Microsatellite Instability (MSI) PCR Test
Short Name: MSI PCR Test
Also known as: MSI Test, Microsatellite Instability Test, MSI-High Test, Mismatch Repair Deficiency Test, MSI PCR Analysis
Microsatellite Instability (MSI) PCR Test test available at DNA Labs India for ₹16,000. Uses Polymerase Chain Reaction (PCR), Fragment Analysis on FFPE Tissue Block samples. Results in Results are available within 10 working days from the date of sample receipt at the laboratory.. Free home collection in 300+ cities across India.
🩺 Medically Reviewed By
Dr Pasupathy Arumugam
Consultant Pathologist · Reg: 21521
Last reviewed: September 7, 2026
Overview
The primary purpose of the MSI PCR test is to detect microsatellite instability in tumor DNA, which helps in: 1. Identifying patients with Lynch syndrome (hereditary nonpolyposis colorectal cancer) and guiding genetic counseling and family screening. 2. Determining eligibility for immune checkpoint inhibitor immunotherapy (e.g., pembrolizumab) in MSI-High tumors. 3. Stratifying prognosis in colorectal, endometrial, gastric, and ovarian cancers. 4. Guiding treatment decisions, including the potential avoidance of adjuvant 5-fluorouracil-based chemotherapy in stage II MSI-High colorectal cancers. 5. Distinguishing sporadic from hereditary causes of MMR deficiency when combined with BRAF V600E mutation testing and MLH1 promoter methylation analysis.
- Test Code
- 1256
- CPT Code
- 81301
- ICD Code
- D48.9
- Price
- ₹16,000
- Sample Type
- FFPE Tissue Block
- Result Time
- Results are available within 10 working days from the date of sample receipt at the laboratory.
- Fasting Required
- No
- Method
- Polymerase Chain Reaction (PCR), Fragment Analysis
Sample Collection
No special preparation or fasting is required. Ensure the FFPE tissue block is available from the pathology laboratory where the biopsy or surgery was performed. A completed test requisition form with clinical history should accompany the sample.
Method: Surgical resection or biopsy tissue preserved in formalin-fixed paraffin-embedded (FFPE) block
Laboratory Analysis
The FFPE tissue block or a minimum of 10 unstained slides (5-10 micron thickness) from the block are collected. If normal tissue comparison is needed, a paired normal tissue block or blood sample may also be requested. The sample is labeled, sealed, and transported at room temperature to the testing laboratory.
Report Delivery
After the tissue block or slides are submitted, the laboratory performs DNA extraction, PCR amplification of the 5 microsatellite markers, and capillary electrophoresis for fragment analysis. Results are available within 10 working days and delivered via online portal, email, or WhatsApp.
Timeline: Results are available within 10 working days from the date of sample receipt at the laboratory.
Patient Instructions
About This Test
Who Should Get This Test
The primary purpose of the MSI PCR test is to detect microsatellite instability in tumor DNA, which helps in:
1. Identifying patients with Lynch syndrome (hereditary nonpolyposis colorectal cancer) and guiding genetic counseling and family screening.
2. Determining eligibility for immune checkpoint inhibitor immunotherapy (e.g., pembrolizumab) in MSI-High tumors.
3. Stratifying prognosis in colorectal, endometrial, gastric, and ovarian cancers.
4. Guiding treatment decisions, including the potential avoidance of adjuvant 5-fluorouracil-based chemotherapy in stage II MSI-High colorectal cancers.
5. Distinguishing sporadic from hereditary causes of MMR deficiency when combined with BRAF V600E mutation testing and MLH1 promoter methylation analysis.
How to Prepare
- Submit the FFPE tissue block or minimum 10 unstained sections (5-10 microns) from the tumor
- Ensure the requisition form includes patient details, tumor type, and clinical history
- Label all slides and containers clearly with patient name and ID
- If a paired normal tissue sample is requested, submit it alongside the tumor sample
- Transport the sample at room temperature; avoid extreme heat or moisture
Doctor's Notes
Reviewed by Dr Pasupathy Arumugam — MBBS, MD (Pathology) · Reg. No. 21521
"Microsatellite instability testing has become a cornerstone of precision oncology. Identifying MSI-High status in a tumor not only aids in diagnosing Lynch syndrome and guiding surveillance for at-risk family members but also opens the door to immunotherapy with immune checkpoint inhibitors such as pembrolizumab. I recommend MSI PCR testing for all newly diagnosed colorectal and endometrial cancers, and in any tumor type where immunotherapy is being considered. Early identification of MSI-High status can significantly change treatment strategy and improve patient outcomes."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Completely necrotic tumor tissue with no viable cells
- Decalcified tissue with severely degraded DNA
- FFPE block with less than 10% tumor cellularity
- Unlabeled or mislabeled samples
- Samples without a completed requisition form
Understanding Your Results
MSI-High (≥2 unstable markers)
The tumor demonstrates high microsatellite instability, indicating a deficient mismatch repair (dMMR) system. This is seen in approximately 90% of Lynch syndrome-associated colorectal cancers and about 15% of sporadic colorectal cancers. MSI-High tumors generally have a better prognosis in early-stage disease and may respond to immune checkpoint inhibitors such as pembrolizumab. Further testing (MLH1 promoter methylation, BRAF V600E) is recommended to distinguish sporadic from hereditary causes.
Action: Genetic counseling and germline testing for Lynch syndrome should be considered. Immunotherapy eligibility should be discussed with the treating oncologist.
MSI-Low (1 unstable marker)
Only one of five markers shows instability. This intermediate category is found in a small percentage of tumors and may indicate borderline MMR deficiency. Additional testing with immunohistochemistry (IHC) for MMR proteins is recommended for clarification.
Action: Correlate with IHC results. Consider expanded molecular testing if clinical suspicion for Lynch syndrome is high.
MSS — Microsatellite Stable (0 unstable markers)
No microsatellite instability detected. The tumor has a proficient mismatch repair (pMMR) system. MSS tumors are unlikely to be associated with Lynch syndrome and may not respond as favorably to immune checkpoint inhibitor monotherapy.
Action: Standard treatment protocols apply. Lynch syndrome is unlikely but not completely excluded if family history is strongly suggestive — consider germline genetic testing.
Consult your oncologist if your MSI PCR test result is MSI-High or MSI-Low, as these findings directly impact treatment decisions including immunotherapy eligibility and the need for genetic counseling for Lynch syndrome. If you have a strong family history of colorectal, endometrial, gastric, or ovarian cancers, discuss genetic testing with your physician regardless of MSI status.
Limitations
- ⚠MSI PCR detects instability at only 5 specific loci and may not capture all cases of MMR deficiency
- ⚠This test requires tumor tissue; it cannot be performed on blood samples alone
- ⚠MSI-Low results may require additional testing (IHC or expanded panels) for definitive classification
- ⚠The test does not distinguish between germline (Lynch syndrome) and sporadic causes of MSI without supplementary testing such as MLH1 promoter methylation or BRAF V600E mutation analysis
- ⚠Newer NGS-based panels may detect MSI from broader genomic data and may be more sensitive in borderline cases
Risks & Considerations
- ●There are no physical risks to the patient as the test is performed on an already collected tissue sample
- ●In rare cases, the tissue sample may have insufficient DNA quality or quantity, requiring re-submission of the sample
- ●False-negative results are possible if tumor cellularity is low in the submitted sample
Interfering Factors
- ●Excessive necrosis in the tumor tissue sample may yield insufficient viable DNA
- ●Decalcified tissue samples may produce degraded DNA affecting PCR amplification
- ●Small biopsy samples may have insufficient tumor cell content
- ●DNA degradation due to improper storage or prolonged fixation in formalin
- ●Low tumor cellularity in the FFPE block (minimum 20% tumor content recommended)
Compare With Similar Tests
| Test | Microsatellite Instability (MSI) PCR Test | Immunohistochemistry (IHC) for MMR Proteins | NGS-Based MSI Detection | MLH1 Promoter Methylation Test |
|---|---|---|---|---|
| Comparison | Microsatellite Instability (MSI) PCR Test | IHC detects loss of MMR protein expression (MLH1, MSH2, MSH6, PMS2) by staining tumor tissue. It is faster and less expensive than MSI PCR but may miss some MSI-High cases. Both tests are complementary and often used together in clinical practice. | Next-generation sequencing (NGS) panels can detect MSI using hundreds of microsatellite loci, providing greater sensitivity. NGS is typically performed as part of a comprehensive genomic profiling panel and may identify MSI that the 5-marker PCR panel misses. | This test determines whether MLH1 gene silencing is due to promoter hypermethylation (sporadic cause) rather than germline mutation (Lynch syndrome). It is recommended when MSI-High status is detected to differentiate hereditary from sporadic MSI. |
Frequently Asked Questions
What is the Microsatellite Instability (MSI) PCR Test?
Why is the MSI PCR test performed?
What sample is required for the MSI PCR test?
Does the MSI PCR test require fasting or special preparation?
What does MSI-High mean in the test results?
What is the difference between MSI PCR and immunohistochemistry (IHC) for MMR proteins?
How long does it take to get MSI PCR test results?
Is the MSI PCR test the same as a genetic test for Lynch syndrome?
Can MSI-High tumors be treated with immunotherapy?
What is the cost of the MSI PCR test at DNA Labs India?
Is the MSI PCR test available in my city?
Is the MSI PCR test covered by health insurance in India?
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