ColoSeq™ - Lynch and Polyposis Syndrome Panel

Questions: 1-800-256-0893

Background

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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 13 genes listed in the table below. Large deletions, duplications, and mosaicism are also detected by the assay and reported. In January 2013, the panel was expanded from to 11 to 13 genes to include SMAD4 and BMPR1A. There is no change to pricing, ordering, or specimen requirements with the expanded panel.

ColoSeq - Polyposis Panel (APC and MUTYH only)

For information on ColoSeq™ Polyposis see ColoSeq - Polyposis Panel

ColoSeq - Single Gene (Pick One Gene To Test)

For information on ColoSeq™ Single Gene see ColoSeq - Single Gene

ColoSeq - Known Mutation (Single-Site Testing)

For information on single site testing of a known mutation in one of the 11 genes listed above see ColoSeq - Known Mutation

Methods

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This assay sequences all exons and flanking intronic sequences of MLH1, MSH2, MSH6, PMS2, EPCAM, APC, MUTYH, CDH1, PTEN, STK11, TP53, SMAD4, and BMPR1A. 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

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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

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

• Ship specimen at room temperature for overnight delivery. Specimen 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

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

CPT Codes and Pricing

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• CPT codes: 81292, 81294, 81295, 81297 (Please note: these are updated to reflect the 2013 CPT coding changes)
• Please contact 1-800-256-0893 for pricing

Billing and Insurance Pre-Authorization

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• We offer insurance pre-authorization services

• 206-616-8605 direct line

• or 1-800-256-0893

• Pre-authorization form

Turnaround Time

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12 weeks (84 days)

Reference Range

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No mutation detected.

Genetic Counseling

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Genetic counseling can be useful to patients and families considering genetic testing. The laboratory can provide referrals to genetics clinics in the patient’s locale or a listing can be found at http://www.genetests.org or http://www.nsgc.org.

Contact Us

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For further information:

• ColoSeq™ Inquiries: 1-800-256-0893

• Other tests offered by the Genetics and Solid Tumor Diagnostic Laboratory

• Supervisor: Deborah Barden, Ph.D.
• Genetic Counselor: Angela Jacobson, M.S., L.G.C.
• Director: Colin C. Pritchard, M.D., PhD.
• Director: Karen Stephens, Ph.D.
• Director: Jonathan Tait, M.D., Ph.D.

References

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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.