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Clinvitae - variant search

Test code: 50002
Turnaround time:

5–12 calendar days (7 days on average)
Preferred specimen:

3mL whole blood in a purple-top tube
Alternate specimens:

Saliva is accepted; assisted saliva and DNA are not accepted
Sample requirements
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Invitae BRCA1 and BRCA2 STAT Panel

Test description

This test analyzes the BRCA1 and BRCA2 genes, which are associated with hereditary breast and ovarian cancer syndrome (HBOC).

Accelerated turnaround time (TAT) may be necessary because physicians and patients often want to make surgical and management decisions as quickly as possible. Individuals with a pathogenic variant have a higher risk of developing another breast cancer and may choose more aggressive surgery and/or different treatment options based on genetic testing results. BRCA1 and BRCA2 have well established medical management guidelines.

This test is appropriate for breast cancer patients with upcoming cancer-related breast surgeries and/or treatment and genetic testing may inform decisions such as lumpectomy versus mastectomy, single versus double mastectomy, or use of other treatments (such as use of PARP inhibitors or other chemotherapy regimens). Identification of a disease-causing variant may also guide testing and management of at-risk relatives. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Genes tested

BRCA1 BRCA2

Order test

Primary panel (2 genes)

Required

BRCA1 BRCA2

Alternative tests to consider

HBOC can also be ordered as part of a broader panel. Depending on the individual’s clinical and family history, one of these broader panels may be appropriate. Any of these broader panels can be ordered at no additional charge.

Clinical information

Disorders tested

hereditary breast and ovarian cancer syndrome (HBOC)

Clinical description

The average woman’s lifetime risk of developing breast cancer is 12%; her risk for developing ovarian cancer is 1.3%. Most cases of these cancers are sporadic and are not due to hereditary factors, but approximately 5%-10% of breast and ovarian cancer cases are hereditary and due to an identifiable pathogenic variant in a disease-causing gene. HBOC accounts for the majority of hereditary breast and ovarian cancer cases in individuals with a strong family history or an early-onset diagnosis.

Individuals who have inherited a pathogenic variant have a dramatically higher risk of developing cancer, and many of these cancers can be difficult to detect and treat. It is extremely helpful to identify these high-risk individuals so that additional screening, surveillance, and interventions can be started. These efforts can result in risk-reduction and early diagnosis, which increases the chances of successful treatment and survival.

Lifetime risks

Individuals with a pathogenic variant in one of these genes have an increased risk of malignancy compared to the average person. However, not everyone with such a variant will actually develop cancer. Further, the same variant can present differently, even among family members. Because we cannot predict which cancers may develop, additional medical management strategies focused on cancer prevention and early detection may benefit most patients who are found to have a pathogenic variant.

Gene	Female breast cancer	Male breast cancer	Ovarian cancer^*	Other associated cancers
BRCA1	Up to 87%	1%-2%	Up to 54%	Pancreatic
BRCA2	Up to 84%	Up to 8.9%	Up to 27%	Prostate, pancreatic, melanoma

^*Ovarian cancer risk includes fallopian tube and primary peritoneal cancers.

Clinical sensitivity

Pathogenic variants in BRCA1 or BRCA2 account for the majority of hereditary breast and ovarian cancer cases in individuals with a strong family history or an early-onset diagnosis.

Inheritance

HBOC is inherited in an autosomal dominant pattern. The gene BRCA2 is also associated with autosomal recessive Fanconi anemia.

Considerations for testing

HBOC syndrome testing should be considered in individuals with a personal and/or family history of features, including:

early onset breast cancer (age 50 or younger)
triple negative (ER-, PR-, HER2-) breast cancer at age 60 or younger
ovarian cancer
male breast cancer
multiple BRCA-associated cancers in the same person
a family history of ovarian, breast, pancreatic, melanoma, or prostate cancer
breast or ovarian cancer and Ashkenazi Jewish ethnicity

References

Management guidelines

For management recommendations, please refer to:

National Comprehensive Cancer Network, Clinical practice guidelines in oncology. Genetic/Familial High Risk Assessment: Breast and Ovarian.

Assay

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene	Transcript reference	Sequencing analysis	Deletion/Duplication analysis
BRCA1*	NM_007294.3
BRCA2*	NM_000059.3

BRCA1: Sequence analysis includes +/- 20 base pairs of adjacent intronic sequence.
BRCA2: Sequence analysis includes +/- 20 base pairs of adjacent intronic sequence.

Resources

Clinical resources

Genes and associated cancers chart Hereditary cancer gene list Hereditary cancer risks and references chart Invitae brochure

Patient resources

Patient guide: Genetic testing for hereditary cancer Patient guide: Genetic testing simplified Patient guide: Hereditary breast cancer Patient guide: Hereditary colorectal cancer

Test information

Forms page Specimen requirements page

References

Headquarters | 458 Brannan Street, San Francisco, CA 94107

Laboratory & Shipping | 475 Brannan Street, Suite 230, San Francisco, CA 94107 | www.invitae.com

In the US | clientservices@invitae.com | p: 800-436-3037 | f: 415-276-4164

Outside the US | globalsupport@invitae.com or visit www.invitae.com/contact

©2015 Invitae Corp. All rights reserved.

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