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ColoSeq™ - Lynch and Polyposis Syndrome Panel

Questions: 1-800-713-5198

Background

ColoSeq - Lynch and Polyposis Gene Panel

ColoSeq™ is a comprehensive genetic test for hereditary colon cancer that uses next-generation sequencing to detect mutations in multiple genes associated with Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC), familial adenomatous polyposis (FAP), MUTYH-associated polyposis (MAP), hereditary diffuse gastric cancer (HDGC), Cowden syndrome, Li-Fraumeni syndrome, Peutz-Jeghers syndrome, Muir-Torre syndrome, Turcot syndrome, and Juvenile Polyposis syndrome. The assay sequences all exons, introns, and flanking sequences of the 19 genes listed in the table below. Large deletions, duplications, and mosaicism are also detected by the assay and reported. In October 2013, the panel was expanded from to 13 to 19 genes to include POLE, POLD1, GALNT12, GREM1, AKT1 and PIK3CA. There is no change to pricing, ordering, or specimen requirements with the expanded panel.

Patient information on next-generation sequencing, Points to Consider, is available.

Gene

RefSeq

Disease Association or Cancer Risk

#Exons

Complete Sequencing

Del/Dup

Added

MLH1

NM_000249.3

Lynch, Muir-Torre

19

Yes

Yes

November 2011

MSH2

NM_000251.1

Lynch, Muir-Torre

16

Yes

Yes

November 2011

MSH6

NM_000179.2

Lynch

10

Yes

Yes

November 2011

PMS2

NM_000535.5

Lynch

15

Yes

Yes

November 2011

EPCAM

NM_002354.2

Lynch

9

Yes

Yes

November 2011

APC

NM_000038.5

FAP, Turcot

16

Yes

Yes

November 2011

MUTYH

NM_001128425.1

MAP

16

Yes

Yes

November 2011

CDH1

NM_004360.3

HDGC

16

Yes

Yes

June 2012

PTEN

NM_000314.4

Cowden

9

Yes

Yes

June 2012

STK11

NM_000455.4

Peutz-Jeghers

10

Yes

Yes

June 2012

TP53

NM_000546.5

Li-Fraumeni

11

Yes

Yes

June 2012

SMAD4

NM_005359.5

Juvenile Polyposis

12

Yes

YES

January 2013

BMPR1A

NM_004329.2

Juvenile Polyposis

12

Yes

Yes

January 2013

POLE

NM_006231.2

Colon, endometrial cancer

Yes

Yes

NEW October 2013

POLD1

NM_002691.3

Colon cancer

Yes

Yes

NEW October 2013

GALNT12

NM_024642.4

Colon cancer

Yes

Yes

NEW October 2013

GREM1

NM_001191323.1

Polyposis

Yes

Yes

NEW October 2013

AKT1

NM_005163.2

Breast, thyroid cancers, macrocephaly

Yes

Yes

NEW October 2013

PIK3CA

NM_006218.2

Breast, thyroid cancer, macrocephaly

Yes

Yes

NEW October 2013

ColoSeq - Polyposis Panel (APC and MUTYH only)

For information on ColoSeq™ Polyposis see ColoSeq - Polyposis Panel

BROCA/ColoSeq - Single Gene (Pick One Gene To Test)

For information on single gene testing see BROCA/ColoSeq - Single Gene

BROCA/ColoSeq - Known Mutation (Single-Site Testing)

For information on single site testing of a known mutation in one of the genes listed above see BROCA/ColoSeq - Known Mutation

Methods

This assay sequences all exons and flanking intronic sequences of MLH1, MSH2, MSH6, PMS2, EPCAM, APC, MUTYH, CDH1, PTEN, STK11, TP53, SMAD4, BMPR1A, POLE, POLD1, GALNT12, GREM1, AKT1, and PIK3CA. A total of 445 kb 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 (1). Large deletions and duplications are detected using methods described by Nord et al. 2011 (2).

Requisition Form and Ordering Instructions

  1. Fill out a Clinical Lab Request - Genetics - available at UWMC Genetics Requisition

  2. Under “Check Test Requested,” check: "ColoSeq™ – Lynch and Polyposis Panel"

Sample Requirements and Specimen Handling

10 mL whole blood in lavender top (EDTA) tube. ACD is also acceptable. Minimum 5 mL.

For additional details regarding specimen collection, handling and transport, see the Laboratory Medicine Online Test Guide for COSEQ

CPT Codes and Pricing

Billing and Insurance Pre-Authorization

Turnaround Time

12 weeks (84 days)

Reference Range

No mutation detected.

Contact Us

For further information:

References

  1. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, Gulden C, Kupfer SS, Swisher EM, Bennett RL, Novetsky AP, Jarvik GP, Olopade OI, Goodfellow PJ, King MC, Tait JF, Walsh T. ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing. J Mol Diagn. (2012)14:357-66. PubMed

  2. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. PNAS (2010) 107:12629-33.

  3. Nord AS, Lee M, King MC, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics. (2011) 12:184.

  4. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. (2010) 11:31-46.

2014-06-11 09:13