We are clearly on the verge of a revolution in medicine—one in which the sequence of As, Ts, Gs, and Cs is as much a part of a patient’s phenotypic profile as are the sounds of the heart or were the colors of the bile. Yet we are clearly not there yet, with many hurdles still to be overcome.
At the recent “Asia Pacific Bioinformatics” conference in Vancouver, Brad Popovic, Ph.D., CSO at Genome BC, moderated a session where stakeholders from pathologists and funders to bioinformaticians and large technology firms discussed how to traverse the technical, political, cultural, and other landscapes while avoiding the hidden mines on the way to viable medical informatics. The panel discussion helped to provide attendees—who Dr. Popovic described as largely trainees, and largely from the broadly defined bioinformatics field—with some guideposts to get from here to there.
Sequencing technology has been advancing at such a clip that in some ways it is outpacing our ability to assemble and interpret the data it is able to generate, said Dr. Popovic.
Among the biggest concerns in medicine—and in medical testing specifically—are whether data is accurate, reproducible, and translatable from one instrument (or algorithm, or lab, or technician) to another.
Jordan Stockton, Ph.D., director of product marketing, computational biology for Illumina, was asked, “How do I know what truth is? How do I know when I see a call, or a variation, or an interesting marker, that I know I’m looking at something real?”
He believes the answer has two parts. On the one hand, vendors like Illumina “own” the “accuracy problem”—of optimizing the fidelity of the calls, and alerting the end user when they should or shouldn’t trust the data. That problem, he said, is “addressable if not solved.”
(A greater challenge is in knowing what the data means, and in what context should it be taken to mean something medically serious or medically actionable, Dr. Stockton said. That is something that will potentially evolve rather than being solved in one fell swoop, and will be tackled by the community and vendors together.)
The medical community wants to see measures of confidence and portability. One way for this to happen—to move the field forward—is to coalesce around a particular set of standards. “I think in the past three years there has been a lot of consensus around various means of variant calling and various means of representation of data,” Dr. Stockton said.
He added that Illumina’s market presence allows the company the opportunity, and to some extent gives it the burden, to impose some standardization. Using a cloud-based system to analyze the data churned out by sequencers, too, “gives people the opportunity to literally be using the same code to execute the same test anywhere in the world.”