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Stephen W. Scherer

Director, The Centre for Applied Genomics
Alternate Contact Name:
Elaine Chang
Alternate Phone:
416-813-7654 ext. 301574
Alternate Email:
Chair Positions:
GlaxoSmithKline Chair, Genome Sciences

Research Positions

Senior Scientist
Genetics and Genome Biology

U of T Positions

Director, McLaughlin Centre

Professor, Department of Molecular Genetics

Senior Fellow, Massey College 


Dr. Stephen Scherer’s research includes understanding the composition of the human genome for studies of genetic disease built around three themes:

  1. gene copy number and structural variation in the human genome,
  2. determining the genetic architecture in autism spectrum and related- disorders and using this information to help families, and
  3. developing infrastructure and capacity in Canada for translational genomics research.

He has co-published over 600 papers and many of these have been in the highest impact periodicals, such as Nature, Nature Genetics, Nature Medicine, the New England Journal of Medicine, and Science. His research discoveries have also headlined in the New York Times, Globe and Mail, The Independent, Time, Newsweek, Scientific American, and he often appears on the Canadian Broadcasting Corporation (CBC), and other national media explaining scientific breakthroughs.

He achieved the distinction of Thomson Reuters Highly Cited Researcher. In 2014, he was selected to join a handful of elite scientists worldwide as a Thomson Reuters Citation Laureate for seminal contributions to the field of Physiology or Medicine “For the discovery of large-scale copy number variation and its association with specific diseases”, placing his name on the lifetime Thomson Reuters Hall of Laureates.

He holds leadership positions on numerous grants, and funding to his program has exceeded $350M, impacting basic science and knowledge translation. He is Director of The Centre for Applied Genomics, managing $100M of revenues in the past 5 years, and Director of the University of Toronto McLaughlin Centre, a $50M endowment that funds research and education in genomic medicine. Through this dynamic translational research program, he has supervised 19 graduate students, 44 post-doctoral fellows, 52 visiting fellows and >200 undergraduate students; and these scientists are now working in 20 countries around the world. He has also delivered over 400 invited presentations in 28 countries. 

Dr. Scherer’s team uses advanced technologies to study genes and how they are involved in health and medicine, in particular the neurobehavioral disorder called autism. They study families, populations of people, and cellular and animal models. Their goal is to identify genetic markers for diagnosis to enable early identification, and to discover molecular pathways for new medicine development.

Dr. Scherer has also founded or co-founded the Autism Genome Project, The Canadian Personal Genome Project, The Database of Genomic Variants, the Autism Speaks MSSNG 10,000 Project, the CANSEQ150, and most recently the Canadian COVID-19 Host Genome Sequencing Project.

Education and experience

  • 2018: D.Sc., Honorary Doctorate of Science, Western University
  • 2017: D. Sc., Honorary Doctorate of Science, University of Waterloo
  • 2000: D. Sc., Honorary Doctorate of Science, University of Windsor
  • 1995: PhD Molecular and Medical Genetics, University of Toronto
  • 1991: M.Sc. Medical Biophysics, University of Toronto
  • 1987: Hons. B.Sc. Biology and Chemistry, University of Waterloo


  • 2019: Killam Prize in Health Sciences, Canada Council for the Arts
  • 2018: Distinguished University Professor, University of Toronto
  • 2017: Distinguished Honorary Affiliate of the Canadian College of Medical Geneticists
  • 2015: World’s Most Influential Scientific Minds
  • 2015–Present: Thomson Reuters (now Clarivate) Highly Cited Researcher
  • 2014: Thomson Reuters 2014 “Nobel-class” Citation Laureate, Physiology or Medicine
  • 2013: Queen Elizabeth II Diamond Jubilee Medal for contributions to Canada
  • 2011: Fellow, American Association for the Advancement of Science
  • 2008: Premier’s Summit Award for Biomedical Research
  • 2006: Fellow, Academy of Sciences, Royal Society of Canada
  • 2004: Steacie Prize in the Natural Sciences
  • 2002–2007: Howard Hughes Medical Institute International Scholar Award
  • 2000: Canada’s Top 40 Under 40 Award for Contributions to Society


  1. *Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, +81 co-authors, and Venter JC, Li PW, Mural RJ, Adams MD, and Tsui LC. (2003). Human chromosome 7: DNA sequence and biology. Science 300, 767-772
  2. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, **Scherer SW and *Lee C. (2004). Detection of large-scale variation in the human genome. Nature Genetics 36, 949-951. 
  3. Marshall, AJHG 2008Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars CEJ, Vos YJ, Ficicioglu C, Kirkpatrick S, Nicholson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P and *Scherer SW. (2008). Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics 82, 477-488 
  4. Yuen RK, Thiruvahindrapuram B, Merico D, Walker S, Tammimies K, Hoang N, Chrysler C, Nalpathamkalam T, Pellecchia G, Liu Y, Gazzellone MJ, D'Abate L, Deneault E, Howe JL, Liu RS, Thompson A, Zarrei M, Uddin M, Marshall CR, Ring RH, Zwaigenbaum L, Ray PN, Weksberg R, Carter MT, Fernandez BA, Roberts W, Szatmari P, and *Scherer SW. (2015). Whole-genome sequencing of quartet families with autism spectrum disorder. Nature Medicine 21, 185-19
  5. Yuen RKC, Merico D, Bookman M, HoweJL, Thiruvahindrapuram B, +70 authors, and Szatmari P, Ring RH, Glazer D, Pletcher MT, and *Scherer SW. (2017). Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nature Neuroscience 20, 602-611.

*Senior and/or equal corresponding author

See a full list of Stephen Scherer's publications

07/2015–06/2022: Scherer (PI).  Genomes to Outcomes in Autism Spectrum Disorders, Canadian Institutes of Health Research (Foundation Scheme), $2,204,198 
07/2016–03/2021: Sebat (PI), Scherer (PI: subaward), Psychiatric GWAS Consortium (PGC3): Finding actionable variation, National Institutes of Health, $1,660,958 USD 
01/2017–03/2022: Scherer (PI), Canada's Genomics Enterprise (CGEN), Canada Foundation for Innovation – Major Science Initiative, $31,975,000 
04/2017–03/2022: Scherer (PI), Strug (Co-PI), The Centre for Applied Genomics (TCAG), Genome Canada, $9,174,603 
10/2017–09/2020: Evans (PI), Scherer (Co-I) et al. Canadian Open Neuroscience Platform Brain Canada, $10,995,000 
10/2017–09/2022: Estivill (PI), Fakhro (PI), Scherer (Co-I) et al. 
Building a national resource for the advancement of knowledge of autism in Qatar, Qatar National Research Fund $1,049,412 USD 
04/2018–03/2023: Anagnostou (PI), Scherer (Co-PI), et al., Province of Ontario Neurodevelopmental Disorder Network (POND), Ontario Brain Institute, $13,000,000 
04/2018–03/2023: Fehlings (PI), Scherer (Co-I), et al., Childhood Cerebral Palsy Integrated Neuroscience Discovery Network “CP-NET” (Phase III), Ontario Brain Institute, $3,750,000 
07/2018–06/2020: Investigator Award (Scherer) Medical Annotation of the Human Genome SequenceSickKids Foundation GSK Chair in Functional Genomic, $309,771 
08/2018–07/2021: Scherer (PI), The role of the PTCHD1-antisense long noncoding RNA in autism, Simons Foundation Autism Research Initiative (SFARI), $974,550 USD 
01/2019–12/2020: Scherer (PI) MSSNG Project management contract to sequence 10,000 genomes of ASD individuals and family members and make the data available to approved researchers Autism Speaks, $550,220 USD 
06/2019–03/2024: Vorstman (PI), Scherer (co-PI), Bassett (Co-PI). Dissecting the effects of genomic variants on neurobehavioral dimensions in CNVs enriched for neuropsychiatric disorders, National Institutes of Health (NIH), $2,667,030 USD. 
05/2020–04/2022: Scherer (PI), Aziz (co-PI), Lathrop (Co-PI), Jones (Co-PI). Canadian COVID-19 Human Host Genome Sequencing Project, Genome Canada, $20,000,000. 

Relevant pages

Relevant articles

COVID-19 molecule

COVID-19 research projects led by SickKids scientists receive funding from federal government

Two COVID-19 research projects led by SickKids scientists will give greater insight into how COVID-19 works, potentially shedding light on future treatment strategies.

Scientist looking into a microscope

High-quality stem cells enable researchers to better study almost any disease

Using whole genome sequencing, a collaborative team at SickKids and the University of Toronto has created high-calibre control induced pluripotent stem cells that can be used to study a variety of diseases.

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Genome testing for siblings of individuals with autism may detect diagnosis before symptoms appear

New research led by SickKids and the University of Alberta found testing the DNA of siblings of individuals with autism may be predictive of a future diagnosis even if symptoms aren’t yet apparent. Findings could lead to earlier therapeutic interventions.

SickKids researchers to benefit from major investment in genomics and precision health research

Eight researchers at SickKids will receive funding as part of two new major investments in genomics research totalling $255 million from federal and provincial governments, as well as research institutions and private sector partners.

Personal Genome Project shows whole genome sequencing could transform how Canadians manage their own health care

Researchers from The Hospital for Sick Children (SickKids) and the University of Toronto behind the Personal Genome Project Canada (PGP-C) are predicting whole genome sequencing will likely become part of mainstream health care in the foreseeable future.

Go to species article

Call for researchers across Canada to sequence the genomes of 150 genetically unexplored species

A new initiative announced at SickKids and led by Canada’s Genomics Enterprise (CGEn) is inviting researchers from across Canada to sequence 150 new genomes from species that have never had their genomes sequenced before.

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Team led by SickKids scientists finds new insight into gene mutations associated with autism

New research from The Hospital for Sick Children (SickKids), the University of Toronto and McMaster University suggests increased activity in neurons that are deficient in the CNTN5 or EHMT2 gene could cause autism-related characteristics in humans.

SickKids team discovers overconnected brain cells may cause autism

Typically nerve cells with fewer connections are associated with autism. A team at SickKids found that nerve cells from children with autism can be overconnected and overactive, leading us to think about the causes of autism in a new way.

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Dr. Stephen Scherer awarded Killam Prize, top health sciences award in Canada

One of The Hospital for Sick Children (SickKids)’s own was awarded the Killam Prize in health sciences today. Dr. Stephen Scherer, Director, The Centre for Applied Genomics (TCAG) and Senior Scientist, Genetics & Genome Biology, joins the prestigious group of Canadians who have received this award.

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