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Whole genome sequencing: The known knowns and the unknown unknowns

Whole genome sequencing: The known knowns and the unknown unknowns

A few years ago, when I spoke with Euan Ashley, MD, associate professor of medicine and of genetics, about the promise of genomics for diagnosing and treating diseases he agreed that the field was in the wild, wild west. Now, in my latest 1:2:1 podcast with him, I asked how would he describe this moment in time, when so much has changed so quickly in whole genome sequencing (WGS). First, he said, the costs of sequencing the genome have plummeted. “At the point we spoke we were just coming off the $20,000 genome,” he told me. “Which seems remarkable, because we’d just been at… $200,000, and before that at the $2 million genome. In looking around in science… in medicine, I have not seen a technology that has changed that much.”

Euan AshleyAshley recently published a paper that my colleague, Krista Conger, has written about; in it, Ashley and his fellow researchers, Michael Snyder, PhD, professor and chair of genetics, and Thomas Quertermous, MD, professor of medicine, analyzed the whole genomes of 12 healthy people and took note of the degree of sequencing accuracy necessary to make clinical decisions in individuals, the time it took to manually analyze each person’s results and the projected costs of recommended follow-up. Quite clearly, Ashley says, the study shows “there are still some challenges, not that these are non-solvable problems.”

Ashley often cites an infamous quote that Donald Rumsfeld, former Secretary of Defense, said when he was asked about the lack of evidence of Iraqi weapons of mass destruction, as he thinks the questions that Rumsfeld raised about WMDs are analogous to the field of genetics today. Ashley told me:

There are really a number of things that we really know that we know, because they’re genetic variants we’ve seen many times. Also, there are a number of known unknowns… which are genes that we know are a problem but maybe variants we haven’t seen before, so they look pretty suspicious… There [are] the complete unknowns, the unknown unknowns… Many genes about which we really do not know very much at this point in time.

Who would have thought Rumsfeld was laying out the future of WGS and not just WMD’s?

Previously: Assessing the challenges and opportunities when bringing whole-genome sequencing to the bedside, Coming soon: A genome test that costs less than a new pair of shoes, Stanford researchers work to translate genetic discoveries into widespread personalized medicine, New recommendations for genetic disclosure released, Ask Stanford Med: Genetics chair answers your questions on genomics and personalized medicine and You say you want a revolution
Photo of Euan Ashley by Mark Tuschman

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