ColoSeq Polyposis

ColoSeq™ Polyposis is a paired polyp-germline panel that aims to discover the genetic cause of polyps in patients with unexplained colon polyposis. While many patients with adenomatous polyposis are found to have germline variants in APC, MUTYH and other genes, some patients with polyposis remain unexplained. Constitutional mosaic APC mutations have been described and current germline testing of peripheral blood and saliva has not been adequate to detect mosaic APC mutations. Uniquely, by testing colon polyps and a germline sample, ColoSeq™ Polyposis tests for constitutional mosaic mutations in APC and other genes to look for a common mutation. In a recent series of 28 patients with unexplained adenomatous polyposis, a total of 18 (64%) were found to have constitutional mosaic APC mutations detected in their colon adenomas, often also present at low allelic fraction in their germline sample (9 of 18 mosaic cases)1. ColoSeq™ Polyposis may also be useful for the evaluation of hamartomatous and juvenile polyps, serrated colon lesions and other rare polyposis syndromes.

ColoSeq™ Polyposis includes both a comprehensive pan-cancer germline analysis of 91 genes associated with hereditary cancer syndromes AND a targeted tumor assessment of select somatic and constitutionally mosaic somatic mutations to aid in the identifying the etiology of colon polyposis. The polyp analysis includes microsatellite instability, detection of loss of heterozygosity and BRAF V600E mutation.

ColoSeq™ Polyposis uses next-generation sequencing to detect most mutations in AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK12, CDKN1B, CDKN2A, CEBPA, CHEK2, CTNNA1, CTNNB1, DDX41, DICER1, EGFR, EPCAM, ETV6, FANCM, FH, FLCN, GATA2, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PIK3CA, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RINT1, RNF43, RPS20, RSPO3, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, SUFU, STK11, TMEM127, TP53, TSC1, TSC2, VHL, and WT1.

Testing is performed on DNA extracted from two colorectal polyps and a germline sample, using next-generation sequencing to detect somatic and germline variants in genes associated with hereditary colon cancer and polyposis. All exons and flanking intronic sequences are analyzed for all panel genes. Promoters and introns are sequenced for the mismatch repair genes and BRCA1/2. Non-coding variants of uncertain significance are assessed with RNA analysis when certain criteria are met. Select patients may be offered long range sequencing if test results suggest an undetected germline variant in a specific gene. Many patients undergoing paired tumor-germline testing have already undergone a lot of testing, and these assays are intended to provide conclusive results whenever possible.  

For an overview of available germline and paired tumor-germline testing for hereditary cancer syndromes, please see: Hereditary Cancer Test Menu: Germline and Paired Tumor-Germline guideline.

For information on the tumor-germline paired ColoSeq™ Tumor Panel and ColoSeq Tumor Single Gene assays for unexplained mismatch repair deficiency see ColoSeq Tumor Panel [CSQTP] and ColoSeq Tumor Single Gene [CSQTS].

For previous versions of ColoSeq™ - Lynch and Polyposis Panel, see ColoSeq - Lynch and Polyposis Panel [COSEQ]

Next-generation sequencing.

This assay sequences all exons, flanking intronic splice site sequences, and select promoter regions of AKT1, ALK, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRAF, BRCA1*, BRCA2*, BRIP1, CDH1, CDK4, CDK12, CDKN1B, CDKN2A, CEBPA, CHEK2, CTNNA1, CTNNB1, DDX41, DICER1, EGFR, EPCAM, ETV6, FANCM, FH, FLCN, GATA2, GEN1, GREM1, HOXB13, KIF1B, KIT, LZTR1, MAX, MBD4, MEN1, MET, MITF, MLH1*, MLH3, MSH2*, MSH3, MSH6*, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PIK3CA, PMS2*, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RNF43, RPS20, RSPO3, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, SUFU, STK11, TMEM127, TP53, TSC1, TSC2, VHL, and WT1.
Gene introns are also sequenced for genes indicated above with an asterisk (*).

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.

Two polyp specimens 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 polyp tissues and a germline specimen (peripheral blood, saliva or normal tissue). Only polyp tissues are required if ColoSeq™ testing on a germline specimen has been done previously at UW Lab Medicine.

1) Two Polyp Tissues:

Polyp specimens 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 polyp specimens are 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 adenomatous 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 germline sample should be submitted in addition to polyp tissue.

2) 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

2. Under “Check Test Requested,” check: "ColoSeq™ – Polyposis/CSQP"

Genetics Preauthorization Form (preauthorization is only available for providers who are external to the UW system).

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

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 following page, CPT codes for Hereditary Cancer Panels (germline and paired).

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.

Genetics Preauthorization Form