ColoSeq Tumor Panel
General Information
- Lab Name
- ColoSeq Tumor Panel
- Lab Code
- CSQTP
- 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
ColoSeq™ Tumor Panel is designed to detect somatic mutations in the genes on the ColoSeq™ Panel, with specific focus on identifying mutations in the mismatch repair genes. Somatic mismatch repair (MMR) mutations have been reported in colon and endometrial cancers which have IHC loss of MMR protein(s) and normal (negative) germline MMR testing.
ColoSeq™ Tumor Panel is an option for patients who have had abnormal MMR IHC but normal germline testing, such as ColoSeq™.
ColoSeq™ Tumor Panel is an assay for tumor samples that detects mutations in the genes included in this panel. MSI testing and BRAF codon 600 testing are included in the panel for colon cancer. Next-generation sequencing is performed on an Illumina instrument to detect single nucleotide variants, insertions, deletions, gene amplifications, and selected translocations.
NOTE: a peripheral blood control sample is needed in addition to tumor tissue if germline ColoSeq™ testing was not performed previously in this laboratory.
ColoSeq Tumor Single Gene [CSQTS] is also available for the analysis of single gene(s) from the ColoSeq™ Tumor Panel.
For information on germline ColoSeq™ Lynch and Polyposis Panel (comprehensive colon cancer risk panel) see, ColoSeq - Lynch and Polyposis Panel [COSEQ]
ColoSeq™ Panel Genes
Gene
Function/Pathway
Heterozygote Cancer Risk*
Associated disease/syndrome
References
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 AXIN2
WNT signaling Colon Colon cancer, oligodontia
15042511 BAPI
BRCA1-associated protein complex Uveal Melanoma, Mesothelioma BAP1 Tumor predisposition syndrome
21874000, 21874003 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 CDH1
Cell adhesion Breast, Gastric Hereditary diffuse gastric cancer
20301318 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 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 GALNT12
O-glycosylation Colon unknown
19617566, 22461326 GREM1
BMP antagonist Colon Hereditary mixed polyposis syndrome
22561515 MBD4
Mismatch DNA repair Uveal Melanoma, myelodyplastic disease, colon polyposis Polyposis, multi-organ tumor predisposition (recessive)
32239153, 35460607, 30049810 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 MUTYH-associated polyposis (recessive)
20301519, 21952991 NTHL1
Base excision repair Colon polyps, Endometrial, Breast, Pancreatic Hereditary cancer with colon polyposis (recessive)
25938944, 26431160 PDGFRA
Protein tyrosine kinase GIST, often somatic Familial, sporadic GIST
25975287, 23036227 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, 37140166 PTCH1
Hedgehog Basal cell carcinoma, PNET Nevoid basal cell-carcinoma syndrome
8681379, 8658145, 20301330 PTEN
PI3K/MAPK Signaling Breast Cowden syndrome
20301661 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 SMAD4
TGF-beta signaling Colon Juvenile Polyposis
20301642 TP53
Cell growth Breast, Ovarian Li-Fraumeni syndrome
22006311, 20301488 For previous versions of ColoSeq™ - Lynch and Polyposis Panel, see Previous Versions, COSEQ.
- References
- Pritchard CC, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 2012, 14:357-66. 22658618
- 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
- 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
- Rhees J, Arnold M, and Boland CR. Inversion of exons 1-7 of the MSH2 gene is a frequent cause of unexplained Lynch syndrome in one local population. Fam Cancer 2014, 13:219-25. 24114314
- Mensenkamp AR, et al. Somatic mutations in MLH1 and MSH2 are a frequent cause of mismatch-repair deficiency in Lynch syndrome-like tumors. Gastroenterology 2014, 146:643-646.e8. 24333619
- Haraldsdottir S, et al. Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology 2014, 147:1308-1316.e1. 25194673
- Salipante SJ, Scroggins SM, Hampel HL, Turner EH, and Pritchard CC. Microsatellite instability detection by next generation sequencing. Clin Chem 2014, 60:1192-9. 24987110
- Synonyms
- AKT1, APC, ATM, AXIN2, BAP1, biallelic somatic, BMPR1A, BRAF, CDH1, CHEK2, ColoSeq, COSEQ, CTNNA1, CTNNB1, double somatic, ENG, EPCAM, GALNT12, GREM1, hereditary nonpolyposis colorectal cancer, HNPCC, Lynch syndrome, MBD4, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NTHL1, PDGFRA, PIK3CA, PMS2, POLD1, POLE, POT1, PTEN, RNF43, RPS20, RSPO3, SMAD4, TP53
- Components
-
Code Name CTPGS ColoSeq Tumor Gene Sequenced CTPRE ColoSeq Tumor Result CTPIN ColoSeq Tumor Interpretation CTPCH ColoSeq Tumor Clinical History CTPMT ColoSeq Tumor Methods CTPDI ColoSeq Tumor Director
Interpretation
- Method
Next-generation sequencing.
This assay sequences all exons, flanking intronic splice site sequences, and select promoter regions of AKT1, APC, ATM, AXIN2, BAP1, BMPR1A, BRAF, CDH1, CHEK2, CTNNA1, CTNNB1, ENG, EPCAM, GALNT12, GREM1, MBD4, MLH1*, MLH3, MSH2*, MSH3, MSH6*, MUTYH, NTHL1, PDGFRA, PIK3CA, PMS2, POLD1, POLE, POT1, PTEN, RNF43, RPS20, RSPO3, SMAD4, TP53. 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
- Ref. Range Notes
No mutations detected.
- Guidelines
Ordering & Collection
- Specimen Type
- Formalin-Fixed Paraffin Embedded Tumor Tissue (FFPE), Purified DNA, Peripheral Blood, cultured cells from skin biopsy, purified DNA from peripheral blood or cultured cells, saliva
- Collection
-
Tumor specimen will be requested directly, by UW Laboratory Medicine, 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.
NOTE: This test requires BOTH tumor tissue and peripheral blood. Only tumor tissue is required if ColoSeq™ testing on peripheral blood has been done previously at UW Lab Medicine.
Tumor Tissue:
Tumor specimen will be requested directly, by UW Laboratory Medicine, 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.
NOTE: If germline MMR testing was performed in a different laboratory, a peripheral blood sample should be submitted in addition to tumor tissue.
Germline control sample:
BLOOD:
- 10 mL whole blood in LAVENDER TOP EDTA tube.
- Also acceptable: YELLOW TOP ACD tube, purified DNA from peripheral blood or cultured cells.
SALIVA:
Contact laboratory for validated collection kit.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).
- Forms & Requisitions
Requisition Form and Ordering Instructions:
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 (internal link).
2. Check "ColoSeq™ – Tumor Panel" or "ColoSeq™ - Tumor Single Gene" as desired.
3. For ColoSeq™ - Tumor Single Gene, specify gene in space provided.
4. Unless prior germline testing was performed at University of Washington, also select: "Normal Control (blood)."
5. Select the appropriate “Specimen Submitted."
6. Submit test requisition with peripheral blood sample and a copy of the tumor pathology report.
NOTE: Tumor specimen will be requested directly, by UW Laboratory Medicine and Pathology, from the originating pathology department, and therefore, in most cases, it is not necessary to submit tumor block or slides.
- Handling Instructions
Attach a copy of the pathology report for the tumor sample being submitted.
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: Tissue: 10 unstained slides plus one H&E-stained; slide or extracted DNA: 5 microgram AND 5 mL control peripheral blood (DNAPRP)
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 98195Tel: 206-598–6429 M–F (7:30 AM–4:00 PM)
Fax: 206-616-4584
Lab email: cgateam@uw.eduTel (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
- Results within 4-6 weeks, once sample arrives in the laboratory.
- Available STAT?
- No
Billing & Coding
- CPT codes
- Billing Comments
For additional test/billing information, see ColoSeq™ Tumor CPT codes.
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.
A letter of medical necessity is highly recommended for ColoSeq™ Tumor testing, and a template is available by emailing genelab@uw.edu.
- LOINC
- 51967-8
- Interfaced Order Code
- UOW2961