In a win for open data, leading diagnostics company Ambry Genetics is releasing genomic information from 10,000 patients with breast and ovarian cancer in a free, public database open to researchers studying hereditary links to these diseases and others.
Dubbed AmbryShare, the database contains anonymized information from patients who had previously used the company’s diagnostic genetic tests, which are designed to spot certain abnormalities or mutations in a person’s DNA that make them at higher risk for certain diseases. The data dump contains no identifying information from the patients, who consented to their test samples being used for research. What makes this information useful to scientists is that it shows the allele frequency, or the percentage of people with a specific gene mutation, with hereditary breast cancer and ovarian cancer.
While other genomic databases exist, this seems to be the first large-scale initiative by a commercial diagnostics company to share such information.
Ambry CEO and founder Charles Dunlop, a stage IV prostate cancer survivor, said the motivation for the database–which cost Ambry $20 million–was scientific necessity. “Science is about helping people, not hoarding data,” Dunlop said in an interview. Dunlop hopes the database will help researchers discover new diagnostic targets and treatments.
The endeavor is in line with President Barack Obama’s Precision Medicine Initiative, rolled out by the White House in February 2015 to advance tailored medical treatments for individual patients based on their unique genetic information.
In the past 25 years, scientists have identified more than 20 genes, notably BRCA1 and BRCA2, associated with both hereditary breast cancer and ovarian cancer. Together, BRCA1 and BRCA2 mutations account for about 20% to 25% of hereditary breast cancers and about 5% to 10% of all breast cancers, according to the National Cancer Institute.
“We’re curious to see how many new genes we’d find with this [database],” Dunlop said.
Ambry took on the cost of conducting whole-exome sequencing–a DNA test that searches all the protein-coding genes in a person’s genome for mutations responsible for disease–on the 10,000 patient samples. The exome represents only about 1% of a person’s entire genome, but it contains around 85% of known disease-related variants. Since 1999, Ambry said it has tested approximately half a million patient samples.
Based on projections from its current sample volumes, Ambry said it plans to add information from around 200,000 patients annually to the database. In addition, Dunlop said he wants to eventually build a similar database for cystic fibrosis.
Before he made the decision to release the information publicly, Dunlop said a pharmaceutical company had approached him about using the data in a private partnership with Ambry. But his own cancer diagnosis, plus the experiences of friends who have children with genetic disorders, made him think twice about the deal and instead open the data up to the public.
“We have a goal. The goal is curing human disease. If we’re ever going to get there, it’s going to come from the genomic information that comes out of the human population,” Dunlop said.
For now, the AmbryShare database is intended for bioinformatics professionals who can understand and interpret the data. But Ambry said the platform will evolve to include information targeted at clinicians and eventually the general public. Ultimately, the database will be compatible with third-party registries and other open-source databases, such as the National Center for Biotechnology Information’s ClinVar, to which Ambry Genetics is a heavy contributor.
Previously, Ambry had been tied up in a bitter patent fight with Myriad GeneticsMYGN +% over both companies’ BRCA1 and BRCA2 tests. Myriad, the first company to offer commercial BRCA1 and BRCA2 genetic testing for breast cancer, was the subject of a historic Supreme Court decision in 2013 in which the court ruled that human genes cannot be patented. In December 2014, a U.S. Court of Appeals for the Federal Circuit ruled in favor of Ambry in a lawsuit with Myriad. The court held that claims from three of the patents covering BRCA1 and BRCA2 tests Myriad asserted against Ambry did not contain subject matter eligible for patent protection.
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