What are the 5 specific genes examined in the Microsatellite Instability (MSI) Polymerase Chain Reaction (PCR) test?

Microsatellite Instability PCR Test: The 5 Genes Examined

The MSI PCR test examines five specific microsatellite markers: BAT-25, BAT-26, NR-21, NR-24, and NR-27, which is the recommended panel due to its higher sensitivity and specificity compared to older panels. 1

Standard MSI PCR Panels

There are two primary panels used in MSI PCR testing:

1. Current Recommended Panel (Pentaplex Mononucleotide Panel):

   • BAT-25
   • BAT-26
   • NR-21
   • NR-24
   • NR-27

2. Original NCI/Bethesda Panel:

   • BAT-25 (mononucleotide)
   • BAT-26 (mononucleotide)
   • D5S346 (dinucleotide)
   • D2S123 (dinucleotide)
   • D17S250 (dinucleotide)

Why the Pentaplex Mononucleotide Panel is Superior

The five poly-A mononucleotide repeat panel has become the current standard because:

• It demonstrates higher specificity and sensitivity in MSI testing 1
• It may obviate the need for normal tissue for comparison 1, 2
• It provides more consistent results across different populations 2

In a comprehensive multipopulation analysis of 1,206 individuals from 55 different populations worldwide, the pentaplex panel showed remarkable consistency, with 87.5% of individuals showing no variant alleles 2.

Clinical Application and Interpretation

MSI is defined as loss of stability in 2 or more of the 5 microsatellite markers 1. This testing is particularly important for:

• Identifying Lynch syndrome and other hereditary cancer syndromes
• Determining prognosis in colorectal and other cancers
• Guiding immunotherapy decisions

A simplified 3-marker assay (BAT-25, BAT-26, and D2S123) has been proposed by some researchers as potentially more accurate for identifying patients with favorable prognosis 3, but the 5-marker panel remains the standard recommendation in clinical guidelines.

Complementary Testing

While MSI PCR is highly sensitive (99.3% in gastric cancers), it is often used in conjunction with immunohistochemistry (IHC) for mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2) 4. The consensus panel from ESMO recommends using both MMR-IHC and MSI-PCR to assess eligibility for treatment with immune checkpoint inhibitors in metastatic colorectal cancer and other cancers of the Lynch syndrome spectrum 1.

Important Considerations

• MSI-low tumors should be included with microsatellite stable tumors, as they have similar clinical behavior 1
• In cases of discordant or indeterminate results between MSI PCR and IHC, complementary testing is required 4
• Next-generation sequencing (NGS) represents an alternative molecular test to assess MSI and has the advantage of simultaneously determining tumor mutational burden 1

MSI testing has significant implications for patient outcomes, as MSI-high tumors generally have more favorable prognosis and may respond differently to certain chemotherapy regimens 5.