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The second panel member, Harvard University medical geneticist Michael Murray asked, “What would you do with your genome?” His answer: “For the most part you would do nothing.” He then asked the audience to think about the case in which while reviewing your whole genome sequencing results you found that you had an unknown variant in the TSG11 gene, a tumor suppressor gene. What would you do with that information?
Murray temporarily set that aside to discuss some cases illustrating how genomic information might or might not be useful. In one case, about 36 percent of people of East Asian heritage have a variant ALDH2 gene which causes them to experience facial flushing, nausea, and a higher rate of heartbeats if they drink alcohol. However, if they take an H2 blocker like Zantac, they can drink and not experience these symptoms. So does taking H2 blockers solve all their problems with regard to flushing? According to Murray the answer is no, because even if they take H2 blockers people with the ALDH2 flushing variant are at a much higher risk of esophageal cancer if they drink.
As an example of how genetic information is being misused Murray cited the case of the Atlas First Sportgene Test. The company tests for variants of ACTN3 gene which it claims is related to athletic predispositions. Supposedly some carry a variant that suits them for sprint/power sports and others for endurance sports. However, Murray pointed out that a recent winner of the Boston Marathon was an East African. The so-called endurance version of the ACTN3 gene is mostly absent in East African genomes.
Murray then returned to the tumor suppressor gene variant case with which he opened. So far something like 1,300 tumor suppressor genes have been identified in the human genome. TSG11, on the basis of very thin data, has been associated with lung cancer. Murray worries that a patient, armed with this equivocal genetic information, might demand that his doctor conduct further (unnecessary) testing such as a lung CT scan. And this is where Murray and Kohane revealed their real concerns: They are mightily annoyed by the prospect that patients will have their genomes sequenced and then bedevil hardworking physicians like themselves with questions, follow-up visits, and requests for further testing. Murray actually said, “I believe that physicians should suppress information that is not useful or is uninterpretable.”
During the question period, Rosalynn Gill, the chief science officer for Sciona—who also happens to be PGP#9, or Personal Genome Project Whole Genome #9—challenged Murray and Kohane to provide actual evidence that doctors are being overwhelmed by the demands of consumers of direct to consumer genetic testing. In addition, the fact that physicians are so overscheduled that they can spend only a few minutes with each individual patient suggests that the health care system is broken, not that information should be suppressed.
What Does Your Genome Say About You?
The last panel of the day was devoted to describing various efforts to interpret genome sequencing results. In a sense the main theme of the entire conference is about how to make genomic information relevant to clinical outcomes cheaply and quickly. Martin Reese, the CEO of Omicia, did a nice demonstration of how his company’s Opal genomic interpretation software suite operates. Opal uses a proprietary algorithm to compare whole genomes from people suffering specific genetic diseases with reference genomes to quickly identify rare variants associated with their diseases. Next up was bioinformatics guru Michael Cariaso, the founder of SNPedia, a wiki supporting personal genome annotation, interpretation, and analysis. He is also the author the Promethease program for interpreting personal genomes. He was correctly introduced as “something of a cult figure in our field.” Cariaso gave the audience a quick run through of the capabilities both SNPedia and Promethease. So far SNPedia contains some 35,000 annotated gene variants. If you’re interested in how Promethease works head on over and take a look at what it tells you about my genome.
My final dispatch from the conference will report on talks focusing on using genetic results to track down your ancestry; what it’s like to open up your whole genome to public scrutiny; and how genetic testing can help babies. For more background, take a look at my first conference dispatch, “Virtual Children, Genome Sequencing for Everyone, and Forget Genetic Privacy.”