ColoSeq - Lynch and Polyposis Panel

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General Information

Lab Name
ColoSeq: Lynch and Polyposis
Lab Code
COSEQ
ORCA Name
ColoSeq, Lynch and Polyposis
Description

ColoSeq™ is a comprehensive genetic test for hereditary colon cancer that uses next-generation sequencing to detect most mutations in AKT1, APC, AXIN2, BMPR1A, CDH1, CHEK2, CTNNA1, EPCAM, GALNT12, GREM1, MLH1, MSH2, MSH3, MSH6, MUTYH, NTHL1, PDGFRA, PIK3CA, PMS2, POLD1, POLE, PTEN, RPS20, SMAD4, STK11, and TP53. Mutations in these genes are associated with Lynch Syndrome (MLH1, MSH2, MSH6, PMS2, EPCAM), familial adenomatous polyposis (APC), MUTYH-associated polyposis, Li- Fraumeni (TP53), Hereditary Diffuse Gastric Cancer (CDH1), Cowden Syndrome (PTEN), Peutz-Jeghers (STK11), Turcot syndrome (APC), PTEN Hamartoma Tumor Syndrome (PHTS), Bannayan-Riley-Ruvalcaba Syndrome (PTEN), Muir-Torre syndrome (MLH1 and MSH2), and Juvenile Polyposis syndrome (SMAD4 and BMPR1A). The assay completely sequences all exons, introns, and flanking regions of these genes AND detects large deletions and duplications. The panel capture detects the MSH2 exon 1-7 inversion (since 2015) described by Rhees, Arnold and Boland 2014. The panel also includes promoter 1B regions of the APC gene including deletions and gastric polyposis causing variants reported in Li et al. 2016.

ColoSeq™ Tumor

Beginning in 2014, ColoSeq™ Tumor is offered for detection of somatic mutations in tumors. Double 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 (Mensenkamp et al. 2014, Haraldsdottir et al. 2014). In the absence of a germline MMR mutation, the presence of double somatic mutations in tumor greatly reduces the likelihood that IHC loss of MMR protein(s) is due to an undetected germline mutation, reducing the likelihood the patient has Lynch syndrome.

ColoSeq™ Tumor is an option for patients who have had abnormal MMR IHC and normal germline testing, such as ColoSeq™. ColoSeq™ Tumor can also assess microsatellite instability in colon cancer (Salipante 2014) and BRAF V600E status. ColoSeq™ Tumor Single Gene and ColoSeq™ Tumor Panel testing are available. See ColoSeq Tumor Panel [CSQTP] for additional information.

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

ColoSeq™ Panel Genes

Gene

RefSeq

Disease Association or Cancer Risk

Complete Sequencing

Del/Dup

Added

MLH1

NM_000249.3

Lynch, Muir-Torre

Yes

Yes

November 2011

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

PMS2

NM_000535.5

Lynch

Yes

Yes

November 2011

EPCAM

NM_002354.2

Lynch

Yes

Yes

November 2011

APC

NM_000038.5

FAP, Turcot

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

MSH3

NM_002439.4

Colon polyposis (recessive)

Yes

Yes

January 2017

CDH1

NM_004360.3

Hereditary diffuse gastric cancer

Yes

Yes

June 2012

CTNNA1

NM_0011903.2

Hereditary diffuse gastric cancer

Yes

Yes

October 2014

PTEN

NM_000314.4

Cowden

Yes

Yes

June 2012

AKT1

NM_005163.2

Cowden-like, Breast, thyroid cancers, macrocephaly

Yes

Yes

October 2013

PIK3CA

NM_006218.2

Cowden-like, Breast, thyroid cancer, macrocephaly

Yes

Yes

October 2013

STK11

NM_000455.4

Peutz-Jeghers

Yes

Yes

June 2012

TP53

NM_000546.5

Li-Fraumeni

Yes

Yes

June 2012

CHEK2

NM_007194.3

Li-Fraumeni-like

Yes

Yes

February 2015

SMAD4

NM_005359.5

Juvenile Polyposis

Yes

Yes

January 2013

BMPR1A

NM_004329.2

Juvenile Polyposis

Yes

Yes

January 2013

POLE

NM_006231.2

Colon cancer

Yes

Yes

October 2013

POLD1

NM_002691.3

Colon cancer

Yes

Yes

October 2013

GALNT12

NM_024642.4

Colon cancer

Yes

Yes

October 2013

GREM1

NM_001191323.1

Polyposis

Yes

Yes

October 2013

AXIN2

NM_004655.3

Colon cancer, oligodontia

Yes

Yes

February 2015

RPS20

NM_001023.3

Colon cancer

Yes

Yes

February 2015

PDGFRA

NM_006206

GIST

Yes

Yes

July 2016

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]

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
  • Li J et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. Am J Hum Genet 2016 May, 5;98(5):830-842. 27087319
  • 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
  • Herman DS, et al. Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog. J Mol Diagn 2018, 20:512-521. 29792936
Synonyms
AKT1, APC, AXIN2, Adenomatous polyposis, BMPR1A, CDH1, CHEK2, CSQTP, CSQTS, CTNNA1, ColoSeq Tumor, Colon cancer, Cowden, EPCAM, FAP, GALNT12, GREM1, HDGC, HNPCC, Hereditary nonpolyposis colorectal cancer, Juvenile Polyposis, Li-Fraumeni, Lynch Syndrome, MLH1, MSH2, MSH3, MSH6, MSI, MUTYH, NTHL1, Next-generation sequencing, PDGFRA, PIK3CA, PMS2, POLD1, POLE, PTEN, Peutz-Jeghers, RPS20, SMAD4, STK11, TP53
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, CTNNA1, EPCAM, GALNT12, GREM1, MLH1, MSH2, MSH3, MSH6, MUTYH, NTHL1, PDGFRA, PIK3CA, PMS2, POLE, POLD1, PTEN, RPS20, SMAD4, STK11, and TP53. A total of 445Kb 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 Pritchard et al. 2012. Large deletions and duplications are detected using methods described by Nord et al. 2011.

Reference Range
See individual components
Ref. Range Notes

No mutations detected.

Ordering & Collection

Specimen Type
ColoSeq™ : Peripheral Blood, cultured cells from skin biopsy, purified DNA from peripheral blood or cultured cells ColoSeq™ Tumor: Formalin-Fixed Paraffin Embedded Tumor Tissue (FFPE), Purified DNA
Collection

ColoSeq™:

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 Maternal Cell Contamination [MCC] for ordering and specimen requirements)

ColoSeq™ Tumor:

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: See ColoSeq™ collection instructions above.

Forms & Requisitions

Complete UWMC Genetics Requisition.

For ColoSeq™:

  • In “Next Generation Sequencing" section of test requisition, check: "ColoSeq™ – Lynch and Polyposis Panel"

For ColoSeq™ Tumor:

  1. In “Next Generation Sequencing" section of test requisition, select: "ColoSeq™ – Tumor Panel" or "ColoSeq™ - Tumor Single Gene". For ColoSeq™ - Tumor Single Gene, specify gene in space provided.
  2. Unless prior germline testing was performed at University of Washington, also select: "Normal Control (blood)".
  3. Select the appropriate “Specimen Submitted".
  4. 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

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: 5 mL 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)
UWMC 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: genelab@uw.edu

Supervisor

Robert Livingston, PhD bobl@uw.edu

Genetic Counselors

Angela Jacobson, MS, LGC agibson@uw.edu
Ginger Tsai, MS, LGC, gjtsai@uw.edu

Faculty

Colin C. Pritchard, MD, PhD
Brian H. Shirts, MD, PhD
Christina Lockwood, PhD, DABCC
Stephen Salipante, MD, PhD
Eric Konnick, MD, MS
Karen Stephens, PhD, FACMG
Jonathan F. Tait, MD, PhD
Vera Paulson, MD, 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 following page: ColoSeq™ – Lynch and Polyposis CPT codes or 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: ngsbill@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
41103-3