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At GET, Researchers Discuss How Sequencing Can Find Causal Variants


By now, the refrain that sequencing is becoming cheaper and cheaper is well-worn. But since sequencing is becoming more economical, researchers are increasingly using it as a go-to method in the lab. As the technology and computing power improves, they also hope to someday have vast numbers of sequenced human genomes on hand — something that may power personalized medicine.

At the recent Genomes, Environment, and Traits conference held in April in Philadelphia, Duke University's David Goldstein said that his lab has switched from mainly using genome-wide association studies to sequencing. Goldstein, who suspects that rare variants are at the heart of common diseases, said that sequencing has enabled his lab to find pathogenic mutations and begin to tease out function. He noted that the role of copy number variants in disease has been overblown, though. "Of all the rare, high-penetrant mutations that are out there influencing schizophrenia and epilepsy, copy number variants might be one or two. We want to find the rest of them and how do we do that? Well, we have to sequence," Goldstein said. "It's as simple as that."

While Goldstein's lab has thus far taken a combined whole-exome and whole-genome sequencing approach, he said that's a stopgap measure: Whole-exome sequencing is an interim method until whole-genome sequencing becomes more affordable.

And it soon will, added the next speaker, Complete Genomics' Rade Drmanac. His company is centralizing human genome sequencing, and hopes that will make it affordable as well as scalable. "Just to understand the genetic basis of disease and other phenotypes, we are going to need millions of genomes," he said, adding that cancer, chronic diseases, and rare diseases may need a million genomes. He suspects that can be done in five to six years.

Other work needs to be done to better connect genotype to phenotype, especially as the field lurches toward personalized medicine, said Columbia University's Dana Pe'er. "We're not getting from genotype to phenotype. We're only explaining a small fraction, and sequencing is not going to be the solution," she said. "We really need new approaches."

As those technological advances proceed, Harvard's George Church added that there needs to be "a cohort to test-drive personalized medicine as it advances."

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