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MSH6/MUTYH/EPCAM Del/Dup Testing by MLPA

Omics test Model
Test Code D5233
Test Summary

This assay detects copy number changes in the MSH6, MUTYH, and EPCAM genes and the two common point mutations in MUTYH, which are associated with Lynch syndrome or MUTYH-associated polyposis (MAP).
Turn Around Time 12 days
Acceptable Sample Types DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA)
Acceptable Billing Types Institutional Billing , Self (patient) Payment
NY Approved No
Self (patient) Price $935.00
Institutional Price $935.00
CPT Codes** 81300(x1), 81403(x1), 81479(x1)
*TAT starts after the sample and all required sample information is received at the processing laboratory.

**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.

This testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.
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Test Code: D5233
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Clinical Genomics Test Requisition Form

Test Description

Multiplex Ligation-Dependent Probe Amplification (MLPA) detects the deletion and duplication of single and multiple exons within a given gene (PMID: 20938835). It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides are amplified by PCR, thus specific for the sequence of interest. This test includes copy number analysis of the MSH6, MUTYH, and EPCAM genes and two common MUTYH mutations, c.536A>G (p.Tyr179Cys) and c.1187G>A (p.Gly396Asp). 

Condition Description

Lynch syndrome (LS, MIM# 120435; formerly known as HNPCC, Hereditary Nonpolyposis Colorectal Cancer) is the most common heritable colorectal carcinoma (CRC) syndrome and is responsible for 2% to 4% of all CRC cases in the Western world. Heterozygous germline mutations in one of the mismatch repair (MMR) genes MSH2 (MIM# 609309), MLH1 (MIM# 120436), MSH6 (MIM# 600678), or PMS2 (MIM# 600259) are responsible for Lynch syndrome (PMID: 20301390). Another cause of Lynch syndrome is the deletion of the 3’ part of EPCAM, leading to constitutional epigenetic silencing of the downstream MSH2 gene. The estimated contribution of the different genes to Lynch syndrome is 15-40% for MLH1, 20-40% for MSH2, 12-35% for MSH6, 5-25% for PMS2 and <10% for EPCAM (PMID: 20301390).

Mutations in the MUTYH gene also result in a hereditary predisposition to colon and gastric cancer, referred to as MUTYH-associated polyposis (MAP). In contrast to LS, MAP is an autosomal recessive disorder. In MAP patients, ten to several hundred colonic adenomatous polyps develop, and in adulthood, these become evident at a mean age of 50. However, colon cancer can also develop in the absence of polyposis. A single defective copy of the MUTYH gene may result in no risk or only a slight increase in risk for CRC. Phenotypes of Lynch (like) syndrome and MAP can partly overlap. There are two common MUTYH mutations, c.536A>G (p.Tyr179Cys) and c.1187G>A (p.Gly396Asp), which are found in ~70% of all MAP patients of European descent. These hotspot mutations are less prevalent in other populations, such as Eastern Asia.

Genes

EPCAM, MUTYH, MSH6

Test Methods and Limitations

MLPA-based assay for detecting deletions/duplications in the MSH6, MUTYH, and EPCAM genes. The MRC-Holland reagent kits and the Applied Biosystem 3730xl DNA Analyzer instrument generate fragment analysis data.

Detailed Sample Requirements

DNA, Isolated
Test Details Page
Collection

Required DNA Quantity by Test Type*:

  • Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
  • Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
  • Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.
Sample Condition * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping Ship overnight at ambient temperature.
Special Sample Instructions
  • Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
  • Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor before submitting a DNA sample from any non-CLIA-certified laboratory.
  • Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Whole Blood (EDTA) (Preferred Sample)
Test Details Page
Collection Container(s) EDTA (purple top)
Collection Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
Special Sample Instructions Clotted or hemolyzed samples are not accepted.
Saliva
Test Details Page
Collection Container(s) Oragene™ Saliva Collection Kit or ORAcollect-Dx kit
Collection Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer's instructions.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature.
Special Sample Instructions Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information.
Dried Blood Spots
Test Details Page
Collection Container(s) Dried blood spot card
Collection

Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.

  • NBS: Please contact Revvity Omics to request the StepOne® kit.
  • Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit.
  • For pre-punched DBS: The required minimum is 6 punches
Sample Condition Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping Follow kit instructions. Double bag and ship overnight at ambient temperature.

Resources

Clinical Genomics Test Requisition Form
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