ColoSeq Tumor Single Gene

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General Information

Lab Name
ColoSeq Tumor Single Gene
Lab Code
CSQTS
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 Single Gene is designed to detect somatic mutations in a single gene of ColoSeq™ Panel. 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 is an option for patients who have had abnormal MMR IHC and normal germline testing, such as ColoSeq™. ColoSeq™ Tumor Single Gene is a multiplexed assay for tumor samples that detect mutations in single gene selected by ordering provider. Next-generation sequencing is performed on an Illumina instrument to detect single nucleotide variants, insertions, deletions, gene amplifications, and selected translocations.

NOTE: If germline MMR testing was performed in a different laboratory, a peripheral blood sample should be submitted in addition to tumor tissue.

For information on the full ColoSeq™ Tumor Panel, see ColoSeq Tumor Panel [CSQTP]

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

RefSeq

Disease Association or Cancer Risk

Complete Sequencing

Del/Dup

Added

AKT1

NM_005163.2

Cowden-like, Breast, thyroid cancers, macrocephaly

Yes

Yes

October 2013

APC

NM_000038.5

FAP, Turcot

Yes

Yes

November 2011

AXIN2

NM_004655.3

Colon cancer, oligodontia

Yes

Yes

February 2015

BMPR1A

NM_004329.2

Juvenile Polyposis

Yes

Yes

January 2013

CDH1

NM_004360.3

Hereditary diffuse gastric cancer

Yes

Yes

June 2012

CHEK2

NM_007194.3

Li-Fraumeni-like

Yes

Yes

February 2015

CTNNA1

NM_0011903.2

Hereditary diffuse gastric cancer

Yes

Yes

October 2014

CTNNB1

NM_001904.3

Desmoid tumors

Yes

Yes

February 2023

EPCAM

NM_002354.2

Lynch

Yes

Yes

November 2011

GALNT12

NM_024642.4

Colon cancer

Yes

Yes

October 2013

MLH1

NM_000249.3

Lynch, Muir-Torre

Yes

Yes

November 2011

MLH3

NM_001040108.1

Mismatch repair deficiency

Yes

Yes

June 2020

MSH2, includes exon 1-7 inversion

NM_000251.1

Lynch, Muir-Torre

Yes

Yes

November 2011

MSH6

NM_000179.2

Lynch

Yes

Yes

November 2011

MUTYH

NM_001128425.1

MUTYH-associated polyposis

Yes

Yes

November 2011

NTHL1

NM_002528.5

Colon polyposis (recessive)

Yes

Yes

July 2016

PDGFRA

NM_006206

GIST

Yes

Yes

July 2016

PIK3CA

NM_006218.2

Cowden-like, Breast, thyroid cancer, macrocephaly

Yes

Yes

October 2013

PMS2

NM_000535.5

Lynch

Yes

Yes

November 2011

POLD1

NM_002691.3

Colon cancer

Yes

Yes

October 2013

POLE

NM_006231.2

Colon cancer

Yes

Yes

October 2013

PTEN

NM_000314.4

Cowden

Yes

Yes

June 2012

RPS20

NM_001023.3

Colon cancer

Yes

Yes

February 2015

SMAD4

NM_005359.5

Juvenile Polyposis

Yes

Yes

January 2013

TP53

NM_000546.5

Li-Fraumeni

Yes

Yes

June 2012

Single Gene Testing available for any gene on ColoSeq™

For information on single gene testing see BROCA/ColoSeq - Single Gene Analysis [SGN]

Known Mutation Testing

Known mutation testing is available for mutations identified at UW Laboratory Medicine. For information on single site testing of a known mutation in one of the genes listed above see BROCA/ColoSeq™ - Known Mutation Testing [KMU]

For information about how University of Washington Department of Laboratory Medicine reports variants, see Variant Classification and Clinical Reporting of Results.

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
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 Single Gene".

3. 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, from the originating pathology department, and therefore, in most cases, it is not necessary to submit tumor block or slides.

Synonyms
biallelic somatic, ColoSeq™, COSEQ, double somatic, EPCAM, hereditary nonpolyposis colorectal cancer, HNPCC, Lynch syndrome, MLH1, MSH2, MSH6, MSI, PMS2, UW-Oncoplex™
Components

Interpretation

Method

Next-generation sequencing.

This assay sequences all exons, non repeating intronic sequences and select promoter regions of AKT1, APC, AXIN2, BMPR1A, CDH1, CHEK2, CTNNA1, CTNNB1, EPCAM, GALNT12, MLH1, MLH3, MSH2, MSH6, MUTYH, NTHL1, PDGFRA, PIK3CA, PMS2, POLE, POLD1, PTEN, RPS20, SMAD4, and TP53. 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.

Reference Range
See individual components
Ref. Range Notes

No mutations detected

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
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 Single Gene".

3. 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, 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: 20 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 98195

Tel: 206-598–6429 M–F (7:30 AM–4:00 PM)
Fax: 206-598–0304
Lab email: cgateam@uw.edu

Tel (EXOME only): 206-543-0459

Manager
Joe Bernal

Genetic Counselors
Angela Jacobson, MS, LGC
Sandra Coe, MS,LGC
Dru Leistritz, MS, LGC(EXOME testing only)

Variant Review Scientist
Ankita Jhuraney, PhD
Sarah Paolucci, MA, MS, LGC
Catherine A. Darcey, MSc
Daniel W. Serber, PhD, MS, LCGC

Faculty
Jillian Buchan, PhD, FACMG
Runjun Kumar, MD, PhD
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 Single Gene 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.

Genetics Preauthorization Form

LOINC
51967-8
Interfaced Order Code
UOW2941