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Test ID: BRMLH MLH1 Hypermethylation and BRAF Mutation Analysis, Tumor

Useful For

An adjunct to MSI / Microsatellite Instability (MSI), Tumor and IHC / Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor testing, when colon 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 tumor from the same patient demonstrates MSI-H and loss of MLH1 protein expression

Profile Information

Test ID Reporting Name Available Separately Always Performed
PBMLH MLH1 Hypermethylation/BRAF Mutation No Yes

Additional Tests

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

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
BMLHH MLH1 Hypermethylation Analysis Yes, (order ML1HM) No
BBRAF BRAF Analysis Yes, (order BRAFD) No

Testing Algorithm

When this test is ordered, BRAF analysis and MLH1 hypermethylation analysis will always be performed. The exception would be if the tissue origin is an endometrial tumor; in those cases only the MLH1 hypermethylation analysis component will be performed.


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

Methylation-Specific Polymerase Chain Reaction (PCR) and Digital Droplet Polymerase Chain Reaction (ddPCR)

Reporting Name

MLH1 Hypermethylation/BRAF Mutation

Specimen Type


Advisory Information

This test is not recommended as a first-tier screening measure for Lynch syndrome. Please refer to MSI / Microsatellite Instability (MSI), Tumor and IHC / Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor.


This test will only be performed on colon tumors demonstrating loss of MLH1 protein expression.

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 both tumor and normal tissue.

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)

Clinical Information

Lynch syndrome is an inherited cancer syndrome caused by a germline pathogenic variant 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 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) etiology, 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 alteration 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 alteration is rarely identified in cases with germline MLH1 pathogenic variants. Thus, direct assessment of MLH1 promoter methylation status and testing for the BRAF V600E alteration can be used to help distinguish between germline etiologyand epigenetic/somatic inactivation of MLH1. Tumors that have the BRAF V600E alteration and demonstrate MLH1 promoter hypermethylation are almost certainly sporadic, whereas tumors that show neither are most often caused by an inherited (germline) pathogenic variant.


Although testing for the BRAF V600E alteration 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 Lynch syndrome, especially when testing is performed in conjunction with MSI / Microsatellite Instability (MSI), Tumor and IHC / Mismatch Repair (MMR) Protein Immunohistochemistry Only, Tumor. 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 interpretive report will be provided.


An interpretive report will be provided.

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

5. 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;17(9):1032-1041

Day(s) and Time(s) Performed

Varies; Varies

Analytic Time

7 days

CPT Code Information

Slide Review

88381-Microdissection, manual


81210-BRAF (v-raf murine sarcoma viral oncogene homolog B1) (eg, colon cancer), gene analysis, V600E variant, if appropriate

81288-MLH1 promoter methylation analysis, if appropriate

LOINC Code Information

Test ID Test Order Name Order LOINC Value
BRMLH MLH1 Hypermethylation/BRAF Mutation In Process


Result ID Test Result Name Result LOINC Value
53223 Result Summary 50397-9
53224 Result 82939-0
53225 Interpretation 69047-9
53226 Specimen 31208-2
53227 Source 31208-2
53228 Tissue ID 80398-1
55139 Method 49549-9
54921 BRAF Analysis No LOINC Needed
54440 MLH1 Hypermethylation Analysis No LOINC Needed
53229 Released By 18771-6

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.


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

2. If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.