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U. Washington's Targeted Gene Panel Pinpoints Breast Cancer Mutations in Quarter of Patients with Negative BRACAnalysis Test Results

BOSTON (GenomeWeb News) – A targeted gene panel developed by University of Washington researchers found that some women, who had a family history of breast and ovarian cancer, and who had received negative test results from Myriad Genetics' BRACAnalysis test, in fact, had BRCA1 and BRCA2 mutations that BRACAnalysis did not pick up.

As UW's Tomas Walsh reported at the American Society for Human Genetics yesterday, he and his colleagues examined nearly 750 families with a history of breast cancer in which one member had undergone commercial testing and received a negative result.

Using their BROCA breast cancer gene mutation test, the researchers were able to determine the genetic root of disease in about a quarter of the families.

Of those resolved families, 39 percent had mutations affecting BRCA1 or BRCA2. Those mutations were likely missed, either because the woman who was tested was indeed wild type, though some of her relatives were not, or because the family harbored a mutation that was not covered by the commercial test.

Still, nearly two-thirds of the resolved families contained mutations in other cancer risk genes.

At a press briefing, UW's Mary-Claire King said that she recommended that patients with a family history of disease be tested using such a gene panel. UW is commercializing the test.

A related study used the same test to determine the genetic source of breast cancer in a population of African-American women, unexpectedly finding a high frequency of mutations in BRCA1, BRCA2, and other genes.

The BROCA test was developed and validated by Walsh and King in 2010, and it became widely available in June after the US Supreme Court struck down certain claims on patents held by Myriad on the BRCA1 and BRCA2 genes.

The BROCA panel now includes some 40 known breast cancer genes, including BRCA1 and BRCA2 along with double stranded break repair genes like ATM and CHEK1 and syndromic genes like p53. The panel can also detect single-base substitutions, indels, and CNVs in those genes. Those genomic regions are captured by a custom Agilent SureSelect panel and sequenced using the Illumina HiSeq 2000, according to the UW website.

Some of those included genes are well-established and confer high risk of disease, though others are more newly established genes that appear to increase risk by a few fold. The panel also contains what Walsh termed emerging risk genes that have been linked to breast cancer, but whose significance is still being worked out.

Myriad's BRACAnalysis test is based on Sanger sequencing, as well as a rearrangement test to detect mutations and some rearrangements affecting the BRCA1 and BRCA2 genes.

To search for the genetic root of breast cancer in patients with family history of the disease but which Myriad's test found to be wild type, Walsh and his colleagues turned to a cohort of 743 families. He later noted that some of those negative results included results indicating the test found variants of unknown significance.

With the BROCA test, the genetic source of breast cancer could be resolved in about a quarter of those families. As Walsh presented at ASHG, of those resolved families, 39 percent had deleterious mutations in BRCA1 or BRCA2. Those mutations, he said, were likely missed by the commercial test because the proband was indeed wild type though others in her family had a BRCA1 or BRCA2 mutation or because the family had a mutation that was not reported by the commercial test.

As an example of the latter, one family had a mutation that appeared to be silent. That mutation, though, through an unknown path, decreased the level of BRCA1 transcripts in patient lymphoblasts, which Walsh and his colleagues found by studying cDNA levels.

Other families contained intronic variants that had not previously been detected, including one that affected a splice site and led to a truncation.

However, about two-thirds of the resolved families had mutations in other genes.

About 37 percent of the families had mutations in genes like CHEK2, PALB, or TP53, whose role in inherited cancers has been established. Another 20 percent of families had mutations in genes like ATM, BARD1, or BRIP1 that have been linked to breast cancer, but that have not been fully characterized — what the researchers called "emerging" risk genes.

At a press briefing King added that Myriad "does what Myriad does well." These results instead indicate that examining a broader range of breast and ovarian cancer-causing mutations with a different technology may help elucidate risk.

A separate study presented by Olufunmilayo Olopade, an oncologist at the University of Chicago applied the BROCA gene panel to a cohort of nearly 400 African-American women diagnosed with breast cancer. African Americans, Olopade noted, are more likely to develop early-onset breast cancer, have triple-negative cancer, and have worse outcomes than white women with breast cancer. In addition, African-American women have been unrepresented in prior breast cancer gene mutation testing and the genes involved in breast cancer risk in this population are not well characterized.

Eighteen percent of women in the cohort had a mutation in one or more of nine known breast cancer genes, including BRCA1 and BRCA2, but also in CHEK2, PALB2, ATM, and others. The results were confirmed through Sanger sequencing.

The laboratory medicine department at UW offers the BROCA test. Physicians can order the test for their patients and have it done at UW. Alternatively, King added, the test has not been patented and other molecular diagnostic labs could develop it. She and Walsh estimated the list price of the test to be approximately $3,800.

At the session, one audience member said that returning results from other genes is "irresponsible."

At a press briefing, King said that clinical patients receive results on a dozen genes, including well-established genes like BRCA1 and BRCA2 as well as the newer risk genes like ATM and CHEK1. They do not receive results on the emerging risk genes.

However, those results are given to the research participants.

The BROCA test has been performed on some 6,000 research participants and 500 clinical patients.

She and Walsh have a study underway using the BROCA panel to examine 7,000 cases and 5,000 controls to further study the emerging risk genes.

A spokesman for Myriad today said that if BRACAnalysis did not pick up certain mutations that BROCA did, BRACAnalysis wasn't designed to do so. As a whole, he added, the field is moving toward gene panels, and in September, Myriad launched its myRisk Hereditary Cancer test, comprising 25 genes associated with eight major cancers cancers — breast, colorectal, ovarian, endometrial, pancreatic, prostate, gastric and melanoma.

Myriad has said that myRisk will replace BRACAnalysis and the company's other hereditary cancer tests by the summer of 2015.

"It's where the future is moving, to these panel tests, and we have a panel test," the spokesman, Ron Rogers, told GenomeWeb Daily News, adding that in colon cancer, myRisk detected 60 percent more mutations in cancer predisposition genes in patients with a prior history of colon cancer and/or polyps.

"We believe the Myriad myRisk Hereditary Cancer represents a significant scientific advancement in hereditary cancer testing for a range of clinically actionable cancers and will improve the quality of patient care by empowering healthcare providers with knowledge about their patients’ risk of hereditary cancer and the appropriate medical management options available based on that risk," he added in a statement.