Stephen W. Scherer | |
---|---|
Born | Stephen Wayne Scherer January 5, 1964 |
Nationality | Canadian |
Alma mater | University of Waterloo (B.Sc.) University of Toronto (M.Sc., Ph.D.) |
Spouse | Jo-Anne Herbrick (m. 2002) |
Children | 2 |
Stephen Wayne "Steve" Scherer (born January 5, 1964) is a Canadian scientist who currently serves as the Chief of Research at The Hospital for Sick Children (SickKids) and distinguished University Professor at the University of Toronto. [1] He obtained his PhD at the University of Toronto under Professor Lap-chee Tsui. Together they founded Canada's first human genome centre, the Centre for Applied Genomics (TCAG). He is a Senior Fellow of Massey College at the University of Toronto. [2] In 2014, he was named an esteemed Clarivate (previously Thomson Reuters) Citation laureate in Physiology or Medicine for the “Discovery of large-scale gene copy number variation and its association with specific diseases.” [3]
Scherer was born in Windsor, Ontario, and attended Riverside High School. He played competitive hockey and baseball winning provincial and national championships. [4] He completed his Honours Science Degree at the University of Waterloo, Master of Science and Doctor of Philosophy in the Faculty of Medicine at the University of Toronto. [5]
Scherer has co-published over 700 scholarly papers and book chapters. [6] He has been on the Thomson Reuters Highly Cited Researcher and World’s Most Influential Scientific Minds list (2015-2018). [7] [8] His Google Scholar h-index=159; 127,143 citations. [9] In 2023, with Ronald D. Cohn and Ada Hamosh, he edited Thompson & Thompson Genetics and Genomics in Medicine, 9th Edition, Elsevier Publishers. [10]
Chromosome mapping
From 1988 to 2003 with Lap-Chee Tsui, Scherer led studies of human chromosome 7, in particular in the mapping phase of the Human Genome Project. [11] [12] [13] Through collaborative research, genes involved in holoprosencephaly, [14] [15] renal carcinoma, [16] Williams syndrome, [17] [18] sacral agenesis, [19] citrullinemia, [20] renal tubular acidosis [21] and many others were identified. His group also discovered the largest gene in the genome, which was later found to be involved in autism. [22] The sum of this work, including contributions from scientists worldwide and J. Craig Venter's Celera Genomics, generated the first published description of human chromosome 7. [23] In other chromosome studies with Berge Minassian, disease genes causing deadly forms of epilepsy were identified. [24] [25] [26]
Discovery of frequent gene copy number variation (CNV) events
Scherer's research contributed to the initial description of genome-wide copy number variations (CNVs) of genes, including defining CNV as a highly abundant form of human genetic variation. [27] Previous theory held that humans were 99.9% DNA identical with the small difference in variation almost entirely accounted for by some 3 million single nucleotide polymorphisms (SNPs) per genome. [28] [29] [30] Larger genomic CNV changes involving losses or gains of thousands or millions of nucleotides encompassing one or several genes were thought to be exceptionally rare, and almost always involved in disease. [31] Scherer's observations of frequent CNV events found in the genomes of all cells in every individual, co-published with Canadian-Korean scientist Charles Lee working at Harvard in 2004, [32] opened a new window for studies of natural genetic variation, evolution and disease. Scherer founded the Database of Genomic Variants, a public database utilized by clinical laboratories around the world to interpret CNV and structural variation data in diagnostics. [33] Scherer, Lee and collaborators led by Matthew Hurles at the Wellcome Trust Sanger Institute, as well as scientists at the University of Tokyo and Affymetrix Corp then generated the first CNV maps of human DNA revealing the structural properties, mechanisms of formation, and population genetics of this previously unrecognized ubiquitous form of natural variation. [34] [35] These studies were also the first to discover that CNVs number in the thousands per genome and encompass at least ten times more DNA letters than SNPs, revealing a 'dynamic patchwork' structure of chromosomes. These findings were further substantiated through work with J. Craig Venter's team, [36] which contributed to the completion of the first genome sequence of an individual. [37]
Autism-associated CNVs and genes
From 2003-2010, Scherer and collaborators went on to discover numerous disease-associated CNVs, and the corresponding disease-susceptibility genes in upwards of 10% of individuals with autism spectrum disorder. [38] [39] [40] These discoveries have led to broadly available tests facilitating early diagnostic information for autism. [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
Similar discoveries to those made in autism were also found in schizophrenia, intellectual disability and other brain disorders (with often the same genes/CNVs involved), thereby establishing a new paradigm to explain how complex human behavioral conditions can have a genetic (biological) basis. With Jacob Vorstman, Christian Schaaf and colleagues, Scherer developed the EAGLE (Evaluation of Autism Gene Link Evidence), which is a highly utilized resource in diagnostic testing for autism. [53]
Determining the genome architecture underlying autism
Scherer has led the Autism Speaks MSSNG project, [54] which uses whole genome sequencing to decode the DNA of thousands of families having a diagnosis of autism. The research underpinned the identification of >100 genes and CNVs involved in autism providing explanations of why autism has occurred for approximately 5-20% of families. [55] [56] [57] [58] [59] [60] [61] These discoveries have enabled faster and more precise diagnoses, early intervention and genetic counselling and have led to the identification of new molecular pathways for the development of therapeutics. [62] [63] [64] [65] In 2022, Scherer’s team published a comprehensive description of the genomic architecture in autism using the largest collection of whole genome sequencing data available to facilitate research studies in autism. [66]
Genome science, data and public policy infrastructure
Scherer co-founded the TCAG genome centre at SickKids in 1998. In 2015 with Marco Marra and Steven Jones at the University of British Columbia and Mark Lathrop at McGill University, the three major Canadian genome centres came together as CGEn, which serves as a Major Science Initiative of the Canada Foundation of Innovation. [67] For the 150th anniversary of Canada (2017), he started the CanSeq150 Project to sequence 150 genomes of species most relevant to Canada’s culture/environment/conservation; notable species completed include many of the “canadensis” members such as the Canadian beaver and Canadian wolverine. [68] [69] [70] Canseq 150 is now part of the Canadian Biogenome Project, an international effort aiming to sequence the genetic material for all complex life on earth. [71] CGEn also led the Covid-19 host genome sequencing project, which completed 10,000 Canadian genomes in April 2022. [72]
Scherer and colleagues launched the Personal Genome Project Canada in 2007, a resource of data that supports evaluation of whole genome sequencing in medicine and public health. [73] [74] These experiences along Scherer’s advocacy with the Canadian Coalition for Genetic Fairness helped to establish Canada’s Genetic Non-Discrimination Act, [75] which passed into law on May 4, 2017. He is also Editor-in-Chief of the scientific journal npj Genomic Medicine, which was co-founded in 2016 with Dr. Magdalena Skipper the current Editor-in-Chief of Nature. [76]
Scherer’s discoveries have appeared in the Globe and Mail, New York Times, Washington Post, Playboy, The Independent, Time, Newsweek, Scientific American and many other periodicals. He has appeared on the Canadian Broadcasting Corporation (CBC), PBS Newshour, TVO Agenda, and other national TV, radio, and media, including Quirks and Quarks, explaining scientific discoveries. [77] [78] [79] [80] [81] [82] [83] [84] [85] His research was featured in Roger Martin's book The Design of Business, [86] Bob Wright’s autobiography the Wright Stuff: from NBC to Autism Speaks, [87] Steve Silberman’s NeuroTribes: The Legacy of Autism and the Future of Neurodiversity, [88] amongst others. In 2013, he spoke at the Canadian Broadcast Glenn Gould Studio: ‘Cracking the Autism Enigma’, [89] and in 2015 was a special guest speaker at the United Nations, New York for World Autism Awareness Day. [90] He has been featured the Genome Giants series of interviews. [91] He served as the scientific consultant for two documentaries, the MediCinema Film creation Cracking the Code, the continuing saga of genetics, [92] and the Gemini Award-winning documentary, After Darwin by GalaFilms-Telefilm Canada. [93] He also hosts the SickKids Discovery Dialogues which takes attendees behind the scenes of research to discuss their research and the path to scientific discovery. [94]
Scherer holds three Honorary Doctorates from the University of Windsor (2001), the University of Waterloo (2017) and Western University (2018). [113] [114] [115] [116]
Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.
In genetics and bioinformatics, a single-nucleotide polymorphism is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population.
Haploinsufficiency in genetics describes a model of dominant gene action in diploid organisms, in which a single copy of the wild-type allele at a locus in heterozygous combination with a variant allele is insufficient to produce the wild-type phenotype. Haploinsufficiency may arise from a de novo or inherited loss-of-function mutation in the variant allele, such that it yields little or no gene product. Although the other, standard allele still produces the standard amount of product, the total product is insufficient to produce the standard phenotype. This heterozygous genotype may result in a non- or sub-standard, deleterious, and (or) disease phenotype. Haploinsufficiency is the standard explanation for dominant deleterious alleles.
The heritability of autism is the proportion of differences in expression of autism that can be explained by genetic variation; if the heritability of a condition is high, then the condition is considered to be primarily genetic. Autism has a strong genetic basis. Although the genetics of autism are complex, autism spectrum disorder (ASD) is explained more by multigene effects than by rare mutations with large effects.
Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. Approximately two-thirds of the entire human genome may be composed of repeats and 4.8–9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype.
Many causes of autism, including environmental and genetic factors, have been recognized or proposed, but understanding of the theory of causation of autism is incomplete. Attempts have been made to incorporate the known genetic and environmental causes into a comprehensive causative framework. ASD is a neurodevelopmental disorder marked by impairments in communicative ability and social interaction and restricted/repetitive behaviors, interests, or activities not suitable for the individual's developmental stage. The severity of symptoms and functional impairment vary between individuals.
22q13 deletion syndrome, also known as Phelan–McDermid syndrome (PMS), is a genetic disorder caused by deletions or rearrangements on the q terminal end of chromosome 22. Any abnormal genetic variation in the q13 region that presents with significant manifestations (phenotype) typical of a terminal deletion may be diagnosed as 22q13 deletion syndrome. There is disagreement among researchers as to the exact definition of 22q13 deletion syndrome. The Developmental Synaptopathies Consortium defines PMS as being caused by SHANK3 mutations, a definition that appears to exclude terminal deletions. The requirement to include SHANK3 in the definition is supported by many but not by those who first described 22q13 deletion syndrome.
The 1000 Genomes Project (1KGP), taken place from January 2008 to 2015, was an international research effort to establish the most detailed catalogue of human genetic variation at the time. Scientists planned to sequence the genomes of at least one thousand anonymous healthy participants from a number of different ethnic groups within the following three years, using advancements in newly developed technologies. In 2010, the project finished its pilot phase, which was described in detail in a publication in the journal Nature. In 2012, the sequencing of 1092 genomes was announced in a Nature publication. In 2015, two papers in Nature reported results and the completion of the project and opportunities for future research.
The Centre for Applied Genomics is a genome centre in the Research Institute of The Hospital for Sick Children, and is affiliated with the University of Toronto. TCAG also operates as a Science and Technology Innovation Centre of Genome Canada, with an emphasis on next-generation sequencing (NGS) and bioinformatics support. Research at TCAG focuses on the genetic and genomic basis of human variability, health and disease, including research on the genetics of autism spectrum disorder and structural variation of the human genome. The centre is located in the Peter Gilgan Centre for Research and Learning in downtown Toronto, Canada.
Complete Genomics is a life sciences company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis. This solution combines the company's proprietary human genome sequencing technology with its informatics and data management software to provide finished variant reports and assemblies at Complete Genomics’ commercial genome center in Mountain View, California.
Neurogenomics is the study of how the genome of an organism influences the development and function of its nervous system. This field intends to unite functional genomics and neurobiology in order to understand the nervous system as a whole from a genomic perspective.
The Center for Applied Genomics is a research center at the Children's Hospital of Philadelphia that focuses on genomics research and the utilization of basic research findings in the development of new medical treatments.
Genomic structural variation is the variation in structure of an organism's chromosome. It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, copy-number variants, insertions, inversions and translocations. Originally, a structure variation affects a sequence length about 1kb to 3Mb, which is larger than SNPs and smaller than chromosome abnormality. However, the operational range of structural variants has widened to include events > 50bp. The definition of structural variation does not imply anything about frequency or phenotypical effects. Many structural variants are associated with genetic diseases, however many are not. Recent research about SVs indicates that SVs are more difficult to detect than SNPs. Approximately 13% of the human genome is defined as structurally variant in the normal population, and there are at least 240 genes that exist as homozygous deletion polymorphisms in human populations, suggesting these genes are dispensable in humans. Rapidly accumulating evidence indicates that structural variations can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.
Cognitive genomics is the sub-field of genomics pertaining to cognitive function in which the genes and non-coding sequences of an organism's genome related to the health and activity of the brain are studied. By applying comparative genomics, the genomes of multiple species are compared in order to identify genetic and phenotypical differences between species. Observed phenotypical characteristics related to the neurological function include behavior, personality, neuroanatomy, and neuropathology. The theory behind cognitive genomics is based on elements of genetics, evolutionary biology, molecular biology, cognitive psychology, behavioral psychology, and neurophysiology.
Joseph D. Buxbaum is an American molecular and cellular neuroscientist, autism researcher, and the Director of the Seaver Autism Center at the Icahn School of Medicine at Mount Sinai. Buxbaum is also, along with Simon Baron-Cohen, the co-editor of the BioMed Central journal Molecular Autism, and is a member of the scientific advisory board of the Autism Science Foundation. Buxbaum is a Professor of Psychiatry, Neuroscience, and Genetics and Genomic Sciences. He is also the Vice Chair for Research and for Mentoring in the Department of Psychiatry at the Icahn School of Medicine at Mount Sinai.
Charles Lee is Director and Professor of The Jackson Laboratory for Genomic Medicine, The Robert Alvine Family Endowed Chair and a board certified clinical cytogeneticist who has an active research program in the identification and characterization of structural genomic variants using advanced technology platforms. His laboratory was the first to describe genome-wide structural genomic variants among humans with the subsequent development of two human CNV maps that are now actively used in the diagnoses of array based genetic tests. Lee served as the President of the Human Genome Organisation (HUGO) 2017 to 2023.
Evdokia Anagnostou is a professor in the Department of Pediatrics at the University of Toronto, and is cross-appointed as pediatric neurologist and a senior clinician scientist at the Holland Bloorview Kids Rehabilitation Hospital in Toronto, Canada. She is a Tier 2 Canada Research Chair in Translational Therapeutics in Autism Spectrum Disorder.
Emmanouil Theophilos Dermitzakis is a Greek human geneticist and professor in the Department of Genetic Medicine and Development at the University of Geneva, where he is also Director of the Health 2030 Genome Center. He is an ISI Highly Cited Researcher and an elected member of the European Molecular Biology Organization. He is a member of the Swiss Institute of Bioinformatics, where his research group is focused on the genetics and genomics of complex traits in humans. He has joined GlaxoSmithKline as Vice President, Computational Biology in R&D.
GeneMatcher is an online service and database that aims to match clinicians studying patients with a rare disease presentation based on genes of interest. When two or more clinicians submit the same gene to the database, the service matches them together to allow them to compare cases. It also allows matching genes from animal models to human cases. The service aims to establish novel relationships between genes and genetic diseases of unknown cause.
Deborah Ann "Debbie" Nickerson was an American human genomics researcher. She was professor of genome sciences at the University of Washington. Nickerson founded and directed of one of the five clinical sites of the Gregor Consortium and was a major contributor to many genomics projects, including the Human Genome Project and the International HapMap Project.
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