BROCA Paired Tumor Panel

General Information

Lab Name

Lab Code

BROCOP

Epic Ordering

Order using "UW Genetics and Solid Tumor Test Request"
Place a separate order to draw the paired blood sample.

See tip sheet for more information (internal link).

Description

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 AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1*, BRCA2*, BRIP1, CDH1, CDK12, CDK4, CDKN2A, CHEK2, CTNNA1, CTNNB1, DICER1, ENG, EPCAM, FANCM, FH, FLCN, GALNT12, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1*, MLH3, MRE11, 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, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SUFU, TP53, TSC1, TSC2, VHL, WT1.

The assay completely sequences all exons of these genes AND detects large deletions and duplications.

*For genes with an asterisk in the list above, intronic regions are also sequenced and analyzed.

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 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].

Gene	Function/Pathway	Heterozygote Cancer risk*	Associated syndrome	References (PMID)
ALK	MYC signaling	Neuroblastoma	Cowden-like	18724359, 28674118
AKT1	AKT signaling	Breast, Thyroid	Cowden-like	23246288
APC	WNT signaling	Colon	Familial adenomatous polyposis	20301519
ATM	Double stranded break repair	Breast, Pancreatic	Ataxia telangiectasia (recessive)	16832357, 19781682, 22585167
ATR	Double stranded break repair	Oropharyngeal	Seckel (recessive)	22341969
AXIN2	WNT signaling	Colon	Oligodontia-colorectal cancer syndrome	15042511
BAP1	BRCA1-associated protein complex	Uveal Melanoma, Mesothelioma	BAP1 Tumor predisposition syndrome	21874000, 21874003
BARD1	BRCA1-associated protein complex	Breast, Ovarian	Hereditary breast cancer	21344236
BMPR1A	TGF-beta signaling	Colon	Juvenile polyposis	20301642
BRAF	Serine/Threonine protein kinase	Typically somatic or mosaic only	Typically somatic only, association with MLH1 promoter hypermethylation in colon cancer and Cardiofaciocutaneous syndrome when mosaic	20301365
BRCA1	BRCA1-associated protein complex	Breast, Ovarian	Hereditary breast and ovarian cancer	22006311, 2270482, 7545954
BRCA2	Fanconi/BRCA	Breast, Ovarian	Hereditary breast and ovarian cancer, Fanconi anaemia FA-D1 (recessive)	22006311, 8524414
BRIP1	Fanconi/BRCA	Breast, Ovarian	Fanconi anaemia FA-J (recessive)	22006311, 17033622, 21964575
CDH1	Cell adhesion	Breast, Gastric	Hereditary diffuse gastric cancer	20301318
CDK4	Cell cycle	Melanoma	Familial melanoma	19585149
CDK12	MAP kinase regulation	Breast, ovarian cancer, frequently somatic	Hereditary breast and ovarian cancer	24554720, 29906450, 24240700
CDKN2A	Cell cycle	Pancreatic, Melanoma	Familial melanoma and pancreatic cancer	19585149
CHEK2	Double stranded break repair	Breast	Hereditary breast cancer	11967536
CTNNA1	Beta-catenin, e-cadherin complex	Gastric	Hereditary diffuse gastric cancer	23208944
CTNNB1	WNT signaling	Typically somatic only	Colon cancer, endometrial cancer, desmoid tumors, colon adenomas	33115416, 37048063
DICER1	Tumor suppressor	Wilms tumor, pleuropulmonary blastoma	DICER1 syndrome	29343557, 28960912, 23625684
ENG	Transforming growth factor-beta (TGFB) receptor complex and binds TGFB1	Colon polyps, telangiectasia	Hereditary Hemorrahagic Telangiectasia, type 1), potential colon polyposis syndrome	23399955, 16287957
FANCM	Fanconi/BRCA	Breast	Fanconi anemia (recessive)	25288723
FH	Tumor suppressor	Renal	Hereditary leiomyomatosis and renal cell cancer	25018647, 11865300, 25004247
FLCN	Tumor suppressor	Renal	Birt-Hogg-Dube syndrome. Primary spontaneous pneumothorax.	12204536, 19659657
GALNT12	O-glycosylation	Colon	unknown	19617566, 22461326
GEN1	Double stranded break repair	Breast	Hereditary breast cancer	2052659
GREM1	BMP antagonist	Colon	Hereditary mixed polyposis syndrome	22561515
HOXB13	Sequence-specific transcription factor which binds preferentially to methylated DNA	Prostate	Familial prostate cancer	36446039, 34799695, 34059701
KIF1B	Tumor suppressor	Neuroblastoma	Hereditary neuroblastoma	18334619, 24469107, 30859632
KIT	Proto-oncogene which encodes a tyrosine-protein kinase that acts as a cell-surface receptor for cytokine KITLG/SCF	Gastrointestinal stromal tumors (GIST), Acute myelogenous leukemia (AML)	Hereditary GIST and AML	36351335, 35821557
LZTR1	RAS ubiquitination/MAPK signaling	Schwannomatosis	Schwannomatosis, Noonan syndrome	24362817, 25335490
MAX	MYC signaling	Pheochromocytoma, Paraganglioma	Hereditary pheochromocytoma and paraganglioma	21685915, 22452945
MBD4	Mismatch DNA repair	Uveal Melanoma, myelodyplastic disease, colon polyposis	Polyposis, multi-organ tumor predisposition (recessive)	32239153, 35460607
MEN1	Gene expression regulation	Endocrine	Multiple endocrine neoplasia type 1	9215689
MET	Tyrosine Kinase receptor	Kidney, Squamous cell carcinomas	Hereditary papillary renal cell carcinoma	11551094, 9140397, 27330189
MITF	Melanocyte inducing transcription factor	Kidney, Melanoma	MITF-related melanoma and renal cell carcinoma predisposition	24290354, 22012259
MLH1	Mismatch DNA repair	Colon, Ovarian, Endometrial	Lynch syndrome	20301390
MLH3	Mismatch DNA repair	Polyposis (recessive)	unknown	30573798
MRE11A	Double stranded break repair	Breast	Ataxia-telangiectasia-like disorder (recessive)	10612394, 19383352
MSH2 (+EPCAM)	Mismatch DNA repair	Colon, Ovarian, Endometrial	Lynch syndrome	20301390
MSH3	Mismatch DNA repair	Polyposis	Familial adenomatous polyposis 4 (recessive)	27476653, 35675019, 38243056
MSH6	Mismatch DNA repair	Colon, Endometrial	Lynch syndrome	20301390
MUTYH	DNA repair	Colon (homozygotes)	MUTYH-associated polyposis	20301519, 21952991
NBN	Double stranded break repair	Breast	Nijmegen breakage syndrome (recessive)	15185344, 9590180
NF1	MAPK signaling	Optic Glioma, Peripheral Nerve Sheath, Breast	Neurofibromatosis	2114220, 23165953, 20301288
NF2	Cellular regulation	Acoustic neuromas, Vestibular Schwannomas	Neurofibromatosis 2	20301380
NTHL1	Base excision repair	Colon	Polyposis (recessive)	25938944, 26431160
PALB2	Fanconi/BRCA	Breast, Pancreatic	Fanconi anaemia FA-N (recessive)	17200668, 17200671, 25099575
PDGFRA	Protein tyrosine kinase	GIST	Familial, sporadic GIST	25975287, 23036227
PHOXB2	Tumor suppressor	Neuroblastoma	Hereditary neuroblastoma	17637745, 28674118
PIK3CA	AKT signaling	Breast, Thyroid	Cowden-like	22729224, 23246288
PMS2	Mismatch DNA repair	Colon, Endometrial	Lynch syndrome	20301390
POLD1	DNA Polymerase	Colon, Endometrial	Familial polyposis, colorectal cancer	23263490, 23770608
POLE	DNA Polymerase	Colon	Familial polyposis, colorectal cancer	23263490
POT1	Telomere maintenance	Melanoma, CLL, Sarcoma, Glioma, Colon, Thyroid, Breast	Multi-organ tumor predisposition	23502782, 24686849, 28853721
PRKAR1A	cAMP signaling	Endocrine	Carney complex (recessive)	4010501
PTCH1	Hedgehog	Basal cell carcinoma, PNET	Nevoid basal cell-carcinoma syndrome	8681379, 8658145, 20301330
PTEN	PI3K/MAPK Signaling	Breast	Cowden syndrome	20301661
RAD51B	Double stranded break repair	Unknown	Hereditary breast and ovarian cancer	24139550
RAD51C	Fanconi/BRCA	Ovarian, Breast	Fanconi anaemia FA-O (recessive)	22006311, 22538716
RAD51D	Fanconi/BRCA	Ovarian, Breast	Fanconi anaemia (recessive)	21822267, 22415235
RB1	Tumor suppressor	Retinoblastoma, Sarcoma, Melanoma	Hereditary retinoblastoma	25621664, 22355046, 20301625
RECQL	DNA repair	Breast	Hereditary breast cancer	25915596
RET	Receptor Tyrosine Kinase	Endocrine	Multiple endocrine neoplasia type 2	20301434
RINT1	DNA checkpoint regulation	Breast, Colon	Multi-organ tumor predisposition	25050558
RNF43	WNT signaling	Colon	Sessile Serrated Polyposis	27329244, 27081527
RPS20	Ribosomal protein	Colon	unknown	24941021
RSPO3	WNT signaling	Typically somatic only	Colon cancer	29127379, 37048063
SDHA	Succinate dehydrogenase complex	Pheochromocytoma, Paraganglioma	Hereditary paraganglioma-pheochromoctyoma	20484225, 21752896
SDHB	Succinate dehydrogenase complex	Pheochromocytoma, Paraganglioma	Hereditary paraganglioma-pheochromoctyoma	11404820
SDHC	Succinate dehydrogenase complex	Pheochromocytoma, Paraganglioma	Hereditary paraganglioma-pheochromoctyoma	11062460
SDHD	Succinate dehydrogenase complex	Pheochromocytoma, Paraganglioma	Hereditary paraganglioma-pheochromoctyoma	10657297
SMAD4	TGF-beta signaling	Colon	Juvenile polyposis	20301642
SMARCA4	SWI/SNF complex	Ovarian	Hereditary small cell carcinoma of the ovary, hypercalcemic	24658002
SMARCB1	ATP-dependent SWI/SNF chromatin remodeling complex	Schwannoma, Pediatric Rhabdoid Tumors (Kidney, CNS, Soft Tissue), Meningioma,	Schwannomatosis, rhabdoid tumor predisposition syndrome type 1	28109176, 29706634
SUFU	Hedgehog Signaling	Basal cell carcinoma, medulloblastoma, meningioma, gonadal tumours	Nevoid basal cell-carcinoma syndrome (Gorlin syndrome)	19533801, 35768194
TP53	Cell growth	Breast, Ovarian	Li-Fraumeni syndrome	22006311,20301488
TSC1	Cell growth	Hamartomas	Tuberous sclerosis complex	10227394, 9924605, 17287951
TSC2	Cell growth	Hamartomas	Tuberous sclerosis complex	8825048, 9829910
VHL	p53 regulation	Kidney, Neuroendocrine	von Hippel-Lindau syndrome	20301636
WT1	WT1 transcription factor	Wilms tumor	Wilms tumor	15150775

*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.

References

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

Forms & Requisitions

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].

Synonyms

AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1*, BRCA2*, BRIP1, CDH1, CDK12, CDK4, CDKN2A, CHEK2, CTNNA1, CTNNB1, DICER1, ENG, EPCAM, FANCM, FH, FLCN, GALNT12, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1*, MLH3, MRE11, 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, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SUFU, TP53, TSC1, TSC2, VHL, WT1

Components

Code	Name
BROPGS	BROCA Tumor Genes Sequenced
BROPRE	BROCA Tumor Result
BROPIN	BROCA Tumor Interpretation
BROPCH	BROCA Tumor Clinical History
BROPMT	BROCA Tumor Methods
BROPDI	BROCA Tumor Director

Interpretation

Method

Next-generation sequencing.

This assay sequences all exons and flanking intronic splice site sequences of AAKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1*, BRCA2*, BRIP1, CDH1, CDK12, CDK4, CDKN2A, CHEK2, CTNNA1, CTNNB1, DICER1, ENG, EPCAM, FANCM, FH, FLCN, GALNT12, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1*, MLH3, MRE11, 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, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SUFU, 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.

Reference Range

See individual components

References

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

Guidelines

Ordering & Collection

Specimen Type: Formalin-Fixed Paraffin Embedded Tumor Tissue (FFPE), Purified DNA, Peripheral Blood, cultured cells from skin biopsy, skin biopsy (direct), saliva, purified DNA from peripheral blood or cultured cells, saliva
Collection: 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.
Forms & Requisitions: 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].
Handling Instructions: 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
Quantity: requested: Entire sample
minimum: 5mL whole blood

Processing

Processing: 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.

Performance

LIS Dept Code

Genetics (GEN)

Performing Location(s)

UW-MT	Genetics Attention: Genetics Lab Clinical lab, Room NW220 University of Washington Medical Center 1959 NE Pacific Street Seattle, WA 98195 Tel: 206-598–6429 M–F (7:30 AM–4:00 PM) Fax: 206-616-4584 Lab email: cgateam@uw.edu Tel (EXOME only): 206-543-0459	Faculty Jillian Buchan, PhD, FACMG Runjun Kumar, MD, PhD Regina Kwon, MD, MPH Christina Lockwood, PhD, DABCC, DABMGG Brian Shirts, MD, PhD Abbye McEwen, MD, PhD Colin Pritchard, MD, PhD Vera Paulson, MD, PhD Eric Konnick, MD, MS He Fang, PhD

Frequency

Typical Turnaround: 4 weeks *Turn around times may vary based on factors such as tissue acquisition and insurance preauthorization.

Available STAT?

Billing & Coding

CPT codes
Billing Comments: 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
LOINC: 47997-2
Interfaced Order Code: UOW3817