BROCA Cancer Risk Panel

Next-generation sequencing.

This assay sequences all exons and flanking intronic sequences of ALK, AKT1, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK12, CDKN2A, CHEK1, CHEK2, CTNNA1, DICER1, FANCM, FH, FLCN, GALNT12, GEN1, GREM1, HOXB13, KIF1B, MEN1, MET, MITF, MLH1, MLH3, MRE11A, MSH2 (+EPCAM), MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PALLD, PDGFRA, PHOXB1, PIK3CA, PMS2, POLD1, POLE, POT1, PRKAR1A, PRSS1, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RNF43, RPS20, SDHB, SDHC, SDHD, SLX4, SMAD4, SMARCA4, TP53, TSC1, TSC2, and VHL. A total of 1.4 Mb (1.4 Million base pairs) are sequenced and the average coverage ranges from 320 to >1,000 sequencing reads per bp. Genomic regions are captured using biotinylated RNA oliognucleotides (SureSelect), prepared in paired-end libraries with ~200 bp insert size, and sequenced on an Illumina HiSeq2000 instrument with 100 bp read lengths, in a modification of a procedure described by Walsh et al. 2010 and 2011. Large deletions and duplications are detected using methods described by Nord et al. 2011.

• Walsh T, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A 2010, 107:12629-33. 20616022
• Walsh T, et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A 2011, 108:18032-7. 22006311
• Nord AS, Lee M, King MC, and Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics 2011, 12:184. 21486468
• Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 19997069
• Shirts BH, et al. Improving performance of multigene panels for genomic analysis of cancer predisposition. Genet Med 2016, 18:974-81. 26845104

For providers interested in more information on interpreting genetic test results for your patient, please see the Guide to Interpreting Genomic Reports: A Genomics Toolkit

BLOOD:

• 10 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)*.

*Prenatal testing requires concomitant testing for maternal cell contamination (see Online Test Guide [[MCC]] for ordering and specimen requirements)

BLOOD:

Preferred: 10 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.
2. Under "Check Test Requested," check: "BROCA - Cancer Risk Panel".
3. For single gene next-generation sequencing or known muatation testing, see Single Gene Analysis [SGN] or Known Mutation Testing [KMU].
4. To order a subset of genes on the BROCA panel, check: "BROCA - Cancer Risk Panel" and note the genes for which testing is being ordered. Custom BROCA pricing is the same as full BROCA panel.
5. To order BROCA panel germline testing with paired tumor control, check "BROCA Paired Tumor Panel". All BROCA panel testing with tumor control require a copy of pathology report to be sent along with the Genetics Requistion form.

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

Genetics Preauthorization Form