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MEDICINE AND BIOMEDICAL SCIENCES IN
MODERN HISTORY
A History of Genomics
across Species, Communities
and Projects
Miguel García-Sancho · James Lowe
Medicine and Biomedical Sciences in Modern
History
Series Editors
Carsten Timmermann
University of Manchester
Manchester, UK
Michael Worboys
University of Manchester
Manchester, UK
The aim of this series is to illuminate the development and impact of medi-
cine and the biomedical sciences in the modern era.The series was founded
by the late Professor John Pickstone, and its ambitions reflect his commit-
ment to the integrated study of medicine, science and technology in their
contexts. He repeatedly commented that it was a pity that the foundation
discipline of the field, for which he popularized the acronym ‘HSTM’
(History of Science, Technology and Medicine) had been the history of
science rather than the history of medicine. His point was that historians
of science had too often focused just on scientific ideas and institutions,
while historians of medicine always had to consider the understanding,
management and meanings of diseases in their socio-economic, cultural,
technological and political contexts. In the event, most of the books in the
series dealt with medicine and the biomedical sciences, and the changed
series title reflects this. However, as the new editors we share Professor
Pickstone’s enthusiasm for the integrated study of medicine, science and
technology, encouraging studies on biomedical science, translational med-
icine, clinical practice, disease histories, medical technologies, medical spe-
cialisms and health policies.
The books in this series will present medicine and biomedical science as
crucial features of modern culture, analysing their economic, social and
political aspects, while not neglecting their expert content and context.
Our authors investigate the uses and consequences of technical knowl-
edge, and how it shaped, and was shaped by, particular economic, social
and political structures. In re-launching the Series, we hope to build on its
strengths but extend its geographical range beyond Western Europe and
North America.
Medicine and Biomedical Sciences in Modern History is intended to
supply analysis and stimulate debate. All books are based on searching
historical study of topics which are important, not least because they cut
across conventional academic boundaries.They should appeal not just to
historians, nor just to medical practitioners, scientists and engineers, but
to all who are interested in the place of medicine and biomedical sciences
in modern history.
This series continues the Science, Technology and Medicine in Modern
History series.
Miguel García-Sancho • James Lowe
A History of
Genomics across
Species, Communities
and Projects
Miguel García-Sancho James Lowe
Science, Technology and Science, Technology and
Innovation Studies Innovation Studies
University of Edinburgh University of Edinburgh
Edinburgh, UK Edinburgh, UK
© The Editor(s) (if applicable) and The Author(s) 2023. This book is an open access
publication.
Open Access This book is licensed under the terms of the Creative Commons Attribution
4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits
use, sharing, adaptation, distribution and reproduction in any medium or format, as long as
you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons licence and indicate if changes were made.
The images or other third party material in this book are included in the book’s Creative
Commons licence, unless indicated otherwise in a credit line to the material. If material is not
included in the book’s Creative Commons licence and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to obtain permission directly
from the copyright holder.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this
publication does not imply, even in the absence of a specific statement, that such names are
exempt from the relevant protective laws and regulations and therefore free for general use.
The publisher, the authors, and the editors are safe to assume that the advice and information
in this book are believed to be true and accurate at the date of publication. Neither the
publisher nor the authors or the editors give a warranty, expressed or implied, with respect
to the material contained herein or for any errors or omissions that may have been made.
The publisher remains neutral with regard to jurisdictional claims in published maps and
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This Palgrave Macmillan imprint is published by the registered company Springer Nature
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The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
Acknowledgements
This book is the culmination of over five years’ work as part of the multi-
disciplinary ‘TRANSGENE: Medical translation in the history of modern
genomics’ project, which was funded by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innova-
tion programme, grant agreement No. 678757. Without this support it
would not have been possible to produce this book. There have been
several full-time members of staff and multiple collaborators associated
with the project in addition to ourselves: Giuditta Parolini, Erika
Szymanski, Mark Wong, Rhodri Leng, Jarmo de Vries and Rodrigo
Liscovsky Barrera all worked on the project, while Ann Bruce, Niki
Vermeulen and Gil Viry were invaluable collaborators. Jarmo de Vries also
undertook a careful copy-editing of the manuscript, and provided insight-
ful comments on the contents and writing style.
More broadly, we would like to thank colleagues within and outside the
University of Edinburgh for their invaluable feedback, some of it at con-
ferences and other events at which we presented our work. The members
of the Advisory Board of our project, along with Robert Cook-Deegan,
devoted considerable time to providing us with guidance and comment-
ing on our ongoing work.
We are grateful to all those who have provided us with access to archives
or agreed to be interviewed, including all those who have informed our
analyses but have not been cited in the book. Furthermore, we appreciate
the additional clarifications and answers to our queries provided by many
of our interlocutors, including Alan Archibald, Jon Beever, David Bentley,
Martin Bobrow, Horst Domdey, Horst Feldmann, Mark Guyer, Barbara
v
vi ACKNOWLEDGEMENTS
“The history of genomics, García-Sancho and Lowe argue, is more than just the
history of the Human Genome Project. Diving deeply into the history of the yeast
and pig genomic project next to those of the human, the authors show how mul-
tifaceted and varied the field of genomics is. What is regarded as a reference
sequence, how it is turned into a useful resource and who participates in the effort
changes from species to species. These insights also change our understanding of
the Human Genome Project. The book is an important addition to the historiog-
raphy of genomics.”
—Soraya de Chadarevian, University of California, USA
Contents
1 Introduction 1
2 Distributed
and Concentrated Strategies in the
Sequencing of the Yeast Genome 41
ix
x Contents
8 Conclusion327
Index361
List of Figures
Fig. 1.1 A genetic linkage map of the six chromosomes of the nematode
worm Caenorhabditis elegans, and a diagrammatic
representation of how a physical map is produced from a DNA
library and assembled into a sequence 10
Fig. 1.2 Timeline representing historical milestones in DNA mapping
and sequencing, as well as genomics more generally 15
Fig. 1.3 An illustration of two hourglass models: of the history of
genomics and of the history of heredity 21
Fig. 1.4 A depiction of events preceding and succeeding the Human
Genome Project (HGP) that accompanied an article published
in Nature in 2011 24
Fig. 2.1 Alan Coulson beside the physical map of C. elegans at Cold
Spring Harbor Laboratory in 1989, and the autoradiograph
resulting from the application of the fingerprinting mapping
technique46
Fig. 2.2 The cover of a 1992 meeting programme at Cold Spring
Harbor Laboratory featuring John Sulston and Robert
Waterston as C. elegans worm cyclists competing with other
organisms in a race to finish their genomes 49
Fig. 2.3 Genetic linkage and physical maps that Mark Johnston used to
sequence chromosome VIII of the yeast Saccharomyces cerevisiae50
Fig. 2.4 Members of the Consortium of the European Commission,
along with representatives from Washington University,
Stanford University, McGill University and the Sanger Institute,
at the final conference of the Yeast Genome Sequencing Project
in Trieste (25th–28th September 1996) 55
xi
xii List of Figures
Fig. 2.5 Several key players and institutions in the sequencing of the
yeast genome: Horst Feldmann’s group at Ludwig-Maximilian
University of Munich; Horst Domdey; and a laboratory during
the early years of Genzentrum 62
Fig. 3.1 Victor McKusick and Frank Ruddle at the first chromosome
workshop, held at Yale University in 1973; and part of the
genetic linkage and physical map of human chromosome 18 90
Fig. 3.2 Part of the genetic linkage map and physical map of human
chromosome 18, as reported in the Fourth International
Workshop devoted to its mapping, held in Boston (USA) in 1996 91
Fig. 3.3 Sydney Brenner with co-discoverer of the double helix of DNA,
Francis Crick; and John Sulston holding a section of the
physical map of C. elegans96
Fig. 3.4 The level of grant support per institution that the UK Human
Genome Mapping Project had awarded by 1992, in thousands
of pounds 102
Fig. 3.5 An outline representation of the Human Genome Project of the
USA, Human Genome Mapping Project of the UK and
European Commission’s Human Genome Analysis Programme 111
Fig. 4.1 A diagram included in the original 1992 application to establish
the Sanger Institute; and a picture of this institution’s Board of
Management131
Fig. 4.2 The first building in which the Sanger Institute operated,
located in the grounds of Hinxton Hall; and the Wellcome Trust
Genome Campus that has developed at the Hinxton site from
1993 onwards 138
Fig. 5.1 Picture of four key members of the Laboratoire Mixte CEA‐
INRA de Radiobiologie Appliquée based in Jouy-en-Josas,
south-west of Paris 170
Fig. 5.2 A Meishan sow and a Large White pig at the Roslin Institute 177
Fig. 5.3 Photograph of an early PiGMaP meeting in Toulouse,
December 1991 178
Fig. 5.4 TJ Tabasco, as preserved on the wall of Lawrence Schook’s
office at the University of Illinois at Urbana-Champaign; and its
cloned offspring 188
Fig. 6.1 Example of a display of a reference genome - Sscrofa11.1 for
Sus scrofa, the pig - on a genome browser: Ensembl 208
Fig. 6.2 Diagrammatic depiction of models of annotation and how they
relate to different stages or levels of annotation 216
Fig. 6.3 Cover and selected page of a manual produced by the
HAVANA team – then at the Sanger Institute – for use by
manual annotators of the pig genome community 237
List of Figures xiii
xv
xvi List of Tables
Table 7.3 Pig ‘genomicists’ who were initial members of the Functional
Annotation of Animal Genomes (FAANG) Consortium 301
Table 7.4 List of members of the International Porcine SNP Chip
Consortium and their institutional affiliations 309
Table 8.1 The main model organisms used in biological research 335
CHAPTER 1
Introduction
In four decades, genomics has transformed the biological sciences and has
penetrated well beyond them. The marriage of DNA sequencing tech-
niques and computational infrastructures built to handle, store and anal-
yse ever-increasing quantities of data has contributed to significant
developments in:
DNA sequencing has gone from being a highly specialised practice, requir-
ing considerable labour and skill, to being routinely applied in ordinary
laboratory work while also being conducted at great scale, speed and accu-
racy in factory-style genome centres. In the late-1970s, manually sequenc-
ing the tiny genome of a bacteriophage (a virus that infects bacteria) was
a monumental task, one that earned Frederick Sanger, who led the group
undertaking it, a Nobel Prize (Brownlee, 2014; Hutchison, 2007). The
determination of the whole human DNA sequence (commonly referred to
as the Human Genome Project) took more than a decade, at a cost initially
estimated at $3 billion. It started in the 1990s and concluded in 2003,
expanding in speed and scale throughout.
Progress since then has been so dramatic that, more recently, well over
fourteen million coronaviruses have been sequenced and shared via the
Global Initiative on Sharing Avian Influenza Data.1 Another example that
illustrates how far genomics has come, is that the cost of sequencing a
whole human genome was estimated to be about £7000 in 2020, multiple
orders of magnitude below the original budget of the Human Genome
Project (Schwarze et al., 2020).2
In 1999, four years before the Human Genome Project was officially
concluded, the National Center for Biotechnology Information of the
USA created a new database called RefSeq. The purpose of this database
was to serve as a centralised repository that would gather the ongoing
reference sequence of the human genome and those of other species com-
pleted or in progress. Those reference sequences were and still are curated
and freely released to the research community. They serve as canonical
representations of their designated species and are graded according to
1
https://www.gisaid.org/ (last accessed 29th November 2022). The COVID-19
Genomics UK (COG-UK) Consortium alone has sequenced over two million SARS-CoV-2
viruses: https://www.cogconsortium.uk/ (last accessed 29th November 2022).
2
Elsewhere, lower figures have been indicated (https://www.genome.gov/about-
genomics/fact-sheets/Sequencing-Human-Genome-cost, last accessed 29th November
2022), though these may not include the full range of costs involved in all aspects of the
sequencing process, including processing, storage and curation of the resulting data.
1 INTRODUCTION 3
3
RefSeq distinguishes “reference genomes”, “representative genomes” and “variant
genomes”. Throughout, when we refer to reference genomes, we are referring to objects
that are designated by RefSeq as “reference genomes” and “representative genomes”. When
the distinction between these becomes relevant in our narrative, we will specify which RefSeq
category we are referring to. For RefSeq, “reference genomes” are “manually selected ‘gold
standard’” high-quality complete genomes. “Representative genomes” are designated stan-
dard genomes for a given species of organism, while “variant genomes” constitute “genome
variations within the species” (Tatusova et al., 2014, p. 135).
4
See https://www.ncbi.nlm.nih.gov/refseq/statistics/ (last accessed 29th November 2022).
4 M. GARCÍA-SANCHO AND J. LOWE
5
Our outline is necessarily brief and focused on the episodes and practices that we examine
in more detail later in the book. For more comprehensive reviews, see Müller-Wille &
Rheinberger, 2012, Chs. 7–8; Morange, 2020, Ch. 27 and our timeline below (Fig. 1.2).
1 INTRODUCTION 5
To use the vulcanizer, clean the area around the hole in the tube
with sandpaper, and cut a piece of rubber of the proper size to fit
over it. Slip one of the prepared cardboard disks into the tin cover,
and clamp the cover and tire with patch into the iron frame, as
shown. Touch a lighted match to the cardboard disk, which will burn
rapidly, but without flame, supplying sufficient heat to vulcanize the
tube.—Thomas W. Benson, Hastings on Hudson, N. Y.
Rudder for a Toboggan
This Rudder for a Toboggan Insures Positive Control, and Prevents Wear on
the Shoes and Clothes of the Rider
Onedeveloping
of the chief difficulties in developing plates in a nonreversible
tank is that irregular development takes place,
because the developer tends to settle more or less, depending on
the time necessary for complete development. The construction of a
reversible tank is a simple matter, and the cost is slight. The tank
described is 3¹⁄₄ by 4¹⁄₄, in. in size, but the dimensions can be varied
for other sizes of plates. The tank is a box having grooves in
opposite ends for the plates. By placing the latter back to back, 12
can be developed at a time. Sheet rubber is fitted between the cover
and the body of the tank, and the cover, upon being screwed down,
makes a water-tight compartment of the box. The asphaltum paint
used is not affected by the developer, and preserves the wood.
Fixing and developing may both be done in the one tank, but it is
preferable to use the tank for developing only.
Assembly Views, Showing the General Construction and Detail of the Cover
The two sides are plain pieces, ¹⁄₂ by 4 by 4¹⁄₂ in. in size. The end
pieces have ¹⁄₈ by ¹⁄₈-in. grooves, ¹⁄₄ in. apart and extending the
length of the piece, which is ¹⁄₂ by 2¹⁄₂ by 4¹⁄₂ in. long. The grooves
can be made either on a power saw, or by chiseling them out by
hand. The bottom piece is ¹⁄₂ by 3¹⁄₂ by 5¹⁄₂ in. in size, with two ³⁄₈-in.
holes bored to receive the bolts. The two bolt supports are ¹⁄₂ by ³⁄₄
by 1 in., and are also bored ³⁄₈ in. to receive the bolts, and are nailed
to the end pieces. The cover is ¹⁄₂ by 3¹⁄₂ by 5¹⁄₂ in. long, with a slot
in each end for the bolts, which are ³⁄₈ by 6-in. carriage bolts.
The Finished Tank, and Details of the Bottom, Ends, and Bolt Supports
The parts are assembled with screws, and the tank is given two
coats of asphaltum paint. Care should be taken, before assembling
the parts, to insure that the plates fit the grooves.
Turned Cane with Snakes Inlaid
The making of a cane is a favorite job for the home craftsman,
especially the veteran who finds himself in need of such a support
and has the leisure to make it. A novelty in constructions of this kind
is a turned cane built up of dark and light-colored woods with snakes
inlaid. That shown in the illustration was made of black walnut and
birch, with a walnut knob. It is made as follows: Glue up a piece of
walnut and a piece of birch, ⁷⁄₈ by 1³⁄₄ by 3 ft. long, as shown at A.
Mark out the snake on the birch surface, and cut it out very carefully
on the band saw, or with a fine hand turning saw. The snake portion
will drop out and is then separated into a walnut and a birch strip,
making two similar snakes. Bore holes for the eyes and plug them
with the opposite kind of wood. Replace the snakes in opposite
positions, the one of birch in the walnut side, and the walnut one in
the birch side. Glue them carefully into place, removing a small
portion of the wood at the ends of the sawed pieces to make a close
fit.
This Novel Cane can be Turned in a Lathe or Planed from the Square Stock,
and Arouses Curiosity as to its Construction
This Dry-Plate Kit is Made of Cardboard and Serves the Purpose Admirably if
Carefully Fitted