DNA sequencing is increasingly being used in medicine, but doctors can have trouble making sense of the data. Now sequencing machine manufacturer Illumina has announced that it will integrate software into its desktop sequencing platform to assist physicians with that task. The most interesting aspect of the analysis tool may be its ability to share, which could be key to unlocking the real promise of genomics in medicine.
Every person’s genome is full of variations—research estimates that the genomes of any two people differ at around three million positions—but most of these differences, called variants, are harmless. But some variants cause disease, and others contribute to the likelihood of disease. When a variant is suspected to affect health, doctors can turn to the scientific literature for clues, but they may not find any useful information there, or they may find data on entire populations that may not apply to an individual patient.
“They want to be able to say, ‘We found this variant in an important gene, it may be causing this effect, and we’d love to see if someone has seen this before,’ ” says Brad Ozenberger of the National Human Genome Research Initiative. But there’s currently no centralized collection of medically relevant variants for doctors to use. Some National Institutes of Health-run databases include genetic variants linked to disease and drug response, but they are more suited for researchers than doctors. To address this issue, the National Human Genome Research Initiative announced this summer that it will fund such a centralized database.
“The grand vision is that whenever any patient gets their genome sequenced and analyzed, doctors will be able to tap those data,” says Ozenberger.
The commercial answer to the question may come from Illumina’s new collaboration with Partners HealthCare, a consortium of hospitals in the Boston area. Partners developed the interpretation software, and has already used it to support its own clinical interpretation of some 24,000 disease cases, says Heidi Rehm, who directs the hospitals’ Laboratory for Molecular Medicine.
The software generates a report that might include information such as how a patient’s variant will affect the behavior of the gene where it’s located and whether one or two copies are needed to see an effect. If a lab has seen the variant before, the report may describe its impact on health. “This notion of a share and share alike network will be very powerful for interpretation of this data,” says Rehm.
In the case of Illumina, some of that initial sharing may happen not with whole genome sequencing, but with disease-focused selective sequencing. Last week, the company began taking orders for its tests for autism, cancer, cardiomyopathy, and a broad range of inherited diseases. By sequencing only targeted genes, clinicians and researchers can increase the speed and reduce the cost of the analysis. Illumina’s customers can use the Partners Healthcare software to generate reports from this data, and that could help strengthen the power of the technique.
“If I found a variant that’s come through my lab that I’ve never seen, I can go out on my network and see if any other labs have seen it before and see the evidence they used to classify it,” says Tim McDaniel, director of Scientific Research in Translational and Consumer Genomics at Illumina. “The dream here is that every lab would be on the network, so that it’s not just, ‘Has my lab seen it before?’ but ‘Has any lab seen it previously?’ “