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Test ID: ML1HM MLH1 Hypermethylation Analysis, Tumor

Useful For

An adjunct to MSI / Microsatellite Instability (MSI), Tumor and Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor when colon or endometrial tumor demonstrates microsatellite instability (MSI-H) and loss of MLH1 protein expression, to help distinguish a somatic versus germline event prior to performing expensive germline testing


An adjunct to negative MLH1 germline testing in cases where colon or endometrial tumor demonstrates MSI-H and loss of MLH1 protein expression

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Testing Algorithm

When this test is ordered, slide review will always be performed at an additional charge.


See Lynch Syndrome Testing Algorithm in Special Instructions.

Method Name

Polymerase Chain Reaction (PCR) Analysis

Reporting Name

MLH1 Hypermethylation Analys, Tumor

Specimen Type


Advisory Information

This test is not recommended as a first-tier screening measure for hereditary nonpolyposis colon cancer (HNPCC). Refer to MSI / Microsatellite Instability (MSI), Tumor and Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor.


Testing will only be performed on colon or endometrial tumors demonstrating loss of MLH1 protein expression by immunohistochemistry.


Mayo's preferred screening test (BRMLH / MLH1 Hypermethylation and BRAF Mutation Analysis, Tumor) includes both MLH1 promoter hypermethylation and BRAF V600E testing.


Extracted DNA from tissues is not an acceptable specimen type.

Necessary Information

Pathology report must accompany specimen in order for testing to be performed.

Specimen Required

Specimen Type: Tissue block or slide

Collection Instructions:

1. Submit formalin-fixed, paraffin-embedded tissue block (preferred) or 1 slide stained with hematoxylin and eosin and 10 unstained, nonbaked slides (5-micron thick sections) of the tumor tissue.

2. Sections should contain tumor tissue.

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)

Clinical Information

Hereditary nonpolyposis colon cancer (HNPCC), also known as Lynch syndrome, is an inherited cancer syndrome caused by a germline mutation in one of several genes involved in DNA mismatch repair (MMR), including MLH1, MSH2, MSH6, and PMS2. There are several laboratory-based strategies that help establish the diagnosis of HNPCC/Lynch syndrome, including testing tumor tissue for the presence of microsatellite instability (MSI-H) and loss of protein expression for any one of the MMR proteins by immunohistochemistry (IHC). It is important to note, however, that the MSI-H tumor phenotype is not restricted to inherited cancer cases; approximately 20% of sporadic colon cancers are MSI-H. Thus, MSI-H does not distinguish between a somatic (sporadic) and a germline (inherited) mutation, nor does it identify which gene is involved. Although IHC analysis is helpful in identifying the responsible gene, it also does not distinguish between somatic and germline defects.


Defective MMR in sporadic colon cancer is most often due to an abnormality in MLH1, and the most common cause of gene inactivation is promoter hypermethylation (epigenetic silencing). A specific mutation in the BRAF gene (V600E) has been shown to be present in approximately 70% of tumors with hypermethylation of the MLH1 promoter. Importantly, the V600E mutation is rarely identified in cases with germline MLH1 mutations. Thus, direct assessment of MLH1 promoter methylation status and testing for the BRAF V600E mutation can be used to help distinguish between a germline mutation and epigenetic/somatic inactivation of MLH1. Tumors that have the BRAF V600E mutation and demonstrate MLH1 promoter hypermethylation are almost certainly sporadic, whereas tumors that show neither are most often caused by an inherited mutation.


Although testing for the BRAF V600E mutation and MLH1 promoter hypermethylation are best interpreted together, they are also available separately to accommodate various clinical situations and tumor types. These tests can provide helpful diagnostic information when evaluating an individual suspected of having HNPCC/Lynch syndrome, especially when testing is performed in conjunction with MSI / Microsatellite Instability (MSI), Tumor and Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor studies. It should be noted that these tests are not genetic tests, but rather stratify the risk of having an inherited cancer predisposition and identify patients who might benefit from subsequent genetic testing.


See Lynch Syndrome Testing Algorithm in Special Instructions.

Reference Values

An interpretative report will be provided.


An interpretive report will be provided. The likelihood of a germline (inherited) mutation is very low in those cases where the tumor demonstrates MLH1 promoter hypermethylation and the normal tissue is unmethylated. The likelihood of a germline mutation is high in those cases where the tumor and normal tissue lack MLH1 promoter hypermethylation. In cases where the tumor and normal tissue demonstrate MLH1 promoter hypermethylation, this result will be interpreted as equivocal and a blood sample will be requested to confirm potential germline hypermethylation.

Clinical Reference

1. Cunningham JM, Kim CY, Christensen ER, et al: The frequency of hereditary defective mismatch repair in a prospective series of unselected colorectal carcinomas. Am J Hum Genet 2001;69:780-790

2. Wang L, Cunningham JM, Winters JL, et al: BRAF mutations in colon cancer are not likely attributable to defective DNA mismatch repair. Cancer Res 2003;63:5209-5212

3. Domingo E, Laiho P, Ollikainen M, et al: BRAF screening as a low-cost effective strategy for simplifying HNPCC genetic testing. J Med Genet 2004;41:664-668

4. Bettstetter M, Dechant S, Ruemmele P, et al: Distinction of hereditary nonpolyposis colorectal cancer and sporadic microsatellite-unstable colorectal cancer through quantification of MLH1 methylation by real-time PCR. Clin Cancer Res 2007;13:3221-3228

Day(s) and Time(s) Performed

Weekly; Varies

Analytic Time

7 days

Test Classification

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 U.S. Food and Drug Administration.

CPT Code Information




LOINC Code Information

Test ID Test Order Name Order LOINC Value
ML1HM MLH1 Hypermethylation Analys, Tumor In Process


Result ID Test Result Name Result LOINC Value
53299 Result Summary 50397-9
53300 Result 82939-0
53301 Interpretation 69047-9
53302 Reason for Referral 42349-1
53303 Specimen 31208-2
53304 Source 85298-8
54447 Tissue ID 80398-1
53305 Released By 18771-6


1. Molecular Genetics: Inherited Cancer Syndromes Patient Information (T519) in Special Instructions

2. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Gastroenterology and Hepatology Client Test Request (T728)

-Oncology Test Request (T729)

Mayo Clinic Laboratories | Gastroenterology Catalog Additional Information: