Software to Help Free Breast Cancer Gene Data

Original article written by Susan Young and published at www.technologyreview.com/view/517666/software-to-help-free-breast-cancer-gene-data/

An effort to build a public database of BRCA gene variants joins with Silicon Valley startup Syapse.

A Silicon Valley genome sciences startup has joined an initiative to help doctors interpret the risks associated with gene variants linked to breast and ovarian cancer.

Syapse develops software platforms for aggregating and structuring medical data, including genomic information, that is collected by diagnostic companies, biotech and hospitals. The idea is to create medical records that are savvy to genomics and other data-intensive biomedical information–so that doctors can better diagnose and treat patients using that data.



One way such medical records could achieve that goal is by promoting data sharing. At this early stage of medical genomics, doctors may not always know how a particular DNA variant can affect their patients’ health. What’s needed is a common database that links DNA variants to medical outcomes.

On Monday, Syapse announced that it will provide the software infrastructure necessary to create such a database for the BRCA1 and BRCA2 genes. Until this June’s ruling by the Supreme Court on gene patents, BRCA1 and BRCA2 had been patented by Myriad Genetics. The court largely overruled the company’s patents (see “U.S. Supreme Court Says ‘Natural’ Human Genes May Not Be Patented”), which freed other companies and researchers to test patients for variants in the BRCA genes.

However, as physician and medical geneticist Robert Nussbaum described in a piece he wrote for MIT Technology Review, Myriad still has control over the vital information that links variants within the genes to clinical outcomes–a private database of DNA mutations and their medical associations:

“This unparalleled record of the natural variation in these important genes, collected from patients, is claimed to be Myriad’s own intellectual property […] Having clinical reports locked up in a single laboratory, treated as intellectual property, with a black-box, nontransparent protocol for assessing the clinical significance of these variants is not good medicine.”

That power over medical data inspired Nussbaum to start an initiative to collect such information from doctors and patients on a volunteer basis (see “Free Our Genetic Data”). Nussbaum started the Sharing Clinical Reports Project about a year ago and he anticipates that the initiative will have tens of thousands of reports in the coming year. That’s where Syapse comes in– the company’s software will let doctors analyze, annotate and organize that data. In a released statement, Sharon Terry, CEO and president of Genetic Alliance, one of the founders of the BRCA data initiative, says that Syapse has the “best platform for integrating complex genomics and clinical data from disparate sources.”

The issue of data sharing is not limited to the case of the formerly patented BRCA genes. If genomics is going to change medicine, doctors from many disciplines will need to share their findings of how genetic variants impacted a patient’s disease and treatment response (see “By Simply Sharing, Doctors Could Unlock the Genome’s Potential”). Competitiveness between diagnostic companies and even hospitals may hinder data sharing, but in some cases it may come down to a lack of a convenient (and privacy-protecting) way to share such data. Companies like Syapse and its competitors could help fill that gap.