Professional development and research paths in

genetics: a two-part tale

1. Scientific societies – what are they and why are they important
2. My research story

Carole Yauk, Dept. of Biology, University of Ottawa

For Western Human Genetics Class
Oct. 17, 2022
Part 1.
Scientific
societies
Environmental Mutagenesis and
Genomics Society
https://www.emgs-us.org/

Anyone can join.

Student membership $25 USD
 What do we do?
• Connect people to exchange knowledge and
information on the latest developments in our field
• Annual meetings
• Share your science and gain new knowledge
• Build networks (academia, government, industry, NGO)
• Personally meet the experts
• Find a mentor
• Find colleagues with shared interests
• Society journal
• Virtual workshops and other events
• Newsletters
• Professional development and leadership opportunities
 13th International Conference on
Environmental Mutagens (ICEM)
53rd Annual Meeting of the Environmental
Mutagenesis & Genomics Society (EMGS)
August 27 – September 1, 2022
OTTAWA, CANADA
 • Multi-sectoral membership (charitable, non-profit
organization)
• Academics studying genetic toxicology and
mutagenesis/genomics
• Industry specialists interested in understanding
how endogenous factors or exposures to
drugs/environmental agents induce mutations
Who are our • Government researchers and regulators
interested in recent knowledge on
members? environmental mutagens and developing
optimal test methods
• Non-profit organizations advocating for sound
decision-making and health protective policies
 Promoting
our vision and
mission to
protect and
advance
public health

Inter
na
supp tional ou
The role of arou orting n treach
n
soun d the w ations
d o
–
Advancing public e m
w l e dge ritical
Kno on of c nd
inati ndings a
deci science rld in s
dis arch fi thods
scientific sion
-mak and
ing
and environmental
health based on
rese ew me
n

societies sound science

P
de rofe
v s r k nt
– n elop sion o
tw e
ur m al
t e Ne lopmram
su an urin nt eve rog ng, -
sci pp d g d p ldi ry
en or – ui to
sci tist ting b ula rch s
pr enti s an reg esea ction
og fi d r ne
ram c
n
s co
Part 2. My
Research
Story
(and its connection to the
Environmental Mutagenesis and
Genomics Society)
EMGS founded
“Ourtomost
protect
vital“Our most vital assets”
assets”
 • The Human Gene Mutation Database contains

Population >350,000 genetic alterations in >13,000 genes that

cause inherited disease:
• single nucleotide variants (SNVs),

health is insertions/deletions (indels), copy number

variants (CNVs), translocations, and complex
rearrangements

inextricably • Majority of these are de novo mutations

linked to the • Major cause of severe early-onset genetic disorders -

production of
intellectual disability, autism spectrum disorder, and
other developmental diseases.

healthy • For example, between 1 in 200-500 offspring are born

with de novo mutations that cause intellectual
developmental disorders*

offspring *McRae JF et al., Nature, 2017. 542(7642): p. 433-438.

 Impacts of small increase in mutation rate on population health
Calculated population impacts of 5 or 25% increase in germline mutation rate:
• Considering only 700 genes involved in intellectual disease
• Applying the mutation spectrum induced by tobacco smoke
• Counting only loss of function mutations

Inheritance Pattern Number of F1 Mutations

5% Increase 25% Increase
Autosomal Dominant 102,000 510,000 Estimated cost:
Autosomal Recessive 238,000 1,190,000 $100 BILLION
X-linked Dominant
12,000 60,000
(Female)
X-linked Recessive
28,000 140,000
(Female)
X-linked (Male) 0 in F1; Would not appear until F2 generation Beal et al. Mutat Res.
Reviews 2017
Total 380,000 1,900,000
11
But no accepted human germ-cell mutagen?
>150 mouse germ-cell mutagens
1971 Nixon • 30 cause mutations in the
declares offspring of exposed males
War on
Cancer
• Ionizing radiation
• ENU, EMS, MNU, MMS
• Cyclophosphamide
• Procarbazine
• Triethylene melamine
• Acrylamide monomer
• Etoposide
• Trophosphamide
• Chlorambucil, Bleomycin
• Melphalan, Chlormethin
 Methodological challenges in studying induced
heritable mutations

~1 mutation in 100 million nucleotides

Require 10 000 offspring to find one mutation in a 10 kb

sequence.

BUT, the genome is large (6 billion nucleotides)

The average child inherits ~60 mutations from parents.

13
 A little about me and why I
do what I do…
My journey to
find human New stuff and select results
germ cell from our lab
mutagens
The NEXT GENERATION!
McMaster University (1989-1998)
 Increased mutation rates in offspring near steel mills
♂
♀ ♀

Yauk et al., PNAS, 1996; Yauk et al., Mutat Res. 2000

All good things
All goodmust come
times good to to an end…
an end…
Take off, eh!
 Research at the University of Leicester

Exposure to radiation and nuclear

fallout induces germline tandem
repeat mutation in humans and
mice

Dubrova et al., Nature Genetics (1993) Dubrova et al., Nature (1996)

 Single Molecule PCR Recombination hotspots

Dilute DNA to 5-10 pg/ml

(approx. 1 molecule/PCR)

PCR Amplify

Run positives on long gel

brain sperm

Yauk et al., Mutat Res. 2002 Yauk et al., EMBO J., 2003
State of the art early genomics (circa, 2000)
Job choices
Translating research innovations in genomics
into regulatory toxicology applications

Canada Research Chair, Genomics and the Environment, Dept. of

Biology
Genomics in Regulatory
and Applied Toxicology
(GReAT) Laboratory

Designed by: Tatiana Kozbenko

 Environmental exposures that are likely
human germ cell mutagens

9/10 people worldwide breathe polluted air (World Health Organization, 2018)
17.7% of Canadians age 12 and over smoked daily or occasionally in 2015 (Health Canada) 24
 Particulate air pollution near steel mills
is a mouse germ cell mutagen
Rural Site Steel Site

0.50 *
Paternal Maternal *
Mutation rate per-band (+ 95% CI)

0.40

0.30

0.20

0.10

0.00
Rural Rural Rural Steel Steel Steel
HEPA male HEPA male
Somers et al., PNAS, 2002; Somers et al., Science, 2004
Yauk et al., PNAS, 2008
 Tobacco smoke is a mouse
male germ cell mutagen

ity

nt
me
lo c
ve

lo p

ili t y
De ly
erm

ve
r
e

on Ea

ert
ag
sp

dF
bry of
am

ic
s
d

ion

Em ition
AD

ce
ce

tat
Active smoking

du
du

ib
DN

Mu

Re
Re

Inh
Mainstream smoke (MS)
SPERM REPRODUCTION

   MS
Sperm
 
SS
Sidestream smoke (SS)
Passive smoking Stem
   MS
Cells
Marchetti et al., PNAS, 2011  SS
No agreement on existence of human germ cell mutagens

Skepticism
Unstable DNA ~ gene mutations?

Mutations in sperm = heritable mutations?

Heritable mutations = genetic disease?

Mutations in mice = mutations in humans?

 The times, they are a-changin’….

1977 2022
Drivers of mutation: parental age is a human germ cell mutagen

Kong et al., Nature, 2012

 Next generation germ-cell mutation research
Male mice exposed to Paternal age-mutation rate shows
mutagens pass on more extensive inter-family variability
mutations to their offspring

Adewoye et al. Nat Comm 2015: increased CNVs by

radiation.

Masumura et al. Mutat Res. 2016: dose-dependent

increases in point mutations by ENU

Beal et al. Comm Biol 2019: increases in point and gain

CNV mutations by BaP Habiballah Shojaeisaadi, in preparation
The hunt for germ cell mutations is on!
• 21,879 families
• 12 individuals with a hypermutated genome
• 2 families had genetic drivers of
germline hypermutation (variants) in
DNA-repair genes
• 5 explained by paternal exposure to
chemotherapeutic agents before
conception

Conclusions
• Germline is well protected from mutagenic
effects
• Hypermutation is rare
Kaplanis et al., Nature, 2022
• More subtle effects unclear
 The future: Duplex Sequencing
An error corrected next-generation sequencing (NGS) technology that improves sequencing
accuracy by independently tracking both strands of DNA

Duplex Sequencing:
- reduces sequencing errors from 1 in 100 to 1 in 10
million
- can be used with any tissue, cell line and species
- measures mutagenesis in endogenous genes
- is more easily integrated with other toxicity tests
NGS Duplex
- simultaneously generates mutation frequency and Sequencing
spectrum in the same assay

32
 Duplex Sequencing (DS): Proof of Concept and Validation Studies

Dose-dependent increases in
PRC

Mutation Frequency
BaP
Mutation Frequency
mutations in mouse bone
marrow following
Benzo[a]pyrene (BaP) and
Procarbazine (PRC) exposure

LeBlanc et al., BMC Genomics,

2022.

Dodge et al., in preparation.

Dose (mg/kg/day) Dose (mg/kg/day)
 The Next Generation
Harness genomic
technologies to define how
environmental exposures
impact male and female
• Must involve collaboration: germ-cell genomes
• Genetic toxicology and genomics experts
• Exposure and biomonitoring experts
• Clinicians
• Epidemiologists
• Bioinformaticians
• Technologists
Characterize
Improve risk
health
assessment
implications
• Harness state of the science tools and resources
• Error-corrected sequencing
• Identify structural variants
• Global sequencing initiatives
Manage, communicate and mitigate the risk of
exposure to human germ-cell mutagens
And how did the EMGS shape these
accomplishments?
• Student member (joined in 1996)
• Travel award recipient
• Poster and platform presentations
• Invited speaker in symposia
• Symposium chair and Program Committee member
• Leader of the Heritable Mutation and Disease Special Interest Group
• Council member
• Leader of the Special Interest Groups
• Guest Editor of Special Issues for the Society’s journal
• Editorial Board member of the Society’s journal
• Associate Editor of the Society’s journal (10 years)
• President of the Society (term ended 2022)
• Co-chair of the International Conference on Environmental Mutagens (2022)
Acknowledgments Canada Research Chairs Program, NSERC, Burroughs Wellcome Fund