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Invitae Breast Cancer STAT Panel
Test description
The Invitae Breast Cancer STAT Panel includes up to 9 well-established genes that are associated with a significantly increased risk of developing breast cancer. Accelerated turnaround time (TAT) is needed because physicians and patients often want to make surgical and management decisions as quickly as possible. Individuals who are identified with an inherited 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.
All genes on this panel have published medical management guidelines and are associated with defined hereditary cancer syndromes.
This test is appropriate for breast cancer patients with upcoming cancer-related breast surgeries and/or treatment where 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
Primary panel
BRCA1 BRCA2 CDH1 PALB2 PTEN STK11 TP53
Add-on ATM Gene
ATM
ATM can be added at no additional charge with the same turnaround time.
Add-on CHEK2 Gene
CHEK2
CHEK2 can be added at no additional charge with the same turnaround time.
Order test
Primary panel (7 genes)
Customized gene selection (0 included, 0 excluded)
BRCA1 BRCA2 CDH1 PALB2 PTEN STK11 TP53
Add-on ATM Gene (1 gene)
Customized gene selection (0 included, 0 excluded)
ATM can be added at no additional charge with the same turnaround time.
ATM
Add-on CHEK2 Gene (1 gene)
Customized gene selection (0 included, 0 excluded)
CHEK2 can be added at no additional charge with the same turnaround time.
CHEK2
Alternative tests to consider
The BRCA1 and BRCA2 genes can be ordered alone with the Invitae BRCA1 and BRCA2 STAT Panel. Report delivery is guaranteed within 5-12 calendar days (7 days on average) of Invitae receiving the sample.
Clinical information
Disorders tested
- Cowden and Cowden-like syndrome
- hereditary breast and ovarian cancer syndrome (HBOC)
- hereditary diffuse gastric cancer syndrome (HDGC)
- Li-Fraumeni syndrome (LFS)
- Peutz-Jeghers syndrome (PJS)
Clinical description
The average woman’s lifetime risk of developing breast cancer is 12%. Most cases are sporadic and not inherited; however, approximately 5%-10% of breast cancer is hereditary and due to a pathogenic variant in a disease-causing gene. 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.
The other genes on this panel are also associated with hereditary breast cancer, and their inclusion is expected to increase the clinical sensitivity of this test. Individuals with a pathogenic variant in one of these genes have a significantly increased risk of developing cancer, and many of these cancers may be difficult both to detect and to treat. Identifying those with an underlying hereditary cancer syndrome enables implementation of surgical and/or treatment decisions at the time of diagnosis. These efforts may also result in risk-reduction and early diagnosis of other cancers, increasing 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, but 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.
For gene-associated cancer risks, download our Cancer risk poster.
Inheritance
All of the genes on this panel have autosomal dominant inheritance for hereditary breast cancer. The BRCA2 and PALB2 genes are also associated with autosomal recessive Fanconi anemia. The ATM gene is associated with autosomal recessive ataxia-telangiectasia.
Considerations for testing
This panel comprises genes for which there are established medical management guidelines. It may be considered for individuals with a personal and/or family history of:
- breast, ovarian, uterine/endometrial, colon, pancreatic, melanoma, sarcoma, and/or prostate cancer, particularly if early onset (<50 years)
- male breast cancer
- breast or ovarian cancer and Ashkenazi Jewish ancestry
There are also some common, general features suggestive of a hereditary cancer syndrome family. These include:
- cancer diagnosed at an unusually young age
- different types of cancer that have occurred independently in the same person
- cancer that has developed in both organs of a set of paired organs (e.g., both kidneys, both breasts)
- several close blood relatives that have the same type of cancer
- unusual cases of a specific cancer type (e.g., male breast cancer)
References
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Breast and Ovarian Management Based on Genetic Test Results. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp. Accessed August 2018.
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Management Guidelines for HBOC. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp Accessed September 2015.
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Genetic/Familial High Risk Assessment: Breast and Ovarian. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp Accessed January 2018.
Management guidelines
For management recommendations, please refer to:
- Fitzgerald, RC, et al. Hereditary diffuse gastric cancer: updated consensus guidelines for clinical management and directions for future research. J. Med. Genet. 2010; 47(7):436-44.
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Breast and Ovarian Management Based on Genetic Test Results.
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 |
|---|---|---|---|
| ATM | NM_000051.3 | ||
| BRCA1* | NM_007294.3 | ||
| BRCA2* | NM_000059.3 | ||
| CDH1 | NM_004360.3 | ||
| CHEK2 | NM_007194.3 | ||
| PALB2 | NM_024675.3 | ||
| PTEN* | NM_000314.4 | ||
| STK11 | NM_000455.4 | ||
| TP53* | NM_000546.5 |
BRCA1: Sequence analysis includes +/- 20 base pairs of adjacent intronic sequence.
BRCA2: Sequence analysis includes +/- 20 base pairs of adjacent intronic sequence.
PTEN: Deletion/duplication analysis covers the promoter region.
TP53: Deletion/duplication analysis covers the promoter region.
Resources
Clinical resources
Genes and associated cancers chart Hereditary cancer gene list Hereditary cancer risks and references chart Invitae brochureReferences
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Breast and Ovarian Management Based on Genetic Test Results. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp. Accessed August 2018.
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Genetic/Familial High Risk Assessment: Breast and Ovarian. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp Accessed January 2018.
- National Comprehensive Cancer Network®, Clinical practice guidelines in oncology. Management Guidelines for HBOC. http://www.nccn.org/professionals/physician_gls/f_guidelines.asp Accessed September 2015.
