Test Catalog

Test Id : LYNCP

Lynch Syndrome Panel, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Establishing a diagnosis of Lynch syndrome or constitutional mismatch repair deficiency allowing for targeted cancer surveillance based on associated risks

 

Identification of MLH1, MSH2, MSH6, PMS2, or EPCAM variants to allow for predictive testing in family members

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 5 genes associated with Lynch syndrome: MLH1, MSH2, MSH6, PMS2, EPCAM (copy number variant only). For additional details see Method Description, Targeted Genes and Methodology Details for Lynch Syndrome Panel.

 

Identification of a pathogenic variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for Lynch syndrome.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Sequence Capture and Next-Generation Sequencing (NGS), Polymerase Chain Reaction (PCR), Sanger Sequencing and/or Multiplex Ligation-Dependent Probe Amplification (MLPA)

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Lynch Syndrome Panel

Aliases
Lists additional common names for a test, as an aid in searching

CMMRD

Colon Cancer Panel

Colorectal Cancer

Constitutional mismatch repair deficiency

Hereditary Colon Cancer

HNPCC

Lynch syndrome

NextGen Sequencing Test

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

This gene panel tests for germline variants in the Lynch syndrome genes. This is not a tumor test or immunohistochemistry (IHC). For information on tumor testing or IHC staining for Lynch syndrome, see TMSI / Microsatellite Instability, Tumor or IHC / Mismatch Repair (MMR) Protein Immunohistochemistry Only

 

For a comprehensive hereditary cancer panel that includes MLH1, MSH2, MSH6, PMS2, and EPCAM genes, consider ordering 1 of the following tests:

-CRCGP / Hereditary Gastrointestinal Cancer Panel, Varies

-PANCP / Hereditary Pancreatic Cancer Panel, Varies

-PRS8P / Hereditary Prostate Cancer Panel, Varies

-BRGYP / Hereditary Breast/Gynecologic Cancer Panel, Varies

 

Additional first-tier testing may be considered/recommended. For more information see Lynch Syndrome Testing Algorithm.

 

Customization of this panel or single gene analysis for any gene present on this panel is available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.

 

Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the genes on this panel. For more information see FMTT / Familial Mutation, Targeted Testing, Varies.

Shipping Instructions

Specimen preferred to arrive within 96 hours of collection.

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file.

-Informed Consent for Genetic Testing  (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Molecular Genetics: Inherited Cancer Syndromes Patient Information Sheet (T519)

3. Targeted Genes and Methodology Details for Lynch Syndrome Panel

4. If not ordering electronically, complete, print, and send a Oncology Test Request (T729)

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Varies (preferred)

Useful For
Suggests clinical disorders or settings where the test may be helpful

Establishing a diagnosis of Lynch syndrome or constitutional mismatch repair deficiency allowing for targeted cancer surveillance based on associated risks

 

Identification of MLH1, MSH2, MSH6, PMS2, or EPCAM variants to allow for predictive testing in family members

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 5 genes associated with Lynch syndrome: MLH1, MSH2, MSH6, PMS2, EPCAM (copy number variant only). For additional details see Method Description, Targeted Genes and Methodology Details for Lynch Syndrome Panel.

 

Identification of a pathogenic variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for Lynch syndrome.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

The lifetime risk of colorectal cancer in the general population is 4% to 6%.(1) Lynch syndrome (also known as hereditary nonpolyposis colorectal cancer: HNPCC) is an autosomal dominant hereditary cancer syndrome accounting for 2% to 4% of all colorectal cancer cases.(2,3)

 

Lynch syndrome is associated with germline variants in the mismatch repair genes, MLH1, MSH2, MSH6, PMS2, or deletions of the EPCAM gene. It is predominantly characterized by significantly increased risks for colorectal and endometrial cancer.(2,3) The lifetime risk for cancer is highly variable and dependent on the gene involved. Other malignancies within the tumor spectrum include gastric cancer, ovarian cancer, hepatobiliary and upper urinary tract carcinomas, and small bowel cancer.(2,3)

 

Individuals with biallelic pathogenic variants in the same mismatch repair gene are at risk for constitutional mismatch repair deficiency, an autosomal recessive childhood-onset hereditary cancer syndrome.(3)

 

The National Comprehensive Cancer Network and the American Cancer Society provide recommendations regarding the medical management of individuals with Lynch syndrome.(2,4)

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

All detected variants are evaluated according to American College of Medical Genetics and Genomics (ACMG) recommendations.(5) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Clinical Correlations:
Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.

 

To discuss the availability of further testing options, or for assistance in the interpretation of these results, Mayo Clinic Laboratory genetic counselors can be contacted at 800-533-1710.

 

Technical Limitations:
Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.

 

This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Insertions/deletions (indels) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller indels.

 

Deletion/Duplication Analysis:

This analysis targets single and multi-exon deletions/duplications; however, in some instances single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.

 

This test is not designed to detect low levels of mosaicism or to differentiate between somatic and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.

 

Genes may be added or removed based on updated clinical relevance. for the most up to date list of genes included in this test. For detailed information regarding gene specific performance and technical limitations, see Method Description, Targeted Genes and Methodology Details for Lynch Syndrome Panel in Special Instructions or contact a laboratory genetic counselor.

 

If the patient has had an allogeneic hematopoietic stem cell transplant or a recent heterologous blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.

 

Reclassification of Variants Policy:
At this time, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages health care providers to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time.

 

Variant Evaluation:
Evaluation and categorization of variants is performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline. Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.

 

Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgement.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Howlader N, Noone AM, Krapcho M, et al: SEER Cancer Statistics Review. 1975-2018. National Cancer Institute. Updated April 2021. Accessed July 7, 2021. Available at: https://seer.cancer.gov/csr/1975_2018

2. Gupta S, Provenzale D, Llor X, et al: NCCN Guidelines Insights: Genetic/familial high-risk assessment: colorectal, version 2.2019. J Natl Compr Canc Netw. 2019 Sep 1;17(9):1032-1041

3. Idos G, Valle L: Lynch syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews (Internet). University of Washington, Seattle; 2004. Updated February 2, 2021. Accessed May 4, 2021. Available at www.ncbi.nlm.nih.gov/books/NBK1211/

4. Smith RA, Andrews KS, Brooks D, et al: Cancer screening in the United States, 2019: A review of current American Cancer Society guidelines and current issues in cancer screening. CA Cancer J Clin. 2019 May;69(3):184-210

5. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing (NGS) and/or Sanger sequencing is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known pathogenic variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for insertions/deletions (indels) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS, multiplex ligation-dependent probe amplification (MLPA), and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. PCR and gel electrophoresis is performed to test for the presence of the 10 megabase inversion of coding exons 1-7 of the MSH2 gene. For details regarding the targeted genes analyzed for each test see Targeted Genes and Methodology Details for Lynch Syndrome Panel.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. For details regarding the specific gene regions not routinely covered see Targeted Genes and Methodology Details for Lynch Syndrome Panel.

 

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.(Unpublished Mayo method)

 

Genes Analyzed: MLH1, MSH2, MSH6, PMS2, and EPCAM (copy number variants only)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

Supplemental

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

3 to 4 weeks

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole Blood: 2 weeks (if available); Extracted DNA: 3 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81319

81403

81292

81295

81298

LOINC® Information

Test Id Test Order Name Order LOINC Value
LYNCP Lynch Syndrome Panel In Process
Result Id Test Result Name Result LOINC Value
Result LOINC Value Tooltip
614755 Test Description 62364-5
614756 Specimen 31208-2
614757 Source 31208-2
614758 Result Summary 50397-9
614759 Result 82939-0
614760 Interpretation 69047-9
614761 Resources In Process
614762 Additional Information 48767-8
614763 Method 85069-3
614764 Genes Analyzed 48018-6
614765 Disclaimer 62364-5
614766 Released By 18771-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports