Microsatellite instability (MSI)

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What is MSI testing?

It is a test that identifies microsatellite instability (looks at DNA microsatellite length changes) in tumor tissue for cancer diagnostics and treatment (colorectal cancer, endometrial cancer, and several other solid tumors).

DNA mismatch repair (MMR ) system —

is a highly conserved biological system that recognizes, removes, and repairs erroneous base-base mismatches and insertion/deletion mispairs generated during DNA replication and recombination.

When the MMR system is deficient (dMMR), many mismatch errors accumulate, leading to genome-wide instability and the appearance of mutations — triggers of cancerogenesis. MMR system includes proteins: [1]:

MSH2 MLH1 MLH3 PMS1 MSH6 PMS2 MSH3 Exo1

DNA microsatellites

Microsatellites are short, organized by tandems, repetitive DNA segments that consist of 1 to 4 base pairs distributed throughout the human genome in both coding and non-coding regions. Due to their repetitive structure, microsatellites are particularly prone to DNA replication errors [1].

Microsatellite instability (MSI)

MSI is a genome instability/alterations due to defects in the MMR system (dMMR) characterized by a wide range of microsatellite repeat length polymorphisms. Defects in the DNA MMR system can be caused by germline (congenital, Lynch syndrome) and somatic and epigenetic changes.

Lynch syndrome (LS)

Lynch syndrome is a genetic disorder associated with an increased risk of developing several cancers such as colorectal, endometrial, gastric, and ovarian.

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Why MSI testing is necessary?

3.8%

of solid malignant tumors

20%

of colorectal and gastric cancers

26%

of endometrial cancers

are characterized by microsatellite instability (MSI-H/high status), i.e., have defects in the DNA mismatch repair system (dMMR).

90%

of colorectal cancers caused by Lynch syndrome also have MSI -high status (MSI-H)

Распространенность MSI-H в различных опухолях *

*Bonneville R, Krook MA, Kautto EA, Miya J, Wing MR, Chen HZ, Reeser JW, Yu L, Roychowdhury S. Landscpe of Microsatellite Instability Across 39 Cancer Types.
JCO Precis Oncol. 2017;2017:PO.17.00073. dol: 10.1200/PO.17.00073. Epub 2017 Oct 3. PMID: 29850653; PMCID: PMC5972025.

Zoom in on the graph

Ministry of Health of the Russian Federation and NCCN (National Comprehensive Cancer Network, USA) guidelines recommend MMR/MSI testing for the patients with colorectal and endometrial cancers for:

cancer prognosis,
to define treatment options,
as a screening test for Lynch Syndrome [4, 9].

dMMR/MSI-High in tumor considers as:

A marker of cancer prognosis
A predictive marker that determines:
- the effectiveness of fluoropyrimidine adjuvant therapy,
- sensitivity to immune checkpoint inhibitors therapy (pembrolizumab, nivolumab, etc.).

A screening test for Lynch Syndrome.. Patients with MSI-H tumors who meet the Bethesda/Amsterdam II diagnostic criteria should be advised to consider Lynch syndrome genetic testing in blood samples.

How does MMR/MSI testing perform?

Two methods are widely used for MMR system deficiency detection:

Immunohistochemistry (IHC)

The expression assessment of 4 proteins encoded by MMR system genes: MLH1, MSH2, MSH6, and PMS2. The negative result is the presence of expression of all 4 proteins, which means the DNA MMR system is not deficient. Loss of expression of ≥1 proteins is defined as a defect in the MMR system, and the sample is scored as MMR-defective (dMMR, positive result).

PCR and quantitative capillary fluorescence electrophoresis [8]

Assessment of changes in the lengths of certain microsatellite repeats. Panels of microsatellite markers can vary from manufacturer to manufacturer and can include from 5-7 or more microsatellite repeats.

Differences in the composition and number of markers in the panel determine differences in the sensitivity and specificity of the test.

90%

expected specificity of detecting cases of Lynch Syndrome by MSI-status assessment by PCR

85%

sensitivity of the method

The following results of the MSI status assessment are accepted:

MSI-stable/MSI-S — no loci with instability
MSI-low/MSI-L
MSI-high (unstable)/MSI-H

However, recently, MSI-stable and MSI-low results are merged into MSI-stable status, with the conclusion indicating that no microsatellite instability was detected.

Laboratory First Genetics conducts MSI testing on the expanded panel of markers consisting of:

13 microsatellite loci

BAT‑25

BAT‑26

BAT‑40

CAT‑25

NR‑21

NR‑22

NR‑24

NR‑27

ABI‑16

ABI‑17

ABI‑19

ABI‑20A

ABI‑20B

2 highly polymorphic pentanucleotide loci for sample identification

PentaD

TH‑01

Pros of using the expanded panel for MSI testing

No additional control of normal tissue

No need to use healthy tissue/blood of the patient for control
Small amount of raw DNA

Only 2 ng of paraffin-embedded DNA (FFPE) needed