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Test Code BRCAT BRCA1/2 Mutation Analysis, Next-Generation Sequencing, Tumor


Ordering Guidance


Multiple oncology (cancer) gene panels are available. For more information see Hematology, Oncology, and Hereditary Test Selection Guide.



Necessary Information


A pathology report (final or preliminary), at minimum containing the following information, must accompany specimen for testing to be performed:

1. Patient name

2. Block number-must be on all blocks, slides, and paperwork (can be handwritten on the paperwork)

3. Tissue collection date

4. Source of the tissue



Specimen Required


This assay requires at least 20% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 216 mm(2)

-Minimum amount of tumor area: tissue 36 mm(2)

-These amounts are cumulative over up to 10 unstained slides and must have adequate percent tumor nuclei.

-Tissue fixation: 10% neutral buffered formalin, not decalcified

-For specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing. In this document, the sizes are given as 4 mm x 4 mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3 mm x 1 mm x 10 slides: approximate/equivalent to 36 mm(2).

 

Preferred:

Specimen Type: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block with acceptable amount of tumor tissue.

 

Acceptable:

Specimen Type: Tissue slides

Slides: 1 Stained and 10 unstained

Collection Instructions: Submit 1 slide stained with hematoxylin and eosin and 10 unstained, nonbaked slides with 5-micron thick sections of the tumor tissue.

Note: The total amount of required tumor nuclei can be obtained by scraping up to 10 slides from the same block.

Additional Information: Unused unstained slides will not be returned.

 

Specimen Type: Cytology slides (direct smears or ThinPrep)

Slides: 1 to 3 Slides

Collection Instructions: Submit 1 to 3 slides stained and coverslipped with a preferred total of 5000 nucleated cells, or a minimum of at least 3000 nucleated cells.

Note: Glass coverslips are preferred; plastic coverslips are acceptable but will result in longer turnaround times.

Additional Information: Cytology slides will not be returned.


Useful For

Identifying specific mutations within the BRCA1 and BRCA2 genes known to be associated with response to PARP inhibitors and sensitivity to platinum-based therapy

 

This test is not intended for the evaluation of patients suspected of having inherited or germline BRCA1 or BRCA2 mutations.

Genetics Test Information

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the BRCA1 and BRCA2 genes. See Targeted Genes and Methodology Details for BRCA1/2 Mutation Analysis for details regarding the targeted gene regions evaluated by this test.

 

This test is performed to evaluate for somatic mutations within solid tumor samples. It does not assess for germline alterations within the genes listed.

Disease States

  • Breast cancer

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Testing Algorithm

When this test is ordered, slide review will always be performed at an additional charge.

Method Name

Sequence Capture and Targeted Next-Generation Sequencing (NGS)

Reporting Name

BRCA1/2 Mutation Analysis, Tumor

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded, except for cytology slides
Extracted nucleic acid (DNA/RNA)		 Reject

Clinical Information

Studies have shown that somatic mutations in the BRCA1 and BRCA2 genes are clinically relevant in the selection of therapy for patients diagnosed with cancer. Patients with ovarian, breast, prostate, and pancreatic tumors that harbor a somatic BRCA mutation may respond to treatment with PARP (poly [ADP-ribose] polymerase) inhibitors and be sensitive to platinum-based therapy.

Reference Values

An interpretive report will be provided.

Interpretation

The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.

Cautions

This test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

 

DNA variants of uncertain significance may be identified.

 

A negative result does not rule out the presence of a variant that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X in a sample with 20% or more tumor content.

 

Point mutations and small deletion-insertion mutations will be detected in the BRCA1 and BRCA2 genes only. This test may detect single exon deletions but does not detect multiexon deletions, duplications, or genomic copy number variants.

 

Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors including, but not limited to: tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment.(1,2)

 

Rare polymorphisms may be present that could lead to false-negative or false-positive results. 

The presence or absence of a variant may not predict response to therapy in all patients.

 

Test results should be interpreted in the context of clinical, tumor sampling, histopathological, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

Reliable results are dependent on adequate specimen collection and processing. This test has been validated on cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure.

Supportive Data

Performance Characteristics:

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delins, formerly indels]) is 5% variant allele frequency and having at least 500x deduplicated coverage.

 

Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins is 99.7% (699/701) and 96.6% (226/234) of variants, respectively. Concordance for the detection of delins was 98.9% (186/188) in variants 1-10 base pairs (bp) in size, 95.8% (23/24) in variants 11-50 bp in size, and 88.9% (8/9) in variants 51-200 bp in size.

Clinical Reference

1. Strom SP. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol Med. 2016;13(1):3-11. doi:10.28092/j.issn.2095-3941.2016.0004

2. Spurr L, Li M, Alomran N, et al. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep. 2018;8(1):7735. Published 2018 May 16. doi:10.1038/s41598-018-25462-0

3. US Food and Drug Administration (FDA): Table of Pharmacogenomic Biomarkers in Drug Labeling. Updated Febuary 10, 2023, Accessed July 31, 2023. Available at www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling

4. Petrucelli N, Daly MB, Pal T: BRCA1- and BRCA2-associated hereditary breast and ovarian cancer. In: Adam MP, Everman DB, Mirzaa GM, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 1998. Updated May 26, 2022. Accessed July 31, 2023. Available at www.ncbi.nlm.nih.gov/books/NBK1247/

5. Tung, NM, Garber, JE. BRCA1/2 testing: therapeutic implications for breast cancer management. Br J Cancer. 2018l;119(2):141-152. doi: 10.1038/s41416-018-0127-5

Method Description

Next-generation sequencing is performed to evaluate the presence of a mutation in all coding regions of the BRCA1 and BRCA2 genes. See Targeted Genes and Methodology Details for BRCA1/2 Mutation Analysis for details regarding the targeted gene regions evaluated by this test.(Unpublished Mayo method)

 

A pathology review and macro dissection to enrich for tumor cells are performed prior to slide scraping

Day(s) Performed

Monday through Friday

Report Available

12 to 20 days

Specimen Retention Time

FFPE tissue block: Unused portions of blocks will be returned within 10-14 days after testing is complete; FFPE tissue/cytology slides: Unused slides are stored indefinitely; Digital images are obtained and stored for all slides used in testing.

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

88381 - Microdissection, manual

81163

LOINC Code Information

Test ID Test Order Name Order LOINC Value
BRCAT BRCA1/2 Mutation Analysis, Tumor 59041-4

 

Result ID Test Result Name Result LOINC Value
617889 Result 82939-0
617890 Interpretation 69047-9
617891 Additional Information 48767-8
617892 Specimen 31208-2
617893 Tissue ID 80398-1
617894 Method 85069-3
617895 Disclaimer 62364-5
617896 Released By 18771-6

NY State Approved

Yes

Forms

If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.