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, ovarian, or prostate 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).

IMPORTANT:
If you are ordering paired tumor testing for evaluation of mismatch repaired deficiency, order ColoSeq Tumor Panel [CSQTP].

If you are ordering paired polyp testing for the evaluation of gastrointestinal polyposis, order ColoSeq Polyposis [CSQP].

For an overview of available germline and paired tumor-germline testing for hereditary cancer syndromes, please see: Hereditary Cancer Test Menu: Germline and Paired Tumor-Germline guideline.

BROCA Paired Tumor Panel is not intended to evaluate for somatic mutations for purposes of cancer treatment. Analysis for these tests is limited to select somatic and constitutional mosaic mutations to aid in the diagnosis of genetic and/or hereditary conditions and not all somatic mutations detected are reported.  

NOTE: A germline sample is required if germline BROCA or ColoSeq ™ testing was not performed previously at the University of Washington. The germline sample is used to evaluate for the presence of the apparently somatic mutations detected in the tumor, including the identification of constitutional mosaicism. 
 
BROCA Tumor uses next-generation sequencing to detect most mutations in AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK12, CDKN1B, CDKN2A, CEBPA, CHEK2, CTNNA1, CTNNB1, DDX41, DICER1, EGFR, EPCAM, ETV6, FANCM, FH, FLCN, GATA2, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PIK3CA, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RNF43, RPS20, RSPO3, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, SUFU, STK11, TMEM127, TP53, TSC1, TSC2, VHL, and WT1. 

The assay completely sequences all exons and flanking introns of these genes and detects large deletions and duplications. Promoters and complete intronic sequencing of BRCA1, BRCA2 and the mismatch repair genes is performed, and non-coding variants of uncertain significance are assessed with RNA analysis when certain criteria are met. Next-generation sequencing is performed on an Illumina instrument to detect single nucleotide variants, insertions, deletions, gene amplifications, and selected translocations. BROCA Paired Tumor Panel is also useful for the detection of homologous recombination deficiency (prostate and ovarian cancer only) and microsatellite instability.

*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 AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1*, BRCA2*, BRIP1, CDH1, CDK4, CDK12, CDKN1B, CDKN2A, CEBPA, CHEK2, CTNNA1, CTNNB1, DDX41, DICER1, EGFR, EPCAM, ETV6, FANCM, FH, FLCN, GATA2, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1*, MLH3, MSH2*, MSH3, MSH6*, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PIK3CA, PMS2*, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RNF43, RPS20, RSPO3, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, SUFU, STK11, TMEM127, TP53, TSC1, TSC2, VHL, and WT1.

Gene introns are also sequenced for genes indicated above with an asterisk (*).

Sequences are aligned to the human genome reference (HG38). 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, CPT codes for Hereditary Cancer Panels (germline and paired).

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