshop will bring together experts on the use
of state-of-the art technologies and technological advances to explore:
• how the design, creation, and analysis of current and next-generation

animal models can inform the practice of precision medicine.
• reproducibility concepts to improve the clinical relevance of animal-based
validation experiments and pre- and co-clinical trials in the context of
precision medicine.
• welfare and regulatory considerations of current and especially next-
generation animal models that would inform the design of targeted, per-
sonalized therapies.
The planning committee will develop the workshop agenda, select and invite
speakers and discussants, and moderate the discussions. An individually au-
thored proceedings of the presentations and discussions at the workshop will be
prepared by a designated rapporteur in accordance with institutional guidelines.
Roundtable, said Lloyd, is to facilitate ongoing discussion and information

exchange on topics of interest to those involved with the science and wel-
fare of laboratory animals. The Roundtable is made up of thought leaders
from academia and the public and private sector, and these workshops
are an opportunity for members and experts to engage in discussion in a
neutral setting that builds trust and promotes problem solving. The hope
is that workshop attendees will be inspired and engaged to share insights
and lessons learned with their colleagues and other stakeholders on these
topics, said Lloyd, and to encourage cross-fertilization and collaboration
between different stakeholders.
ORGANIZATION OF THIS PROCEEDINGS OF A WORKSHOP

The workshop was organized by an independent ad hoc planning com-
mittee, in accordance with the procedures of the National Academies. The
agenda for the workshop is presented in Appendix A, and the biographical
sketches of the planning committee and speakers are presented in Appen-
dixes B and C.
This publication summarizes the presentations and discussions that
occurred throughout the workshop. Chapter 1 presents an overview and

history of precision medicine, the regulatory scheme and challenges for

regulating precision medicine, issues relating to public opinion and commu-
nity involvement, and the ethical considerations involved in animal-based
research. Chapter 2 presents existing precision medicine initiatives, both
in the United States and internationally. Chapter 3 explores the promises
and perils of animal modeling: presenters discussed successes, challenges,
and unique approaches to animal-based research. Chapter 4 covers issues
with reproducibility and predictivity in precision medicine and animal-
based research. Chapter 5 looks at in vitro alternatives to animal models,
including induced pluripotent stem cells (iPSCs) and microphysiological
systems. Presentations that are summarized in Chapter 6 discussed the use
of animal models, and the integration of animal and human data, for safety
and toxicology assessments. Chapter 7 presents two patient perspectives on
precision medicine. Finally, Chapter 8 is a summary of Kent Lloyd’s reflec-
tions on the workshop.1
WHAT IS PRECISION MEDICINE AND HOW DID WE GET HERE?

India Hook-Barnard, director of research strategy at University of
California, San Francisco, opened the workshop with a definition of preci-
sion medicine: “An emerging approach for disease prevention and treatment
that takes into account people’s individual variations in genes, environment,
and lifestyle” (NIH, 2015). This definition was first used by the National
Institutes of Health (NIH) in the announcement of the Precision Medicine
Initiative in 2015, but Hook-Barnard explained that the concept of preci-
sion medicine had begun years earlier. In the 1980s, scientific knowledge
and technology had reached a point at which it became possible to imag-
ine sequencing the entire human genome. In 1988, the National Research
Council published a blueprint for this project, Mapping and Sequencing
the Human Genome, that explored technical, legal, and ethical issues as
well as funding and organizational needs (NRC, 1988). In 2000, President
Bill Clinton announced that the majority of the human genome had been
sequenced, and in February 2001, 90% of the human genome sequence was
published in the journals Nature and Science. Ten years after this achieve-
ment, Francis Collins, director of the National Institutes of Health and
former director of the National Human Genome Research Institute, wrote
a commentary for Scientific American in which he reflected on the progress
1 This Proceedings of a Workshop was prepared by the workshop rapporteurs as a factual
summary of what occurred at the workshop. The planning committee’s role was limited to
planning and convening the workshop. The views contained in the proceedings are those of
individual workshop participants and do not necessarily represent the views of all workshop
participants, the planning committee, or the National Academies of Sciences, Engineering,
and Medicine.

made and the challenges ahead for precision medicine. In this commen-
tary, Collins repeated Amara’s law: “The First Law of Technology says we
invariably overestimate the short-term impact of a truly transformational
discovery, while underestimating its longer-term effects” (Collins, 2010).
In 2011, said Hook-Barnard, the National Research Council released
the report Toward Precision Medicine, which explored the idea of creating
a new taxonomy of disease, based on molecular data and disease mecha-
nisms. The report concluded that “realizing the full promise of precision
medicine . . . requires that researchers and health-care providers have access
to very large sets of health and disease-related data linked to individual
patients” (NRC, 2011, p 7). Hook-Barnard pointed out that the state-
ment of task and the background for that report did not mention precision
medicine by name, but that the committee thought about the issues very
broadly and determined that a new taxonomy of disease would require
these large datasets and linkages to patient data. The report envisioned
an “information commons” structure for health data in which each layer
contains a specific type of information about patients, for example, data
about symptoms, exposures, genome, and microbiome. The information
commons approach would be similar to GIS mapping systems, said Hook-
Barnard, in that data could be captured, stored, and analyzed using one
or more layers (see Figure 1-1). Hook-Barnard added that the report also
stressed the importance of participant engagement and health justice. As
the field of precision medicine moves forward, it is critically important that
representation, inclusion, and engagement be considered and built into the
system, said Hook-Barnard.
FIGURE 1-1 Building a knowledge network.

FIGURE
SOURCE: 1-‐1 Building
Hook-Barnard, slidea 13.
knowledge network
SOURCE: Hook-‐Barnard, Slide 13

With a slightly different perspective on precision medicine, David Valle,

the Henry J. Knott Professor and director of the McKusick-Nathans Insti-
tute of Genetic Medicine at the Johns Hopkins University School of Medi-
cine, argued that “precision medicine” may be an oxymoronic term. The
dictionary definition of precise is “exactly or sharply defined,” or “strictly
conforming to a pattern, standard or convention”; however, human biol-
ogy is anything but precise, said Valle. Valle compared two systems—a
watch and human biology—and noted that, while both are complex, they
differ considerably. A watch is an intentionally designed closed system,
with precise yet interchangeable parts. On the contrary, human biology is
an imperfect, messy system that developed through evolutionary trial and
error. While organs, such as liver and heart, may be partially interchange-
able, no two humans are precisely alike. In addition, human biology is an
open system, in which human beings are constantly exposed to environ-
mental factors that affect and interact with their biological systems. Valle
noted that, in contrast to the old intelligent design theory about human
development—in which humans were compared to a watch—the theory of
evolution is like a tinkerer without a plan. Valle prefers the term “individu-
alized medicine” rather than “precision medicine,” because it acknowledges
the fact that each individual has unique strengths, weaknesses, and needs.
However, he noted that the term “precision medicine” has taken hold and
he is not likely to change it now.
This said, Valle continued with a description of four principles of
precision medicine. First, all disease has both a genetic and an environ-
mental component. He noted that while in some cases—such as Mendelian
disorders—the genetic component of the disease is obvious, in reality every
disease is the result of an interaction between genetic and environmental
factors. Second, everyone has their own disease. That is, two individuals
with the same diagnosis may respond quite differently to treatment and may
experience the disease in a very different way. Third, disease and risk fac-
tors must be considered across the lifetime of an individual. While a preci-
sion medicine approach may forestall the onset of a disease when there are
known risk factors, this may result in unintended consequences later in the
individual’s life. Finally, Valle said that, while change is difficult, the field
of medicine can do better and should vigorously pursue precision medicine
and what it has to offer patients.
REGULATION OF PRECISION MEDICINE

Robert Califf, Donald F. Fortin MD Professor of Cardiology at Duke
University and former commissioner of the U.S. Food and Drug Adminis-
tration (FDA), added another way of defining precision medicine: the right
treatment at the right dose at the right time for the right patient. Califf

noted that, while the term “precision medicine” is fairly new, the FDA has
focused on this goal since 1962 with the passage of the Kefauver-Harris
Amendments to the Federal Food Drug and Cosmetic Act. These amend-
ments required drug manufacturers, for the first time, to provide evidence
that their drugs were effective for the intended use—in other words, that
the right patient was getting the right treatment, at the right dose, at the
right time.
Califf gave a general overview of the FDA’s mission and responsibilities.
The FDA’s mission is “protecting the public health by assuring the safety,
efficacy, and security of human and veterinary drugs, biological products,
medical devices, our nation’s food supply, cosmetics, and products that emit
radiation,” reported Califf (U.S. FDA, 2017). Importantly for precision
medicine, Califf added that the FDA is also “responsible for advancing the
public health by helping to speed innovations that make medical products
more effective, safer, and more affordable and by helping the public get
the accurate, science-based information they need to use medical products
and foods to maintain and improve their health” (U.S. FDA, 2017). The
FDA also regulates labeling of both food and drugs, ensuring that truthful,
well-supported, and non-misleading information is available to consumers,
he added.
Moving on to the topic of discovery, development, and regulatory ap-
proval of precision medicine approaches, Califf noted a number of issues
that complicate the process. First, the current drug discovery and develop-
ment process is years long, and only a very small percentage of initial can-
didate compounds end up as FDA-approved drugs. There is no reason to
believe that the process of developing precision medicine approaches would
be any shorter; if anything, it is likely to be longer and more complex. Sec-
ond, Califf said that there is a dearth of high-quality evidence to support
current clinical practice guidelines, even for the average patient (Tricoci
et al., 2009). Given this, producing enough high-quality evidence to sup-
port a more personalized clinical approach for specific patients will be an
enormous challenge. Finally, Califf suggested that changes in the regulatory
scheme for new technologies would be needed. Traditionally, tests are regu-
lated one test at a time. For technologies like next-generation sequencing
(essentially 3 billion tests all done at one time), Califf believes there needs
to be an extensive evidence base underpinning this technology. Otherwise,
the regulation of next-generation sequencing still won’t be accomplished
years from now. He added that for other advances, such as gene editing, it
is critical to have high-quality animal models that can help us understand
the potential for off-target effects and long-term effects.
Despite these challenges, Califf stated that he believes that there is
great promise in precision medicine. Califf said that in order to realize
the vision of precision medicine, it is critical that the research community

develops an ecosystem for nonhuman or animal studies that accounts for

this complexity, develops reproducible predictive models, and can respond
rapidly to the need for co-clinical mechanistic studies. At the same time, the
challenge for the FDA is developing a system that ensures safety in the face
of all these scientific advancements, while not inhibiting the opportunity
for innovation.
Califf told workshop participants about the Project Baseline Study,
a collaboration among Verily, the Duke University School of Medicine,
Stanford University, Google, and the American Heart Association. Project
Baseline is aimed at developing gold standard data, tools and technologies
to provide a holistic view of human health and more efficiently and effec-
tively conduct clinical research. Participants in the study undergo compre-
hensive assessments, including the following:
• Genomics, proteomics, transcriptomics, metabolomics, microbi-

ome, etc.
• Eye exam, audiometry
• Personal and family medical history
• Imaging chest X-ray, coronary computed tomography, echocar-
diography, etc.
• Cognitive and physical tests
• Blood, urine, stool, saliva tests, microbiome
Some of the information gathered by the Baseline Study is collected

through passive sensors, such as watches that continuously record physi-
ological and environmental data, sleep sensors, and an app that works as
an interface for self-reported as well as passive data collection. Using these
technologies is a huge advance, said Califf, because previous longitudinal
studies were limited by the need to get participants into the clinic repeatedly
for data collection.
Another precision medicine initiative that is under way is PCORnet,
also known as the National Patient-Centered Clinical Research Network,
said Califf. PCORnet, which is funded by the Patient-Centered Outcomes
Research Institute, is a large, highly representative, national patient-centered
clinical research network that seeks to conduct large-scale, relevant clinical
research, with the end goal of enabling people to make informed healthcare
decisions. The data in PCORnet come from more than 122 million patients,
collected by 34 different health systems. This large-scale data network
enables researchers to perform passive observational studies as well as
prospective studies, Califf noted.
Califf concluded with his “regulatory dream” of what would be needed
in order for precision medicine to realize its promise of delivering the right
treatment at the right dose at the right time for the right patient:

• Integrative nonclinical models that provide reliably probabilistic

estimates of translation into human biology
• Quality management systems that enable assurance about data
provenance, analytical appropriateness, and reproducibility
• Rapid, less expensive, and scalable models to test mechanisms
when unexpected results occur
• Ecosystem engagement in rapid learning, given the new capacity to
acquire, store, and analyze digital information
• Deliberate risk taking to advance beyond regulatory inertia to
move the field forward
ETHICAL CONSIDERATIONS OF ANIMAL-BASED RESEARCH

Elizabeth Heitman, professor in the Program in Ethics in Science and
Medicine at the University of Texas Southwestern Medical Center, opened
her presentation by saying how important it was that this workshop was
being held, noting that it was the perfect time to discuss the ethical issues
surrounding precision medicine and animal-based research. She explained
that, if ethical discussions are held too early in the process of developing a
new scientific advancement, there is not enough known about it to predict
its likely future manifestations, potential applications, and possible effects.
However, if these discussions are held too late, the technology may already
be so diffused into clinical care that it is too late for ethical considerations
to have any impact through professional norms and standards, formal
policy and regulation, or public opinion.
Heitman noted that workshops held by the National Academies are
often designed to explore emerging technologies with an eye to anticipa-
tory governance. In other words, the workshops are designed to engage
stakeholders in strategic, policy-oriented discussions about risk reduction
and management, using predictive processes to identify key decision points
and the necessary steps for managing the development, application, and ef-
fects of new technologies. She expressed her hope that this workshop would
contribute significantly to future governance of animal-based research for
precision medicine.
Consideration of ethics and values is essential for anticipatory gover-
nance, said Heitman. Professional ethical standards of practice shape how
new scientific developments unfold and inform how they are applied. The
public’s diverse values support—or oppose—scientific developments and
new technologies, often from distinctly different perspectives than those
of the scientific community. Heitman noted that, while the public has been
engaged in the Precision Medicine Initiative, there has been little ethical
discussion around the role of animal-based research for precision medicine.
Ethicists, like most other participants in anticipatory governance, are

challenged by the need to predict how a technology will develop and be

applied. Typically, clear ethical standards in science have been articulated
retrospectively, such as after a crisis or scandal or after dramatically new
capability challenges the status quo. Ethicists must rely on others’ reports
about new scientific developments to identify their potential ethical impact
and make recommendations about their ethical use, Heitman said, thus
discussion of animal models in precision medicine is still too new to have
generated a related ethical discourse. Heitman pointed out that, in fact, the
first outline about animal models in precision medicine was published in
2016, in the article quoted by Kent Lloyd in his introductory remarks (see
p. 2; Lloyd et al., 2016).
To begin the discussion about the ethics of animal-based research for
precision medicine, Heitman walked workshop participants through the
three “Rs” of animal-based research (Russell and Burch, 1959).
Replace: Researchers should use animals of the lowest level of

evolutionary complexity and consciousness possible to answer the
research question, and should replace animal models with alterna-
tives whenever possible.
Reduce: Research protocols should be based on thorough knowl-

edge of past work, and research should be designed to reduce the
number of animals and experiments to the fewest necessary in or-
der to answer the research question in a statistically significant way.
Refine: Researchers should continuously refine their procedures in

order to eliminate or at least minimize animal pain and distress.
With these ethical principles for animal-based research in mind,

Heitman, referring to the definition at the National Library of Medicine
website,2 identified four elements of precision medicine research that would
affect the practice and implementation of the three Rs:
1. The reliability, sharing, and use of animal data

2. Modeling genetic effects on environmental exposures
3. Modeling genetic effects on lifestyle and behavior exposures
4. Modeling genetic effects over a lifetime
2 See https://ghr.nlm.nih.gov/primer/precisionmedicine/definition (accessed March 5, 2018).

Data
Precision medicine will require large databases for storing, analyzing,
and sharing data on both humans and animals. Heitman said that collab-
orative databases can help support the goals of reduction and replacement,
because researchers can answer research questions using already existing
data, rather than carrying out new animal experiments. She noted that the
ethical norms and best practices for data sharing are still being defined
and adopted, and that funding is needed in order to establish collaborative
databases and to facilitate sharing and communication. Furthermore, data
sharing and coordination remain challenging, both in terms of creating
systems that can “talk” to one another, and in terms of patient confidential-
ity and institutional policies about data sharing. She listed several existing
collaborative databases for animal-based research:
• WormBase
• FlyBase
• Mount Sinai’s Center for Personalized Cancer Therapeutics’ data-
base of fruit fly tumor avatars and effective chemotherapy
• Zebrafish International Resource Center (ZFIN)
• The Knockout Mouse Project
• International Mouse Phenotyping Consortium
• International Mouse Strain Resource
• Immuno Polymorphism Database/Non-Human Primates Database
Gene–Environment
One type of precision medicine research that is likely to utilize animal-
based models is research on how gene variants interact with exposure to
environmental factors, such as pollution. Heitman noted that this type
of research has the potential to conflict with existing standards for safe
animal housing, particularly when the research focuses on studying com-
plex environmental exposures such as multiple pollutants or sick building
syndrome (situations in which people who live or work in buildings experi-
ence adverse health effects that seem to be linked to spending time in the
building, but there is no specific illness or cause identified). She also noted
that research on environmental factors has the potential to run counter
to the goal of reduction: when there is already a public health solution
for an issue (e.g., reduce industrial pollution), it may be unethical to con-
duct research on animals rather than pursuing the public health solution.
Finally, Heitman observed that these types of studies may be problematic
not just for animals but for humans as well. She suggested that research
that is aimed at ameliorating the impact of environmental factors—for

example, developing a drug to counter an industrial pollutant’s effects on

heart health—risks doing injustice to humans by medicalizing what would
otherwise be an environmental issue.
Gene–Lifestyle
Another potential area of animal-based research for precision medi-
cine is the study of how genes interact with behaviors or lifestyle choices.
In designing this type of research, Heitman said, researchers will need to
carefully distinguish between behavior that is volitional—for example, ciga-
rette smoking—and factors that are not volitional—for example, exposure
to wood smoke. She said that this type of research may require the use
of more sentient animals that can express volition rather than be passive
participants in an environmental hazard, and noted that this would conflict
with the goal of replacement.
Longitudinal Data
In order to fully understand how different genes lead to different out-
comes over a lifetime, researchers may need to collect data on animals for
their entire natural lifespan. Heitman said that this may conflict with the
goal of refinement. Collecting data about prolonged, chronic, and terminal
illnesses may conflict with the goal of using refined, early end points in
animal studies; research animals would normally be humanely euthanized
before they were subjected to diseases such as advanced cancer. In addition,
using animal models for studies on diseases linked to long-term environ-
mental exposures will require exposing animals to harmful and potentially
stressful settings for long periods of time, which conflicts with the ethical
standards of housing and care currently employed.
Heitman concluded that, in addition to these four examples, there will
likely be old, new, and potentially unexpected ethical issues that arise with
the use of animal-based research for precision medicine. Stakeholders—
including researchers, journal editors, Institutional Review Boards, fund-
ing agencies, and patients—need to be on the lookout for these ethical
issues and be ready to engage the public in a discussion of how to design
high-quality research that is consistent with the three Rs of animal-based
research.
BIOETHICS, PUBLIC OPINION, AND

COMMUNITY ADVISORY BOARDS
Richard Sharp, professor of biomedical ethics and medicine and di-
rector of the Biomedical Ethics Research Program at the Mayo Clinic,

said that there is a “perfect storm” around the issue of animal research
that involves declining public support for animal-based research, increas-
ing concerns about certain kinds of research—particularly around genetic
modification—and increasing political activism about these issues. Sharp
said that the percentage of Americans who believe it is “morally accept-
able” to perform medical testing on animals has dropped from 65% in
2001 to 51% in 2017, representing a significant slide (Gallup News, 2017).
At the same time, emerging technologies, such as CRISPR/Cas-9, are gener-
ating public concern about the ability to fundamentally alter the genomes of
organisms; these concerns fall into several general categories. First, there is
public concern about catastrophic global consequences, for example, from
genetically modified mosquitos. Second, there are concerns about animal
experimentation that would make animals more like human beings for the
purpose of investigating their biology, said Sharp. Third, there are experi-
ments that raise concerns about the integrity of species, for example, the
human neuron mouse that was proposed at Stanford over a decade ago.
In the context of animal modeling for precision medicine, Sharp fore-
sees potential for controversy in several areas. First, the public’s concerns
over animal research often center on the question of whether it is reason-
able to inflict suffering on animals for what may be an uncertain benefit
to human beings. Certain precision medicine initiatives in particular may
spark this concern, for example, the mouse “hospitals” in which humans
and mice undergo co-clinical trials to inform treatment of the human (see
Chapter 3). While this model may be promising for identifying effective
therapies for patients, it may be a disturbing image for many people in the
public, said Sharp. The fact that strains of animals would be engineered
solely in order to benefit an individual patient could generate significant
controversy and opposition. Second, animal research raises the question
of how many mice should be sacrificed in order to save a human life. As
precision medicine research advances, it is likely that animal models will
play a significant role, and this increase in the need for animals in research
may draw opposition. While these general areas of concern about animals
are not novel, the rise of precision medicine may put increased focus on
animal research.
Given this potential for controversy, Sharp had suggestions for mov-
ing forward. First, he said that we are often in a state of discourse without
dialogue, in which people talk at, but not with, each other. The challenge,
said Sharp, is to move beyond this and to really engage in conversation
with people in order to understand where these concerns are coming from.
Second, Sharp said that there is a lack of trust in the scientific community
that can result in opposition to some forms of research. He quoted E.F.
Einsiedel, who said: “While public concerns are often dismissed as naïve
or misguided, the public use of dystopian images also reflects their lack of

trust in the scientific community and their skepticism in the capacity of

government to regulate in the public interest” (Einsiedel, 2005, p. 154).
Sharp said that more effective engagement and dialogue with “opponents”
can help bridge this divide and increase trust in the scientific community.
Finally, Sharp encouraged scientists to learn from historical mistakes such
as the story of Henrietta Lacks and the Havasupai controversy.
The key to improving dialogue and engendering trust is community
engagement, said Sharp; one way to accomplish this is through Commu-
nity Advisory Boards (CABs). These CABs, which exist across the country
and comprise people from various parts of the local community, can be
extremely effective for providing researchers with insights about whether
and how members of the community might object to the work they are
doing. The Mayo Clinic, said Sharp, has three CABs that meet a handful
of times throughout the year and provide input to researchers with regard
to governance structures, procedures, and donor engagement. In addition
to providing ongoing feedback, a CAB can also work with researchers to
engage the community on specific topics or areas of concern. For example,
Sharp said that there was an issue concerning partnerships with industry
and the commercialization of biobank samples, and it was necessary to do
a deep dive with the members of the CAB and really discuss the issues at
hand.
As an example of how CABs can operate, Sharp gave a few details
about one of the Mayo CABs. Advisors on the CAB are drawn from the
southeastern Minnesota area and the Biobank participant population and
serve a term of 2-3 years. They attend five or six meetings per year, and re-
ceive $75 compensation for each meeting. Advisors receive regular commu-
nications between meetings and are expected to interact respectfully with
one another, recognizing the plurality of views among the advisors. Sharp
said that the Mayo Clinic makes it clear to the CAB advisors that their role
is to serve as representatives of their communities, but not as regulators.
He said that the advisors are not asked to approve or disapprove research
projects, and he believes it is important to be clear with CAB members what
authority is being granted. The Mayo Clinic CAB has advised the Biobank
leadership on topics, including the following:
• Informed consent process

• Communications about biobank research
• Underrepresented minorities
• Return of genetic findings
• Partnerships with industry
• Commercialization of biobank samples
• Use of new technologies, such as whole-genome sequencing

Sharp stressed that the goal of CABs is not necessarily to come to

consensus, nor to argue opponents into submission. Rather, the value of
CABs is to clarify moral differences and identify areas where there seems
to be some irreconcilable, substantive, and moral disagreement in play,
and perhaps to find agreement on certain moral positions for which there
may be agreement. This process requires recognizing marginalized voices
and recognizing divergent moral views. Ultimately, “by engaging opposing
views we may not be able to reach consensus but we may be able to find
some type of compromise position for which no one is happy but everyone
is at least satisfied,” said Sharp. The value in this type of dialogue, said
Sharp, is that it might help “avoid political entrenchment and the kind of
moral extremism that’s become all too common in political debates in the
U.S.” Sharp added that CABs are not the only mechanism by which these
difficult goals can be met, and that there are more formal and less formal
ways to structure these types of conversations.
Given the potential for controversy in precision medicine research,
Sharp said that the scientific community should expect there to be public
concerns and should engage the public in conversations in order to build
trust and increase the transparency of the work. He cautioned, however,
that, while this engagement is valuable and necessary, it is unlikely to
reduce these debates to a place where all stakeholders come together and
rally in support of the same goals. Despite the challenges, Sharp said that
discussions about precision medicine research should be expanded in order
to include the debates about animal research. Although this may be an un-
comfortable thing to do, Sharp said that discussions about animal research
will be an essential part of the conversation that needs to take place.

Existing Precision Medicine Initiatives
Key points:
• The current time and labor-intensive system for diagnosing
individual patients is not scalable or sustainable. (Kaufmann)
• The future of genomic medicine is dependent on deep and ac-
curate phenotyping of clinical and model organisms and the
use of precision animal models to validate genetic findings and
to test potential treatments. (Smedley)
• Global collaboration is critical for diagnosing patients with
rare disease. (Kosaki)
S trategic initiatives on precision medicine are emerging in a number

of countries. This chapter presents information from both days
regarding the efforts in the United States, United Kingdom, France,
and Japan and a new initiative by the World Economic Forum.
It is meant to highlight these parallel and related efforts and to
comment on how global collaboration could ensure success in the
future of precision medicine.
UNITED STATES: ALL OF US

Petra Kaufmann, director of the Office of Rare Diseases Research at
the National Center for Advancing Translational Sciences, told workshop
16

EXISTING PRECISION MEDICINE INITIATIVES 17
participants about the All of Us research program that is under way at the
National Institutes of Health. The program is an effort to move precision
medicine forward by collecting and analyzing a wide array of data from at
least 1 million Americans. Kaufmann first laid out the rationale behind the
program, observing that the current system of research and clinical care
has disadvantages for patients, providers, and researchers. Clinical treat-
ments are usually geared toward the average patient, and finding the right
treatment for any individual patient may be the result of years of trial and
error. Providers lack the time to thoroughly analyze each patient’s biology,
medical history, and symptoms, and there are too few data underpinning
the available clinical guidelines. Kaufmann described the challenging pro-
cess for a provider trying to do the detective work to diagnose a patient:
Internet research, emails to people in the field, and “pulling together puzzle
pieces from PubMed” to diagnose one patient. She noted that this process
is not sustainable or scalable in the current healthcare environment, but
that precision medicine initiatives like All of Us may address these issues.
Challenges for researchers, she said, include difficulties in collecting large
and diverse sample sizes, building and maintaining systems for storing and
analyzing the data, and sharing and collaborating with other researchers.
The mission of All of Us is to accelerate health research and medical
breakthroughs, enabling individualized prevention, treatment, and care for
all Americans (https://allofus.nih.gov), said Kaufmann. This goal will be
met by nurturing relationships with 1 million participant partners, develop-
ing a large and rich biomedical dataset, and catalyzing a robust ecosystem
of researchers and funders to use and support the system. The program will
collect clinical, environmental, lifestyle, and genetic data, with participants
consenting to data collection on an ongoing basis throughout their lifetime.
Data will be collected using a wide variety of methods, including biospeci-
mens, wearable technologies, electronic health records, and surveys. The
program seeks to recruit a highly diverse group of participants and will par-
ticularly over-recruit populations who are traditionally underrepresented
in biomedical research. Participants will have access to information about
themselves, and the program will seek to earn the trust of participants
through engagement and full transparency. Kaufmann noted the pervasive
concern about data privacy and said that, while of course it is critically im-
portant to protect privacy, she does not want the pendulum to swing too far
toward not collecting or sharing data that could lead toward treatments and
cures for disease. The program will seek participation from a diverse group
of researchers, from citizen scientists to premier university labs. By making
the data accessible to all, All of Us hopes to apply “more brainpower per
problem” and be a catalyst for innovative research. Kaufmann said that All
of Us is seeking to transform the traditional method of research—in which
data are brought to researchers through a complex maze of issues including

data sharing protocols, huge infrastructure, and cumbersome access—to a

new approach that brings researchers to the data quickly and efficiently.
Currently, the program is in the closed beta phase. In this phase,
Kaufmann said, the program will enroll 10,000-15,000 participants and will
expand across the country slowly. All aspects of the program—including
the website, consent forms, online tools, and staff workflow—will be tested
and refined during this time, and participants will be asked to give feedback
on their experiences. The national launch for the program is set for spring
2018.
UNITED KINGDOM: 100,000 GENOMES

Damian Smedley, director of genomic interpretation at Genomics
England, explained the United Kingdom’s 100,000 Genomes project. The
project involves sequencing 100,000 genomes, including genomic, pheno-
typic, and other clinical data from 70,000 patients with rare diseases or
cancer. The project is not just a genomic research project, said Smedley, but
rather is aimed at transforming the healthcare system. While the main goal
is to benefit patients in the UK healthcare system, a second goal is to kick-
start the development of a UK genomics industry by creating the capacity,
capability, and legacy of personalized medicine in the United Kingdom. The
project utilizes 13 National Health System (NHS) genomic medicine centers
around the country, responsible for recruiting patients, obtaining informed
consent, and collecting samples. Sequencing is performed, and electronic
health record data on the patients are collected and stored at a specially
commissioned data center that is government-approved, secure, and behind
an NHS firewall. Researchers can access and analyze de-identified data
through a system akin to a reading library, which is designed to protect
patient data while also making translations from research to the healthcare
system quicker and more efficient. Academic researchers who want access
to the data become members of a Genomics England Clinical Interpretation
Partnership.
One of the primary reasons for and benefits of the project is being
able to diagnose rare diseases. To do so, internal curation teams curate
gene panels for every recruited disease category to look for variants us-
ing two software tools, Exomiser and Genomizer. Finally, all of the data
and analysis are merged together for clinicians to review and share with
patients. Smedley gave two examples of successful diagnoses stemming
from the 100,000 Genomes project. One patient, a 4-year-old girl named
Jessica, presented with epilepsy and developmental delay, and all of the
standard genetic tests had not revealed the cause. After a genome-wide
scan, researchers found more than 6 million variants in her genome, around
600,000 of which were rare. About 3,000 of these were predicted to cause

change in a protein, and only 67 of those were different from her parents’
genes. One of those was a gene that was listed in PanelApp, a crowdsourc-
ing tool developed by Genomics England. A de novo mutation in SLC2A1
was identified as the cause of her Glut 1 deficiency syndrome, and she is
now being successfully treated with a ketogenic diet. Another successful
diagnosis was for a young girl named Georgia, who had developmental
delays and multiple medical problems. Despite extensive genetic testing, no
cause had been identified. 100,000 Genomes researchers found a de novo
truncation in KDM5B, a newly recognized disease gene. While there is cur-
rently no treatment for her disease, the diagnostic odyssey has ended and
gives her parents reassurance about the low risk of recurrence if they have
another child, said Smedley.
The treatment cycle for diagnosing and treating a patient with a rare
disease requires a complex chain of operations, most of which have not
been designed or optimized for the purposes of genomic medicine, said
Smedley. In particular, in order to integrate clinical and genetic data, the
clinical data need to be captured and recorded in a standardized way across
the system. Genomics England has created a clinical data capture system
for rare disease diagnostics that includes defined Human Phenotype Ontol-
ogy (HPO) terms for each disease category and a standardized system for
imaging and lab test results. Based on the patient’s phenotypes, clinicians
can decide on the relevant gene panels.
Genomics England is wrapping up a pilot test for rare diseases, and
Smedley shared some of the results stemming from almost 5,000 enrolled
patients with 170 different conditions. HPO phenotyping allowed for
12,966 positive and 43,088 negative annotations to be collected. The di-
agnostic rate is currently around 20-25%, but Smedley expects it to rise
as further analysis is performed, because the diagnostic rates improve as
more data are collected. The pilot project also demonstrated the benefit of
software like Exosimer. Smedley said that, for the first 1,000 patients who
received a likely diagnosis based on internal clinical review, Exosimer iden-
tified the right variant in 59% of the cases and identified the variant as a
top five candidate in 88% of the cases. Exosimer has also found additional
diagnoses for patients. For example, the gene panel for cataracts did not
include a deletion in the SORD gene, due to limited evidence. However,
after Exosimer flagged this mutation as a top five candidate for a patient
with congenital cataracts, researchers found a mouse model with both the
mutation and cataracts. This demonstrates the utility of the model organ-
isms, said Smedley, as most useful in this realm of research candidates in
the undiagnosed cases.
Animal models, said Smedley, will have two main purposes in the
100,000 Genomes research: to validate the variants, and to test potential
treatments. He noted that they are likely to end up with 10,000 to 15,000

rare disease cases that do not have a diagnosis, and that model organisms
will be critical for new disease gene discovery. He is particularly intrigued
by the potential for using CRISPR/Cas-9 to quickly and efficiently develop
precision animal models for functional validation and treatment testing.
Smedley noted that the Genome Editing Mice for Medicine (GEMM) pro-
gram, available for researchers to request mouse models, puts out a call
every 9 months, and Genomics England has submitted several applications.
He noted that similar programs are available in other countries as well, and
that the International Mouse Phenotyping Consortium, with its huge num-
ber of mouse models, also takes requests for new ones. Genomics England
is also participating in the Matchmaker Exchange program, which seeks to
connect patients, diseases, and model organisms around the world to aid
in diagnosis and mechanistic discovery, and also performs computational
matching of rare disease patients across clinical and public sources.
Smedley concluded that the future of genomic medicine is dependent
on deep and accurate phenotyping of clinical and model organisms and the
use of precision animal models to validate genetic findings and test potential
treatments. The 100,000 Genomes project will drive genomic medicine into
the NHS by building capacity and capability for precision medicine, with
the hope of achieving diagnoses, therapies, and opportunities for patients.
FRANCE: THE FRENCH PLAN FOR GENOMIC MEDICINE

Catherine Nguyen, director of ITMO Génétique, Génomique et Bio-
informatique, told workshop participants about France’s recent foray into
genomic medicine. Nguyen started by noting that, when a patient presents
to a provider, there are a number of questions that are not immediately
answerable, such as whether the patient’s therapeutic regime would be
effective at this stage of the disease, what kind of rare disease this patient
may have, what treatment is best suited for this patient, can the evolution
of diabetes in this individual be predicted. Genomic medicine, said Nguyen,
will hopefully provide new tools to start answering these types of questions.
Providing the historical context regarding the French plan, Nguyen
explained that in 2015 the French prime minister asked Aviesan (the French
National Alliance for Life Sciences and Health) to examine the current land-
scape of genomic medicine and its role in medicine, and to propose a plan
to integrate genomics into France’s healthcare system and industrial sector.
The prime minister specifically asked for a proposal of a long-term model
that integrates the issues of insurance coverage along with the establishment
of an industrial sector to support such an initiative. More than 160 people
collaborated to answer the prime minister’s call and to produce a report
entitled Genomic Medicine France 2025.
The report, said Nguyen, set a plan for genomic medicine over the next

10 years, with two major goals. First, sequencing should be integrated into
routine clinical practice. Specifically, the goal is to implement a general
healthcare pathway for all French patients with cancer, rare diseases, or
common diseases that includes access to genomic medicine for all those
concerned (patients and eventually family members depending on diagno-
sis) by 2025. Second, work must be done to develop a national genomic
sector. Specifically, the goal is to place France among the leading countries
in the field of genomic medicine in the next 10 years, to export its expertise
developed in this area, and to establish a medical and industrial sector of
genomic medicine.
Nguyen further elaborated that, on the first goal of integrating sequenc-
ing into routine healthcare, the report outlined a basic model for integration
that included putting clinical and genetic data into a national database, and
a framework for exchange between the diagnostic laboratory and clinical
decision makers and patients. The report identified several needs that each
stakeholder would have in such an integrated system. For example, the pa-
tient would want a diagnosis based on the integration of genomic data with
clinical data, and adequate care by the healthcare system. The practitioner
would need validated indications, digital files with genomics and clinical
data for each patient, a system for identifying variants for a particular
pathology, and tools for exploring data and developing therapeutic strate-
gies. Based on the needs of stakeholders, there were three broad objectives
identified: (1) implement the tools for a genomic healthcare pathway, (2)
ensure operational implementation and growth, and (3) implement moni-
toring and management tools. Fourteen actions were identified that would
help support these objectives. For example, in order to implement the tools
for a genomic healthcare pathway, there were three actions that needed to
be performed:
1. Create a network of sequencing platforms

2. Create a Central Analyzer of Data to process and use the volume
of data generated
3. Allow the integration and use of patient data in the healthcare
pathway
In order to test these objectives and actions, several pilot studies were
initiated on diabetes, rare disease, and variant analysis of the general
population. As part of this process, centers for reference, innovation, and
expertise (CReflX) are being created. These centers will test innovations,
evaluate the quality of data, and educate stakeholders.
Animal models, Nguyen said, will be important to the advancement
of precision medicine in several ways: for increasing knowledge on gene
function, for understanding variations in the genome and environmental

conditions, for enhancing knowledge of molecular mechanisms, and for

validating therapeutic hypotheses. Importantly, there are drawbacks and
limits to the use of animal models, including societal concerns about ani-
mal research generally, issues with reproducibility of animal studies, and
determining the relevance of animal models to human health.
JAPAN: INITIATIVE ON RARE AND UNDIAGNOSED DISEASES

Kenjiro Kosaki, director of the Center for Medical Genetics at Keio
University School of Medicine, told workshop participants about Japan’s
Initiative on Rare and Undiagnosed Diseases (IRUD). IRUD is designed to
help patients who have remained undiagnosed because their disease is so
rare that doctors do not know it, or because their disease is a completely
new and unknown condition. IRUD accepts undiagnosed patients who meet
at least one of the enrollment criteria: congenital onset, familial occurrence,
and/or multi-organ involvement. The IRUD process is multi-step, collabora-
tive, and iterative, utilizing regional participating hospitals, clinical centers,
and analysis centers. Eligible patients are referred up through the system,
phenotyping and genetic sequencing are performed, and information and
analysis are filtered back down to clinicians and patients for genetic coun-
seling and potential treatment.
To analyze and evaluate the patients’ genetic information, IRUD uses a
program that includes information about mouse phenotypes and associated
human diseases. Normal Japanese variants are filtered out, using informa-
tion from whole genome sequencing on 3,500 controls as well as a database
of centenarians and super centenarians (i.e., over 110 years old). Kosaki
noted that any variants that are observed in these long-living individuals
are unlikely to be associated with one of the rare diseases.
IRUD started in July 2015, and in the 2 years since its inception,
has already identified and published about 10 new diseases, said Kosaki.
Twenty-five hundred patients have been accepted to the program, and the
diagnostic success rate is around 30%. Kosaki gave two examples of new
diseases that have been identified. In the first case, an 18-year-old undi-
agnosed patient with overgrowth, scoliosis, fragile skin, and intellectual
disability was matched to three other patients from Japan and the United
States with similar phenotypic features. Genetic analysis revealed that all
patients had de novo mutations in the PDGFRB gene, though the muta-
tions were not identical (Minatogawa et al., 2017). In addition to the three
signaling pathways associated with overgrowth syndrome—IGF1, TGFb,
and AKT1 receptors—the IRUD research demonstrated that PGDFRB can
also cause overgrowth. A Belgian research group read the IRUD research
findings and subsequently conducted in vitro studies that showed that the
PDGFRB mutation could be suppressed by imatinib, a kinase inhibitor

(Arts et al., 2016). At the same time, another patient in Minnesota with
a different mutation in PDGFRB was identified. Based on further in vitro
work by the Belgian researchers, this patient was treated with imatinib,
resulting in “objective improvement of debilitating hand and foot contrac-
tures and significant improvement in quality of life” (Pond et al., 2018).
Kosaki said that this experience shows that making a diagnosis can lead to
potential treatment, and that it took only 3 years between the discovery of
the condition to the first human trial.
The second example Kosaki gave was a patient who suffered from
intellectual disabilities, lymphedema of the legs, and increased platelet size
with concomitant decreased platelet count. Genetic analysis showed a novo
mutation in CDC42, which in mouse models was associated with large,
albeit fewer, platelets, and brain defects. Kosaki presented this case at a
local genetics meeting in Japan, and one of the attendees recognized the
phenotype from one of his patients. This attendee’s patient had the same
de novo mutation, while several more patients have been identified since
then with the same or similar mutations and similar phenotypes. This new
disease—a diagnosis of thrombocytopenia and intellectual disability, with
a CDC42 mutation—has been classified as Takenouchi-Kosaki syndrome.
Kosaki noted that the process of identifying Takenouchi-Kosaki syn-
drome was dependent on a very astute audience member with a photo-
graphic memory, as well as the previous publication of CDC42 knockout
mice studies. He warned, however, that we should not be relying on these
types of fortuitous circumstances but should instead rely on more structured
approaches, such as cross-species phenotype ontology and systematic case
matching. The HPO is one tool that can help with this type of systematic
approach, said Kosaki, as it provides a standardized vocabulary of pheno-
types associated with human disease and allows researchers from around
the world to compare cases and find matches. Kosaki reported that they
have succeeded in using Google translation technology to translate Japanese
medical items directly into HPO, which is a versatile method for not only
Japan but other countries. Kosaki said that the IRUD project has begun
collaborations beyond the borders of Japan and has analyzed samples from
37 patients from other countries. This type of global collaboration is es-
sential to identifying rare and undiagnosed diseases and, hopefully, finding
effective treatments for these patients.
WORLD ECONOMIC FORUM:

CENTER FOR THE FOURTH INDUSTRIAL REVOLUTION
The World Economic Forum (WEF), said Genya Dana, project head
for the Precision Medicine project, is a membership-based, international
organization that serves as a convening platform for bringing together lead-

ers and stakeholders around the world who are committed to shaping the
future of the world and making it a better place. In recent years, the WEF
has moved beyond a convening function into taking a more active role, said
Dana. As part of these efforts, WEF launched the Center for the Fourth
Industrial Revolution in March 2017, focused on emerging technological
areas. This project is aimed at developing and testing policy frameworks
and protocols that maximize the benefits of emerging technologies while
minimizing the risks to societies. The project has nine program areas: Ar-
tificial Intelligence and Machine Learning; Blockchain (Distributed Ledger
Technology); Future of Drones and Tomorrow’s Airspace; Future of Urban
and Autonomous Mobility; Internet of Things and Connected Devices;
Digital Trade and Cross-Border Data Flows; Environment and the Fourth
Industrial Revolution; Future of Production; and Precision Medicine.
The Fourth Industrial Revolution project collaborates with global part-
ners, including companies that are committed to a leadership role in the
revolution, as well as partners at all levels of government. These govern-
ment partners will send a representative to the WEF Center in San Francisco
for up to 18 months; these representatives will collaborate with each other
and other partners on co-designing pilot projects and will help guide the
development of governance norms, protocols, partnerships, and standards.
Rwanda and Japan have signed on as government partners, and corporate
partners include Kaiser Permanente, Microsoft, and the American Heart
Association.
The Precision Medicine project, said Dana, has the objective of shap-
ing the trajectory of precision medicine to promote societal benefits while
minimizing risk, and will do so by collaboratively designing and testing
governance approaches for precision medicine through pilot projects. Dana
noted that precision medicine has long been an interest and a topic of dis-
cussion among WEF’s members, but that this specific project is new and
in the earliest stages. The project will be divided into three phases. First,
the landscape of precision medicine will be surveyed, key stakeholders will
be identified, and the barriers that are preventing precision medicine from
moving forward will be described. Next, the project will work with its
government partners to determine what some of the priority areas are and
how they could be translated into a pilot project. For example, if partners
are concerned about data sharing, WEF would look at the barriers to data
sharing, the policy challenges involved, and how current initiatives could
be joined or utilized as part of a pilot project. Finally, pilot projects will
be designed and launched in collaboration with government partners and
other stakeholders. An assessment after 9 months will evaluate the proj-
ects and determine whether and how they could be expanded into other
communities.

Dana enumerated the challenges identified thus far by the Precision

Medicine project:
• Evidence of efficacy generation

• Data sharing and infrastructure
• Regulatory environments
• Integration into clinical practice
• Pricing and reimbursement pathways
• Patient and public engagement
Dana said that the Precision Medicine project is a global scoping ex-
ercise and a global endeavor; therefore she welcomes the opportunity to
collaborate with all relevant stakeholders from around the world.

The Promise and Perils

of Animal Models1
Key points:
• Animal models are key for confirming causation, for under-
standing pathophysiology, and as surrogates for treatment
studies. (Valle)
• Animals are not a perfect analogy for humans. We need to
be aware of what question we are trying to answer, and if a
certain animal model is an appropriate way to look for these
answers. (Kuhn)
• It is important to choose the right animal model for the phe-
notype that is being investigated. (Haendel)
• Using animal models can present issues with face validity, con-
struct validity, and predictive validity. (Burgess)
• New approaches to animal modeling, such as co-clinical trials,
can improve the usefulness of animal models and their transla-
tion to human health. (Clohessy)
• Comparative oncology is a promising approach for translating
from animals to humans. (LeBlanc)
1 Nicholas Katsanis of the Duke University Medical Center spoke during this session, but
due to technical problems, his presentation is not summarized here. His presentation is avail-
able at http://nas-sites.org/ilar-roundtable/roundtable-activities/precision-medicine-workshop/
webcast.
26

THE PROMISE AND PERILS OF ANIMAL MODELS 27
his chapter focuses on defining elements of “precise” and apply-

T
ing precision when modeling diseases in animals. Presenters first
explored the translatability, alignment, and relevance of current
animal models to the human condition. Subsequent presentations
focused on new approaches to disease modeling, including devel-
oping “non-model” model systems and new modeling platforms.
MOUSE MODELS
Introduction to Model Organisms

David Valle introduced workshop participants to the five most com-
monly used model organisms for research: Escherichia coli (bacterium),
Saccharomyces cerevisiae (brewer’s yeast), Caenorhabditis elegans (round-
worm), Drosophila melanogaster (common fruit fly), and Mus musculus
(house mouse). Valle stressed that each of these organisms has unique fea-
tures and that researchers should choose the model that is most appropriate
to answer the research question at hand.
Valle said that there are three main ways that animal models—mice in
particular—can be used to advance the purposes of individualized medicine.
First, animals can be used to confirm causation. When researchers perform
genomic sequencing to find the genetic variant responsible for a pheno-
type, there is often a short list of prospective variants. Animal models can
quickly confirm which variant, or combination of variants, is relevant to
the phenotype. Second, animal models can serve as experimental systems
for understanding pathophysiology. Finally, animal models can act as sur-
rogates for treatment studies, particularly studies that may be difficult or
time consuming to test in humans.
Confirming Causation
As an example of using mouse models to confirm causation, Valle told
participants about the Centers for Mendelian Genomics. These four centers
are seeking to identify all genes that have high-penetrance variants (i.e.,
genetic variants that often result in expression of the associated phenotype).
Researchers recruit families or cohorts with identified and unexplained
phenotypes, and collect genetic information. Using family relationships,
allele frequency data, functional predictions, model organism results, and
functional studies, researchers are able to identify the genes and vari-
ants responsible for the phenotypes. Valle said that over the last 5 years,
the Centers for Mendelian Genomics have identified around 1,000 novel
disease genes and have also expanded the phenotypic spectrum of known

disorders. In some instances, these genes are high-quality candidates, but

in others, animal models were needed to confirm the relationship between
gene variant and phenotype. However, he noted that there is a long way to
go to identify every gene variant and explain every currently unexplained
phenotype. Valle noted that other species can also be used to study can-
didate genes; a zebrafish model has been used to research bicuspid aortic
valve, which is a genetically heterogeneous disorder that occurs in 1-2% of
the general population.
Valle cautioned that the common approach of simply knocking out a
candidate gene in a mouse model runs the risk of missing the nuances of
biology and causation. He said that, while many disease genes are associ-
ated with only one phenotype, some genes have many discrete phenotypes,
depending on the specific allele. He gave the example of two patients who
have very different phenotypes but who have a mutation on the same gene.
To fully understand this allelic heterogeneity, it is essential to insert specific
allele variants into animal models and observe their effect on the phenotype.
Understanding Pathophysiology
Animal models can help contribute to understanding the pathophysiol-
ogy of a disease. One example, said Valle, is in research on Marfan syn-
drome. The gene responsible for Marfan syndrome—FBN1—was identified
in 1991. In the years since this identification, researchers have been able to
determine that the mutation on FBN1 causes a disruption of the extracellu-
lar matrix with elevated levels of free TGFβ, which then affects the elasticity
and function of tissues. These discoveries explain many of the phenotypic
characteristics of Marfan syndrome and point toward TGFβ antagonist as
an appropriate therapy.
Surrogates for Treatment Studies

Valle told workshop participants about a powerful example of using
animal models as surrogates for potential treatments. A rare disease called
gyrate atrophy, caused by mutations in the OAT gene, results in retinal
degeneration, due to abnormal levels of ornithine accumulation caused by
deficiency of the enzyme ornithine aminotransferase. Researchers specu-
lated that an arginine-restricted diet would lower the levels of ornithine, but
because patients differed significantly in terms of age, stage of degeneration,
compliance with diet, and allelic variations, it was difficult to conduct a
controlled study over the many years that it would take to show an effect.
Using mouse models allowed researchers to have complete control over the
diet and to observe retinal degeneration at a much faster pace. Despite dif-
ferences in eye structure between mice and humans, researchers were able

to show that an arginine-restricted diet was therapeutically beneficial for

this disorder.
International Mouse Phenotyping Consortium

Steve Brown, director of the Mammalian Genetics Unit, MRC Harwell,
United Kingdom, discussed the International Mouse Phenotyping Consor-
tium (IMPC) and its importance to precision medicine. The IMPC involves
21 research centers that are collaborating to solve a key problem in ge-
nomics: the lack of knowledge about the function of the majority of genes.
Knockout models have been generated and analyzed for only a fraction of
mouse genes, and data for these genes is patchy, dependent on the interests
and experience of the investigator. Pleiotropy—in which one single gene
produces two or more phenotypic traits—is particularly poorly understood,
said Brown. Pleiotropy is manifest across a whole range of genetic phe-
nomena, including variable expressivity and phenotypic expansion. More
data about pleiotropy will be essential to understand human phenotypes
and to ensure that animal models are appropriate comparators for human
disease states.
To address these gaps in knowledge, IMPC is seeking to generate and
comprehensively phenotype a mouse mutant for every single gene in the
mouse genome. These phenotype data are uploaded from IMPC centers to
the IMPC Data Coordination Centre, where they are analyzed to determine
gene function, to identify disease models, and to build a deep and pleio-
tropic view of gene function. All of the data, as well as the mouse models
themselves, are open source and available for researchers to use. For ex-
ample, programs collecting data from vast numbers of patients—such as
the 100,000 Genomes project—can use the IMPC data to provide informa-
tion on gene function, to validate potential gene–phenotype relationships,
and to perform synergistic analyses with the multidimensional genetic and
phenotypic data that are collected.
Brown told workshop participants that all mice in the IMPC are co-
isogenic and bred on a black 6N background to reduce unwanted sources
of variation. Many of the allele mutants are now generated using CRISPR/
Cas-9, which is faster and cheaper. Each mutant allele is studied at each
phase of life, each mutation is assessed for fertility and viability, and gross
morphology and histopathology of both mutant embryos and placenta are
performed. Mutant adult mice are assessed for gross pathology, whole body
plethysmography, body composition, and morphology and histopathology.
All of the data are validated, checked for quality, and analyzed before being
placed in the core data archive.
IMPC has developed nearly 7,000 genotype-confirmed lines thus far,
approximately one-third of the mouse genome. More than 50 million data

points have been collected, nearly 400,000 images have been stored, and
phenotype data from nearly 5,000 phenotyped lines are available. The work
of the IMPC has resulted in a number of novel insights into the mammalian
genome, said Brown, including the following:
• Extensive new collection of disease models, new candidate disease

genes, and new functional knowledge
• Novel insights into gene function (e.g., metabolism, deafness)
• Revelations about pervasive sexual dimorphism
• Opportunities for the identification of new gene and phenotype to
elicit novel biological mechanisms
• Insights into human disease from the analysis of mouse lethal (es-
sential) genes
The IMPC project is a substantive step toward a comprehensive cata-

log of mammalian gene function, Brown said. These large-scale and mul-
tidimensional data will facilitate a new era of comparative genomics that
will transform the opportunities for rare disease and precision medicine
initiatives, particularly with respect to the pleiotropic nature of genes.
Phase II of the IMPC is now under way, said Brown, with a new focus
on the identification and characterization of late-adult phenotypes, which
will bring new insights to the study of late-onset disease. By early 2018,
IMPC expects to have delivered mutants and phenotypes for one-third of
the coding genome.
Essential Genes
Mary Dickinson, professor and Kyle and Josephine Morrow Endowed
Chair and associate dean for research at Baylor College of Medicine,
picked up on Brown’s presentation regarding the IMPC’s phenotyping
efforts to explain that, as part of this effort, her research focuses on
identifying and phenotyping embryonic lethal genes (i.e., genes that are
essential). Dickinson explained that, while there are many different ways
to define “essential genes,” she defines them as genes that are needed to
produce a viable animal that survives to birth and weaning. By creating
standardized lethal phenotyping pipelines, researchers have the opportu-
nity to investigate development in different stages and to identify which
genes are critical to survival at these stages. The pipeline is divided into
four different embryonic stages, measured by embryonic days: E9.5, E12.5,
E15.5, and E18.5. Each stage offers insight into different types of defects
and causes of death:

9.5: Pre-implantation, gastrulation, organization of the body plan,

E
heart formation
E12.5: Heart function, placenta formation, circulation
E15.5 and E18.5: Organogenesis, heart failure
Dickinson has found that the largest percentage of mutated mice die
prior to E9.5 (nearly half). The second largest window of lethality is after
E18.5; Dickinson said that many mice are perfectly healthy at E18.5 but
die shortly before or after birth. The phenotype information often helps
to identify the reasons the mice die, said Dickinson, but in some cases the
reasons remain completely unknown.
Fully understanding the defects of these embryos is valuable for iden-
tifying mechanistic relationships between genes and development, and un-
derstanding potential implications for human disease, said Dickinson. One
tool for fuller understanding of the phenotypes of these animals is 3D high-
resolution micro computed tomographic (microCT) scanning. Traditional
sectioning of each embryo would be time intensive and cost prohibitive,
said Dickinson, so using the microCT (using an iodine-based dye that cre-
ates variable contrast reflecting the density of different tissues) allows the
researchers to capture histology-level data from entire embryos and to look
for structural phenotypes that, in digital format, can be shared with the
research community for the data to be interrogated in different ways. These
images from the embryonic pipeline research are made available to the
public through a data-coordination center. “The legacy of these data will
be realized many, many years from now,” said Dickinson. An additional
tool used for this research is automated phenotyping, such as automated
volumetric analysis, which can facilitate identification and quantitation of
phenotypes that may not be obvious to the person reading the data.
Dickinson told workshop participants about several interesting phe-
notypes that have been found. First, a gene called Tmem132; mutations in
this gene cause embryos to be smaller, with limb abnormalities and spina
bifida, and internal imaging shows abnormalities including kidney agenesis
or duplications in kidney tissue. The second interesting find was a gene
called SMDT1, which is a gene of unknown function. Mutant embryos
showed excessive brain foliation and mysteriously died shortly after E12.5.
Dickinson said there is no visible structural defect in the heart, and that
they are not exactly sure what is responsible for the lethality.
In 2016, Dickinson and her colleagues published the first analysis of
their research on essential genes (Dickinson et al., 2016). This report is
based on the first 1,751 knockouts produced by the IMPC; 410 (23%) of
these genes were found to be lethal and 198 (11%) subviable. Dickinson
noted that, while the research has expanded to 4,245 knockout lines, the
percentages of lethal, subviable, and viable genes have remained remarkably

stable. In looking at how these essential genes in mice may be relevant to

human health, Dickinson said that, of 399 lethal murine genes, 126 have
human homologs with known disease associations. At the time of the pub-
lication, 52 of these constituted mouse models were reported for the first
time, demonstrating the importance of this project. Comparisons of human
and mouse essential genes have shown a strong correlation, but much work
is still needed to determine any overlap. Dickinson further noted that, when
comparing essential genes, differences between humans and mice are quite
relevant. One such difference is that mice can die at birth for a variety of
reasons that would be treatable or preventable in humans; for example,
mice born with a cleft palate are not treated in a neonatal intensive care
unit. Another difference is that the human genome is more robust. Genes
that cause lethality in mice may just cause loss-of-function in adult humans.
Dickinson explained that this could be due to redundancy or compensa-
tion by other genes in the human genome. Dickinson stressed that, despite
these differences, the null mouse alleles are key to understanding disease
mechanisms.
One interest within Dickinson’s group is the cardiovascular develop-
ment and associated required genes. To study this area more in depth,
Dickinson’s team developed advanced microCT methods to image the em-
bryo with the yolk sac and placenta intact. These techniques were used to
look at embryos with mutations in Alg10B, which are lethal between E9.5
and E12.5. The mouse phenotypes showed abnormal vascular development
and other defects often indicative of impaired cardiac function. In humans,
this gene is associated with a reduced susceptibility to a drug-induced long
QT syndrome, meaning it still affects cardiovascular function. Dickinson
said that these types of scenarios—in which mutations manifest differently
but within the same system—present opportunities to look at very precise
disease-related alleles and compare them directly to null information.
Precision Mouse Models

Robert Burgess, principal investigator of the Jackson Center for Preci-
sion Genetics, started his presentation by asking, “What are we modeling
precisely?” There are three different ways in which an animal can model a
human phenotype or disease: face validity, construct validity, and predic-
tive validity. Face validity means that the model looks right—it has the
same phenotype and presentation of disease seen in humans. Construct
validity means that the phenotype is appearing for the same reason that it
is appearing in the human patient, for example, because of the same ge-
netic mutation. Burgess noted that face validity and construct validity do
not necessarily go hand in hand, and the relative importance of each may
have to be balanced. For example, research to develop a treatment based

on pathophysiology may need better face validity, while a treatment that

is based on the core mechanism of the disease might need better construct
validity. Predictive validity—where results in the model translate into results
in human patients—is the real goal of modeling, concluded Burgess, though
he cautioned that even the best model has its limitations.
Burgess discussed the challenges in developing appropriate animal
models, using his work on Charcot-Marie-Tooth (CMT) disease as an ex-
ample. CMT is not a single disease but a collection of related diseases that
result in peripheral neuropathy. CMT is rare, affecting around 1 in 2,500
people, and there are likely 100 different loci in the human genome that can
cause CMT. As a consequence, each individual form of CMT is extremely
rare. Burgess said that creating animal models for CMT is essential, as vitro
models are challenging due to the complexity of this adult-onset degenera-
tive disease. Burgess gave two examples of mouse models for CMT, though
he noted that models have also been created in other organisms, including
rat, zebrafish, and drosophila. Burgess discussed models developed for two
versions of CMT: CMT 4D and CMT 2D.
CMT 4C is a recessive demyelinating neuropathy caused by muta-
tions in SH3TC2. Mouse models have been developed that re-create the
phenotype and loss of function seen in humans. Burgess noted that these
models can recapitulate the phenotype with either a targeted knockout or a
spontaneous mutation of the gene, and that because there are no treatments
for this disease, predictive validity is not relevant at this point. CMT 2D
is a dominant axonal neuropathy caused by mutations in the GARS gene.
This pathogenesis is either related to a dominant negative or a neomorphic
activity causing the mutant protein to take on a new pathological function,
Burgess said. Researchers have discovered two alleles that create mice with
good face and construct validity for the disease.
Based on the success of modeling the GARS mutation in mice, research-
ers sought to validate the pathogenicity of a de novo mutation that had
been identified in a 4-year-old girl who suffered from a severe motor neu-
ropathy and whose whole exome sequencing had identified a 12-base pair
deletion in GARS. Researchers wanted to validate this mutation through
mouse modeling and were also hoping to develop a gene therapy approach
toward treatment. The patient mutation was introduced into the mouse
genome using CRISPR/Cas-9, and a control model with the wildtype se-
quence was also created. Researchers found that the patient mutation did
cause a dominant axonal neuropathy in the models, while the control mice
were normal. Based on previous studies, researchers knew that transgenic
expression of wildtype GARS did not suppress the neuropathy, so they
sought to decrease the expression of the mutant form of the protein. Allele-
specific knock-downs of interfering RNA (RNAi) were delivered using
adeno-associated virus 9 (AAV9), an approach that showed benefit even

post-onset of the neuropathy in multiple mouse models, including the one

with the human-patient mutation. Burgess noted that, while the molecular
mechanism is still not entirely understood, the treatment (the only one
available to date) appears to work. He added that the treatment requires
testing multiple RNAi sequences for every different allele associated with
the disease, and that gene therapy delivered through AAV9 is still somewhat
of an experimental delivery system.
Burgess briefly discussed the rigorousness of these preclinical studies.
The researchers tried to perform well-powered studies with a sufficient
number of mice and used blinded analysis to the extent possible. They
developed multimodal clinically relevant outcome measures including be-
havioral, electrophysiological, and histological measures. Key biological
variables, such as age, were considered, since CMT is a degenerative dis-
ease. Finally, the therapy was tested in more than one model with more
than one mutation of GARS.
Burgess concluded with a discussion about the importance of the ge-
netic background of mouse models (see Figure 3-1). He noted that every
FIGURE 3-1 Genetic background of mouse models.

SOURCE: Burgess, slide 13.
FIGURE 3-1: Genetic Background of Mouse Models
SOURCE: Burgess slide 13

FIGURE 3-2 Idealized mouse models.

SOURCE: Burgess, slide 14.
FIGURE 3-2: Idealized Mouse Models

inbred murine strain has idiosyncrasies, and that testing on multiple back-
Source- burgess slide 14
grounds can help expose the potential degree of variability in response to
treatment, can reveal how robust the treatment is, and can improve pre-
dictive validity. He said that testing 1,000 C57 black 6 mice is similar to
testing 1 C57 black 6 mouse 1,000 times, making it difficult to extrapolate
findings. He again emphasized the importance of seeking predictive validity,
rather than exact face or construct validity, noting that the precise mutation
in the mouse is unlikely to be the same as that in the human, but that a simi-
lar mechanistic pathway is the key to translating findings from the animal
model into patient therapies. An idealized mouse model (see Figure 3-2),
said Burgess, would be one in which the patient variant introduced into the
mouse resulted in face validity and construct validity, the phenotype was
tested on multiple backgrounds, and the model had good predictive validity
and could improve patient care.

UNIQUE ANIMAL-BASED APPROACHES
Opossum
Jennifer Maier, postdoctoral research associate at the University of
California, Los Angeles, introduced workshop participants to a novel spe-
cies for animal-based research. Monodelphis domestica—otherwise known
as the opossum—is a small, pouchless marsupial native to South America.
Maier noted that this opossum is a different species than Didelphis virgin-
iana, the opossum common to the United States. The monodelphis opossum
breeds year-round, with litters of up to 13 pups. It is a genetically diverse,
U.S. Department of Agriculture (USDA)-regulated species that is easy to
care for, requiring a standard rat cage with nesting and bedding material,
and commercially available opossum chow. However, being a nonsocial
species, these animals cannot be group-housed after a certain age.
Opossums have some advantages over mice, including a shorter gesta-
tion period (14 days versus 21), slow development, and the fact that there
are some human orthologs present in opossums but absent in mice. The
pups are born at a stage that is equivalent to a 10.5-12.5-day-old mouse
embryo, take 2 months to wean, and because the opossum does not have
a pouch, the pups are exposed during this time and can be observed and
manipulated, said Maier. Compared to mice, opossums take 8 months to
reach full maturity and live about 3 years in captivity. The unique biologi-
cal characteristics of opossums make them a relevant model for studying
certain diseases; for example, they have a slower metabolic rate and a lower
body temperature than placental mammals.
Maier said that the opossum research community is growing, and that
many of the techniques that are used in mice can be adapted to opossums.
There are a number of resources available for monodelphis research, includ-
ing a well-annotated genome, husbandry guides, transcriptome libraries, a
well-established embryology guide, and the OpossumBase website, which
contains genetic and genomic data for the species.
The research that Maier presented focused on the development and
evolution of the limbs. She noted that mammalian limbs have a huge mor-
phological diversity, from the wings of a bat to the pectoral fin of a dolphin
to the arm of a human. Research on the limb system is well established,
particularly in animals such as the mouse and the chicken, and many of the
required genes are known and conserved in the opossum. Congenital limb
malformations are quite common in humans, caused by genetic mutations
or environmental triggers.
One area of research in Maier’s lab focuses on the effects of retinoic
acid on opossum limb and craniofacial development. Retinoic acid is a de-
rivative of vitamin A that is contained in some pharmaceuticals, including

acne treatments. Pregnant opossums were treated orally with retinoic acid
and the embryos were collected just before birth. All of the animals that
were treated with retinoic acid had missing digits (oligodactyly), and some
sort of craniofacial defect. Researchers determined that these malforma-
tions were associated with disruption of the expression of fibroblast growth
factor in the two major limb-signaling centers (the apical ectodermal ridge
and the zone of polarizing activity).
Another area of opossum research involves thalidomide, a well-known
teratogen that caused thousands of children to be born with limb, cranio-
facial, and vascular deformities in the mid-1950s. Mice and rats are not
susceptible to thalidomide, making it difficult to study in traditional animal
models. Research in which pregnant opossums were injected with thalido-
mide revealed that the animal is susceptible to the teratogen, with high
penetrance of mild deformation and recapitulation of several more severe
human thalidomide phenotypes. Opossums exposed to thalidomide gave
birth to pups with defects of the heart, blood vessels, limbs, amniotic sac,
and craniofacial area. Research is under way for molecular characterization
of these phenotypes, said Maier.
In addition to these areas of research on limb formation, monodelphis
is also currently being used to study the formation of the mammalian
middle ear and intervertebral discs, spinal regeneration, ultraviolet-induced
melanoma, and diet-induced hyperlipidemia. Despite the benefits of using
monodelphis as a model organism, there are also some drawbacks, Maier
said. One major challenge is the absence of techniques to create knockout
or other genetically modified opossums, which complicates functional test-
ing. Maier’s lab has received a grant to develop a method for making a
transgenic opossum, and the lab is currently studying a method in which
spermatogonial stem cells are cultured, expanded, and modified in vitro
before being transplanted into testes. In conclusion, Maier said that opos-
sums are an excellent model for biomedical and evolutionary questions, and
that advances in genetic modification of the species will make the opossum
an even more useful species for research.
Precision Pathology
Keith Mansfield, director of Discovery and Investigative Pathology
at Novartis Institutes for Biomedical Research, spoke to workshop par-
ticipants about using molecular pathology to evaluate animal models for
precision disease modeling. He started with a basic definition of molecular
pathology, describing it as focused on the study and diagnosis of disease
through the examination of molecules (generally DNA, RNA, and pro-
tein) within organs, tissues, or bodily fluids. Molecular pathology is mul-
tidisciplinary in nature, integrating genomics, genetics, proteomics, and

physiology with morphology, and it utilizes a number of tools, including

immunohistochemistry and in situ hybridization. Mansfield said that mo-
lecular pathology is used to delineate the molecular basis of morphologi-
cal or structural changes in tissues and how those changes are related to
functional alterations. Molecular pathology is frequently used in the clinical
diagnosis and management of cancer patients and is one of the foundations
of precision medicine. Mansfield’s presentation focused on describing a few
of the main molecular pathology techniques and tools and how they may
relate to precision medicine.
One key technique in molecular pathology is molecular localization,
the ability to define the spatial distribution of molecules, such as proteins
or nucleic acids, in tissue sections. Molecular localization allows the pa-
thologist to understand how alterations in the spatial orientation of these
molecules relate to functional deficits in the organism. Molecular localiza-
tion can be performed using tools such as immunohistochemistry or in situ
hybridization.
Immunohistochemistry is a technique that uses antibodies—usually
linked to an enzyme or a dye—to test for disease markers in a tissue sample.
Mansfield said that immunohistochemistry has advanced enormously over
the past decade; automated staining platforms have increased the efficiency
and reproducibility of the assay, reducing the length of the process from 12
to 1-2 hours. However, he noted that a shortcoming of these assays is the
quality of commercial antibodies, and the resulting difficulty in validating
an assay before use in the clinic or an experiment. There is no single gold
standard to validate an immunohistochemistry assay, said Mansfield. In his
experience, most commercially available antibodies are not specific or sensi-
tive for the target. Traditional immunohistochemistry assays can be used
to simultaneously analyze 5-6 antibodies. However, new platforms—such
as image-amassed cytometry, or laser ablation inductively coupled plasma
amassed imaging—are highly multiplexed assays, allowing the analysis of
up to 20 or 30 markers simultaneously. Mansfield noted that these tech-
nologies are not yet ready for routine use, but they have a lot of potential
utility.
In situ hybridization allows pathologists to identify specific chromo-
somes in tissue through the hybridization (attachment) of probes that
have been linked to a dye. Like immunohistochemistry, automated staining
platforms have made in situ hybridization more efficient and reproducible.
A new generation of probes has improved sensitivity and specificity, said
Mansfield, because they can detect splice variants and single-nucleotide
polymorphisms (SNPs).
Biobanks are a sometimes forgotten but critical resource in molecular
pathology, said Mansfield. Biobanks that contain well-curated collections
of normal and diseased human biological samples, in combination with

samples from animal models, can help researchers determine the similarities
and differences in morphology and molecular alterations between humans
and animal models. This side-by-side comparison can determine the com-
parative relevance as well as the potential limitations of animal models and
inform the selection of models that most closely parallel the aspects of the
disease under investigation. Such careful selection of animal models can
reduce the number of animals needed to complete an experiment. Mansfield
gave an example of the importance of choosing the right animal model: in
comparative molecular pathology research of pancreatic adenocarcinoma,
researchers found that there were significant differences in the morphology
between human and mouse tumor cells. Mansfield noted that, in this case,
genetically engineered organoids were better at reproducing the morphol-
ogy than mouse models. Mansfield stressed that these differences between
human and animal models do not mean that animal models are not useful,
but that we need to understand how differences in morphology may impact
the relevance of the disease in modeling human cancer.
Digital pathology has advanced the field of molecular pathology in
significant ways, said Mansfield. In traditional pathology, tissue samples are
collected, processed, stained, and delivered to the pathologist who looks
at them through a microscope and writes a report. The slides are archived,
but there is little ability to access information contained in the slide or in
the report at a later date. In contrast, in digital pathology slides are scanned
and stored in a database along with all associated metadata. This allows
pathologists to review slides and data at any time and to analyze morpho-
logical diagnoses along with patient metadata in order to discover novel
patterns associated with diseases. In addition, digital pathology facilitates
whole-slide image analysis, allowing a pathologist to quantitatively measure
things such as staining intensities, cell number, cell morphology, and the
spatial relationship between cells.
Tissue microarrays—in which one slide contains samples from many
cases—is another advance in molecular pathology. Tissue microarrays can
hold 100 or more samples on a single slide, and custom arrays can be cre-
ated that focus on a single species, organ, or disease process. Mansfield
noted that the commercially available tissue microarrays are inconsistent
in quality, so he finds internal creation of the assays to be beneficial. The
automated platforms for immunohistochemistry and in situ hybridization
can be used for these tissue microarrays, and thousands of samples can be
analyzed in a matter of hours. Image analysis software can be used to as-
sess and measure the images that are generated with this high-throughput
analysis.
Other new technologies in molecular pathology include spatial tran-
scriptomics and genomic expression profiling. Spatial transcriptomics al-
lows the pathologist to profile several thousand genes within a single slide,

and to resolve the spatial orientation of changes within that gene expres-
sion. Genomic expression profiling can be coupled with morphological
interpretation of tissue to assist in elucidating the pathogenesis of disease.
Paired samples are routinely taken for genomic profiling and processing
for histological analysis, said Mansfield. The analysis involved in genomic
expression profiling is complex because changes in overall gene expression
may result from alterations in individual cells as well as from changes in the
cellular composition of tissue. Molecular localization studies can be used to
confirm expression changes and cellular source.
Mansfield concluded that molecular pathology advances our under-
standing of comparative pathogenesis of human disease in relevant animal
models. He said that molecular pathology is a rapidly advancing field that
integrates traditionally anatomical pathology skills with molecular biology
and bioinformatic approaches. Mansfield stressed that the interrogation of
tissues from precision animal models should be made in conjunction with
the evaluation of human disease tissues in order to better understand the
models’ relevance and limitations. Future advances in the field of molecu-
lar pathology will build on the use of bioinformatics, particularly highly
multiplex localization assays and computational interrogation of digital
slide databases.
Mouse Hospital Co-Clinical Trials

John Clohessy, director of the Mouse Hospital/Preclinical Murine Phar-
macogenetics Facility at Beth Israel Deaconess Medical Center and Harvard
Medical School, presented a unique and promising approach in animal-
based research for precision medicine. The “mouse hospital” model allows
clinical trials to be held simultaneously with mice and humans, enabling
rapid, real-time transfer of information from mouse experiments to human
trials. For these trials, appropriate genetically engineered mouse models
(GEMMs) are identified based on tumor genetics to act as surrogates for
the human patient, or patient tumors are engrafted in immunodeficient mice
to create patient-derived xenograft (PDX) models. The mouse models are
used to test sensitivity of tumors to treatments, and real-time integration
of these data is used to inform patient treatment protocols and improve
patient outcome.
Clohessy explained that the genesis of the mouse hospital model came
out of an acknowledgment that every patient has a unique disease in terms
of its molecular characterization and its progression and response to treat-
ments. The traditional drug development process does not reflect this, while
also suffering from a number of shortcomings. Traditionally, diseases and
cancer types are classified based on antiquated nomenclature and histopa-
thology, said Clohessy, rather than the tumors’ molecular profiles. Drugs

are evaluated based on statistical trends in patient response, with response

rates as low as 20% often deemed adequate for approval. A low response
rate does not necessarily mean that the drugs are not useful, said Clohessy,
but that perhaps the patient populations are not as well defined as they
could be. Clohessy noted that, although there are many promising agents,
and much has been invested in the quest to find new cancer drugs, the
number of new drugs approved by the U.S. Food and Drug Administration
(FDA) has decreased in recent years. In addition, cancer is revealing itself to
be a very sophisticated disease capable of modifying itself and developing
resistance to treatments.
For these reasons—the unique and complex nature of cancer and the
inadequate current drug development system—Clohessy said there is a need
for improved disease models and a new system of disease classification and
drug development. This ideal new system would provide disease models,
including patient surrogates, to account for the complexity of biologic
systems and the inherent inter- and intra-patient heterogeneity of human
cancers. The system would link agents to their molecular targets using
predictive modeling. Finally, there would be improved clinical trial designs
based on predictive biomarker validation strategies, which could be tested
and validated with a single trial.
The mouse hospital’s mission is to provide expertise in the design and
implementation of preclinical trials to test new drugs in mouse models of
human disease. By performing pre- and co-clinical trials with GEMMs and
PDX models, researchers can determine which patients are more likely to
respond to novel therapeutic agents, on the basis of their genetic makeup.
In addition, the progress from bench to bedside for promising new agents,
or combinations of already approved drugs, can be streamlined. The mouse
hospital, said Clohessy, is a state-of-the-art animal facility, with person-
nel who are trained in diseased mouse care, husbandry, and therapeutic
treatments, as well as dedicated areas in the vivarium for in vivo imaging,
behavioral testing, and surgical procedures.
The ultimate goal, said Clohessy, is to have mouse hospitals throughout
the country and the world. These hospitals would be credentialed and ac-
credited, and the data from the pre- and co-clinical trials would be centrally
deposited. Clohessy explained that the mouse hospital is currently in the
proof-of-concept phase, working in concert with the cancer clinical center
and the cancer research institute at Beth Israel Deaconess Medical Center.
Clohessy said that the collaboration between the patient care teams and the
researchers is an iterative process that allows patient treatments and patient
care to be tailored to improve outcome.
Clohessy explained the ideal structure of these co-clinical trials (see
Figure 3-3). First, when a patient is diagnosed with a tumor, a mouse model
is either selected (GEMM) or created (PDX). While the patient is undergo-

FIGURE 3-3 Co-clinical mouse trials for cancer.

FIGURE
SOURCE:3Clohessy
-‐3 Co-‐clinical mouse
and Pandolfi, 2015.trials for cancer
SOURCE: Clohessy, J. G. and P. P. Pandolfi. 2015. Mouse
hospital and co-‐clinical trial project-‐-‐from bench to bedside.
ing standard-of-care treatment, a mouse clinical trial is conducted to screen
Nat Rev Clin Oncol. 12(8):499.
treatments. The findings from the initial mouse trials are used to adjust the
treatment strategy for the human patient, and at the same time, the initial
outcomes of the human patient are used to inform the direction of research
in the mouse models. Final outcomes from the mouse trial, along with in-
formation about how the human patient has responded to treatments, are
used to optimize the treatment of the human patient.
In order to fully realize the potential of mouse co-clinical trials, a num-
ber of challenges need to be overcome, said Clohessy.
1. Reevaluation and Repurposing of Existing Models

There may be improved ways to utilize the multitude of available
cancer models, Clohessy said, and described ongoing research that uses
GEMMs to study lung cancer at a single-cell level. Researchers focus on
subpopulations of tumor cells to understand how these respond to treat-

ment, to predict the emergence of resistance or to identify populations of

cells that may be resistant at an early stage of the disease. These data from
the animal models are used in concert with data from primary human tu-
mors to more fully understand cancer at the cellular level and develop more
precise treatments.
2. New Approaches for Model Development

Using GEMMs in a co-clinical trial approach is lengthy and costly,
said Clohessy, as it takes a significant amount of time to develop and
breed mouse cohorts that are appropriate models for a single patient. To
address this challenge, the mouse hospital has developed a platform called
orthotopic graft of GEMM-derived organoids (OGGO). This platform has
allowed researchers to isolate prostate cells, grow organoids in vitro, and
manipulate their genetic makeup. These organoids can be placed into ge-
netically homogeneous mice to allow researchers to track the development
of disease and study the diversity of human cancers.
3. Co-clinical Implementation of Models Toward Therapy

Leukemia mouse models are used to develop and evaluate novel thera-
peutic approaches, said Clohessy. Mutations in the IDH2 gene occur in
about 20% of patients with acute myeloid leukemia. A recently developed
mouse model allows the study of the dependence of the disease on IDH2
expression. Through a serial transplantation protocol, researchers have de-
veloped a number of models with variable sensitivity to the de-induction of
the mutation. These models are compared using metabolomics, genomics,
and transcriptomics, and through this comparison, researchers have identi-
fied both novel resistance mechanisms and novel vulnerabilities. Clohessy
said that clinical trials for therapeutic approaches based on these findings
are in development.
Pets with Naturally Occurring Tumors

Amy LeBlanc, director of the National Cancer Institute’s Comparative
Oncology Program, told workshop participants about how the Compara-
tive Oncology Program (COP) may present an opportunity to further the
field of precision medicine. Through the Comparative Oncology Trials
Consortium, COP facilitates clinical trials for pets with cancer at 22 veteri-
nary teaching schools in North America. These trials offer pets (and their
owners) the chance to receive treatments, while also offering researchers
an opportunity to assess new treatments with naturally occurring cancer
models and to collect relevant data on toxicity, response, drug dosing, bio-

markers, and histology. In addition, COP has a laboratory that is currently

focused on the biology and metabolism of metastasis in osteosarcoma in
dogs, and the development of molecular imaging tools to help interrogate
laboratory findings and translate them into the clinical trial setting. About
4.2 million dogs are diagnosed with cancer every year, and cancers in dogs
and humans are remarkably similar, said LeBlanc. Dogs develop cancer in
many of the same areas of the body as humans. While dogs and humans
are not always a perfect match, there are many types of cancer in dogs that
are appropriate models for humans, said LeBlanc.
Comparative oncology trials provide an iterative process where stud-
ies on dogs can inform studies on humans, and vice versa, with the overall
gain in knowledge advancing the understanding of cancer and potential
treatments, said LeBlanc (see Figure 3-4). For example, initial studies on
dogs with tumors can produce data about potential treatments, including
activity, toxicity, pharmacokinetics, and pharmacodynamics. These data
FIGURE 3-4 Comparative

FIGURE 3-4 Comparative oncology with dogs.
SOURCE: Paoloni and Khanna, 2008. oncology with
dogs
SOURCE: Paoloni, M. and C. Khanna. 2008. Translation of new
cancerCopyright
treatments from pet dogs to humans. Nature Reviews
National Academy of Sciences. All rights reserved.
can then inform phase I human clinical trials, and data from both of these
trials can inform further research on the dog and human patients on dose,
regimen, and biomarkers.
LeBlanc gave two examples of successful comparative oncology tri-
als. One trial focused on a novel immunocytokine (NHS-IL12), which the
manufacturing company was ready to give up on. Dogs receiving the im-
munocytokine responded favorably. The efficacy data resulted in enough
enthusiasm to generate an Investigational New Drug application to the
FDA, and eventually phase I clinical trials. The data also helped in bio-
marker selection. The second example was a trial to compare three TOPO-1
inhibitors in dogs with lymphoma. The data from dogs suggested that one
of the drugs was more biologically active than the other two, a result that
was not obvious from preclinical mouse research.
The initiation of a new clinical trial by COP is being done to meet
a specific need that is unmet by human drug development and fill a gap,
said LeBlanc. She said that data on drug efficacy may not always be the
top priority; trials may focus on target modulation or pharmacodynamic
and pharmacokinetic relationships. The FDA views data from comparative
oncology trials as important but supplementary; according to LeBlanc, the
agency has stated that data from comparative oncology trials will not derail
the clinical development of a drug or result in a clinical hold.
Regarding precision medicine, LeBlanc said that the biggest area yet to
be addressed is the genetic landscape of canine cancers. Most comparative
oncology research to this point has focused on clinical observations, rather
than on collecting and analyzing genetic data about potential mutations
associated with cancers. In order to move precision medicine forward,
comparative oncology researchers will need analytic tools and expertise to
collect genetic information; LeBlanc noted that because they are not bound
by privacy rules regarding human data collection, there is an opportunity
to build a robust set of data in this area.
LeBlanc discussed new funding initiatives from the National Can-
cer Institute (NCI) that pertain to precision medicine. In 2016, the NCI
distributed eight awards (totaling about $4 million) for cancer centers to
characterize the molecular landscape of selected canine cancers. The goals
of these awards are to
• sequence (by whole exome sequencing and RNAseq) at least 25

canine tumors, including B-cell lymphoma, glioma, osteosarcoma,
melanoma, bladder cancer, and mammary cancer;
• determine the mutational load in the cancers chosen for study;
• use appropriate computational tools to characterize neoantigens
that can strongly bind canine MHC antigens; and

• describe and characterize the T lymphocyte numbers and subsets,

as well as other relevant aspects of the tumor microenvironment,
within the canine tumors.
The second step of this initiative was a Request for Application (RFA)
for studies investigating the utility of dogs with cancer as models for immu-
notherapy development. The short-term goals of this RFA are to establish
a network of laboratory scientists and canine clinical trialists to study the
anti-tumor effects of immunotherapy agents and novel combinations of
immunotherapy and other modalities, and also to establish a coordinating
center to implement the clinical protocols and manage data from these tri-
als. In the long-term, the NCI will use these data to establish the suitability
of canine models for studying immunomodulating agents, and to eventually
translate the findings to human studies. The awards from this RFA were
announced in mid-2017, with five institutions receiving about $15 million
in total.
LeBlanc concluded that finding success in precision medicine in this
area depends on the advancement of our knowledge regarding cancers in
dogs. She said, however, that there has been significant progress in recent
years in terms of awareness, advocacy, funding, and research, and that
comparative oncology presents a great opportunity to learn more and con-
tribute to the care and treatment of both humans and dogs.
CHALLENGES OF USING ANIMAL MODELS

FOR PRECISION MEDICINE
Big Data
Clinical care and research on humans and animals generate a huge
amount of data, said Melissa Haendel, associate professor of medical in-
formatics and clinical epidemiology at Oregon Health & Science Univer-
sity. There are data from individual patients regarding clinical phenotypes,
-omics, socioeconomic factors, environmental exposure, and other factors;
there are population-level data on population frequencies, disease correla-
tions, risk statistics, and exposure data; and there are data stemming from
model organism research. Despite this plethora of data, most clinical di-
agnostic pipelines leverage only a tiny fraction of it. Haendel said that the
challenge lies not in producing more data but in improving the utilization
of data.
One of the problems, said Haendel, is that different communities—
including researchers, clinicians, patients, and animal scientists—use dif-
ferent terms to describe signs and symptoms of the same clinical entity.” A
disorder characterized by thickening of the skin on the palms and soles may

be called by the clinician “palmoplantar hyperkeratosis,” by the patient

“thick hand skin,” and by an animal scientist “ulcerated paws.” Haendel
noted that human patients are often described in terms of billing or elec-
tronic health record codes, while model organisms are described fairly
specifically in terms of anatomy, morphology, and other characteristics. The
issue, said Haendel, is that these data are not relatable to one another, and
the language barriers between fields become very problematic. Because of
this wide variety in terms, it is quite challenging for researchers to work
across multiple research or clinical datasets.
Haendel said that there are hundreds, if not thousands, of standards
used to describe phenotypic features. The Human Phenotype Ontology
project attempts to bridge this phenotypic semantic confusion by using a
logic structure to classify phenotypes according to standardized terms. The
project uses species-neutral ontologies and homologous concepts, drawing
from evidence from the literature, database resources such as OMIM and
Orphanet, and other existing clinical and research ontology standards. The
logic model can deduce that palmoplantar hyperkeratosis and ulcerated
paws are the same phenotype, based on the underlying phenotypic profile
and the terms used to describe the phenotype. This approach makes it pos-
sible to integrate data from both clinical and model organism sources. Each
source has its own ontology, but the application of species-neutral ontology
allows the data to be harmonized. Haendel noted that between—or even
within—data sources, the same phenotype is sometimes associated with a
different component of the genotype, and that harmonizing these sources
creates an opportunity to find novel associations.
Using these data for diagnosis depends on the use of a fuzzy matching
algorithm that compares patient genotypic and phenotypic data against
similar data from human and model organism sources. Through this pro-
cess, the algorithm may, for example, find that an ortholog of “Gene
M” from a mouse with a similar phenotype might be a candidate for the
disease of “Patient A.” In addition to the new insight into a potential
gene–phenotype association, this process also may result in collaboration
between a clinician and a researcher, each of whom have expertise to share,
said Haendel.
The use of such data-harmonizing technology, Haendel said, has im-
proved the diagnostic rate of the NIH’s Undiagnosed Diseases Program by
10 to 20%. The technology also facilitates the matching of patients across
the globe through a site called Matchmaker Exchange. By matching undi-
agnosed patients using both clinical and public data sources, candidate vari-
ants can potentially be validated, and patients and providers from around
the world can collaborate to find diagnoses.
Haendel closed by stressing the importance of developing the right
model for a disease. She said that researchers sometimes settle on models

that generally recapitulate some phenotypic aspects of the disease, rather

than using precise phenotypic data to find which aspects of the phenotype
are actually being recapitulated. While a model organism is unlikely to
recapitulate every aspect of the phenotype, having more information about
similarities and dissimilarities between the organism and humans will en-
able researchers to learn more about the disease. She added that, in some
cases, nontraditional organisms may be the best choice for a model—for
example, aged cats are good models for Alzheimer’s disease, armadillos are
a natural host of the myobacterium that causes leprosy, and pig eyes most
closely resemble human eyes. Haendel said that she and her colleagues are
currently working on new strategies to assess the suitability of different or-
ganisms for modeling specific phenotypes, so that organisms are not chosen
simply because they are the ones “we happen to have in our basement.”
The Animal Rule and Appropriate Modeling

Jens Kuhn, virology lead at the NIH/National Institute of Allergy and
Infectious Diseases Integrated Research Facility (IRF) at Fort Detrick, began
with a brief description of the work performed by the IRF. The IRF seeks
to develop prevention and treatment options for infectious human diseases,
whether naturally emerging or deliberately introduced (e.g., in a bioterror
attack). He noted that the infectious agents that IRF focuses on tend to be
quite rare, with outbreaks few and far between. The one notable exception,
he said, is Ebola, which has received more money and attention since the
2014 epidemic, and as a result is better understood than the other agents.
Kuhn said that the goal of IRF is the rapid development and the licensure
of efficacious countermeasures against diseases caused by these agents. The
infectious agents that they focus on have the ability to migrate quickly,
with a short incubation period, and tend to appear in areas that lack the
resources for proper testing, treatment, and supportive care. He noted that,
while most natural outbreaks of these diseases are small and isolated, the
potential for bioterrorism implies the need to have something ready to treat
a lot of patients. Due to the deadly nature of the agents being investigated,
animal models are essential for understanding the mechanisms of disease
and testing the safety and efficacy of potential countermeasures.
The FDA’s Animal Rule was designed with this type of research in
mind, where human efficacy trials are not feasible or ethical due to the na-
ture of the agent being studied. The rule, which was implemented in 2002
amidst concerns about bioterrorism, allows the FDA to rely on evidence
from animal studies when considering approval of a medical counter-
measure. In order to fall under the auspices of the animal rule, there are
a number of criteria that must be met: There must be a “reasonably well
understood pathophysiological mechanism,” the effect of the countermea-

sure must be “demonstrated in more than one animal species . . . predictive

for humans” or in a single species that is “sufficiently well-characterized”
for predicting the response in humans, the animal study end point must be
“clearly related to the desired benefit in humans,” and the pharmacokinetic
and pharmacodynamic modeling must allow “selection of an effective dose
in humans” (21 CFR Sec. 314.610).
Kuhn said that it would be extremely challenging for research on rare
infectious agents to meet these criteria for a number of reasons. The details
of the human clinical disease for most of these agents are not well-defined.
Because outbreaks tend to be rare and in isolated, resource-poor areas, the
phenotypic descriptions of these diseases are limited to a few observations
that doctors have made, for example, noting that the patient has rash, pale
skin, and tremor. With such a lack of information, how can researchers
develop a reasonable model that faithfully recapitulates the human disease?
Kuhn said the emphasis has long been on developing models with face va-
lidity (i.e., models that recapitulate the symptoms), but that this approach
is problematic and leads to using animal models that may not, in fact, be
particularly relevant. For example, mice infected with Ebola do not develop
a rash, whereas nonhuman primates (NHPs) do. This phenotypic differ-
ence, combined with the fact that NHPs are closely related to humans, has
sometimes led researchers to conclude that NHPs are the gold standard in
research and to dismiss the use of other animal models. However, there are
two issues with this conclusion. First, said Kuhn, the gold standard animal
model becomes reified despite significant differences between the model and
humans. For example, even though gorillas share 99.6% of human genes,
they are vegetarians and thus would be a terrible model for studying the ef-
fects of meat consumption on the human body. Second, the non-expression
of a specific phenotype does not necessarily mean that the disease is not
recapitulated. That is, the pathway of the disease may be the same in an
animal model and in humans, but the animal model may not express the
phenotype due to some other factor, for example, a stop codon.
Kuhn concluded with a quote from Thomas Hartung: “If there was
an animal model good enough to substitute for people we would not have
a 92% failure rate in clinical trials” (Dolgin, 2013, p. 118). Kuhn noted
that the issue is not whether animal models are useful, but rather that the
research community has not thought in depth about how to best develop
and utilize the models. He suggested that inertia has led researchers to
continue to use the same models they have always used, and to look for
face validity rather than at deeper pathways and more relevant mechanisms.
Kuhn imagined a future scenario in which animal models would be highly
relevant and useful for all types of clinical trials: “we would have tons of
different animal models at our fingertips that are very well characterized
all the way to the genomic and mutational and allele level, and we would

have . . . 1 million human genomes available and they are also fully char-
acterized and span the entire spectrum of ethnicities.” Kuhn said that in
order to reach this future, researchers must start not with the practical and
regulatory concerns about what is possible or acceptable, but instead by
choosing the best animal model and the best approach for answering the
scientific question at hand.

Reproducibility and Predictivity
Key points:
• Science as a whole has a reproducibility issue, and animal
studies may be in even more trouble regarding reproducible
outcomes. (Hoitinga)
• The ARRIVE Guidelines were an important step, but they need
to be adopted and followed in order to be effective. (Hoitinga)
• There are structural and systematic problems in research, such
as the concept of multiplicity, that lead to lack of reproduc-
ibility. (Manrai)
• The paradox of precision medicine is that, in order to make
medicine truly “personalized” for a specific individual or group
of individuals, research necessarily involves a small number of
people, which makes results far less reliable. (Kimmelman)
he fourth chapter recapitulates the discussions around essential

T
elements of reproducibility that have been studied in translational
fields, such as stroke research, or that arise through the use of com-
munal and large datasets, and how reproducibility can be sustained
in the context of precision modeling.
51

TRANSLATIONAL STROKE RESEARCH: THE

“WORST PRACTICES” OF ANIMAL RESEARCH
Ulrich Dirnagl, professor and director of the Department of Experi-
mental Neurology, Charité Universitätsmedizin Berlin, Germany, took a
different tack than some of the earlier speakers in the workshop. Rather
than talking about the successes or opportunities of animal research, he
discussed his work in translational stroke research as a cautionary tale.
Dirnagl said that learning from the “worst practices” of his field could help
other researchers do better in the future. Over the last decades, researchers
studying stroke in animal models have published “thousands of articles
in top journals,” using “millions of animals” while consuming “a lot of
money.” However, the treatments that were found to be highly effective in
animal models had no effect—or even a negative effect—once they were
translated into clinical trials on humans. For example, a meta-analysis
of animal studies on neuroprotectants found a mean treatment effect of
roughly 30%. When tested on humans, these neuroprotectants had no ef-
fect or even may have harmed patients. There remains only one clinically
proven pharmacological therapy for acute ischemic stroke, and no proven
way to protect or regenerate the brain, said Dirnagl.
“If translation is possible—at least in principle—then why have we not
succeeded in neuroprotection” posited Dirnagl. While the easiest answer
is that animals are simply different than humans and cannot be used to
predict human response, Dirnagl said that he feels this is highly unlikely.
Citing several examples in which animal models were useful for stroke re-
search, Dirnagl said that there are several reasons why stroke drug research
in animals has been unsuccessful.
First, said Dirnagl, many of the animal studies published in the stroke
field suffer from a lack of internal validity. There is selection bias, with
randomization practiced around 30% of the time. In addition, there is high
performance and detection bias, with blinding also practiced around 30%
of the time. Attrition bias is widespread: treatment and control groups often
have different sizes, which is often due to loss of animals/group that is not
adequately explained.
Second, many of these studies also suffer from a lack of external and
construct validities. Dirnagl compared a group of mouse subjects, all of
whom are young inbred twins who have been raised in isolation and fed on
a strict diet of granola, to the diversity of the human population, who vary
widely by age, sex, comorbidities, medications, and exposure to pathogens
and antigens throughout life. All of these cofounders in humans are not
replicated in the animal model and make it difficult for such research to
predict the response of human patients. As examples, Dirnagl presented one
study in which a drug had an effect on males but not females (Harhausen

REPRODUCIBILITY AND PREDICTIVITY 53
et al., 2010), and another where the drug only worked in younger subjects
but not older (Thériault et al., 2016). Another study found that an interven-
tion worked only in subjects that were not hypotensive (De Geyter et al.,
2013). Factors such as gender, age, and co-morbidities are highly relevant
for human patient populations, but animal research often does not account
for this variability, said Dirnagl.
A third issue is the high degree of standardization in animal models;
subjects are usually kept in identical environments and treated identically,
to the extent possible. While this is often seen as a benefit to animal studies
because it removes the influence of known variables, it can lower external
validity by finding “truths” that are only valid in the controlled environ-
ment of the study (Richter et al., 2009). This effect makes the research less
reproducible and less predictive of the response seen by the human patient,
said Dirnagl.
A fourth issue is the use of specific pathogen free housing facilities,
which are free from certain infectious organisms in order to prevent these
organisms from interfering with the experiment. These conditions result in
mice with the immune status of a newborn, which may have tremendous
consequences for the ability to translate data from these mice into humans.
Finally, there is a complete power failure in the way experiments are
done, said Dirnagl. A meta-analysis found that the mean group size in
stroke mouse studies was eight subjects (Holman et al., 2016), which gives
these studies a mean statistical power of around 45%. This means, said
Dirnagl, that the false-positive rate and the overestimation of true effects
are both around 50% (Dirnagl, 2016).
Dirnagl addressed the issue of avatar mouse models (i.e., co-clinical
trials), in which mice are transplanted with patient-derived xenografts in
order to screen for anti-cancer drugs for an individual patient. While this
approach has promise, Dirnagl cautioned that this personalized animal
research may suffer from the same issues as traditional animal model
research, such as lack of statistical power, lack of internal and external
validity, and lack of attention to the effect of comorbidities and other con-
founders. The lack of a mature immune system in mouse models may be
particularly problematic for xenotransplant research. Dirnagl concluded
that most of the issues, which have confounded population models, would
remain problematic in our personalized models, so attention must be paid
to them.
SYSTEMATIC REVIEWS
Merel Ritskes Hoitinga, professor in evidence-based laboratory animal
science at Radboud University Medical Center in the Netherlands, said
that in order to move forward with animal-based research for precision

medicine, it is important to first reflect on the current situation, which

unfortunately, is a “reproducibility crisis.” A 2015 analysis reported that
the non-reproducibility of preclinical studies is somewhere between 51%
and 89% (Freedman et al., 2015). One consequence of this reproducibility
crisis, said Hoitinga, is a translation crisis. As Ulrich Dirnagl discussed, the
translation success rate in stroke research is “abysmally low,” and the fact
that the number of drugs being approved annually by the U.S. Food and
Drug Administration (FDA) has declined in recent years suggests that there
is a problem. The reproducibility crisis has a number of possible causes,
said Hoitinga, including the following (Prinz et al., 2011):
• Lack of reporting of methodological details

• Lack of standardization
• Incorrect statistical analysis, insufficient sample sizes
• Interaction with different environmental influences
• Selective reporting of results
• Bias toward publishing positive results
• Significance chasing
• Errors undetected in the current peer-review system
Fortunately, said Hoitinga, there is a solution to this crisis: system-

atic reviews. Systematic reviews are an appropriate avenue for providing
transparency in support of the quality of animal studies and will hopefully
trigger improvement in the field. Hoitinga and her group at the Systematic
Review Centre for Laboratory Animal Experimentation (SYRCLE) teach
researchers how to perform systematic reviews. SYRCLE holds workshops,
provides coaching and supervision, develops guidelines and tools, and has
started an international network of ambassadors who promote systematic
reviews of animal studies in their local areas. In addition, SYRCLE executes
systematic reviews and attempts to identify success factors for translation
of animal studies. The six steps of a systematic review are fairly simple, but
it is important to perform them carefully and objectively in order to reach
evidence-based conclusions, said Hoitinga.
1. Phrase the research question

2. Search for all evidence
3. Select relevant studies
4. Extract characteristics (e.g., species, sex, dose)
5. Assess study quality
6. Perform data meta-analysis
The benefits of systematic reviews are myriad, according to Hoitinga.

Systematic reviews can help researchers make an evidence-based choice

of animal models. For example, a series of systematic reviews revealed

that rodents were a poor choice for modeling cartilage defect and that
large-animal models would be more appropriate (de Vries et al., 2012).
Systematic reviews are linked to more translational transparency and can
help with implementing the three Rs across animal-based research (replace,
reduce, refine). For example, a systematic review found that there had been
many animal studies showing that chemotherapy reduces wound healing
(Jacobson et al., 2017); now this is a known effect, and the experiments do
not need to be repeated, said Hoitinga. Finally, systematic reviews make re-
porting quality transparent. By gathering and analyzing all relevant studies,
a systematic review can reveal where there are issues with the quality of the
research, for example, whether the studies reported the use of randomiza-
tion and blinding. This last benefit is extremely important for translation.
Fifty to 80% of studies do not report if they used randomization or blind-
ing; when a study does not report on these factors it is unclear whether or
not the results are reliable or reproducible as the results could overestimate
the effect of an intervention and—upon translation—unnecessarily expose
patients to potential harms (Horn et al., 2001; Sena et al., 2010).
Improving the reporting quality of animal studies is the goal of the Ani-
mal Research Reporting In Vivo Experiments (ARRIVE) guidelines, which
were first published in 2010 and have since been adopted by hundreds of
journals. The ARRIVE guidelines provide a checklist of details to include
in submitted papers, including species and strain of animals used, random-
ization and blinding procedures, and drug formulation and dose (Kilkenny
et al., 2010). The guidelines are included in the instructions to authors
for journals that have adopted them. Unfortunately, there has been hardly
any improvement in publication quality of animal studies, said Hoitinga.
A report in Science indicated that researchers are either unaware of the
guidelines or are simply ignoring them (Enserink, 2017). There are efforts
afoot to improve the uptake of ARRIVE, but it will take commitment and
culture change among those involved, including funders, editors, academics,
and laboratory animal veterinarians.
Hoitinga concluded with a simple statement: “Transparency provided
by systematic reviews leads to subsequent improvements in quality of re-
porting,” and high-quality reporting leads to a more reliable assessment
of the translation potential of data. Moving forward in precision medicine
will require the use of animal models that are chosen based on high-quality
evidence from well-reported and replicable studies. Performing systematic
reviews of studies will help ensure transparency and high quality.

REPRODUCIBILITY IN LARGE SHARED DATASETS

Arjun Manrai, instructor at the Department of Biomedical Informatics
at Harvard Medical School, began with a quote from Karl Popper: “Non-
reproducible single occurrences are of no significance to science” (Popper,
1959, p. 86). Reproducibility is a very old concept, he said, that has gained
a great deal of attention lately. The crisis of reproducibility in science has
been particularly prominent in drug development, but he noted several
efforts to monitor it, including Retraction Watch, a blog that tracks retrac-
tions as a window into the scientific process (retractionwatch.com), and
multiple studies that have identified numerous instances of irreproducible
data (e.g., Begley and Ellis, 2012).
Attempts to improve the reproducibility of biomedicine and animal sci-
ence, said Manrai, have largely focused on the responsibilities and obliga-
tions of the individual researchers. A 2016 survey by Nature asked 1,500
scientists what could improve reproducibility: the top two answers were
“better understanding of statistics” and “better mentoring and supervision”
(Baker, 2016). However, said Manrai, it is not just an issue of individual
knowledge and responsibility. There are critical structural factors that
influence the reproducibility of study findings that need to be understood
and addressed. One of these structural factors—hidden multiplicity—is
particularly relevant for precision medicine research.
Manrai discussed two technologies common in precision medicine—the
simple nucleotide polymorphism (SNP) chip and the large shared database.
He said that multiplicity is explicitly and rigorously addressed in the con-
text of the SNP chip, but almost never addressed in the context of a large
shared database. The database resembles high-throughput technologies in
scale but not in synchrony: it is a tool utilized by many investigators for
multiple studies, but the studies are conducted over many years. Because of
the lack of synchrony, there is little attempt to address the issue of multiplic-
ity in these database studies. Manrai said that a 2005 paper titled “Why
Most Published Research Findings Are False” by John Ioannidis provides
a framework to think about the reproducibility of an entire field of science
(Ioannidis, 2005). Ioannidis applied the concept of PPV—usually used to
describe the positive predictive value of a diagnostic test—to a given scien-
tific field. Calculating PPV involves assessing several parameters, key ones
being “R” (the pre-study odds, i.e., the ratio of non-null to null relation-
ships that are being studied in the field) and “u” (bias term describing the
proportion of findings that are published that would not be published if
studies had been conducted perfectly).
Manrai has worked to extend the Ioannidis model to large datasets and
to develop a calculation for a new metric called “the dataset positive pre-
dictive value” (dPPV; Manrai et al., 2018). The math involved is complex,

but the general idea is to look at two key factors: how many researchers
are investigating different relationships, and how well these different stud-
ies are powered. Manrai noted that dPPV is a stochastic process that can
be written as the ratio of Poisson binomial distributions; that is, dPPV
is a time-varying random variable. A Poisson binomial distribution is a
generalization of the binomial distribution with non-equal probability of
success on each trial. Communal science settings that use large databases
are ubiquitous, said Manrai, for example, large federal datasets, such as
the National Health and Nutrition Examination Survey, as well as large-
scale genomics datasets, such as the Genome Aggregation Database and
the Mouse Phenome Database. In a recent publication documenting the
importance of reproducible precision medicine, Manrai examined classifica-
tions of patient records at a leading testing laboratory, and he found that
genetic variants were misclassified and that these misclassifications dispro-
portionately affected African Americans as compared to other populations
(Manrai et al., 2016). Understanding communal scientific inquiry through
frameworks like dPPV may help avoid such irreproducible data.
Using a simple scenario Manrai showed workshop participants how
to calculate the dPPV. In this scenario, 1,000 relationships are being stud-
ied, using a shared dataset. One study is performed per relationship, with
a significance threshold set at p < 0.05 for each study. The pre-study
odds—the ratio of non-null to null findings—is 0.001, and the studies are
well-powered at 0.8. It might seem, said Manrai, that this is a good setup.
However, if only the studies that survive the 0.05 threshold are reported,
the expectation of the reproducibility of the findings from this dataset is less
than 2%. Manrai explained that, although the statistical power exceeds the
false-positive rate by a factor of 16, the null relationships dwarf the non-
null relationships by a factor of a thousand. For some real-life examples
of the many paths researchers can take during data analysis that may be
unaccounted for, Manrai referred workshop participants to an article by
Gelman and Loken (2014).
The reproducibility of findings from a large shared dataset is influenced
by several factors, said Manrai. First, reproducibility is lowered when re-
searchers who arrive late to the dataset pursue hypotheses that are a priori
less likely. In this scenario, the key parameter is the ratio of non-null to
null hypotheses, represented by “R.” Researchers who had earlier access
to the dataset may have investigated relationships that were a priori more
likely. However, Manrai said that the reproducibility of research on less
likely hypotheses could be improved by performing studies with greater
power. When the first genome-wide association studies were conducted,
said Manrai, researchers learned about the effect size spectrum and com-
pensated by increasing sample sizes to the tens or hundreds of thousands
of individuals in order to find genome-wide significant associations. Effect

sizes may have been lower than initially hoped for, but the results were
much more reliable compared to previous work in human genetics and
candidate gene era studies.
Manrai noted that some of the findings of his work are counterintui-
tive. For example, he found that more studies per relationship tend to lower
the mean and increase the variance of dPPV. Although one would assume
that more studies would help to corroborate relationships, he explained
that, when there are many studies being conducted on a given relationship,
if the findings are selectively reported then the ones that are reported tend
to be less reproducible over time. Another finding, said Manrai, is that
dPPV variance reduces with more liberal data governance. That is, when
data are open and any researcher can conduct a study, the dPPV tends to
be less variable than when there are a small number of studies being con-
ducted on a dataset.
In concluding, Manrai stressed that multiplicity in large shared data
sets must be addressed. He also emphasized that, while individual respon-
sibility for reproducible data is very important, structural factors are just
as influential and critical.
THE PARADOXES OF PRECISION MEDICINE

Jonathan Kimmelman, associate professor in the Biomedical Studies
Unit/Social Studies of Medicine at McGill University, Canada, introduced
workshop participants to the five paradoxes of precision medicine. These
paradoxes, he said, are creating a very heavy demand for and an expecta-
tion about the quality of preclinical evidence, while concomitantly reducing
the ability to produce high-quality, reproducible evidence.
The first paradox, said Kimmelman, involves the issue of smaller sam-
ples. Precision medicine is aimed at taking heterogeneous populations and
dividing them into smaller groups that are more homogeneous (e.g., in
terms of response to medication). However, by breaking up the large groups
into smaller ones, research on the small groups has lower statistical power
with a higher degree of variance. Relying on traditional randomized con-
trolled trials may not be possible in these situations, said Kimmelman, so
researchers may need to combine different forms of evidence.
The second paradox is the issue of boundaries. Kimmelman explained
that one goal of precision medicine is to develop diagnostic techniques that
allow the stratification of patients. Diagnostic techniques typically rely
on establishing a boundary—a cut-off point that assigns individuals into
different categories. However, there may be a variation of alleles whose
location in regard to the boundaries is unclear. While it may be possible to
determine with a high degree of certainty how a specific individual with a
specific allele reacts to a drug, there may be uncertainty about how other

alleles will affect this response. Using multiple diagnostic techniques further
muddies the waters, said Kimmelman, because each technique has its own
boundaries and commensurate uncertainty about whether these boundaries
are drawn correctly. This creates a “proliferation of imprecision.”
The third paradox is the issue of algorithms and interpretation of data.
The data and algorithms used to determine how to match patients to treat-
ments are, obviously, critical to an accurate matching. The use of preclinical
data in these determinations can be controversial, said Kimmelman. Some
clinicians have chosen not to include any preclinical evidence due to con-
cerns about reproducibility, while others have determined that preclinical
evidence is clinically actionable in the absence of other higher forms of
evidence. The need for high-quality evidence to inform patient classification
algorithms compounds the demands on the quality of preclinical evidence.
The fourth paradox concerns the rapid evolution of knowledge and di-
agnostic techniques in the area of precision medicine. As precision medicine
advances, information is constantly accruing about treatment approaches
and patient populations, and techniques that evolve based on these new
data. By the time a study is published, said Kimmelman, the techniques or
algorithms used may already be outdated.
Finally, the fifth paradox is about integrating diverse datasets.
Kimmelman said that in non-precision medicine, large clinical trials with
a low degree of variance can be synthesized into a meta-analysis regarding
the clinical utility of a treatment. However, in precision medicine, the trials
are much smaller and may be testing different drugs or different diagnostic
techniques to classify patients. Aggregating such disparate information—
together with preclinical research—is a considerable challenge.
One other way that precision medicine is creating pressures on pre-
clinical research is the occasional reliance on preclinical research to make
clinical decisions. Kimmelman gave an example of a study on pediatric
solid tumors, in which the majority of findings on clinically actionable
mutations were based on preclinical research or even just “expert opinion”
(Harris et al., 2016). Kimmelman also reported a case in which a patient
was offered personalized off-label therapy, based on preclinical data that
was published in Nature (Al-Marrawi et al., 2013). In precision medicine,
he said, a treatment does not “necessarily have to go through clinical trials
to get to clinical practice, [which] creates some real pressures on getting the
preclinical evidence exactly right.”
In addition to these five paradoxes, Kimmelman discussed factors that
challenge the ability to make clinically generalizable inferences from pre-
clinical evidence. Kimmelman said that there are three steps in the cycle of
translation, with challenges or threats at each one. The first step is research
design. Threats at this step include design choices that lead to poor internal
and external validity. For example, lack of blinding or randomization, or

reliance on a study population that does not simulate the patient popula-
tion well. The next step, said Kimmelman, is reporting. As other speak-
ers discussed, there is a tendency to publish only positive studies, which
Kimmelman said is a real problem in the context of precision medicine. As
an example, he said that a meta-analysis of sorafenib research found that
the mean effect size dropped by about 37% when statistically corrected for
non-published preclinical studies (Mattina et al., 2016). The third and final
step is uptake, which depends in great part on the inferences made about
the preclinical research. Kimmelman noted that an experiment is valid only
insofar as the interpretation or clinical inferences made from the study are
accurate. Kimmelman’s team has done a systematic study of the quality of
inferences from preclinical research that revealed that experts were remark-
ably poor at predicting whether studies would be reproducible (Benjamin
et al., 2017).
Kimmelman made several recommendations for moving forward given
the paradoxes and the challenges he identified. The first recommendation
was to produce “clinical-grade preclinical evidence.” Because preclinical
evidence may be used to inform clinical decision making, it is critical that
preclinical research be of high quality. Such research should be highly
powered, should use randomization and blinding, and should have a pre-
specified hypothesis, and there should be a mechanism (e.g., prospective
registry) to protect against publication bias. Kimmelman’s second recom-
mendation was to improve the quality of the reporting of studies. He
noted that only 37% of trials of drugs that do not get FDA approval are
published, in contrast with 75% of trials of drugs that do receive FDA ap-
proval. There is a great deal of information loss from these unsuccessful
drug development studies, he said, and it is “unconscionable that we toler-
ate this degree of non-publication.” He added that non-publication also
leads to highly biased datasets.
The third recommendation concerns the issue of uptake. Noting that
physicians are the primary decision makers, Kimmelman said that their
ability to make inferences and decisions can be improved through training
on the content of the research, training to avoid or to better utilize biases
and heuristics, and being provided feedback on their decisions. The pub-
lished literature on decision making suggests that the best kinds of decisions
and prediction contexts are those in which humans work in concert with
machines. In the current healthcare context, said Kimmelman, there is no
existing system or technology to help healthcare providers make better
inferences from research and better clinical decisions.

In Vitro Alternatives to Animal Models
Key points:
• In vitro models can recapitulate phenotypes, allowing us to test
toxicity and efficacy. (Burridge)
• In vitro models allow us to find and validate genetic differences
that cause disease or sensitivity. (Burridge)
• In vitro models allow us to test without any risk or death to
animals or humans. (Wikswo)
• In vitro models are not necessarily a substitute for animal mod-
els; rather, they should be used as an adjunct to animal studies.
(Taylor)
he following chapter explores how rapid advances in in vitro

T
technologies offer new opportunities to improve modeling of the
human condition and how they are both a valuable adjunct to and
a potential replacement for precision modeling in animals.
iPSCs TO MODEL CHEMOTHERAPY-INDUCED CARDIOTOXICITY

Paul Burridge, assistant professor of pharmacology at Northwestern
University, said that induced pluripotent stem cells (iPSCs) can help answer
unique questions that are otherwise inaccessible. For example, iPSCs can be
used to predict which patients will experience negative effects from a drug,
61

identify the genetic cause and pathway of the drug response, and develop
drugs to modify that drug response.
In the clinical care of the future, Burridge believes, vast amounts of data
from each patient will allow large-scale comparisons and the identification
of genetic mutations associated with specific phenotypes. Once a mutation
is identified, iPSCs can be used to validate the association, allowing clini-
cians to predict which patients would suffer negative effects from certain
drugs, and researchers to develop therapies based on an individual’s genetic
information.
iPSCs are now simple and cheap to produce, said Burridge, and are a
powerful tool for genomics. A very small volume of blood (e.g., a small
blood draw or a finger prick) is expanded and transformed into pre-iPSCs.
Burridge’s lab has developed chemically defined, cost-effective methodolo-
gies to generate around 100 iPSC lines annually. The time from blood draw
to ready-to-use iPSCs is about 3.5 months, at a cost of $500. iPSCs are, in
essence, human genomes captured in culture, capable of differentiating into
any of the cell types in the body, said Burridge.
Burridge’s lab focuses specifically on differentiating iPSCs into cardio-
myocytes to recapitulate cardiac diseases with known genetic causes. Beyond
using these cells to study diseases with a known genetic makeup, his lab ex-
plores whether cardiomyocytes can be used to recapitulate patient-specific
drug responses, by focusing on doxorubicin, a common chemotherapy drug
(Burridge et al., 2016). Doxorubicin is used in nearly 1 million patients an-
nually, despite well-established dose-dependent cardiotoxicity that occurs in
8 to 10% of patients. The dose of doxorubicin that breast cancer patients
can receive is limited by its cardiotoxicity, so eliminating or predicting
toxicity would allow patients to receive a higher dose and improve the ef-
ficacy of their chemotherapy treatment, said Burridge. Researchers tested
iPSCs and cardiomyocytes from patients with cardiotoxicity symptoms
and their controls and discovered that the iPSCs/cardiomyocytes accurately
recapitulate a patient’s predilection to doxorubicin-induced cardiotoxic-
ity. However, even though the cells recapitulated a patient’s phenotype,
Burridge said, there were multiple causes of toxicity, including reactive oxy-
gen species (ROS) production, DNA damage, calcium overload, sarcomeric
disarray, and mitochondrial dysfunction.
To find out the genetic basis for doxorubicin’s cardiotoxic effects,
Burridge’s lab collaborated with the Canadian Pharmacogenomics Network,
which had performed a genome-wide association study (GWAS) on more
than 400 patients, and discovered a retinoic acid receptor variant (RARG)
that correlated with doxorubicin-induced cardiotoxicity (Aminkeng et al.,
2015). Validating this variant using the iPSC model was not as simple as
it seemed, said Burridge. The original GWAS population had to be inter-
rogated to identify patients with only the RARG variant, among all other

IN VITRO ALTERNATIVES TO ANIMAL MODELS 63
variants associated with cardiotoxicity. The selected patients had to be re-

recruited, a process that involved “nurse practitioners driving hundreds of
miles to collect blood in high school bathrooms.” Finally, said Burridge,
the data showed that patients with the RARG variant exhibited higher
sensitivity to doxorubicin. The data further confirmed that this variant
was associated with the phenotypes seen earlier, including DNA damage
and ROS production. Overexpression and knockout mouse models of
the variant produced the same phenotype. Aiming for the gold standard
answer, the research team performed a SNP correction, which reversed
the doxorubicin hypersensitivity. Expanding on this information, Burridge
and his colleagues are investigating whether specific RARG agonists could
stimulate the RARG receptor to act as a cardio protectant for patients with
doxorubicin toxicity
IN VITRO CARDIAC DISEASE MODELS

Megan McCain, assistant professor and the Chonette Early Career
Chair in the Department of Biomedical Engineering and the Department of
Stem Cell Biology and Regenerative Medicine at the University of Southern
California, presented her work using in vitro models to study cardiac dis-
ease. She noted that the heart’s key function to contract and pump blood
is achieved by the myocardium. The structure–function relationship of the
cardiomyocytes is critical to the proper functioning of the organ. For ex-
ample, in populations of elongated, rectangular cardiac myocytes with all
of their microfibrils aligned in the same direction, when the microfibrils’
sarcomeres contract they do so in the same direction and thus achieve opti-
mal efficiency. Understanding these structure–function relationships, which
are present throughout the heart, said McCain, is essential to understanding
the function of the healthy organ and how function can decline in certain
diseases.
Conventional animal models for cardiac disease have several limita-
tions. While these models allow researchers to study native physiology in
intact organisms, it is difficult to study or control the microenvironment
of the heart. Conventional in vitro models, such as cell cultures, allow
researchers to study human cardiac cells at a low cost and with high
throughput, but they lack the native tissue structure and thus have limited
functional outputs.
Given the limitations of conventional models, McCain proceeded to
describe her research on building disease models that are modular, scal-
able, and adaptable to other applications (such as drug screening), robust,
quantitative, relevant to humans, and patient specific. She first described the
Muscular Thin Films, developed in Kevin (Kit) Parker’s laboratory at Har-
vard University. Building this platform begins with laser engraving small

windows onto a glass coverslip, which is then coated with a temperature-

sensitive polymer that remains in solid state in the incubator but melts at
room temperature. The coverslip is then coated with polydimethylsilioxane
(PDMS), a silicone elastomer, and micro-printed with different patterns
designed using computer-assisted design software. Cardiac myocytes are
seeded, and they adopt the pattern that has been printed. This model al-
lows researchers to control tissue architecture and creates films that actually
contract once the temperature-sensitive layer melts away. Using an electrode
to control the myocytes’ pacing rate, one can monitor and calculate the
contractility. McCain noted that this type of in vitro modeling is mostly
done with neonatal rat cardiomyocytes.
An in vitro model for inherited Barth syndrome cardiomyopathy, de-
veloped in collaboration with William Pu and Gang Wang at Children’s
Hospital in Boston, depends on human cells. Barth syndrome is the result
of a mutation in TAZ, a transacylase localized to the mitochonrdial mem-
brane. There are few therapeutic approaches or animal models available,
and patients commonly need a heart transplant by adolescence. Using iPSCs
and Muscular Thin Films, Pu found that cardiomyocytes from patients with
Barth syndrome had dramatically less contractility compared to normal
controls. Researchers validated that the disease is directly caused by the
mutation in the TAZ gene, after recovering the normal phenotype by re-
expressing TAZ, said McCain.
Using these in vitro models allows for hypothesis-driven research, bet-
ter understanding of mechanisms of disease, and, ultimately, the identi-
fication of potential therapeutic targets in a human-relevant platform,
concluded McCain.
HUMAN MICROPHYSIOLOGICAL SYSTEMS

John Wikswo, the Gordon A. Cain University Professor, the A.B.
Learned Professor of Living State Physics, and professor of biomedical
engineering, molecular physiology and biophysics at Vanderbilt University,
discussed microphysiological systems (MPSs) as models for studying the
enormous complexity of biological systems on a scale that is small and
controllable.
All current methods for testing drug efficacy and toxicity, said Wikswo,
have disadvantages. Traditional in vitro experiments that are conducted on
two-dimensional cell cultures test cells that “from a cynical point of view
could be argued to have cancer, are inbred, are diabetic, are potatoes on
a stiff plastic couch without exercise, enjoy neither gender nor sex, live
almost entirely in the dark, gorge themselves on sugar once a day, may be
slowly suffocating in an increasingly acidic environment, live in their own
excrement, never bury their dead, may take a complete or only partial

bath every day or two, and talk only to cells of like mind. Clearly we have
learned a lot of biology from these cells, since one can get reproducible,
statistically significant results, but are they relevant to human biology and
disease?” While these experiments may end up with reproducible and sta-
tistically significant results, their relevance to human biology and disease
is questionable, said Wikswo. Animal models also have genetic and physi-
ological differences that affect their relevance to human biology as well.
Although humans are ultimately the best model for human disease, MPSs
such as organs-on-chips, tissue chips, 3D transwells, and self-assembling or-
ganoids can recapitulate the human-specific dynamic interactions between
drugs and organs without harming human beings.
Organ-on-a-Chip
A number of organ-on-a-chip technologies have been developed for
organs, including the lung, the brain, the liver, and the heart, as well as
lymph node-on-a-chip and mammary-gland-on-a-chip. These chips are all
designed slightly differently, and many researchers, Wikswo said, are trying
to create a 2D, 2D+, or 3D architecture with perfusion to more accurately
recapitulate the in vivo environment. Organs-on-chips are expensive to
produce and are not yet fully validated. However, they potentially have
some significant advantages over traditional methods of toxicity testing:
• Better than 2D biology

• Ideal for barrier functions
• Can reproduce physiological flows
• Provide thick extracellular matrix for scaffolding and drug/factor
binding
• Support organ–organ interactions
• Sufficient tissue for multi-omics analyses of tens to thousands of
variables
• Require minimal media volumes
• May ultimately reduce drug costs
• May ultimately enable the construction of a single-patient homun-
culus (i.e., single-patient miniature human)
• May ultimately enable the construction of animals-on-chips
Organoids
Organoids are three-dimensional, self-organizing microphysiologi-
cal systems, models with tissue-level functions and disease phenotypes—
essentially, miniature in vitro organs. Organoids, said Wikswo, have a
number of advantages: they are better models than 2D biology, they can

demonstrate development, and they are transplantable. However, individual

organoids are hard to replicate and difficult to integrate with other organ
systems.
Wikswo said it is his career goal to introduce two new “species” to the
biomedical research ecosystem: Homo minutus (MicroHuman) and Homo
chippiens (NanoHuman). These miniature “humans” (homunculi) could be
used in any number of research areas, including drug development, envi-
ronmental toxicology, physiology, and understanding disease mechanisms.
There are several areas of research in which MPSs could be immedi-
ately applied, said Wikswo. Within the category of disease biology and
pharmacology, MPSs could be used to discover novel mechanisms of hu-
man diseases, to identify novel compounds and clinical candidates, and to
unravel the mechanism of action of drug candidates. In clinical pharmacol-
ogy, MPSs can help identify problematic human haplotypes and drug–drug
interactions, and to improve prediction of human exposure for compounds
and clinical formulations. In toxicology research, MPSs have value for early
termination of toxic drugs and avoiding inappropriate drug terminations
(Watson et al., 2017). In addition to these immediate applications, there
are research applications that are on the cutting edge of MPS, including
re-creating the full metastatic cascade and testing immuno-oncology drugs.
MPS models can be particularly helpful in the late preclinical stages
of research and development. If a drug had entered phase I clinical trials
with unexpected results, MPSs could be used for high content analysis to
decipher the problem, said Wikswo. The U.S. Food and Drug Administra-
tion has stated its vision of “clinical trials in a dish,” where MPSs are used
across multiple areas of drug development, including areas where animal
models are currently used: “If properly validated, there is the potential for
clinical trials in a dish to replace animal testing, some types of clinical tri-
als, or to be used to select patient populations or even individual patients
most likely to benefit or least likely to be harmed by therapies” (Strauss
and Blinova, 2017). Another vision for MPSs, said Wikswo, is a human-
on-a-chip, made from cells from patients, that would be able to predict the
patient’s response to a drug and whether there would be negative effects—
before the human patient is put at any risk (Watson, 2017).
QUANTITATIVE SYSTEMS PHARMACOLOGY

AND MICROPHYSIOLOGICAL SYSTEMS
D. Lansing Taylor, distinguished professor and Allegheny Foundation
Professor of Computational and Systems Biology and director of the Uni-
versity of Pittsburgh Drug Discovery Institute, said that there are two main
challenges to developing precision therapeutics today. First, animal models
do not always exhibit concordance with human mechanisms of disease

and toxicology. Second, the variability in the genetic makeup of patients

demands a research approach that focuses on this diversity in humans.
Given these challenges, technologies such as iPSCs and humans-on-a-chip
can serve as complementary research platforms for human-specific biology
using an in vitro approach. Echoing the previous speaker, Taylor said that
the human biological system is incredibly complex, with interactions and
pathways between multiple organs, cells, and tissues, and many potential
molecular targets for drugs. Quantitative systems pharmacology (QSP) is
a system for “determining the mechanism(s) of disease progression and
mechanism(s) of action of drugs on multi-scale systems through iterative
and integrated computational and experimental methods to optimize the
development of therapeutic strategies” (Stern et al., 2016, p. 522).
The Drug Discovery Institute at the University of Pittsburg, Taylor
said, has developed a step-by-step platform to implement QSP in the drug
discovery process. The process is complex but has 12 basic steps, each of
which may inform the others and loop back in an iterative process:
1. Analyze patients and clinical samples, informed by validated target

knowledge and discovery
2. Infer pathways of disease progression and identify potential drug
targets
3. Utilize machine learning to predict drugs that may interact with
those targets
4. Create and test phenotypic models of disease and safety, using
technologies such as RNA interference (RNAi), CRISPR/Cas-9, and
MPS
5. Perform high-content screening and analysis of treatments
6. Identify drugs that are active for the target
7. Use medicinal chemistry to optimize targets
8. Develop mammalian models of disease and safety
9. Identify high-probability targets using chemical proteomics and
RNAi
10. Build initial computational models based on the available data
11. Use the predictions from the computational models to inform opti-
mal therapeutic strategy, pharmacodynamic biomarkers, and prog-
nostic and predictive biomarkers
12. Use the predictions from the computational models to inform clini-
cal trial design and simulation
Human Microphysiological Systems

QSP can supplement and inform other forms of research, such as
microphysiological models, iPSCs, and animal models. Taylor, building

on Wikswo’s presentation about MPSs, described the effort to create a

liver MPS, a tool to investigate both liver diseases as well as drug toxic-
ity. The newest-generation liver MPS is a vascularized liver acinus MPS
(vLAMPS), which consists of all primary human cells obtained from the
same patient (i.e., hepatocytes, endothelial cells, stellate and Kupffer cells);
it also includes a number of iPSCs and cells with a fluorescent biosensor,
under continuous flow. The model is made primarily of glass and plastic,
with minimal amounts of polymer, because polymers absorb hydrophobic
molecules like drugs very well. This system is also scalable so multiple MPSs
can be run simultaneously.
This MPS model has helped researchers induce immune-mediated
hepatotoxicity and methotrexate-induced fibrosis. For the methotrexate
experiment, researchers engineered stellate cells to express a green fluo-
rescent protein. Subsequent imaging revealed fibrosis due to methotrexate
exposure, identified by an increase in α-smooth muscle actin and collagen
alpha 2(I) chain. The vLAMPS model, said Taylor, allows for cancer cell
extravasation, immune cell infiltration, and delivery of factors from other
organs. From his perspective, in order to fully understand liver disease and
develop appropriate treatments, it is important to implement the full QSP
platform, starting with patients, patient samples, and data, as well as de-
velop multi-scaled experimental and computational models of liver diseases
for drug discovery and toxicity testing.

Assessing Safety and Toxicology
Key points:
• Humans cannot be used for toxicity testing so animal models
or animal data are needed and required in order to develop
assessments for humans. (Thayer)
• One major drawback of animal research is that the study
population tends to be homogeneous, in contrast to the great
diversity within human populations. (Harrill)
• There is great diversity within human populations that has im-
plications for differences in susceptibility or response to toxins
or drugs. (Harrill)
rom the perspective of data from large population cohorts this

F
chapter provides discussions around preclinical drug safety and
environmental toxicology.
PATIENT SUSCEPTIBILITIES IN PRECLINICAL

DRUG SAFETY ASSESSMENT
Brian Berridge, senior GlaxoSmithKline (GSK) fellow and director and
head of WW Animal Research Strategy at GSK, talked about the successes
and challenges of testing for patient susceptibilities in preclinical drug safety
assessment. There are many modeling platforms used throughout the drug
development process, but animal models are used strategically throughout
69

the process to help in critical decision making regarding target identification

and validation, candidate selection, and preclinical safety. The dependence
on animal models is in large part due to extensive similarities in anatomy,
physiology, response to injury, pathobiology, and pharmacology between
animals and humans. Berridge noted that the cardiovascular system, in
particular, is well conserved in animal models. While there are differences
that have to be accounted for, Berridge said there is a logical rationale for
the dependence on animals as a surrogate for the human system.
Citing a study that investigated the concordance of drug toxicity be-
tween humans and animals, Berridge said that the use of animal models,
and the high level of concordance, has helped protect patients from harm
in the early stages of clinical trials (Olson et al., 2000). Despite this confi-
dence, serious adverse events resulting in severe toxicity, irreversible harm,
and even death have occurred in phase I clinical trials, said Berridge (e.g.,
Eddleston et al., 2016; Suntharalingam et al., 2006). In these events, there
was no indication from preclinical studies that these toxicities could occur.
While these acute toxicity events are extremely unfortunate, they are very
rare, said Berridge. More troublesome, in his opinion, is the possibility of
chronic effects in susceptible patients. For example, a clinical trial for the
use of bardoxolone methyl in type 2 diabetes and stage 4 chronic kidney
disease was halted when an increase in cardiovascular events in the treat-
ment group was discovered. By that time, patients had been exposed to the
study drug for an average of 7 months. This is the type of adverse event
that, unfortunately, is usually not detected until data from large numbers
of patients over long periods of time are analyzed. The reasons for the dis-
connect between animal studies and clinical settings are not hard to find,
said Berridge. Experimental animals tend to be young, healthy, genetically
homogeneous, and live in a controlled environment, whereas patient popu-
lations tend to be all ages, usually sick, genetically heterogeneous, and live
in uncontrolled and variable environments (Olson et al., 2000). Berridge
noted that one reason why animal model studies operate under such con-
trolled conditions is that such control leads to more discrete data, which
makes it easier to make a decision. Unfortunately, the more controlled the
platform, the less similar it is to human patients, he said.
Another complication, said Berridge, is that patient susceptibility to
toxicity varies, perhaps due to synergy between the drug and the patient’s
disease or genetic predisposition, or due to other reasons. Cancer treat-
ments give us an opportunity to study toxicities and the concordance
between animal and human studies, because higher levels of toxicity from
cancer drugs are generally tolerated. One study on cardiovascular liabilities
associated with cancer drugs found that, while there was an overall low
incidence of most events, the intra-patient incidence varied widely, suggest-
ing that individual patients are more susceptible, Berridge said.

ASSESSING SAFETY AND TOXICOLOGY 71
Despite these challenges, the current approach to safety assessment pro-

tects patients quite effectively. Citing a study on first-in-human clinical tri-
als, Berridge said that animal safety studies have a high negative predictive
value (Monticello et al., 2017). That is, when a lack of toxicity is observed
across multiple species of animals, and there is concordance across those
species, there is a high degree of confidence that the compound will be safe
in humans. Opportunities to improve this system, particularly how well
models can predict liabilities in susceptible patients, include next-generation
vivaria and alternative models.
Next-Generation Vivaria
Berridge noted that, when humans visit a doctor, certain parameters
(e.g., blood pressure, weight, and body temperature) are always measured,
regardless of the reason for the visit. Some of these parameters are difficult
to routinely measure in animals. Technological developments in vivaria,
said Berridge, will enable researchers to monitor animals in a more holistic
way. The data from these physiological parameters will add to, and give
context to, the data already routinely measured in animal studies.
Alternative Models
Rather than using animal models that are homogeneously young and
healthy, the use of alternative models—animals with diseases or stresses—
can help elucidate potential susceptibilities. For example, a study on doxo-
rubicin found that hypertensive rats were more sensitive to doxorubicin
cardiotoxicity (Herman et al., 1985).
Berridge concluded that, on the whole, the current approach to assess-
ing preclinical drug safety largely protects patients from harm. However,
the system is not designed to identify those rare clinical events associated
with individual patient susceptibilities. As precision medicine advances,
there may be an expectation that preclinical assessment will identify these
individual susceptibilities, and as technological capabilities advance, it may
be possible to do so.
CO-EXPRESSED GENE NETWORK ANALYSIS AS A

BRIDGE FOR EXTRAPOLATION BETWEEN SPECIES
Biological systems are incredibly complex, said James Stevens, distin-
guished research fellow at the Lilly Research Laboratory. This complexity
makes it challenging to model pathophysiology in a way that allows for
meaningful mechanistic inferences. To address this challenge, a European
Innovative Medicine Initiative II (IMI2) project called Translational and

Quantitative Systems Toxicology1 is developing a multi-level computational

modeling approach to bridge cell, tissue, organ, and whole organism signal-
ing and response to injury.
One foundational component of this effort is the application of
weighted gene co-expression network analysis (WGCNA). WGCNA is
not used to examine individual gene changes, but rather to assess highly
connected networks of genes—called “modules”—that frequently respond
together or are “co-expressed.” Though the approach is currently focused
on transcriptomic data (i.e., mRNA), it could be applied more generally to
other -omic data sets, said Stevens. By mapping networks to pathways and
other biological information, the approach leverages the inter-dependence
of biological functions and signaling represented by the modules and gene
regulatory networks.
Stevens said that focusing on modules of genes can define biological or
pathophysiological responses while reducing complexity compared to anal-
ysis at individual gene level, thus avoiding the “curse of dimensionality”—
that is, the need for more and more data as the dimensions of the data
increase. At the same time, modules retain biological content and help
improve data interpretation through network visualization, rather than
analysis of individual elements or genes.
There are several fundamental principles behind WGCNA, said Stevens.
First, cellular biology is driven by coalescent properties. This means that
individual genes and protein activities are not random, but act in integrated
and coordinated ways. Second, these activities are co-regulated with many
basic biological functions that are highly conserved across species. Third,
statistical models are good at defining patterns in complex data.
Stevens gave an example of the use of WGCNA to study toxic liver
injury (Sutherland et al., 2017). First, an open source WGCNA algorithm
(Langfelder and Horvath, 2008; https://labs.genetics.ucla.edu/horvath/
CoexpressionNetwork/Rpackages/WGCNA) was applied to gene expres-
sion data from the public database DrugMatrix. The data represented
about 1,000 treatments that induced a wide spectrum of toxic responses.
The algorithm defined self-assembling modules from these data; 415 mod-
ules were defined for rat liver. This approach, said Stevens, was validated
by comparing the preservation of modules to a similar database built by
the Japanese National Toxicogenomics Program (TG-GATES; Igarashi et
al., 2015), in which 95% of the modules were preserved. Modules were hi-
erarchically clustered to form a dendrogram, using their average eigengene
scores for all modules across all experiments—modules cluster in regions
with similar responses. An eigengene score is a single statistical measure
of perturbation of all of the genes in the module for a given treatment. By
1 See http://transqst.org.

overlaying the dendrograms with pathway and GO terms enrichment clus-

ters of modules with complementary functions are found in specific regions
of the dendrograms. Important pathophysiological associations become
recognizable as patterns of modular gene responses in the dendrogram.
Importantly, said Stevens, mapping to pathways in the Molecular Signa-
tures Database (MSigDB) to modules reveals blank regions in the WGCNA
dendrogram with high association with the co-occurrence of pathology but
for which no pathway has been defined for the modules, suggesting there is
much to be learned regarding mechanisms of pathogenesis by better defin-
ing the biology represented in the gene networks.
Stevens told workshop participants that correlation of individual his-
tological morphologies of injury with changes in WGCNA modules reveals
identifiable and interpretable patterns. For example, modular gene changes
in a rat model of bile duct ligation demonstrate that the WGCNA module
activity parallels the changes in traditional measures of liver injury, such
as histological morphology and serum biochemistry. In addition, assessing
the activation of the c-Jun N-terminal kinase (JNK) pathway (common to
many forms of pathological injury) by looking for the binding of c-Jun (the
transcription factor that controls JNK activation) reveals enrichment in
modules that are active with bile duct ligation.
WGCNA can also differentiate stereotypic or non-specific responses to
injury from compound or mechanism-specific responses, said Stevens. He
gave the example of liver responses in a rat model of partial ischemia. Us-
ing this model, and analyzing the module expression in ischemic and non-
ischemic liver at 4 hours post-ischemia, researchers found distinct responses
such as heat shock, cell cycle arrest, and cell–cell junction changes in the
ischemic lobes, compared to ribosomal DNA processing in the non-ischemic
lobes. However, similar activities (i.e., convergent pathobiology) are pres-
ent in both ischemic and non-ischemic regions at 24 hours post-ischemia;
both regions show DNA replication, ribosomal biogenesis, and tubulin
formation. Stevens said that a similar phenomenon is observed by looking
at other surgical liver injury models, such as partial hepatectomy.
Stevens said that additional applications of WGCNA include com-
parison of biological responses across models within a species (e.g., whole
organs versus cell response in vitro), and across species for the same organ.
For example, he cited work showing that mouse liver is more predictive of
responses in rat liver than cultures of primary rat hepatocytes (Sutherland
et al., 2016). Stevens told workshop participants that WGCNA offers an
opportunity to get a better sense of the comparative relevance or predictiv-
ity of preclinical animal models for responses in human patients.

USING GENETICALLY DIVERSE MICE TO

TEST SUSCEPTIBILITY TO TOXINS
Alison Harrill, a geneticist at the National Toxicology Program of
the National Institute for Environmental Health Sciences, said assessing
the susceptibility of humans to environmental chemicals is challenging
for a number of reasons. First, although humans are routinely exposed to
chemicals in their environments, few, if any, data about specific exposure
levels and health effects are available. Second, exposure and susceptibility
to these chemicals vary considerably between populations. For example,
people exposed to chemicals as part of their job have longer-duration ex-
posures compared to the general population. Infants may be more at risk
of exposure to certain toxins because they put things in their mouth and
have lower body weight. Third, genetic variations are linked to different
susceptibility levels; for example, susceptibility to methyl mercury exposure
can vary 50,000-fold between individuals due to genetic differences. Un-
derstanding these population dynamics can help inform the establishment
of safe exposure thresholds.
The risk assessment process for environmental chemicals involves col-
lecting data on a number of factors. These data are generally collected from
whole animal studies and in vitro research. Data are needed to answer
questions such as the following:
• What is the hazard to the body and what tissues are affected?
• What dose and potency exposure carries an agreeable risk?
• Is the risk different depending on whether exposure is acute or
cumulative?
• Are certain populations more susceptible, based on, for example,
age or life stage?
Safety assessment of chemicals has traditionally focused on determining

the average “safe” exposure, rather than taking into consideration all of
the variability in genetics and susceptibility. New genetically diverse mouse
models have made it possible and desirable to study genetic diversity in
chemical safety assessments. The Diversity Outbred (DO) mouse popula-
tion is a rationally interbred population with highly randomized polymor-
phisms that mimics human genetic diversity, said Harrill. These mice were
created through a genetic reshuffling of genes from eight founder strains,
each with a different genetic profile and different propensities for diseases
(see Figure 6-1). This genetic profile of the population allows researchers
to look at chemical toxicity on a background of comorbidities that is very
similar to that in the human population.

FIGURE 6-1 Founder strains of Diversity Outbred mice.

SOURCE: Harrill, slide 8.
These mice are used
• to identify specific polymorphisms associated with xenobiotic

toxicity,
• to evaluate biomarker performance toward assessing human clini-
cal adverse outcomes, and
• as a tool for population-based estimates of chemical potency for
risk assessment.
To Identify Specific Polymorphisms Associated with Xenobiotic Toxicity

A diverse mouse population can be used to identify specific gene vari-
ants that influence susceptibility to drug and chemical toxicity. Harrill gave
an example from her own research (Church et al., 2015), in which DO
mice were given a short-term oral dose of a component of green tea extract
(epigallocatechin gallate). Among the two-thirds of the susceptible popula-
tion, a very small subpopulation showed extreme sensitivity analogous to
the severe idiosyncratic liver injuries observed in humans. Harrill noted
that these idiosyncratic toxicities had been difficult to study because the
dose–response relationship was unclear, and the mechanism of action was
not well understood. GWAS analysis identified a peak on chromosome four.
Mice that inherited alleles from one specific founder strain (NOD) were less

susceptible to this toxicity. Subsequently, researchers sought to validate the

candidate SNPs from the identified region using data from humans who had
experienced hepatotoxicity associated with the green tea extract.
To Evaluate Biomarker Performance Toward

Assessing Human Clinical Adverse Outcomes
Harill said that often the identification of biomarkers is conducted in
a specific (limited) genetic background (e.g., Sprague Dawley rats), prior
to clinical studies. Using the DO mice, Harrill compared the gold standard
biomarkers of creatinine and blood urea nitrogen (BUN) to newly identi-
fied protein biomarkers, following exposure to cisplatin and the subsequent
proximal renal tubule injury. The response to cisplatin was variable, with
13 of the 45 mice showing no signs of renal tubular necrosis. Twenty-six
mice showed signs of necrosis, with 17 showing grade 1 necrosis and 9
showing grade 2 necrosis. BUN levels, as expected, did not increase until
grade 2 necrosis was present. Unexpectedly the other urinary biomarkers
were similarly not elevated until grade 2 necrosis was established. This find-
ing suggests that these new biomarkers do not represent an improvement
over BUN, said Harill.
As a Tool for Population-Based Estimates of

Chemical Potency for Risk Assessment
A study to examine benzine toxicity used DO mice to calculate its
benchmark concentration (the concentration of a substance that produces a
defined response). Research on 44 human subjects had found a benchmark
concentration at 7.2 parts per million. However, the calculated value from
data collected from the DO mice was 0.205 parts per million—orders of
magnitude lower. This type of study may help to inform risk assessments
for humans that result in more protective levels of acceptable exposure,
concluded Harill.
INTEGRATING EVIDENCE FROM ANIMAL AND HUMAN STUDIES

The Integrated Risk Information System (IRIS) was created in 1985
to enable consistent evaluations of chemical toxicity, said Kristina Thayer,
who serves as director of the IRIS Division at the Environmental Protection
Agency (EPA). Prior to the establishment of IRIS, multiple divisions at the
EPA conducted independent assessments and often came up with conflict-
ing results. The comprehensive IRIS risk assessments involve a rigorous,
multi-step review process, with opportunities for public input, and provide
toxicity values for both cancer and non-cancer effects. These technical as-

sessments, when combined with additional information, such as exposure

levels, cost of cleanup, and regulatory options, are used to make regulatory
decisions under the Clean Water Act, the Safe Water Drinking Act, the
Toxic Substances Control Act, and other laws.
The IRIS assessments use data from both animal and human studies,
conducting wide and deep analysis of the literature to find research that is
relevant to the chemical in question. The assessments are performed using
a systematic review method that screens and evaluates the quality of the
evidence at each step, and synthesizes and integrates the evidence using a
structured framework. The end result of the systematic review process is a
conclusion about the toxicity of the chemical, accompanied by a confidence
rating for the conclusion—that is, based on the quality of the evidence, how
confident the assessor is in the conclusion about toxicity.
The assessment begins with determining the exact parameters of the
assessment, performing a literature review to find relevant research, and
extracting the data. Once studies have been identified—both human and
animal—each study is individually evaluated on criteria incl uding internal
validity, bias, sensitivity, applicability to the question, and reporting quality.
For example, the bias analysis might look at whether or not the study used
randomization; sensitivity analysis might look at the variation in exposure
levels; applicability analysis might determine how relevant a specific animal
model is to human health; and reporting quality analysis might look at
whether the specific form of the chemical was reported. Each of these crite-
ria receives an overall score of good, adequate, poor, or critically deficient.
Based on these ratings, each study is given a score of high, medium,
low, or uninformative. Thayer compared this scoring to a heat map, in
which a study with a lot of green (i.e., criteria scored as “good”) would
fare better than a study with a lot of red (i.e., criteria scored as “poor”
or “critically deficient”). Figure 6-2 demonstrates this visualization (taken
from Taylor, 2017):
High: No notable deficiencies or concerns identified; potential for bias
•
unlikely or minimal and sensitive methodology.
Medium: Possible deficiencies or concerns noted, but resulting bias or
•
lack of sensitivity would be unlikely to be of a substantive degree.
Low: Deficiencies or concerns were noted, and the potential for sub-
•
stantive bias or inadequate sensitivity could have a significant impact
on the study results or their interpretation.
Uninformative: Serious flaw(s) makes study results unusable for hazard
•
identification. (Ibid)
After the individual evaluation of each study, the studies are examined
together to synthesize the information within evidence streams. A similar
heat map approach is used in this step, with, for example, all animal stud-

FIGURE 6-2 Individual epidemiological study ratings.

FIGURE
SOURCE: 6-2:
Thayer, slide 7. Individual epidemiological study ratings
SOURCE: Thayer, Slide 7
ies displayed in one table (see Figure 6-3). The synthesis process considers
questions such as the following:
• What outcomes are relevant to each health hazard domain and at

what level (e.g., health effect or subgroupings) should synthesis
occur?
• What populations were studied (e.g., general population, occupa-
tions, life stages, species, etc.)?
• Can study results be described across varying exposure patterns,
levels, duration, or intensity?
• Are there differences in the confidence in study results for different
outcomes, populations, or exposure?
• Does toxicokinetic information influence differences in responses
across route of exposure, other aspects of exposure, or life stages?
Human and animal studies are synthesized separately, but their evi-
dence streams are integrated together, a step that also includes mechanistic
evidence that can inform the study results. Mechanistic evidence is particu-
larly important when the studies are of lower quality and a determination
cannot be made on the studies alone. In these cases, if mechanistic evidence
supports the findings of the studies, this may increase the confidence in the
overall conclusion. Evidence is organized into a table that describes the gen-

Other sensitivity concerns
FIGURE 6-3 Across study evaluations.

SOURCE: Thayer, slide 8.
FIGURE 6-3: Across study evaluations
eral findings, the factors that increase or decrease confidence in the findings,
a judgment rating about the strength of the evidence, the inference across
evidence streams, and a final conclusion about the evidence (see Figure 6-4).
Thayer noted that each step of these assessments relies heavily on the
judgment of experts: generally two experts perform parts of the assessments
independently and then reconcile their answers. If there is an abundance of
studies, the assessment will focus on those that are of medium or high con-
fidence levels, and those studies rated as “poor” or “critically deficient” will
be dropped from the analysis. Inconsistencies between studies may be due
to the stratification of the evidence—for example, different studies show
different results because they focused on different populations or durations
of exposure. However, if the inconsistencies are unexplained, the confidence
level of the assessment is downgraded. Thayer noted that some studies can-
not be used in their assessments because of a lack of complete information
about features such as randomization, blinding, or exact chemical used, a

80

FIGURE 6-4 Table to summarize evidence
FIGURE synthesis
6-4: Table and integration judgments.
to summarize evidence synthesis and
SOURCE: Thayer, slide 13.
integration judgments

statement that echoes comments made by Dirnagl and Hoitinga during their
presentations at the end of the first day.
The current approach to integration of animal and human studies is
largely qualitative, said Thayer, though structured frameworks like IRIS are
becoming more commonplace. Animal models in environmental health are
assumed to be relevant to human health unless there are data to suggest oth-
erwise. “Exact findings in animals and humans aren’t necessarily required.
. . . [T]he animal models can be canaries in the coal mine,” she said.

Patient Perspectives
Key points:
• Most patients have never heard of personalized medicine, but
when informed, see that it has major benefits. (Pritchard)
• Personalized medicine can have a real, profound effect on
patients. (Pritchard)
• Patient data are critical for advancing understanding of dis-
ease, because ultimately humans are the best model for human
disease. (Fiske)
his chapter summarizes the perspectives of representatives from

T
patient advocacy organizations.
PERSONALIZED MEDICINE COALITION

Daryl Pritchard, senior vice president for science policy at the Person-
alized Medicine Coalition, invited workshop participants to change gears
and focus on “the most important stakeholder in this process—the patient.”
Pritchard started by drawing an analogy between precision medicine and
modern aviation. He explained that traditional medical treatment—involv-
ing trial and error and symptom-based taxonomy—is akin to early aviation,
when pilots had few tools to guide them and “basically looked out the side
of the cockpit for signs that they were going in the right direction.” In con-
82

PATIENT PERSPECTIVES 83
trast, precision medicine and modern aviation involve the use of complex
and precise technologies that help guide the provider or the pilot to the
right treatment or destination. Expanding this analogy further, Pritchard
said that each of the instruments of precision medicine is analogous to a
step in flying a plane. Susceptibility biomarkers—which can help predict
the risk of developing a disease and indicate the need for increased surveil-
lance or prevention strategies—are similar to flight planning. Mechanistic
biomarkers—which can help select the right treatment by indicating that
the candidate drug occupies the intended target—are akin to a pilot’s navi-
gation system. Finally, pharmacogenetic biomarkers—which can help select
the right dose and duration by indicating dose-dependent target modulation
and/or pathway inhibition—correspond to a plane’s landing instrumenta-
tion. These biomarkers “make sure that you get to that destination without
an adverse event.”
Pritchard turned to the advances in personalized medicine over the last
decade or so. In 2005, the cost to sequence a single human genome was
$100 million. Today, said Pritchard, the price is around $1,000. In 2005,
there were 14 personalized medicines on the market, and today there are
more than 160, with many more in development. Pritchard reported on
a study commissioned by the Personalized Medicine Coalition with Tufts
Medical Center that showed that 42% of all the drugs in the pharmaceuti-
cal pipeline in 2015 were personalized medicines, and a full 73% of oncol-
ogy drugs in development were personalized (Tufts Center for the Study of
Drug Development, 2015). In concert with the availability of personalized
drugs, the market for genetic testing products has expanded dramatically.
As of 2017, more than 65,000 genetic testing products were on the market
(Concert Genetics, 2017). In short, said Pritchard, we are in an era of un-
precedented discovery.
Noting the variety of new major research projects around the world,
including the 100,000 Genomes project and the All of Us research pro-
gram, Pritchard said that these large-scale human genome databases are
an ambitious start that will need to be supplemented with research about
mechanisms and molecular pathways of disease, and clinical relevance of
variants will need to be validated through animal-based and in vitro mod-
els. Perhaps most importantly, findings need to be reproducible in order to
be translatable. Pritchard imagined the process like a loop where findings
from large database studies feed into animal-based and in vitro research,
which in turn feed back into analysis of the large database, and eventually
into translation to the clinic.
Of the key stakeholders in precision medicine, researchers, regulators,
and the diagnostic and drug industries are on board. However, the stake-
holders that are most critical for moving precision medicine into the clinic—
payers, providers, and patients—are more cautious, remarked Pritchard.

Patients, in particular, need more information and more dialogue regarding

the value of precision medicine. The Personalized Medicine Coalition per-
formed a survey in 2014 and found that 62% of those surveyed had never
even heard of personalized medicine, said Pritchard. Only 10% of people
said that their doctor had discussed personalized medicine with them or
recommended a targeted treatment. However, the survey also found that,
when participants were told of the benefits of personalized medicine, they
were quick to see how it could help them as patients.
Pritchard closed with two narratives. First, he talked about the progress
made on leukemia and lymphoma in the last 60 years. In the 1950s, these
diseases were simply referred to as diseases of the blood. In the 1970s,
they had been differentiated into a few categories. Today, there are nearly
90 different subcategories of leukemia and lymphoma, each with its own
optimized care pathway for effective treatment, said Pritchard. The effects
of this have been remarkable, with the 5-year survival rate climbing from
about 0% in the 1950s to about 70% today. Second, Pritchard told the
story of a patient, Deb Smith, who was diagnosed with advanced non-
small-cell lung cancer 5 years ago. She and her doctors had not expected
her to survive long, so she had focused on spending her remaining time with
her son so he could have memories of his mother. She was fortunate to be
enrolled in two different clinical trials and is alive and well today, saying,
“I’ve been taking trips with my son that I never thought I would be able
to take . . . what I’ve been trying to do is give him some good memories
. . . and in the process, I’ve found that my life is more complete than ever
before.” These stories, said Pritchard, demonstrate that the impact of per-
sonalized medicine is patient centered and is profound.
PARKINSON’S DISEASE
The Michael J. Fox Foundation for Parkinson’s Research (MJFF), said
Brian Fiske, senior vice president for research programs, is dedicated to
finding a cure for Parkinson’s disease through an aggressively funded re-
search agenda, and to ensuring the development of improved therapies for
those living with Parkinson’s today. MJFF has invested nearly $750 mil-
lion in research programs to date, funding both domestic and international
projects in both the non-profit and for-profit sectors. MJFF funds and
coordinates research in two areas that are particularly germane to animal
modeling for precision medicine. First, MJFF works to develop tools for
researchers, including new preclinical models. Second, MJFF supports the
collection of extensive clinical and biological data from patients, who, Fiske
notes, are the best models of Parkinson’s Disease. Both the tools and the
data are made available to the research community.
Parkinson’s disease is an ideal target for a precision medicine approach,

PATIENT PERSPECTIVES 85
said Fiske. People with Parkinson’s vary greatly in progression, symptom

severity, and response to treatment, suggesting that there are potential sub-
types of the disease. The cause is thought to be multifactorial, with both
identified and unidentified genetic forms as well as many idiopathic cases.
The biological understanding of the disease suggests that many cellular
systems are involved, including mitochondrial function, cellular protein
handling pathways, and lysosome biology. It is unclear at this stage whether
or how these pathways intersect or interact with one another, but it is clear
that there are multiple mechanisms involved, said Fiske. As Parkinson’s
shares some similarities with other neurodegenerative diseases, whether
these diseases should be reclassified based on their biology and mechanisms
rather than clinical description remains an open question.
Recalling Hook-Barnard’s presentation that compared human data to
the layers of a GIS map, Fiske said that, in order to fully understand and
thus effectively model Parkinson’s, there should be a map that includes data
from molecular information all the way to the patient’s daily experience
with the disease. Understanding each of these layers, and how they interact
with one another, will lead to a clearer understanding of the disease and its
subtypes. Fiske noted that the description and classification of Parkinson’s
has not changed significantly since it was first identified 200 years ago.
The disease is still largely diagnosed on the basis of motor symptoms, such
as bradykinesia, rigidity, resting tremors, and postural instability, despite
the fact that there are a number of non-motor symptoms associated with
Parkinson’s, such as cognitive impairment, mood disorders, autonomic
dysfunction, and REM sleep behavior disorder.
While the diagnosis of Parkinson’s has not changed significantly, re-
search on the underlying pathology has changed the understanding of the
disease and the work on potential treatments. Some of the symptoms of
Parkinson’s—primarily motor—are associated with the loss of dopami-
nergic neurons in the substantia nigra and the presence of Lewy bodies
(abnormal aggregates of the protein alpha-synuclein) in the brain. These
criteria are used for neuropathological confirmation of the disease, and
have been the primary drivers for development of potential therapies for
Parkinson’s. However, a number of other pathologies as well as brain cell
degeneration have been observed in Parkinson’s patients, suggesting that
the classification of Parkinson’s is more complex than a simple description
of symptoms and pathology.
Parkinson’s is a progressive disease that changes over time, said Fiske.
The early signs of the disease tend to be largely motoric, the progression
of which can be somewhat slowed with currently available treatments. As
the disease progresses, the non-motor symptoms become more prevalent. In
order to make better treatments for people with Parkinson’s, it is important
that models can reflect all stages and symptoms of Parkinson’s, said Fiske.

However, even understanding or classifying the clinical differences seen in

patients is challenging. Patients are often classified into two clinical sub-
types of Parkinson’s: tremor dominant or postural instability gait disorder
(PIGD). A large prospective cohort study funded by MJFF, however, found
that these classifications were not particularly stable over time (Simuni et
al., 2016). Patients who had been classified as tremor dominant at baseline
(i.e., when newly diagnosed) tended to largely stay that way after 1 year;
however, a significant number of patients who had been classified as PIGD
had switched to tremor dominant after a year. Fiske said that whether these
clinical differences represent true disease subtypes or just snapshots of the
same disease over time remains a major question in the field.
A number of animal models have been developed to study Parkinson’s,
but to date none are considered predictive of the human condition, said
Fiske. These models are divided into two categories: those that model
environmental triggers, such as neurotoxins or inflammation, and those
that model genetic triggers using strategies such as knockouts or transgen-
ics. One of the most critical needs in Parkinson’s research, said Fiske, is
finding a way to accurately measure alpha-synuclein in the brain. Because
there is currently no way to image the protein in the brain, attempts have
been made to measure it elsewhere (e.g., spinal fluid) and use those data as
biomarkers for Parkinson’s. Animal models will be essential to this work.
One model in particular is based on the idea that alpha-synuclein pathol-
ogy might physically spread from cell to cell in the brains of people with
Parkinson’s. The model meets some face and construct validity criteria for
the human disease, but its predictive validity is still uncertain and debate
remains in the field about whether this spread is a true feature in human
Parkinson’s disease.
Fiske concluded that, while models can be extremely useful for under-
standing more about Parkinson’s, ultimately the best model of Parkinson’s
disease is people with the disease. With this in mind, the MJJF has spent
much time and effort on a major project called the Parkinson’s Progression
Marker Initiative (PPMI), which collects data from cohorts of patients over
time in order to build a clearer picture of disease and inform modeling. An
emerging online version of the PPMI, called Fox Incite, uses a variety of
emerging technologies and collection tools, such as wearables, to collect as
much data as possible in order to better understand what Parkinson’s is so
it can be better treated.

Reflections on the Workshop
“This has been an unusual meeting,” said Kent Lloyd in the final ses-
sion of the workshop. While the workshop presentations demonstrated
how far we have come in precision medicine and modeling, there is still
more to be done. Lloyd identified four persistent challenges for precision
medicine research:
• The growth in translational research has increased the incidence of

exposing animal-based research that lacks reproducibility, which is
not a good predictor of human response or disease.
• There have been only modest gains in successful treatments; slow
and expensive drug pipelines often end in failure in diverse patient
populations.
• The path from genotype to mechanism to phenotype is not as
simple and straightforward as once thought. Issues such as pleiot-
ropy, heterogeneity, variable penetrance, and sexual dimorphism
are complicating—but also enriching—our understanding of how
genotypes and phenotypes are related.
• Due to the expansion of genome sequencing, we have identified an
exponentially increasing number of variants of unknown signifi-
cance, while suffering from a lack of sufficient specific biomarkers
of disease.
The utility of model organisms for precision medicine, Lloyd said, lies
in their predictive value and their proximity to the patient. Referring back
to Valle’s presentation he reiterated that three of the best uses of animal
87

models are to confirm causation, to help us understand pathophysiology,

and as surrogates for treatment studies. To those he added a fourth, experi-
mental interrogation.
Based on the presentations and discussions at the workshop, and the
needs and obstacles that had been identified, Lloyd developed eight “calls
to action.” First, there is a need to complete a comprehensive, encyclopedic
functional annotation of the genome. He explained that this project would
require collection and integration of data from both humans and animals,
and would require experimentation to test hypotheses. While there is much
focus on the protein-coding regions of the genome, a full understanding
will require work on the non-coding variants, the regulatory regions, and
mRNA, and issues such as pleiotropy and sexual dimorphism will need to
be elucidated.
Second, there is a need for formal linkages between model organ-
ism communities and databases with precision medicine initiatives, Lloyd
continued. Such linkages would facilitate cross-talk and improve ontolo-
gies and comparative phenotyping. Third, and relatedly, there is a need to
enhance processes and expand availability of tools to apply comparative
ontologies and develop computable phenotypes. These processes and tools
will improve the ability to align phenotypes, mechanisms, and genotypes,
and will improve the rigor, reproducibility, and reliability of research, said
Lloyd.
Lloyd’s fourth “call to action” is to integrate animal ontologies with in
vitro analyses, humans-on-a-chip, and patient data to identify knowledge
gaps that propel precision modeling of specific human variants. The integra-
tion of these different models and data sources can accelerate the process
of distinguishing correlated and causal factors, and can help researchers
optimize the selection of model organisms. The thoughtful integration of
models may reduce the need for animal models and may improve decision
making by creating better evidence with less noise.
Fifth, there is a need to promote, incentivize, and reward a culture of
synergistic, clinical outcomes-focused networks and collaborations between
translational researchers, clinician scientists, and patient groups, said Lloyd.
Collaborations between these sometimes-siloed groups can inform and im-
prove preclinical and clinical trials, can help realize the “regulatory dream”
that Califf had presented, and can keep the focus of research centered on
patients and health outcomes.
As researchers continue to identify variants that are potentially relevant
to human disease or health, we need to expand model organism resources
and technology development for rapid assessment of variants, said Lloyd.
These resources and technologies may include things like model-on-demand
programs, expanded biorepositories and tissue/specimen banks, improved
phenotypic validation, and steps to ensure predictive validity of models.

REFLECTIONS ON THE WORKSHOP 89
The seventh and eighth “calls to action” that Lloyd presented were to
establish clinical utility of a precision modeling paradigm to advance and
accelerate diagnostic decision making, targeted therapeutic development,
and predictable disease prevention strategies and to ensure accessibility of
resources, tools, and networks of precision modelers to the global commu-
nity. Ensuring accessibility to the global community will help “transcend
cultural and socioeconomic divisions, reduce and overcomes disparities,
increase access, and increase opportunities,” Lloyd concluded.
Through the eight sessions of the workshop, speakers identified specific
challenges to the development of predictable, reproducible, and reliable
animal models to support rapid and accurate identification and prioritiza-
tion of causative factors of disease to support precision medicine research.
Model organisms can improve precision medicine outcomes, provided
that formal collaborations are established between researchers using animal
models and precision medicine initiatives so that processes and projects
such as comparative phenotyping, ontologies and functional annotation
of the genome can move forward in tandem. Precision medicine has been
embraced on a global scale, thus global collaboration would help ensure
shared knowledge and resources.

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Appendix A
Agenda
Advancing Disease Modeling in Animal-Based
Research in Support of Precision Medicine
A Workshop of the Roundtable on Science and Welfare

in Laboratory Animal Use with support from the
Office of Research Infrastructure Programs,
National Institutes of Health
October 5-6, 2017
2100 C Street NW, Washington, DC

Historic National Academies of Sciences Building
Fred Kavli Auditorium
An ad hoc planning committee will plan and conduct a public work-

shop to explore the potential of ongoing and future research in animal
models with implications for precision medicine. This workshop will bring
together experts on the use of state-of-the-art technologies and technologi-
cal advances to explore
• how the design, creation, and analysis of current and next-

generation animal models can inform the practice of precision
medicine;
• reproducibility concepts to improve the clinical relevance of ani-
mal-based validation experiments and pre-and co-clinical trials in
the context of precision medicine; and
• welfare and regulatory considerations of current and especially
next-generation animal models that would inform the design of
targeted, personalized therapies.
According to the National Institutes of Health, precision medicine “is

an approach for disease treatment and prevention that takes into account
individual differences in lifestyle, environment, and biology.”1 During the
1 See https://allofus.nih.gov/about/about-all-us-research-program.
95

next 2 days state-of-the-art, animal-based research and its relevance to

precision medicine will be presented and discussed. The workshop’s ses-
sions will explore ways with which in vivo “precision modeling,” next-
generation animal models, and phenotyping platforms can catalyze and
accelerate the advent of precision medicine. Complementary in vitro and
in silico approaches to advance the three Rs and means to ensure reproduc-
ibility of methods and data will be prominent features of the sessions and
discussions.
Thursday, October 5
8:00-9:00am Registration
8:45 Opening Remarks
9:00 Where We Are Today in Precision Medicine

Moderator: Kent Lloyd, University of California, Davis
(Organizing Committee Co-Chair)
This session will provide the historical context and roots
of precision medicine; present the current definitions and
framework of the field; discuss the anticipated goals and
outcomes of the Precision Medicine Initiative; and ex-
pand on the hurdles to achieve these goals. It will also
provide an overview of the regulatory framework and
the ethical and welfare challenges relating to the use of
animals in precision medicine.
The evolution and foundations of precision medicine

India Hook-Barnard, University of California, San
Francisco
The vision and goals of the All of Us Research Program

Petra Kaufmann, National Center for Advancing
Translational Sciences
The regulatory landscape of precision medicine

Robert M. Califf, Duke University School of
Medicine (remotely)
(Organizing Committee Member)

APPENDIX A 97
Ethical and welfare considerations regarding precision

animal modeling
Elizabeth Heitman, University of Texas Southwestern
Medical School
10:15 Coffee Break
10:30 Defining “Precise”: Translation and Human Relevance

of Current Animal Models
Moderator: Melissa Haendel, Oregon Health & Science
University
In their most classic use, animal models express phe-
notypic alignment rather than biological relevance at
the molecular level. Do precise animal models currently
exist? What characteristics should a precise animal
model embody to be relevant in the context of precision
medicine? This session will explore the translatability,
alignment, and relevance of current animal models to
the human condition.
Elements of precision in the design, creation, use, and

data analysis of current animal models
David Valle, Johns Hopkins University
Comprehensive phenotyping of the mouse genome

Steve Brown, Medical Research Council, United
Kingdom
Functional analysis of genes essential for life

Mary Dickinson, Baylor College of Medicine
Exploring genetic variability using precision pathology

in animals
Keith Mansfield, Novartis
Lunch (Will be served for speakers, committee members

12:10pm
and Roundtable members in the Member’s Room. We
have only ordered enough lunch for these parties.)
1:00 Applying “Precise”: New Ways of Modeling Diseases in

Animals

Moderator: Rhonda Wiler, Genentech (ILAR

Roundtable Member)
Improving the relevance of animal models to human
diseases is at the heart of preclinical and translational
research. Focusing on the application of precision, this
session will explore new approaches to disease model-
ing, e.g., can modeling platforms improve the clinical
relevance of current animal models, and what lessons
have we learned from transformative uses of animals to
support human clinical trials?
Precision Disease Modeling in Animals
Genetic modeling in zebrafish and other animals

Nicholas Katsanis, Duke University School of
Medicine (remotely)
Improving diagnostics and therapeutics for Mendelian

diseases using precision mouse models
Robert Burgess, The Jackson Laboratory
Co-clinical trials of mice and human patients

J. Sean Clohessy, Beth Israel Deaconess Medical
Center
New Approaches to Disease Modeling
Developing new “non-model” model systems

Jennifer Maier, University of Illinois
Making connections between human and animal

phenotypes
Melissa Haendel, Oregon Health & Science
University
The Animal Rule: A holistic approach to “precision”

Jens Kuhn, National Institutes of Health/National
Institute of Allergy and Infectious Diseases Integrated
Research Facility at Fort Detrick
3:20 Coffee Break

APPENDIX A 99
3:35 Improving Predictivity in Precision Medicine

Experimentation—Reproducibility Considerations
Moderator: Cory Brayton, Johns Hopkins University
School of Medicine
This session will begin with an overview of the essential
elements that uphold and strengthen the reproducibility
of study design. Subsequent presentations will examine
ways with which reproducibility can be sustained in the
context of precision modeling.
The translational potential of animal models

Ulrich Dirnagl, Charité, Berlin, Germany
Systematic reviews, meta-analysis, and reproducibility

Merel Ritskes Hoitinga, Radboud University Medical
Center, the Netherlands
Biomedical computing, large databases, and

reproducibility
Arjun Kumar Manrai, Harvard Medical School
Reproducibility in the alignment of the individual

human patient and the “precise” animal model
Jonathan Kimmelman, McGill University, Canada
5:15 Adjourn for the Day
Friday, October 6
8:30am Precision Modeling In Vitro
Moderator: Brian Berridge, GlaxoSmithKline
(Organizing Committee Co-Chair)
Rapid advances in technologies involving iPSCs and mi-
crophysiological systems offer new opportunities to im-
prove modeling of the human condition. This session will
explore how these capabilities are both a valuable adjunct
to and a potential replacement for precision modeling in
animals.
Disease modeling and human iPSCs

Paul Burridge, Northwestern University

Modeling Barth syndrome–associated cardiomyopathy

with human iPSCs and microphysiological systems
Megan McCain, University of Southern California
Functional coupling of human microphysiological

systems
John Wikswo, Vanderbilt University (remotely)
Quantitative systems pharmacology and the bridge from

in vitro to in vivo toxicity testing
D. Lansing Taylor, University of Pittsburgh
10:10 Coffee Break
Precision Safety and Toxicology in the Age of Precision

10:25
Medicine
Moderator: Jill Ascher, U.S. Food and Drug
Administration (ILAR Roundtable Member)
Protecting the public’s health and increasing the longev-
ity of the human population present unique challenges.
This session will explore how precision medicine may
change two scientific disciplines that depend on data from
large population cohorts: drug safety and toxicology. At
the level of the individual patient, speakers will explore
modeling and monitoring of drug safety; at the level of
population health, the session will focus on population
outcomes looking at the example of modeling environ-
mental exposures to potential intoxicants. How can data
from animal models inform the transformation from
healthcare that depends on population outcomes to one
exploiting solely an individual’s unique characteristics?
Defining “precise” while modeling patient

susceptibilities to drug-induced toxicity
Patient susceptibilities in preclinical drug safety
assessment
Brian Berridge, GlaxoSmithKline
Co-expressed gene network analysis as a bridge for

extrapolation between species
James Stevens, Eli Lilly and Company

APPENDIX A 101
Defining “Precise” in Environmental Toxicology and

Public Health
Using diversity outbred mice to mimic human

population dynamics in susceptibility to environmental
chemicals
Alison Harrill, National Institute of Environmental
Health Sciences, National Toxicology Program
Approaches to integrating evidence from animal and

human studies in chemical assessments
Kristina Thayer, U.S. Environmental Protection
Agency
12:10pm Lunch (Will be served for speakers, committee members

and Roundtable members in the West Court. We have
only ordered enough lunch for these parties.)
1:00 Precision Medicine Around the World

Moderator: Brian Berridge, GlaxoSmithKline
The speakers of this session will present a number of
national approaches and strategies to creating precision
medicine initiatives. The session will provide a platform
to highlight the rationales, expected outcomes, and possi-
ble convergence of these different approaches. The speak-
ers will also address how central animal-based research is
or can be to these initiatives, and strategies to sharing the
data generated at a global scale.
The United Kingdom’s 100,000 Genomes Project

Damian Smedley, Genomics England, United
Kingdom
The French Plan for Genomic Medicine

Catherine Nguyen, ITMO Génétique, Génomique &
Bioinformatique (GGB), Paris, France
Japan’s Initiative on Rare and Undiagnosed Diseases

Kenjiro Kosaki, Keio University School of Medicine,
Japan

The World Economic Forum’s Precision Medicine Effort

Genya Dana, Center for the Fourth Industrial
Revolution, World Economic Forum
2:15 Linking Animal-Based Research to Precision Medicine:

The Patient’s Perspective
Moderator: Donna Matthews Jarrell, Massachusetts
General Hospital (ILAR Roundtable Member)
Patients are powerful supporters and advocates for sus-
taining research to improve care and treatment. How
do patient advocacy groups understand the relevance of
animal-based research in the era of precision medicine?
How could researchers explain new approaches to re-
search with and without the use of laboratory animals?
Patient advocacy in the context of precision medicine

Daryl Pritchard, Personalized Medicine Coalition
Pets with naturally occurring tumors—A natural model

for improving cancer care and treatment
Amy K. LeBlanc, National Cancer Institute
Using precision medicine to help patients with

Parkinson’s Disease
Brian Fiske, The Michael J. Fox Foundation for
Parkinson’s Research
Community advisory boards and research in precision

medicine
Richard Sharp, Mayo Clinic
3:30 What Can We Expect from Integrating Precision Animal

Modeling Into the Precision Medicine Paradigm?
The speaker will discuss a possible future in which animal
precision models are integral to fulfilling the promises of
precision medicine for improving human health.
Kent Lloyd, University of California, Davis
4:15 Adjourn Meeting

Appendix B
Planning Committee Biographies
Brian R. Berridge (Co-Chair) is a senior GlaxoSmithKline (GSK) fellow

and director and head of WW Animal Research Strategy in the Office of
Animal Welfare, Ethics and Strategy at GSK. In that position he leads ef-
forts to advance the scientific impact of animal and non-animal modeling
in support of pharmaceutical development. He has held previous positions
as a director of Regulatory & Discovery Pathology at GSK and principal
research pathologist at Eli Lilly and Company. Dr. Berridge is an Oklahoma
State University–trained veterinarian with residency and Ph.D. training
from Texas A&M University. He is a diplomate of the American College of
Veterinary Pathologists and holds an adjunct associate professor position in
the Department of Population Health and Pathobiology at North Carolina
State University. He additionally teaches cardiovascular toxicology at the
University of North Carolina. He is a member of the executive board and
board of trustees for the International Life Sciences Institute Health and
Environmental Sciences Institute (HESI), where he also serves as treasurer
and co-chairs the HESI Cardiac Safety Technical Committee and the Inte-
grated CV Strategies Working Group. Dr. Berridge also chairs a CV Spe-
cialty Interest Group within the Society of Toxicologic Pathologists and a
Microphysiological Systems Working Group within the IQ Consortium. He
is a member of the Interagency Coordinating Committee on the Validation
of Alternative Methods.
K.C. Kent Lloyd (Co-Chair) is a veterinarian and research scientist studying

genome-wide mutagenesis in laboratory mice. Dr. Lloyd graduated with his
bachelor of science degree from the University of California, San Diego,
103

with an emphasis in biology and biochemistry. He was accepted into the

School of Veterinary Medicine at the University of California, Davis (UCD),
from which he graduated in 1983 with his doctor of veterinary medicine
degree. After a clinical internship at the New Bolton Center, University of
Pennsylvania School of Veterinary Medicine, surgery residency at the UCD
Veterinary Medical Teaching Hospital (VMTH), and brief appointment as a
clinical faculty member in the VMTH, Dr. Lloyd matriculated in the School
of Medicine at the University of California, Los Angeles (UCLA) where in
1992 he received his doctor of philosophy (Ph.D.) in physiology under the
mentorship of Doctors John H. Walsh and Jared Diamond. After gradua-
tion, he joined the UCLA faculty as an Assistant Professor in the Depart-
ment of Physiology where he established his National Institutes of Health
(NIH)-funded research laboratory investigating the mechanisms of entero-
gastric reflexes. During the next 3 years, Dr. Lloyd served concurrently
as a visiting scientist at the European Molecular Biology Laboratory in
Heidelberg, Germany, where he engaged in pioneering work on conditional
mutagenesis in the mouse. After earning a promotion to associate professor
in 1996, Dr. Lloyd was recruited to the School of Veterinary Medicine at
UCD as a tenured faculty member in the Department of Anatomy, Physiol-
ogy, and Cell Biology and as a founding faculty member of the Center for
Comparative Medicine. In 2001 he was promoted to full professor and was
appointed as associate dean for research and graduate education. Dr. Lloyd
assumed the role of director of the UCD Mouse Biology Program in 2002,
taking over from founding director Dr. Stephen Barthold. In 2013 Dr. Lloyd
was recruited to the UCD School of Medicine, where he is a professor in
the Department of Surgery. Dr. Lloyd has an active NIH-funded research
program that emphasizes the development and application of genetically
altered mice for research that seeks to understand the biological functions
of genes as well as the genetic basis of disease pathogenesis. He is an active
participant in the education and training of undergraduate, graduate, and
professional students and scholars. He also serves on many councils and
committees at the school and campus level, in professional organizations
(e.g., American Veterinary Medical Association), and at federal agencies
(e.g., NIH). His current research is focused on in vivo precision modeling
using next-generation molecular techniques for genome editing and ma-
nipulation in animals. He was recently named associate director of in vivo
precision modeling at the UCD Center for Precision Health.
Cory Brayton is associate professor and director of Phenotyping and Pa-

thology Core Facility at Johns Hopkins University, School of Medicine. She
is a diplomate of the American College of Laboratory Animal Medicine
and the American College of Veterinary Pathologists (ACVP). She served as
president of ACVP in 2014, as well as on ACVP Council 2009-2012, and as

APPENDIX B 105
president elect, 2013. She received her D.V.M. from Cornell University and
did postdoctoral research and pathology training in New York City at the
Animal Medical Center, Cornell University, and The Rockefeller University.
At The Rockefeller University (1989-1992), she became specifically inter-
ested in the pathology and characterization (phenotyping) of genetically
engineered mice, and continued to pursue this interest at several institu-
tions while heading the Facility for Comparative Studies at the Hospital for
Special Surgery (1992-1998). At Baylor College of Medicine (1998-2004),
she headed the Comparative Pathology Laboratory, and was responsible for
health surveillance and diagnostic pathology for a diverse research popula-
tion including more than 150,000 mice. She was also associate professor
in pathology, associate director of the Center for Comparative Medicine,
and interim attending veterinarian, and served on the Institutional Animal
Care and Use Committee while pursuing research collaborations and teach-
ing initiatives and developing national and international conferences on the
characterization and pathology of genetically engineered mice. In 2004 she
moved to Johns Hopkins University to develop a collaborative phenotyping
core based in the Department of Molecular and Comparative Pathobiology,
where veterinarian postdoctoral trainees and faculty investigators provide
a unique comparative and translational research resource, in an institution
with exceptional resources for multidisciplinary biomedical research. She
has been on the ILAR council and co-editor-in-chief of the ILAR Journal
since 2012.
Robert M. Califf is Donald F. Fortin, MD Professor of Cardiology at Duke

University School of Medicine. He was the commissioner of food and drugs
in 2016-2017 and deputy commissioner for medical products and tobacco
from February 2015 until his appointment as commissioner in February
2016. Prior to joining the U.S. Food and Drug Administration (FDA),
Dr. Califf was a professor of medicine and vice chancellor for clinical and
translational research at Duke University. He also served as director of the
Duke Translational Medicine Institute and founding director of the Duke
Clinical Research Institute. A nationally and internationally recognized
expert in cardiovascular medicine, health outcomes research, healthcare
quality, and clinical research, Dr. Califf has led many landmark clinical
trials and is one of the most frequently cited authors in biomedical science,
with more than 1,200 publications in the peer-reviewed literature. Dr. Califf
became a member of the National Academy of Medicine (NAM) in 2016,
one of the highest honors in the fields of health and medicine. Dr. Califf
has served on numerous NAM committees, and he has served as a member
of the FDA Cardiorenal Advisory Panel and FDA Science Board’s Subcom-
mittee on Science and Technology. Dr. Califf has also served on the Board
of Scientific Counselors for the National Library of Medicine, as well as on

advisory committees for the National Cancer Institute, the National Heart,
Lung, and Blood Institute, the National Institute of Environmental Health
Sciences, and the Council of the National Institute on Aging. He has led
major initiatives aimed at improving methods and infrastructure for clinical
research, including the Clinical Trials Transformation Initiative, a public–
private partnership co-founded by the FDA and Duke. He also served as the
principal investigator for Duke’s Clinical and Translational Science Award
and the NIH Health Care Systems Research Collaboratory coordinating
center and co-principal investigator of the Patient Centered Outcomes Re-
search Institute Network. Dr. Califf is a graduate of Duke University School
of Medicine. He completed a residency in internal medicine at the Univer-
sity of California, San Francisco, and a fellowship in cardiology at Duke.
Melissa Haendel co-leads the Monarch Initiative, which aims to provide

open integrated access to model organism and human phenotype-genotype
data for the purposes of disease hypothesis exploration. She also partici-
pates in the Open Research Information Framework, a community standard
designed to collect and disseminate information about all types of scholarly
products (such as code, material resources, etc.) and the contribution roles
that scholars have in their generation. She also participates in development
of interoperability standards, such as the new Phenopackets Phenotype Ex-
change Standard, is an Open Biomedical Ontologies Foundry coordinator,
and is on the International Society for Biocuration executive board. Her
research interests are in using semantic technologies to promote open and
synthetic science through connections within biomedical data, and pushing
toward a cultural shift to use of information science during the course of
research for more effective science, publication of science, and collaborative
science practices.
John P.A. Ioannidis is the C.F. Rehnborg Chair in Disease Prevention at

Stanford University, professor of medicine and of health research and
policy, at the School of Medicine; professor of statistics (by courtesy) at
the School of Humanities and Sciences; co-director of the Meta-Research
Innovation Center at Stanford; and director of the Ph.D. program in Epi-
demiology and Clinical Research. Dr. Ioannidis was born in New York City
in 1965 and grew up in Athens, Greece. He was valedictorian at Athens
College, received the National Award of the Greek Mathematical Society,
graduated in the top rank of his medical school class from the University
of Athens in 1990, and received a doctorate in biopathology from the same
institution. Dr. Ioannidis trained at Harvard and Tufts in internal medicine
and infectious diseases, then held positions at the National Institutes of
Health (NIH), Johns Hopkins, and Tufts. Dr. Ioannidis has chaired the De-
partment of Hygiene and Epidemiology at the University of Ioannina Medi-

APPENDIX B 107
cal School in 1999-2010 and has been adjunct faculty for Tufts University
since 1996 (professor rank since 2002). He was director from 2008 to 2010
of the Center for Genetic Epidemiology and Modeling at Harvard School of
Public Health and is adjunct professor of epidemiology at Harvard School
of Public Health and visiting professor of epidemiology and biostatistics at
Imperial College. Dr. Ioannidis is a member of the executive board of the
Human Genome Epidemiology Network and senior advisor on knowledge
integration at National Cancer Institute/NIH, and served as president for
the Society for Research Synthesis Methodology. Dr. Ioannidis is an edito-
rial board member of many leading journals (including PLoS Medicine,
Lancet, Annals of Internal Medicine, JNCI, Science Translational Medicine,
Clinical Chemistry, Molecular and Cellular Proteomics, AIDS, IJE, JCE,
Clinical Trials, and PLoS ONE, among others) and as editor-in-chief of the
European Journal of Clinical Investigation.

Appendix C
Speaker Biographies
Steve Brown earned his Ph.D. at Cambridge University, and before

he joined the Medical Research Council, he was professor of genetics at
Imperial College, London. His research interests cover mouse functional
genomics, including the use of mouse mutagenesis and comparative genomic
analysis to study the genetic basis of disease and to develop pre-clinical
disease models. A particular focus has been the use of mouse models to
study the molecular basis of genetic deafness. Along with Karen Steel, he
discovered myosin VIIA as the gene underlying the shaker1 mutant, one
of the first deafness genes to be identified. Subsequently, he has developed
interests in the protein complexes that are involved with stereocilia elonga-
tion in hair cells in the inner ear. In addition, over the last 10 years he has
led a substantial research effort in the genetics of otitis media or glue ear,
a common cause of hearing loss in children, employing mouse models to
elaborate the key genetic pathways involved and develop novel therapeu-
tic strategies. He has served on numerous advisory boards, and his current
appointments include the Advisory Council for the National BioResource
Centre, Japan; Science Advisory Board (SAB) for the Helmholtz Centrum,
München; SAB for the Centre Intégratif de Génomique (CIG), University
of Lausanne; and the Strategic Policy Committee, Institut de Génétique et
de Biologie Moléculaire et Cellulaire, Strasbourg. He is the current chair
of the International Mouse Phenotyping Consortium Steering Committee.
Robert Burgess’s lab seeks to understand the molecular mechanisms of

synapse formation and maintenance at two sites in the nervous system:
the peripheral neuromuscular junction and the retina. In all of these studies,
108

APPENDIX C 109
the Burgess lab is addressing basic molecular mechanisms, but these basic
mechanisms have relevance to human neuromuscular and neurodevelop-
mental disorders. The lab’s continued research on the genetics underlying
these disorders, and the continuing effort to identify new genes involved in
these processes, will increase our understanding of the molecules required to
form and maintain synaptic connectivity in the nervous system. Dr. Burgess
received his B.S. in biochemistry from Michigan State University, and his
Ph.D. in neuroscience from Stanford University. After doing postdoctoral
research at Washington University, St. Louis, he joined the faculty of The
Jackson Laboratory in Bar Harbor, Maine, in 2001. Dr. Burgess’s research is
funded by the Muscular Dystrophy Association and the National Institutes
of Health. Among other leadership positions, he is the principal investigator
of The Jackson Center for Precision Genetics.
Paul Burridge is an assistant professor in the Department of Pharmacology

at Northwestern University Feinberg School of Medicine and founding fac-
ulty of the Center for Pharmacogenomics. Dr. Burridge began his career in
genomics and bioinformatics at the Sanger Institute working on the human
and mouse genome projects. He completed a Ph.D. in Human Stem Cell
Biology at the University of Nottingham before pursuing postdoctoral fel-
lowships at the Johns Hopkins University Institute for Cell Engineering in
Pediatric Oncology and then at Stanford University Institute for Stem Cell
Biology and Regenerative Medicine. Dr. Burridge became an instructor in
cardiovascular medicine at Stanford in 2013 before joining Northwestern in
2015. For more than a decade, he has worked on the applications of human
induced pluripotent stem cells disease modeling, specifically the pharma-
cogenomic and molecular mechanisms of chemotherapy-induced cardio-
myopathy and heart failure. Dr. Burridge is the recipient of the National
Institutes of Health National Heart, Lung, and Blood Institute Pathway to
Independence Award and a Dixon Young Investigator Award, and in 2016
he was elected a fellow of the American Heart Association.
John (Seán) Clohessy is director of the Mouse Hospital/Preclinical Murine

Pharmacogenetics Facility at the Beth Israel Deaconess Medical Center
and Harvard Medical School (BIDMC/HMS) in Boston, Massachusetts.
Dr. Clohessy received his Ph.D. in 2005 from University College London,
where he studied the role of BCL2 family proteins in the regulation of
apoptosis and leukemia. Following this, he completed post-graduate train-
ing at Memorial Sloan Kettering Cancer Center and then at the Beth Israel
Deaconess Medical School/Harvard Medical School, where he is currently
instructor in medicine. His current focus as director of the Mouse Hospital
at BIDMC/HMS focuses on the development of best practices approaches
for implementation of pre- and co-clinical trials in mice, with the aim to

develop a “Mouse Hospital” whereby genetically engineered mouse models

that faithfully model human disease can be treated in a manner similar to
how they would be treated in human patients. In particular, he is interested
in the development and utilization of genetically engineered mouse models
for pre- and co-clinical applications to facilitate genetic stratification of
patients for focused and rapid clinical evaluation of novel therapies and
therapeutic strategies in the treatment of cancer. In addition, Dr. Clohessy
has an active research interest in the role of the ribosome and cellular
translation in disease.
Genya Dana joins the Forum from the U.S. Department of State where
she spent 5.5 years working at the nexus of science and foreign policy
in the Office of the Science and Technology Adviser to the Secretary of
State. She is an internationally recognized expert on the policy and science
of synthetic biology and other emerging biotechnologies, and she led the
development of the U.S. position and outreach on synthetic biology and
gene editing at the international level. She served as a negotiator on science,
technology, and innovation in multilateral organizations like the United
Nations, worked to advance science, technology, and innovation for sus-
tainable development with a focus on Africa, and developed international
partnerships to support scientific research on brain science and biological
engineering. Dr. Dana grew up on a small family farm in Mississippi, com-
pleted a bachelor’s degree in biology from Emory University in Atlanta, and
spent several years working in finance before returning to graduate school
to combine science and policy. She has an M.Sc. in science, technology, and
environmental policy and a Ph.D. in ecological risk assessment, both from
the University of Minnesota.
Mary Dickinson is an internationally recognized expert in imaging, genet-

ics, bioengineering, and vascular biology with more than 100 peer-reviewed
publications. Her work involves the development of novel imaging strate-
gies to define the genetic and environmental causes of congenital birth
defects and understand mechanisms underlying angiogenesis and vascular
remodeling. In addition to Dr. Dickinson’s research efforts, she serves as
the director of the Optical Imaging and Vital Microscopy core, as an execu-
tive member of the Cardiovascular Research Institute, and as a principal
investigator for the National Institutes of Health Knockout Mouse Project.
Dr. Dickinson is also a fellow of the American Institute of Medical and
Biological Engineers and recently became the associate dean of research at
Baylor College of Medicine.
Ulrich Dirnagl’s research focuses on stroke, cerebral blood flow regulation,

and brain imaging. In preclinical models, as well as clinical trials, he and his

APPENDIX C 111
coworkers and collaborators explore mechanisms by which brain ischemia

leads to cell death, and develop novel methods to intercept mechanisms
of damage in acute brain damage, as well as to foster regeneration and
repair of the lesions. Dr. Dirnagl is particulary interested in how the brain
protects itself (“endogenous neuroprotection”), and how the brain interacts
with other systems of the body after it has been injured. Closely linked
to his interest in stroke pathophysiology is his interest in the coupling
of regional blood flow to neuronal acitivity, the mechanism underlying
functional brain imaging with magnetic resonance (MR) and positron-
emission tomography. Beyond imaging structure and function of the cen-
tral nervous system he and his team are developing, validating and using
techniques that allow the non-invasive imaging of brain biochemistry
and molecular signaling. To this end they use optical, MR, and nuclear
medicine approaches in mice and humans. To improve the predictiveness of
preclinical translational research he is actively promoting the introduction
of quality standards for experimental design and reporting, as well as in-
ternational collaboration in large, phase III-type preclinical trials. Through
meta-research he is trying to identify opportunities for improving research
practice and to obtain evidence for the impact of targeted interventions. At
the Charité Universitätsmedizin Berlin Dr. Dirnagl serves as director of the
Department of Experimental Neurology. Since 2017 he is also the found-
ing director of the Center for Transforming Biomedical Research (CTBR)
at the Berlin Institute of Health. CTBR aims at overcoming the roadblocks
in translational medicine by increasing the value and impact of biomedical
research through maximizing the quality, reproducibility, generalizability,
and validity of research.
Brian Fiske is the senior vice president for research programs at The
Michael J. Fox Foundation (MJFF) for Parkinson’s Research. Dr. Fiske co-
manages a team of professionals who stay closely linked to the Parkinson’s
community in order to develop an aggressive and innovative agenda for
accelerating research and drug development for Parkinson’s disease. This
ensures that MJFF priorities reflect and best serve the ultimate needs of
patients. Dr. Fiske regularly meets with academic and industry scientists
around the world to identify promising ideas to support, providing trou-
bleshooting and ongoing management of projects as they go forward. He
currently oversees the teams focused on MJFF’s strategies for developing
disease-modifying and symptomatic therapies for Parkinson’s patients. Dr.
Fiske earned an undergraduate degree in biology from Texas A&M Uni-
versity and a Ph.D. in Neuroscience from the University of Virginia. After
completing postdoctoral research at Columbia University, Dr. Fiske spent
several years as an editor for the prestigious scientific journal, Nature Neu-

roscience. He brings this broad experience and knowledge to the Founda-

tion to help bring new treatments to people with Parkinson’s.
Alison Harrill is a geneticist at the National Institutes of Health/National

Institute for Environmental Health Sciences in the Division of the National
Toxicology Program (NTP). Her research interests include investigating the
role of genetic sequence variation and population dynamics as it relates to
toxicity susceptibility for the purposes of risk management. In addition,
she has used rodent population models, like the Diversity Outbred mice,
to investigate differential modes of action of toxicity susceptibility using
toxicogenomic investigations in resistant and susceptible individuals. At the
NTP, she is currently working toward qualification of cell-based screens to
assessing potency of developmental neurotoxic agents using mouse popula-
tion models in order to better extrapolate risk to genetically diverse human
populations. She currently serves as an associate editor for Toxicologi-
cal Sciences, co-chair of the Health and Environmental Sciences Institute’s
(HESI’s) Application of Genomics to Mechanism-Based Risk Assessment
Technical Committee, co-chair of the HESI miRNA Biomarkers Working
Group, co-chair of the Society of Toxicology, Contemporary Concepts
in Toxicology Committee, and past secretary/treasurer of the Toxicology
Division within the American Society for Pharmacology and Experimental
Therapeutics. Dr. Harrill received her Ph.D. in Toxicology from the Univer-
sity of North Carolina at Chapel Hill (2009). Dr. Harrill and her research
team have received several awards, including the Burroughs Wellcome Fund
Award for Innovation in Regulatory Science (2013-2016), the Society of
Toxicology Outstanding Published Paper in Advancing the Science of Risk
Assessment Award (2009), and the Society of Toxicology Best Paper Pub-
lished in Toxicological Sciences (2016).
Elizabeth Heitman is a professor in the Program in Ethics in Science and

Medicine at the University of Texas Southwestern Medical Center in Dal-
las, Texas. Her work focuses on cultural issues and international aspects
of ethics in medicine, biomedical science, and public health; her research
examines international standards of research ethics, education in the re-
sponsible conduct of research, and trainees’ awareness of professional and
cultural norms. She is co-director of the research ethics education program
“Formação Colaborativa na Ética em Pesquisa (Collaborative Research
Ethics Education),” sponsored by the National Institutes of Health Fogarty
International Center, with colleagues from Vanderbilt University Medical
Center in Nashville, Tennessee, and the Universidade Eduardo Mondlane in
Maputo, Mozambique. Dr. Heitman previously directed a similar program
with the Hospital Nacional de Niños in San José, Costa Rica, and was
principal investigator of the National Science Foundation–funded study

APPENDIX C 113
“Research Integrity in the Education of International Science Trainees.” She

is a member of the Board on Life Sciences’ Standing Committee on Educa-
tional Institutes for Teaching Responsible Science. Through the National
Academies, Dr. Heitman has taught in international faculty development
projects on responsible science in the Middle East and North Africa, as well
as Malaysia and Indonesia. She previously chaired the National Academies
Committee on the Elaboration of a National Curriculum in Bioethics and
Responsible Conduct of Science for Algeria, advising the Algerian Ministry
of Higher Education, and recently served as co-chair of the Committee on
Gene Drive Research in Non-Human Organisms: Recommendations for
Responsible Conduct. Dr. Heitman received her Ph.D. in Religious Studies
in 1988 from Rice University’s joint program in biomedical ethics with the
University of Texas–Houston Health Science Center.
Merel Ritskes Hoitinga is a professor in evidence-based laboratory animal

science at the Department for Health Evidence at the Radboud University
Medical Center, Nijmegen, the Netherlands. She founded SYRCLE (www.
syrcle.nl) in 2012, focusing on education, coaching, and research in the
field of systematic reviews of animal studies. Systematic reviews lead to
the actual implementation of the 3Rs, a more evidence-based choice of
animal models and transparency in quality and translation of animal stud-
ies. In 2017 SYRCLE won the Cochrane REWARD 2nd prize, illustrating
the importance of this work for Cochrane and the Lancet REWARD Alli-
ance campaign (increasing value and reducing waste in research). SYRCLE
participates in international networks: CAMARADES, Evidence-Based
Toxicology, Evidence-Based Research Network, GRADE and Evidence
Synthesis International, and is preparing an application for a Cochrane
methods group. From 1997 to 2005 Dr. Ritskes Hoitinga was a professor
in laboratory animal science and comparative medicine at the Faculty of
Health Sciences, University of Southern Denmark. In 2017 she was a visit-
ing professor at the Department for Clinical Medicine at Aarhus University.
India Hook-Barnard is director of research strategy and associate director,

precision medicine at the University of California, San Francisco (UCSF).
She serves as director of the UCSF Precision Medicine Platform Commit-
tee, which aims to conceptualize and build precision medicine as a central
overarching institutional vision at UCSF. She helped launch and serves as
executive director for the California Initiative to Advance Precision Medi-
cine. In the UCSF Office of Science Policy and Strategy, she works with
scientific experts and leaders from across academia, industry, and govern-
ment sectors to identify and frame scientific opportunities, technical feasi-
bility, and organizational challenges. She develops and supports efforts to
secure major research and infrastructure funding, supports research train-

ing programs, and provides advice, consultation, and analysis on scientific

initiatives. Dr. Hook-Barnard’s primary interests are in areas of emerg-
ing science, technology, and medicine, spanning fundamental discovery to
translational application, clinical practice, and population health research,
including issues of policy, regulation, ethical and societal concerns, and
workforce. From 2008 to 2015, she worked as a senior program officer
with the National Academy of Sciences (NAS) and the Institute of Medicine
(IOM). At the NAS and the IOM, she developed and administered a variety
of programs, working with academic faculty, scientists, engineers, clinicians,
business leaders, and policy experts. She served as the study director for six
National Academies reports, including Toward Precision Medicine: Building
a Knowledge Network for Biomedical Research and a New Taxonomy of
Disease (2011), Determining Core Capabilities in Chemical and Biological
Defense Science and Technology (2012), and Sharing Clinical Trial Data:
Maximizing Benefits, Minimizing Risk (2015). Dr. Hook-Barnard was a
postdoctoral research fellow at the National Institutes of Health. She earned
her Ph.D. in microbiology-medicine from the Department of Molecular
Microbiology and Immunology at the University of Missouri.
Nicholas (Nico) Katsanis obtained his baccalaureate degree in genetics

from the University College London in 1993 and his doctorate degree from
Imperial College London in 1997. While at Imperial College, he worked
with Dr. Elizabeth Fisher on the genetics of Down syndrome. He completed
his postdoctoral work in the laboratory of Dr. James Lupski within the
Department of Molecular and Human Genectis at Baylor College of
Medicine in Houston and transitioned his studies to Bardet-Biedl syn-
drome. In 2002, he established his independent research lab at the Institute
of Genetic Medicine, Johns Hopkins University, where he led studies that
unified several allied conditions under the ciliopathy umbrella. Dr. Katsanis
demonstrated that Bardet-Biedl syndrome is caused by centrosomal/basal
body dysfunction, establishing that dysfunction at the primary cilium can
give rise to a large group of disorders with both clinical and genetic
overlap (the ciliopathy model). In 2009, he moved to Duke University to
establish the Center for Human Disease Modeling (CHDM) and is the di-
rector. He developed a structure that aims to facilitate collaboration across
disciplines and to develop physiologically relevant tools to study variation
found in human patient genomes. As part of that effort, Dr. Katsanis
leads the Taskforce for Neonatal Genomics. This multidisciplinary group of
physicians and basic scientists strives to synthesize genomic and biological
data for the faster diagnosis, improved/focused clinical care, and potential
therapeutic paradigms for infants and neonates with genetic conditions.
In parallel, the CHDM pursues questions centered on the signaling roles of
vertebrate cilia, the translation of signaling pathway defects on the causality

APPENDIX C 115
and possible treatment of ciliary disorders, and the dissection of second-site

modification phenomena as a consequence of genetic load in a functional
system. In recognition of his work, Dr. Katsanis was awarded the Young
Investigator Award from the American Society of Nephrology in 2009, the
E. Mead Johnson Award from the Society for Pediatric Research in 2012,
and the Curt Stern Award from the American Society of Human Genetics
in 2017 and has delivered several distinguished lectures. Dr. Katsanis is a
professor in the Departments of Cell Biology and Pediatrics and holds the
Jean and George Brumley Distinguished Professorship.
Jonathan Kimmelman is associate professor at McGill University in the

Biomedical Ethics Unit/Social Studies of Medicine, with a cross appoint-
ment in Experimental Medicine. His research centers on ethical, policy, and
scientific dimensions of drug and diagnostics development, and he founded
and directs the Studies of Translation, Ethics and Medicine. In addition to
his book, Gene Transfer and the Ethics of First-in-Human Experiments
(Cambridge Press, 2010), major publications have appeared in Science,
JAMA, BMJ, and Hastings Center Report. Dr. Kimmelman received the
Maud Menten New Investigator Prize (2006), a Canadian Institutes for
Health Research (CIHR) New Investigator Award (2008), and a Humboldt
Bessel Award (2014). He has served on various advisory bodies within the
National Heart, Lung, and Blood Institute, the U.S. National Academy of
Medicine, and the CIHR, and makes frequent appearances in the news
media. He chaired the International Society of Stem Cell Research Guide-
lines for Stem Cell Research and Clinical Translation revision task force
2015-2016.
Kenjiro Kosaki received clinical and research training in medical genetics at

the University of California, San Diego, and Baylor College of Medicine and
received board certification in clinical genetics from the American Board
of Medical Genetics. Currently, he is serving as the co-principal investiga-
tor for two government-funded national research projects of Japan in the
field of medical genomics and rare diseases. He was the organizer of the
Fourth International Conference on Rare and Undiagnosed Diseases held
in Tokyo in November 2016.
Jens H. Kuhn is a principal at Tunnell Government Services (TGS), Inc.,

Bethesda, Maryland, tasked as the lead virologist (contractor) at the
Integrated Research Facility (IRF). He is also TGS team leader for all IRF-
Frederick TGS contractors. Dr. Kuhn specializes in highly virulent viral
pathogens. He is the author of Filoviruses: A Compendium of 40 Years of
Epidemiological, Clinical, and Laboratory Studies (Vienna: Springer, 2008)
and co-author of The Soviet Biological Weapons Program—A History

(Cambridge: Harvard University Press, 2012) and has studied and worked in
Germany, Italy, Malta, Russia, South Africa, and South Korea. In the United
States, he rotated through or worked at Harvard Medical School, Boston,
Massachusetts; the Arthropod-Borne Infectious Disease Laboratory in Fort
Collins, Colorado; the Centers for Disease Control and Prevention in At-
lanta, Georgia; and the U.S. Army Medical Research Institute of Infectious
Diseases in Frederick, Maryland. Dr. Kuhn was the first Western scientist
with permission to work in the former Soviet biological warfare facility
SRCVB “Vector” in Siberia, Russia, within the U.S. Department of Defense
Cooperative Threat Reduction Program. Dr. Kuhn was a contributor to
the Center for International and Security Studies at Maryland’s Control-
ling Dangerous Pathogens Project and a member of the Center for Arms
Control and Nonproliferation’s Scientists Working Group on Chemical/
Biological Weapons. He is currently chairing the International Committee
on Taxonomy of Viruses Filoviridae and Mononegavirales Study Groups
and is a subject-matter expert for the National Center for Biotechnology
Information for all mononegaviruses; is a member of the editorial boards of
Applied Biosafety—Journal of the American Biological Safety Association,
Archives of Virology, BioMed Research International, Journal of Bioter-
rorism and Biodefense, PLoS ONE, PLoS Pathogens, Viruses, Virologica
Sinica, Voprosy Virusologii, and World Journal of Virology; was a member
of the U.S. National Academy of Sciences’ committee on animal models for
assessing countermeasures to bioterrorism agents; and is continuously in-
volved with the American Association for the Advancement of Science and
the U.S. Department of State bioengagement efforts in the Broader Middle
East and North Africa region, Turkey, and the Newly Independent States.
Amy K. LeBlanc is the director of the intramural National Cancer Insti-

tute’s Comparative Oncology Program. In this position she conducts pre-
clinical mouse and translational canine studies that are designed to inform
the drug and imaging agent development path for human cancer patients.
She also advises leading pharmaceutical companies as well as the National
Cancer Institute’s (NCI’s) Division of Cancer Treatment and Diagnosis on
the inclusion of pet dogs with cancer into the development path of novel
approaches for a variety of malignancies, including immunotherapeutics,
targeted small molecules, oncolytic viruses, and cancer imaging agents.
She directly oversees the NCI Comparative Oncology Trials Consortium,
which provides infrastructure necessary to connect participating veterinary
academic institutions with stakeholders in drug development to execute fit-
for-purpose comparative clinical trials in novel therapeutics and imaging
agents. Prior to her appointment at the National Institutes of Health,
Dr. LeBlanc was an associate professor with tenure and director of trans-
lational research at the University of Tennessee College of Veterinary Medi-

APPENDIX C 117
cine and Graduate School of Medicine. Dr. LeBlanc’s group at the University
of Tennessee published the first comprehensive studies describing molecular
imaging of dogs and cats using positron-emission tomography/computed
tomography, focusing on the forward and back-translation of 18F-labeled
radiopharmaceuticals.
Jennifer Maier is a postdoctoral research associate at the University

of California, Los Angeles, in the lab of Karen Sears. Prior to moving to
UCLA, she was in the Sears lab at University of Illinois at Urbana-Cham-
paign. Her Ph.D. work was done at the University of Florida under Brian
D. Harfe, where she focused on the development of the intervertebral disc
using a variety of transgenic and mouse models. Her interests are broadly
in evolutionary developmental (evo-devo) biology and using non-classical
mammalian models to study diversity. She has worked on a number of
projects in the Sears lab, including investigating mammalian limb diversity,
mammalian digit reduction, and teratogenesis. Currently she is character-
izing the spermatogonial stem cells of the gray short-tailed opossum (Mono-
delphis domestica) and developing methods to generate the first transgenic
marsupials.
Arjun (Raj) Manrai is an instructor at the Department of Biomedical Infor-

matics at Harvard Medical School. Dr. Manrai received an undergraduate
degree in physics from Harvard College and completed his Ph.D. in bioin-
formatics and integrative genomics at the Harvard-Massachusetts Institute
of Technology Division of Health Sciences and Technology. Dr. Manrai
works on machine learning and statistical methods to improve the use of
genomic and laboratory data in the clinic. His work has been published
in the New England Journal of Medicine and the Journal of the American
Medical Association, and featured in The Wall Street Journal and The New
York Times and on National Public Radio.
Keith Mansfield is director of Discovery and Investigative Pathology at

Novartis Institutes for Biomedical Research and heads a molecular pathol-
ogy laboratory in Cambridge, Massachusetts. Prior to joining Novartis,
Dr. Mansfield was an associate professor of pathology at Harvard Medical
School. He was principal investigator of a number of National Institutes
of Health (NIH) grants funded through the National Institute of Allergy
and Infectious Diseases, National Institute of Aging, and National Insti-
tute of Diabetes and Digestive and Kidney Diseases and was a permanent
member and chair of the NIH Comparative Medicine Review Committee.
During this time he was director of a T32 NIH training grant in compara-
tive pathology and mentored a number of postgraduate veterinarians. His
research was focused on the experimental pathology of infectious diseases,

and he is author/co-author on more than 200 peer-reviewed research pub-

lications. Since joining Novartis in 2011, he has led a molecular pathology
laboratory utilizing precision models in drug discovery and development.
In 2016 he received a Novartis outstanding scientist award for his work.
He obtained his bachelor’s and D.V.M. degrees from Cornell University
and is currently an adjunct professor at Cornell University, School of Vet-
erinary Medicine. He trained in veterinary pathology at Harvard Medical
School and is board certified in veterinary pathology by the American
College of Veterinary Pathologists.
Megan McCain is an assistant professor and the Chonette Early Career

Chair in the Department of Biomedical Engineering and the Department of
Stem Cell Biology and Regenerative Medicine at the University of Southern
California (USC). Dr. McCain earned her B.S. in biomedical engineering at
Washington University in St. Louis and her Ph.D. in engineering sciences
at Harvard University. As a graduate student, she engineered cardiac cells
and tissues to investigate mechanotransduction in the context of cardiac
development and disease. She continued as a postdoctoral researcher at the
Wyss Institute for Biologically Inspired Engineering at Harvard University,
where she engineered microscale human cardiac tissues on platforms with
integrated functional assays, known as “heart-on-a-chip,” for patient- spe-
cific disease modeling and medium-throughput drug screening. In 2014,
Dr. McCain joined USC and established the Laboratory for Living Systems
Engineering to engineer and implement novel “organ-on-chip” platforms
for human disease modeling and drug screening, with a focus on cardiac
and skeletal muscle. Dr. McCain is a recipient of a Scientist Development
Grant from the American Heart Association and a Starter Grant from the
Amyotrophic Lateral Sclerosis Association. She has also been recognized as
a Top Innovator Under 35 by the Massachusetts Institute of Technology
Technology Review and a Rising Star by the Cellular and Molecular Bioen-
gineering sub-group of the Biomedical Engineering Society.
Catherine Nguyen has worked since 1984 in experimental biology, mainly

in molecular biology. In 1991 Dr. Nguyen became interested in gene expres-
sion analysis using large-scale approaches to question human diseases. She
currently serves as the director of the ITMO Genetique in Paris, France.
Dr. Nguyen received her Ph.D. in immunology from the University of Aix-
Marseille II.
Daryl Pritchard is the senior vice president of science policy at the Person-
alized Medicine Coalition (PMC), where he leads PMC efforts to increase
awareness and understanding of personalized medicine; identify and address
barriers to the adoption of personalized medicine into the healthcare system;

APPENDIX C 119
and develop and promote appropriate clinical, healthcare infrastructure,

regulatory, and payment policies. Before coming to PMC, Dr. Pritchard
served as the director of policy research at the National Pharmaceutical
Council (NPC), where he led NPC’s policy research, alliance development,
and government relations efforts in the areas of personalized medicine, the
heterogeneity of treatment effects, and recognition of the value of specialty
biopharmaceuticals. Prior to joining the NPC, Dr. Pritchard served as the
director of Research Programs Advocacy and Personalized Medicine at the
Biotechnology Industry Organization, where he developed and expanded
the organization’s diagnostics and personalized medicine policy program.
He also spent 3 years as the director of government affairs for the Ameri-
can Association for Dental Research, and the American Dental Education
Association. Dr. Pritchard received his Ph.D. and master’s degree in genet-
ics from The George Washington University, and completed a postdoctoral
research fellowship at the Children’s National Medical Center. He was
awarded the first American Society of Human Genetics/National Human
Genome Research Institute Fellowship in Genetics and Public Policy, where
he worked as a health legislative assistant in the House of Representatives.
Richard Sharp is the director of the Biomedical Ethics Program at the Mayo
Clinic. Prior to joining Mayo Clinic in July 2013, he was director of bioeth-
ics research at Cleveland Clinic and co-director of the Center for Genetic
Research Ethics and Law at Case Western Reserve University, one of six
National Institutes of Health Centers of Excellence in Ethics Research. Dr.
Sharp has published widely on topics in biomedical ethics, including clini-
cal ethics consultation, informed consent, financial conflicts of interest, and
ethical tensions in patient advocacy. His current research is examining how
patients and healthcare providers view new forms of personalized medicine
and clinical interventions enabled by molecular diagnosis. Dr. Sharp fre-
quently advises healthcare organizations on ethical issues and has served
on advisory committees for the National Institutes of Health, Institute of
Medicine, American College of Medical Genetics, and U.S. Environmental
Protection Agency.
Damian Smedley is director of genomic interpretation for Genomics

England, overseeing the clinical analysis of the rare disease and cancer
genomes emerging from the National Health System’s 100,000 Genomes
Project. He is also a senior lecturer at Queen Mary University London,
where his research focuses on the use of phenotype data to obtain novel
insights into disease causes and mechanisms. His team is involved in trans-
lational aspects for a number of projects, such as the International Mouse
Phenotyping Consortium. In collaboration with other members of the Mon-
arch Initiative he has developed tools that utilize phenotype comparisons for

candidate gene prioritization, particularly for next-gen sequence interpreta-

tion of rare disease patients, as in the Exomiser software suite.
James Stevens is a distinguished research fellow at Lilly Research Labora-

tories and is recognized internationally as an expert in drug safety science
and the application of systems biology in safety testing. For over 4 decades
in government, academics, and industry he has studied molecular and cellu-
lar responses to the metabolism and toxicity of drugs and xenobiotics. His
current research focuses on application of systems biology to elucidate the
molecular basis of pathogenesis using network-based approaches. Dr. Ste-
vens received his Ph.D. in pharmacology from the University of Minnesota
in 1980 and did postdoctoral training at the National Institutes of Health
(NIH) as a National Institute of General Medical Science-Pharmacology Re-
search Associate Training Fellow. Prior to joining Lilly Research Laboratory
in 2000, he held positions at NIH, the U.S. Food and Drug Administration,
the University of Vermont, and the W. Alton Jones Cell Science Center, where
he was executive director. He has served on a variety of national advisory
committees, including the Health and Environmental Sciences Institute
Board of Trustees, National Advisory General Medical Sciences at NIH,
National Toxicology Program Board of Scientific Councilors, the Environ-
mental Protection Agency Subcommittee on Chemical Safety for Sustain-
ability, as well as the boards of directors for Argonex Pharmaceuticals and
Upstate Biotechnology. As a member of the Translational Safety Strategic
Governance Group for the Innovative Medicine Initiative he was instrumen-
tal in launching the Translational Quantitative Systems Toxicology project
in January 2017, a 5-year project including more than 30 pharmaceuti-
cal and academic partners. He received the Achievement Award from the
Society of Toxicology in 1994 and was elected a fellow of the American
Association for the Advancement of Sciences in 1996.
D. Lansing Taylor’s laboratory has embraced the Quantitative Systems

Biology approach to drug discovery and development that integrates ex-
perimental and computational methods, especially in metastatic breast
cancer, neurodegenerative diseases, and liver diseases. Dr. Taylor began
his academic career at Harvard University and remained at Harvard
until 1982, developing and using novel fluorescence-based reagents and
imaging technologies to investigate fundamental cellular processes in living
cells. He then moved to Carnegie Mellon University (CMU) as a profes-
sor of biological sciences and as director of the Center for Fluorescence
Research in the Biomedical Sciences continuing to develop and to apply
novel fluorescence-based technologies in biology and medicine. Dr. Taylor
co-founded Biological Detection Systems in the early 1990s to commercial-
ize research light microscope imaging systems and the multi-color cyanine

APPENDIX C 121
dyes for fluorescence detection in the life sciences, which is now part of
General Electric Life Sciences. Dr. Taylor left CMU in 1996 to start and
lead a series of companies: Cellomics-High Content Screening, now part
of ThermoFisher; Cellumen-early safety assessment, now part of Cyprotex,
and finally a private company, Cernostics-cancer diagnostics. Dr. Taylor
returned to academia at the end of 2010 to continue his academic interests,
which now link large-scale cell and tissue profiling with computational and
systems biology to optimize drug discovery and diagnostics. In addition,
Dr. Taylor has collaborated with investigators in the University of Pittsburgh
Drug Discovery Institute to develop methods to detect and to quantify bio-
logically relevant heterogeneity in phenotypic assays and in pathology tissue
sections. He has also led a team that has developed human organs on chips,
starting with the liver, in order to explore acute and chronic toxicity, as well
as to create long-term human models of disease.
Kristina Thayer has served as the Integrated Risk Information System

(IRIS) division director, located within the U.S. Environmental Protection
Agency (EPA) National Center for Environmental Assessment since January
2017. IRIS assessments identify the potential for a chemical to cause cancer
or non-cancer health effects in people and are considered the top tier source
of toxicity information used by EPA and other agencies to inform national
standards, clean-up levels at local sites, and set advisory levels. IRIS uses
systematic review methods to evaluate epidemiological and toxicological
literature and include consideration of relevant mechanistic evidence. Prior
to joining EPA, Dr. Thayer was deputy division director of analysis at the
National Toxicology Program (NTP) and director of the NTP Office of
Health Assessment and Translation (OHAT) located on the campus of the
National Institute for Environmental Health Sciences (NIEHS). As deputy
division director of analysis, she oversaw OHAT and the NTP Office of
the Report on Carcinogens. She has also worked in the NTP Office of Li-
aison, Policy, and Review, the NIEHS Office of Risk Assessment Research,
and the NTP Center for the Evaluation or Risks to Human Reproduction.
Prior to joining the NTP/NIEHS, she was a senior scientist at the World
Wildlife Fund and then at the Environmental Working Group. She is con-
sidered an expert on the application of systematic review methods to envi-
ronmental health topics and the use of specialized software and automation
approaches to facilitate conducting reviews.
David Valle is the Henry J. Knott Professor and Director of the McKusick-
Nathans Institute of Genetic Medicine with a co-primary appointment in
the Department of Pediatrics and joint appointments in the Departments
of Molecular Biology & Genetics and Ophthalmology at Johns Hopkins
University School of Medicine. His research interests include human ge-

netic disease with an emphasis on inborn errors of metabolism, inherited

retinal degenerations, rare Mendelian disorders, and identification and
understanding of genetic factors that contribute increase susceptibility for
neuropsychiatric diseases, such as schizophrenia. Dr. Valle is a member of
the Institute of Medicine of the National Academy of Science, Association
of American Physicians, and a fellow of the American Association for the
Advancement of Science. He is a past president of the American Society of
Human Genetics and is the senior editor of The Metabolic and Molecular
Bases of Inherited Disease. He is also director of the Predoctoral Training
Program in Human Genetics and the Johns Hopkins Center for Inherited
Disease Research as well as co-director of the Short Course in Medical
and Experimental Mammalian Genetics at The Jackson Laboratory. In
2003 Dr. Valle received the Colonel Harland Sanders Award for Lifetime
Achievement in Genetics Research and Education from the March of Dimes
Foundation, the 2014 Victor A. McKusick Leadership Award, and, in 2016,
the Arno Motulsky–Barton Childs Award for Excellence in Human Genet-
ics Education, both from the American Society of Human Genetics. He was
director of the Pediatric Genetics Clinic of The Johns Hopkins Hospital
from 1976 to 1989, past president of The Society of Inherited Metabolic
Disorders, and member and chair of the National Institutes of Health Study
Sections in Mammalian Genetics and Genetic Basis of Disease. He served
on the Board of Scientific Overseers of the Jackson Laboratory and the Ad-
visory Council of the National Human Genome Research Institute. He has
been a member of the editorial boards of The American Journal of Human
Genetics, Human Molecular Genetics, Human Mutation, European Journal
of Human Genetics, Annual Review of Nutrition, and Annual Review of
Genomics and Human Genetics. Dr. Valle earned his B.S and M.D. from
Duke University. He completed his pediatric residency on the Harriet Lane
Service at The Johns Hopkins Hospital. He is a diplomate of the American
Board of Pediatrics and the American Board of Medical Genetics, and has
published more than 250 papers in reviewed journals and contributed close
to 40 book chapters.
John Wikswo is the Gordon A. Cain University Professor, the A. B. Learned

Professor of Living State Physics, and professor of biomedical engineering,
molecular physiology and biophysics, and physics at Vanderbilt Univer-
sity, and the founding director of the Vanderbilt Institute for Integrative
Biosystems Research and Education (VIIBRE). Trained as a physicist, he
received his B.A. degree from the University of Virginia and his Ph.D.
from Stanford University. He has been a member of the Vanderbilt faculty
since 1977. His research has included superconducting magnetometry; the
measurement and modeling of cardiac, neural, and gastric electric and
magnetic fields; and non-destructive testing of aging aircraft. Since 2001,

APPENDIX C 123
VIIBRE has developed a breadth of optical instruments and software for

studying how living cells interact with each other and their environment
and respond to drugs, chemical and biological agents, and other toxins,
thereby providing insights into systems biology, physiology, medicine, and
toxicology. For the past 5 years, Dr. Wikswo has been guiding VIIBRE en-
gineers and scientists in the development of microfabricated organ-on-chip
bioreactors that include an National Center for Advancing Translational
Sciences (NCATS)-funded neurovascular unit/blood–brain barrier and the
associated perfusion controllers, microclinical analyzers, and other devices
that are required to integrate multiple organs-on-chips to create an in vitro
micro-homunculus. His group’s most recent innovations include the ongo-
ing development of 96-channel microformulator, funded by AstraZeneca,
and a smart well plate for organs-on-chips and high-throughput biology,
funded by NCATS Small Business Innovation Research Program to CFD
Research Corporation. VIIBRE is also the home of the Systems Biology and
Bioengineering Undergraduate Research Experience, a year-round, multi-
year program funded by Gideon Searle. Dr. Wikswo has published more
than 200 peer-reviewed papers, is a fellow of seven professional societies,
holds 24 patents (several of which have been licensed), has multiple patents
pending, and nurtures innovation among his trainees. He loves teaching and
learning and sharing his enthusiasm for research and inventing with high
school students, undergraduates, and graduate students.


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Advancing Disease Modeling in Animal-Based Research in

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National Academies of Sciences, Engineering, and Medicine 2018. Advancing

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Erin Hammers Forstag and Lida Anestidou, Rapporteurs

Roundtable on Science and Welfare in Laboratory Animal Use

Institute for Laboratory Animal Research

Division on Earth and Life Studies

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