The annual meeting of the American Society for Human Genetics, which brings together population geneticists, clinical geneticists, technology providers, and basic researchers, is something of a bellwether for the state of the science. The tone at this year’s meeting, under way in San Francisco through Saturday, suggests that the industry has shifted its attention from genome-wide association studies to whole-genome sequencing.
Among the more than 6,000 scientific participants here is a delegation of seven scientists from the New York Genome Center who are exploring new uses for technologies and the massive troves of data now available and getting a clearer picture of what this new phase of genomics will look like. “The latest research findings are communicated here," said Nancy Kelley, the founding executive director of the New York Genome Center. "There are informal meetings between scientists — where real information is shared — as well as announcements around services and technologies. It's the biggest and most important genetics meeting in the world.”
Several sessions explore the understanding and interpretation of variants using functional and regulatory data. The conference offers an opportunity to discuss new ideas about integrating and making use of such data. One example is the recent work by ENCODE, the collaborative effort to describe all the functional elements of the human genome that produced a wealth of publications in September. Such findings on functional elements of the genome may be applicable to the interpretation of newly discovered sequence variants, said NYGC bioinformatics scientist Vladimir Vacic.
The dizzying abundance of data could itself be a conference theme. The challenge is now in analysis, in standardizing the information and figuring out a way to make it all make sense, said NYGC bioinformatics scientist Nicholas Robine.
No major methodological breakthrough is on the agenda this year. Instead, many sessions reflect the gradual turn toward using sequencing in the clinic. “Last year at ASHG there were a lot of questions about the clinical significance of whole-genome sequencing — how and whether it would be applied,” said Kelley. “I think those questions are in the past. This year, the sense of the conference is: We’re doing it. How fast is it going to go?”
In prenatal and perinatal diagnostics, genomics technologies can be used to identify genetic abnormalities that are not detected with standard methods. Brynn Levy of Columbia University is using SNP-based microarray analysis to understand the causes of miscarriages by diagnosing fetal abnormalities that would otherwise be missed. Jacob Kitzman of the University of Washington described the new technique of fetal whole-genome sequencing using samples of maternal blood.
Other sessions focus on ways to create reliable, standardizable tests from high-throughput screening — work that will be required to make this technology a standard clinical tool. “In the last several years we've seen lots of genes implicated as disease causes,” said NYGC bioinformatics scientist Avinash Abhyankar. “Everything has been in the research setting, and now it’s time to see it in the clinic.” The challenges are practical: How to produce a meaningful report out of the deluge of data generated by exome sequencing, or standards by which variations should be described in relation to a reference sequence. The hurdles are also ethical, regulatory, and legal — considerations that will be taken up during the next days of the meeting.
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Kat McGowan is a journalist and editor specializing in health, medicine and science. She's the editor of Discover's single-topic special issues, and she writes for a range of other magazines including Self, Redbook and Archeology. She writes mostly about neuroscience, genetics, psychology, and other kinds of science that affect how we understand ourselves as individuals and as a society.