ColoSeq Tumor Panel

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

For previous versions of ColoSeq™ - Lynch and Polyposis Panel, see Previous Versions, COSEQ.

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.

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).

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.

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

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.

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.

Genetics Preauthorization Form