Microsatellite instability testing

Published 21/06/2010

Microsatellite instability

No of
detectable
markers:

Lab method:

Fragment analysis

TAT:

3 weeks

Specimen requirements:

Paraffin-embedded, formalin-fixed block of tumor tissue from colon and normal tissue

The best material of tumor tissue is pre-treatment biopsy.
The best material of normal tissue is surgical resection or 2-4 ml of blood (with anticoagulant EDTA).
Storage and transport temperature for paraffin-embedded, formalin-fixed tissue blocks is 20-25°C.
Testing results cannot be guaranteed when DNA quality is poor or DNA is too fragmented due to previous tissue fixation process.

Ordering information:

Go to online ordering or download sample submission form

Indications for genetic testing:

1. Testing of individuals with colorectal or other Lynch-associated cancers to estimate the probability of mutations in mismatch repair genes
2. Determination of disease prognosis
3. Genetic counseling

Microsatellite instability (MSI) is the mutational signature found in colorectal cancers that evolve as a result of inactivation of the DNA mismatch repair system. Defects in the genes involved in mismatch repair lead to an accumulation of somatic mutations in a cell, which may result in the cell becoming malignant. Germline mutations in mismatch repair genes are associated with developing hereditary non-polyposis colon cancer. Approximately 90% of colon cancers from families meeting Amsterdam criteria have MSI.

Lynch Syndrome/Hereditary Non-Polyposis Colon Cancer – HNPCC

Published 22/04/2010

Lynch Syndrome
NGS panel

Genes
(full coding
region):

MLH1, MSH2, MSH6

Lab method:

NGS panel with CNV analysis

TAT:

6-9 weeks

Specimen requirements:

2-4 ml of blood with anticoagulant EDTA

1 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.

Ordering information:

Go to online ordering or download sample submission form

Single Gene Sequencing

Genes:

MLH1, MSH2, MSH6

Lab method:

Sanger sequencing

TAT:

2-4 weeks

Specimen requirements:

2-4 ml of blood with anticoagulant EDTA

2 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.

Ordering information:

Go to online ordering or download sample submission form

Deletion/duplication analysis

Genes:

MLH1, MSH2, MSH6

Lab method:

MLPA

TAT:

4-6 weeks

Specimen requirements:

2-4 ml of blood with anticoagulant EDTA

2,5 µg DNA in TE, AE or pure sterile water at 100-250 ng/µl
The A260/A280 ratio should be 1.8-2.0. DNA sample should be run on an agarose gel as a single band, showing no degradation, alongside with a quantitative DNA marker.

Ordering information:

Go to online ordering or download sample submission form

Referral for molecular testing of Lynch syndrome:

Tumour tissue analysis to evaluate the MMR proteins expression by immunohistochemical analysis (IHC) and DNA microsatellite instability (MSI) testing is suggested for the individuals meeting Amsterdam II/Bethesda criteria.
If absence of the MLH1/PMS2 proteins expression is observed by IHC, methylation analysis of the MLH1 gene promoter and/or testing of the somatic BRAF V600E mutation is recommended in order to exclude sporadic colorectal cancer cases.
If tumour with MMR deficiency and MSI high is detected, further mutation analysis from peripheral blood/normal tissue of the MMR genes is indicated.

Indications for mutation analysis:

1. Testing of individuals meeting Amsterdam II/Bethesda criteria
2. Testing of individuals with family history of colorectal cancer or other Lynch syndrome-related cancers
3. Testing of at-risk family members for known mutations
4. Genetic counseling

Lynch syndrome, also called hereditary non-polyposis colon cancer (HNPCC), is characterized by an increased risk of colon cancer and other cancers (e.g., of the endometrium, ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, and skin). Lynch syndrome is inherited in an autosomal dominant manner and it is associated with germline mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. Mutation carriers have a lifetime risk of up to 80% for colorectal cancer, 20-60% risk of endometrial cancer, as well as other tumors. Lynch syndrome is associated with early onset of cancer, the average age of diagnosis is 45 years.