BRCA Mutation Testing — Identifying Risk for Hereditary Breast and Ovarian Cancer

James, L. Patrick, MD
Senior Medical Director, National
Quest Diagnostics
Lenexa, Kansas
Also by this Author 

Compared to the general population, patients with a confirmed BRCA mutation have a significantly increased risk of developing cancer during their lifetime - up to an 85% risk of breast cancer, up to a 40% risk of ovarian cancer, and up to a 20% risk of prostate cancer.1 Their immediate family members have a 50% chance of possessing the same autosomal dominant mutation and facing comparable risks.1

Dr. Patrick James, Senior Medical Director, Quest Diagnostics discusses how genetic testing provides physicians with valuable information to help identify patients with Hereditary Breast and Ovarian Cancer (HBOC) Syndrome and provides a basis for potentially life-saving interventions.2. 3 He reviews how technology has evolved to offer physicians different testing options and more precise information regarding their patients’ potential risk.

Scientific Background

Over the last forty years, developments in DNA sequencing have enabled researchers studying hereditary cancers to examine genetic changes in members of families with a high incidence of certain cancers. Having identified that some families have a much higher incidence of breast and ovarian carcinomas, a condition termed hereditary breast and ovarian cancer (HBOC) syndrome, researchers in the 1990s identified the two genes linked to this syndrome – the BRCA1 and BRCA2 genes. BRCA1 and BRCA2 are genes that produce tumor suppressor proteins, which help repair damaged DNA.  When either of these genes contains mutations, cells are more likely to develop additional genetic alterations that can lead to cancer.4

“The mode of transmission of these gene mutations is autosomal dominant and these genes have relatively high expression,” says Dr. James, “so it’s clearly important for individuals with a particular family history to learn whether they have a mutation in one or both of the genes as early as possible. Testing is now available to determine whether someone carries the mutation, so they can be presented with choices for prophylactic therapy, such as surgical or chemotherapeutic intervention, or hormonal manipulation, which would greatly decrease the risk of developing these cancers.”

Genetic Testing for BRCA Mutations

Following a Supreme Court Decision in June 2013, a choice of BRCA mutation tests, is now available. “In considering a genetic test, you need to look at two aspects,” notes Dr. James. “First, how the sequencing is performed and second, the bio-informatics and annotations component, which combines all the information provided by the sequencing and allows you to understand the biological implications for the patient being tested.”

The original technology used for genetic sequencing was Sanger sequencing, which is the technology used by others, including the original BRCA mutation test. Newer tests, including Quest Diagnostics BRCAvantage™ test, are based on next generation sequencing, or massively parallel sequencing. “This technology rapidly obtains sequences for a large number of multiple, overlappingfragments of DNA of interest, and works faster and at a lower cost than traditional sequencing,” explains Dr. James. While both assays sequence all the coding exons in BRCA1 and BRCA2, Quest Diagnostics uses an approach for exon capture called RNA bait tile array. “This is important,” continues Dr. James, “because in traditional Sanger sequencing the necessary chemical reactions may cover up some of the areas to be sequenced, leading to certain mutations being missed. The RNA bait tile array approach minimizes the potential that areas harboring mutations may be hidden.” 

For deletions and duplication analysis, Quest Diagnostics uses multiplex ligation-dependent probe amplification (MLPA) to reduce the potential for missing duplications or deletions. “This is the current approach for interrogating all large gene rearrangements, some of which could otherwise be missed,” notes Dr. James.

BRCAvantage™ Test

BRCAvantage™ consists of four test options. The most complete is the BRCAvantage™ Comprehensive Evaluation, which includes next generation sequencing, analysis by both standard and proprietary alignment software, and testing for deletions, duplications, rearrangements using the MLPA approach. “This test is most appropriate for individuals who have a family history of hereditary breast or ovarian cancer risk, but where there is no known family mutation,” says Dr. James.

For the Ashkenazi Jewish population, which has a much higher incidence of BRCA1 andBRCA2 mutations, there is the BRCAvantage™ Ashkenazi Jewish Evaluation, which includes detection of the three hereditary breast and ovarian cancer founder mutations. “Those are the most common mutations found in this group and we believe this the best first-tier test to assess the risk in the Ashkenazi Jewish population,” explains Dr. James. “For those receiving a negative result from this panel, the Comprehensive test can be used as a second tier assay to look more completely at the exon areas for BRCA1 and BRCA2.”

The BRCAvantage™ Re-arrangement Evaluation tests specifically for large deletions and duplications. “We feel this test is best suited for individuals who, may only have had testing for BRCA1 or BRCA2 without analysis for rearrangements, raising concern about BRCA1 or BRCA2. This is a targeted assay for a specific population.”

The fourth test is a BRCAvantage™ Single Site/Known Familial Variant test for families who have a known point mutation or large rearrangement in the BRCA1 or BRCA2 genes. The test interrogates the genome for those mutations only.

Test results are presented as either positive – a known deleterious mutation has been identified, negative - no deleterious mutation has been identified, or variant of uncertain clinical significance (VUS). With a positive result, the report provides information about the specific mutation identified and its implications for the patient. When a VUS is identified, the provider is informed that there will be regular follow-up and that further information will be reported when the biological implication of the variant is determined.

Applying Bio-informatics to Minimize Uncertainty

Recognizing the challenge presented by VUS detection, Quest Diagnostics aims to minimize the VUS rate through extensive use of bioinformatics. Cross-referencing a range of proprietary and public databases for known mutations in BRCA1 and BRCA2 can determine whether a variant not recognized initially is truly unknown. If a variant is not recognized, it can be entered into these databases to be watched over a period of time. “We check on a regular basis for any updates, so we can report back to the provider as soon as possible and ensure the patient is informed,” says Dr. James. “The increased use of BRCA testing, combined with a commitment by testing providers to transparency, will allow us to learn the biological significance of these variants more quickly. We feel confident about our bioinformatics capability. The VUS rate for the first 521 patients we tested was 1.9%, which compares favorably to levels reported by other providers.”

Provider and Patient Resources

Quest Diagnostics provides a range of support services regarding genetic testing for both healthcare providers and patients. “We want to ensure that the right tests are performed on the right patients, and that any questions about test reports are directed to the right individual, so the appropriate information is made available to the provider,” says Dr. James.

A website,, provides extensive information about the test, the four test offerings, and appropriate patient selection. There is a toll-free number, 866-GENE-INFO, for providers to call with questions about the test, test ordering and preauthorization. Experts are also available to help with the pre-authorization required by some insurance companies.

Genetic Counseling is an important part of BRCA testing. For physicians, Quest Diagnostics offers consultations to answer questions related to genetic testing and test selection. Many patients already have access to genetic counseling services through their primary healthcare provider. For those who don’t, Quest Diagnostics will link individuals considering genetic testing to a genetic counselor.

Genetic testing is a rapidly evolving field. As more test information is generated and providers’ understanding grows, it’s likely to play an increasingly important role in identifying patients at risk from hereditary disease and enabling them to make well informed decisions about treatment options.


  1. Cancer.Net. American Society of Clinical Oncology (ASCO). Cancer.Net Editorial Board, Feb 2010. Available from: Accessed August 6, 2013.
  2. National Comprehensive Cancer Network. NCCN clinical practice guidelines in oncology. Genetic/familial high-risk assessment: breast and ovarian. V4.2013. Accessed December 9, 2013.
  3. American College of Obstetricians and Gynecologists. ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome. Obstet Gynecol. 2009;113:957-966. December 9, 2013.
  4. BRCA1 and BRCA2: Cancer Risk and Genetic Testing. National Cancer Institute at the National Institutes of Health. Accessed March 18, 2014