BROCA Paired Tumor Panel

BROCA Paired Tumor Panel is useful for the evaluation of both somatic and germline variants, including patients with a suspected hereditary cancer predisposition, with a focus on syndromes that include breast or ovarian cancer as one of the cancer types. Depending on the causative gene involved, these cancers may co-occur with other cancer types (such as colorectal, endometrial, pancreatic, endocrine, or melanoma).

BROCA Tumor uses next-generation sequencing to detect most mutations in ALK, AKT1, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRCA1*, BRCA2*, BRIP1, CDH1, CDK4, CDK12, CDKN2A, CHEK1, CHEK2, CTNNA1, DICER1, EPCAM, FANCM, FH, GALNT12, GEN1, GREM1, MEN1, MET, MITF, MLH1*, MLH3, MRE11A, MSH2*, MSH6*, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PIK3CA, PMS2*, POLD1, POLE, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RPS20, SDHB, SDHC, SDHD, SMAD4, SMARCA4, TP53, TSC1, TSC2, and VHL. The assay completely sequences all exons of these genes AND detects large deletions and duplications.

• BROCA Paired Tumor Panel is also useful for the detection of actionable somatic (tumor) mutations, such as somatic BRCA1/2 and PIK3CA mutations, as well as homologous recombination deficiency (ovarian cancer only) and microsatellite instability.
• The test uses next-generation sequencing to detect mutations in the genes listed in the table below. The assay completely sequences all exons, select promoter regions of these genes and detects single nucleotide variants, small insertions and deletions (indels), large deletions, duplications, constitutional and somatic mosaicism. For genes indicated with *above, intronic regions are sequenced and analyzed.
• See BROCA Cancer Risk Panel [BROCA] for germline only testing.
• Single Gene Analysis [SGN] (next generation sequencing) can be ordered for any gene on the BROCA panel.
• Known Mutation Testing [KMU] testing can be requested for relatives of probands with pathogenic/likely pathogenic mutations previously detected in via testing at the UW Genetics Laboratory. Known mutation testing can also be requested for patients where mutations were detected, in UW Genetics Laboratory somatic testing, that are suspected to be germline.
• Custom BROCA can be ordered by specifying genes for which testing is requested on the Genetics Requisition; pricing is the same as full BROCA Paired Tumor Panel.
• For patients with a suspected hereditary colon cancer syndrome, see ColoSeq - Lynch and Polyposis Panel [COSEQ] or ColoSeq Tumor Panel [CSQTP].

*Only the most commonly associated cancer types are listed. A more detailed description of cancer risk for some BROCA genes can be found at GeneReviews.

Next-generation sequencing.

This assay sequences all exons and flanking intronic splice site sequences of ALK, AKT1, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK12, CDKN2A, CHEK1, CHEK2, CTNNA1, DICER1, FANCM, FH, GALNT12, GEN1, GREM1,MEN1, MET, MITF, MLH1, MLH3, MRE11A, MSH2 (+EPCAM), MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOXB1, PIK3CA, PMS2, POLD1, POLE, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RPS20, SDHB, SDHC, SDHD, SMAD4, SMARCA4, TP53, TSC1, TSC2, and VHL. Sequences are aligned to the human genome reference (hg19). Test performed by targeted capture for listed genes followed by next-generation sequencing with Illumina technology. This test was developed and its performance characteristics determined by the University of Washington Department of Laboratory Medicine. It has not been cleared or approved by the US Food and Drug Administration. This laboratory is certified under the Clinical Laboratory Improvement Amendments (CLIA) as qualified to perform high complexity clinical laboratory testing. This test is used for clinical purposes. It should not be regarded as investigational or for research.

NOTE: This test requires BOTH tumor tissue and a germline sample such as peripheral blood.

Tumor Tissue:

Tumor specimen will be requested directly, by UW Laboratory Medicine & Pathology, from the originating pathology department. In order to facilitate this, a pathology report should be submitted with the test requisition, blood control and other clinical and billing paperwork.

If the tumor specimen is being submitted by the ordering provider, tissue samples (FFPE) either (a) slides, OR (b) tissue block are required.

(a) Instructions for slide specimens: 1 slide at 4-micron thickness stained with hematoxylin-and-eosin AND 20 unstained, non-baked slides at 10-micron thickness (a minimum of 10 unstained slides is acceptable). Unstained slides can be on charged or uncharged slides. Note: Sections should contain as much tumor tissue as possible.

(b) Instructions for tissue block specimen: Provide complete tissue block containing tumor tissue. If there is more than one tissue block, please provide the block that has the greatest amount of tumor tissue. Tissue block will be returned at completion of testing. Ship at room temperature.

Germline sample:

BLOOD:

Preferred: 5 mL whole blood in LAVENDER TOP EDTA tube.

Also acceptable: YELLOW TOP ACD tube, purified DNA from peripheral blood or cultured cells.

SKIN BIOPSY:

Collection and transport: Obtain 2-4 mm punch biopsy of skin sample under sterile conditions and place in transport media (e.g. Alpha-MEM media, RPMI). Transport media can be supplied by the lab; call 206-598-4488 to request. If transport media is not available, the following media are acceptable alternatives if shipping time will not exceed 24 hours: lactated Ringer's solution, viral transport medium, or sterile saline. DO NOT USE formaldehyde, formalin, alcohol, or 5% dextrose, or tissue culture medium buffered with bicarbonate.

CULTURED CELLS:

(2) T23 or (1) T75 flask (minimum 1-T25 flask).

SALIVA:

Contact laboratory for validated collection kit.

Genetics preauthorization form (preauthorization is only done for providers who are external to the UW system).

1. Fill out a Genetics Requisition form.

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, SCCA, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request." See tip sheet for more information.

2. Under "Check Test Requested," check: "BROCA Paired Tumor Panel".

3. For single gene next-generation sequencing or known muatation testing, see Single Gene Analysis [SGN] or Known Mutation Testing [KMU].

Ship specimen at room temperature for overnight delivery.

Blood specimens can be held for up to 7 days before shipping if refrigerated.

Ship specimens to:

UW MEDICAL CENTER

LABORATORY MEDICINE - GENETICS LAB

1959 NE PACIFIC ST, ROOM NW220

SEATTLE, WA 98195-7110

Blood: Refrigerate whole blood

Unacceptable Conditions: Frozen or clotted specimens

Stability (collection to initiation of testing): Ambient: 5 days; Refrigerated: 7 days; Frozen: Unacceptable

Purified DNA: Refrigerate DNA specimens. Frozen is acceptable.

For additional test/billing information, see following page: BROCA Cancer Risk Panel billing information.

For pricing information, contact Client Support Services 206-520-4600 or 800-713-5198.

Billing and Insurance Pre-Authorization

We offer insurance pre-authorization services (preauthorization is only done for providers who are external to the UW system).

Email: gpab@uw.edu or call 1-855-320-4869 for more information.

Genetics Preauthorization Form