Lawsuits didn’t do it, public shaming didn’t do it, patients and doctors banding together to “free the data” couldn’t do it: For 22 years Myriad Genetics, one of the oldest genetic testing companies, has refused to make public its proprietary database of BRCA1 variants, which lists more than 17,000 known misspellings in that major “cancer risk” gene, along with the medical significance of each. The database lists which mutations increase the risk of breast and ovarian cancer, which do not, and which have an unknown health effect.
But now a blitzkrieg of biology has hacked the secret cache of life-and-death data.
By deliberately causing every possible mutation of the kind that occurs most commonly in BRCA1, and tracking how cells growing in lab dishes respond, scientists at the University of Washington determined which mutations are pathogenic and which are benign, they reported on Wednesday in the journal Nature. They also made that call for more than 2,000 variants whose health consequences have been unknown, a breakthrough that promises to spare thousands of women the anxiety of not knowing if their BRCA1 variant is a ticking time bomb or nothing to worry about.
Calling the research “provocative,” Dr. Stephen Chanock of the National Cancer Institute, an expert on cancer genes, said in an essay accompanying the paper that it “should turn heads.”
“We’re bullish about using this data clinically,” said geneticist Jay Shendure of the Brotman Baty Institute for Precision Medicine at the University of Washington School of Medicine, co-leader of the study. “If it were my relative” deciding what to do after learning she has a BRCA1 mutation whose meaning has been unclear up to now, he said, “I would be comfortable using this to tip the balance.”
About 12 percent of women will develop breast cancer, but 72 percent of those who inherit a harmful BRCA1 mutation will. Just over 1 percent of women will develop ovarian cancer, but 44 percent with a harmful BRCA1 mutation will. But because there are many genetic and environmental causes of cancer, BRCA1 mutations account for only 5 to 10 percent of breast cancer diagnoses overall and 15 percent of ovarian cancers.
Information on the meaning of BRCA1 variants has been known for the most common ones and for variants whose cancer-causing abilities are unambiguous. It can be found in publicly available BRCA databases such as ClinVar, run by the National Institutes of Health, whose data come from individual researchers, testing labs that compete with Myriad, and other sources.
Myriad has the largest and, it says, best source of what-does-it-mean information. But it is available only to women who get its $3,000 BRCA test, not any of the less expensive BRCA tests that have been commercially available since the U.S. Supreme Court invalidated Myriad’s gene patents in 2013.
For hundreds of variants, however, Myriad doesn’t know the cancer-risk significance either. With the new data, said Lea Starita of the Brotman Baty, who co-led the study, “we can move 90 percent” of the variants of unknown significance in public databases “one way or the other,” deeming them pathogenic or benign. “For rare variants, this might be the only data that’s out there.”
Myriad declined a request for comment. It passed 1 million BRCA tests in 2013.
The NCI’s Chanock was more cautious. “It might be tempting to make immediate use” of the information to interpret puzzling variants found when women undergo BRCA tests, he wrote, but it “should not be used as the basis for medical advice — at least until the approach has been clinically validated.”
That’s the gold standard for variant interpretation: whether women with a specific variant developed cancer or not. “But there isn’t a lot of that clinical data, or it’s in a silo held by Myriad,” Starita said.
She and her colleagues therefore aimed to figure out the consequences of BRCA1 variants by marching through the gene like General Sherman through Georgia.
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