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Highly sensitive duplex MSI test and BAT40 germline polymorphism.

So Young Kang1, Kyoung-Mee Kim1,2

  • 1Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine.

APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica
|August 3, 2021
PubMed
Summary
This summary is machine-generated.

A new triplex PCR test using BAT26 and CAT25 markers accurately identifies microsatellite instability (MSI) in Korean cancer patients, offering a simpler alternative to pentaplex assays. This method shows promise for predicting response to immune checkpoint blockade therapy.

Keywords:
BAT26CAT25microsatellite instabilitymononucleotide repeatpolymorphismtumor mutation burden

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Area of Science:

  • Oncology
  • Molecular Diagnostics
  • Genetics

Background:

  • Tumors with DNA mismatch repair deficiency and microsatellite instability (MSI) respond to immune checkpoint blockade.
  • Current pentaplex MSI assays have limitations, including marker sensitivity issues, and require validation in diverse populations.
  • Previous MSI marker studies primarily focused on Western populations.

Purpose of the Study:

  • To evaluate the efficacy of a triplex PCR assay using BAT26, CAT25, and BAT40 MSI markers in a Korean advanced cancer patient cohort.
  • To compare the triplex assay results with a standard pentaplex MSI test and tumor mutation burden (TMB).
  • To assess the clinical utility of a simplified duplex MSI test (BAT26 and CAT25) in this population.

Main Methods:

  • A triplex PCR assay (BAT26, CAT25, BAT40) was performed on 300 Korean advanced cancer samples.
  • Results were compared against a pentaplex MSI test and TMB status.
  • Further validation was conducted on 60 additional MSI-high (MSI-H) cancers, including analysis of BAT40 germline polymorphism.

Main Results:

  • The triplex PCR identified 1.3% of tumors as MSI-high.
  • BAT40 showed high instability (21%) but was attributed to common germline polymorphisms (90%) in the Korean population, associated with higher TMB.
  • A duplex assay (BAT26 and CAT25) demonstrated 100% concordance with the pentaplex assay in validation cohorts, showing equivalent sensitivity and specificity.

Conclusions:

  • The triplex PCR assay, particularly a duplex (BAT26 and CAT25) approach, is a sensitive and specific method for MSI detection in Korean cancer patients.
  • BAT40 instability in this cohort is largely due to germline polymorphism, not true MSI, and is linked to increased TMB.
  • This simplified MSI testing method can aid in patient selection for immune checkpoint blockade therapies.