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A Compelling Look at Variation

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  • Title: Senior Research Fellow, University of Washington
  • Education: PhD, Stanford University School of Medicine, 2006
  • Recommended by: Evan Eichler, Debbie Nickerson

When Greg Cooper applied to two postdoc positions at the University of Washington — one with Evan Eichler, the other with Debbie Nickerson — what he really wanted was to move from mammalian genomics research to work that had more direct application in understanding human genetics and population characterization. Accepted by both PIs, Cooper is now doing a joint postdoc project that has put him right in the thick of the very research he found so appealing.

The project, which began in 2006, aims to connect structural variation data from the human genome to the common traits linked to them. He began by studying the genetic effects of statin response, but the rapid progress in technology for interrogating structural variation, as well as scientists' understanding of the mechanisms involved in it, prompted him to expand his scope. Studying variation in the HapMap samples has, for example, become a major focus of Cooper's lab work, he says.

A key goal is to find the real links between this kind of variation and its phenotypic effect. While much of the community has gotten tremendously excited about genome-wide association studies, Cooper notes that the problem so far is that most of the results have provided "minimal information" about variations of "modest effect." That isn't going to radically change patient care, he says. "As a predictive tool, that's almost useless. That's not clinically relevant to tell somebody" about a variant of negligible effect, he adds. "The only way to make good on that is to learn about the biology," he says. His goal is "coming up with ways to provide a mechanistic understanding to explain the associations that we're observing."

One possible reason that would explain why so many genetic variants don't appear to have a major effect is the possibility that much of the phenotypic variation is actually caused by rare variants, Cooper says. "Copy number variants are a great example of this." But tracking down the rare variants will be particularly challenging, requiring not only significant drops in the cost of sequencing but also access to samples from enormous populations. "It's going to come down to sequencing and picking up all those rare SNPs," he says.

A key to coming up with the "compelling biology" explanations will be improved functional annotation, Cooper says. Back in his grad school days at Stanford University School of Medicine where he earned his genetics PhD with advisor Arend Sidow, Cooper was involved in the ENCODE project that has placed a premium on this kind of work.

Publications of note

To get more of a sense of his work, Cooper says it's a good idea to check out "Systematic assessment of copy-number variant detection via genome-wide SNP genotyping," a paper he co-authored that was published in Nature Genetics. The paper builds on previous work from the Eichler lab analyzing genomic data for nine individuals that was published earlier this year.

And the Nobel goes to …

Not me, Cooper says. "I see genomics as becoming such a collaborative enterprise," he says, "it seems like the notion of a Nobel prize being awarded to a single person for a discovery" is a paradigm that won't work much longer for the field. "I wish I had an answer that I was on the verge of something extraordinary," he laughs.

The Scan

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.

Estonian Biobank Team Digs into Results Return Strategies, Experiences

Researchers in the European Journal of Human Genetics outline a procedure developed for individual return of results for the population biobank, along with participant experiences conveyed in survey data.

Rare Recessive Disease Insights Found in Individual Genomes

Researchers predict in Genome Medicine cross-population deletions and autosomal recessive disease impacts by analyzing recurrent nonallelic homologous recombination-related deletions.

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.