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MLH1/MSH2/MSH6/PMS2/EPCAM Somatic Tumor MMR Sequencing and Deletion/Duplication Test
Clinical Genetic Test
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offered by
Impact Genetics
View lab's test page
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GTR Test Accession: Help GTR000558509.9
CAP
INHERITED DISEASECANCERDIGESTIVE SYSTEM ... View more
Last updated in GTR: 2024-10-10
View version history
Last annual review date for the lab: 2024-10-15 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Drug Response; Monitoring; ...
Conditions (6): Help
Hereditary nonpolyposis colon cancer; Colorectal cancer, hereditary nonpolyposis, type 2; Familial colorectal cancer more...
Genes (5): Help
EPCAM (2p21); MLH1 (3p22.2); MSH2 (2p21-16.3); MSH6 (2p16.3); PMS2 (7p22.1)
Methods (3): Help
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
Patients with tumors that show abnormal IHC and/or MSI testing …
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
Impact Genetics
View lab's website
View lab's test page
Test short name: Help
Somatic MMR tumor testing
Specimen Source: Help
  • Buccal swab
  • Cell culture
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Paraffin block
  • Peripheral (whole) blood
  • Saliva
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
Test Order Code: Help
MLH1/MSH2/MSH6/PMS2/EPCAM Somatic Tumor MMR Sequencing and Delet
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Lab contact: Help
Jaime Jessen, MSc, CGC, Certified Genetic counselor, CGC, Genetic Counselor
[email protected]
647-631-3266
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
For U.S. customers test is ordered via LabCorp test code 481472. Tumor procurement, buccal swab home sampling, pre-authorization services and shipment provided by Impact Genetics/LabCorp. To order test in U.S. clinic must have a LabCorp account. If your institution does not have a LabCorp account or you wish to start …
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Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Genetic counseling
    Comment: Available for U.S. patients
Result interpretation
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Yes
Test strategy: Help
NGS is performed on MLH1, MSH2, PMS2, MSH6 and EPCAM in tumor. If no sequencing variants are detected MLPA will be performed on tumor tissue to detect copy number changes. All suspicious variant will be confirmed by Sanger sequencing or analogous methods in tumor and germline (blood).
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Conditions Help
Total conditions: 6
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 5
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 3
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Mutation scanning of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina HiScan™SQ system
Targeted variant analysis
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose: Help
Diagnosis; Drug Response; Monitoring; Mutation Confirmation; Predictive; Recurrence; Risk Assessment; Screening; Therapeutic management
Target population: Help
Patients with tumors that show abnormal IHC and/or MSI testing who have had normal germline MMR testing (Lynch) This test looks at MLH1, MSH2, MSH6, PMS2 and EPCAM in the tumor. Can also be used as first line test prior to germline as all pathogenic or likely-pathogenic variants found in … View more
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
If a VUS is found we first continue to analyze all exons of the genes tested. If no other mutation is found to be disease causing, we analyze the VUS. First we search the database for previous reports of the variant, and then analyze the previous analysis of the variant … View more

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
No.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes. If variant interpretation changes we will issue a new report to the ordering physician detailing the changes and reasons for the changes.
Sample reports:
Sample Negative Report Help
Sample Negative Report

Sample Positive Report Help
Sample Positive Report
Recommended fields not provided:
Clinical validity, Clinical utility, Is research allowed on the sample after clinical testing is complete?
Technical Information
Test Procedure: Help
A new dilution of the stock patient tumor DNA along side blood DNA is tested using the same or different method.
Test Confirmation: Help
A new dilution of the stock patient tumor DNA along side blood DNA is tested using the same or different method.
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Sensitivity to detect MLH1, MSH2, MSH6, PMS2 and EPCAM mutations are validated to detect over 99% of described mutations.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
VUS:
Software used to interpret novel variations Help
SIFT, Polyphen-2, AlignGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finde
Recommended fields not provided:
Assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: Not Applicable
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.