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Updated: Jun 29, 2025

Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
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Microsatellite Instability Detection in Cancer: A Multiplex qPCR Approach that Obviates the Need for Matching Normal

Wei Chen1, Yan Helen Yan1, Blake Young1

  • 1NuProbe USA, R&D and Innovation Department, Houston, TX, United States.

Clinical Chemistry
|April 6, 2024
PubMed
Summary
This summary is machine-generated.

VarTrace, a new quantitative PCR assay, accurately detects microsatellite instability (MSI) in tumor DNA without normal samples. This rapid, low-cost method improves MSI testing efficiency, especially for low tumor percentages.

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Area of Science:

  • Molecular Biology
  • Oncology
  • Genetics

Background:

  • Microsatellite instability (MSI) signifies DNA mismatch repair deficiency in cancers like colorectal cancer.
  • Current PCR-capillary electrophoresis (CE) methods require normal samples and specialized equipment.
  • VarTrace, a quantitative PCR (qPCR) assay, was developed to assess MSI using only tumor DNA.

Purpose of the Study:

  • To develop and validate VarTrace, a rapid, low-cost qPCR assay for MSI detection.
  • To eliminate the need for matching normal DNA samples in MSI testing.
  • To assess VarTrace's performance against a standard PCR-CE assay.

Main Methods:

  • 101 formalin-fixed paraffin-embedded (FFPE) tumor samples were tested with VarTrace and compared to the Promega OncoMate assay (PCR-CE).
  • Limit of detection was evaluated using contrived samples and synthetic reference standards.
  • Analytical sensitivity, specificity, and input requirements were assessed.

Main Results:

  • VarTrace successfully analyzed all 101 FFPE samples with 100% sensitivity and 98% specificity versus OncoMate.
  • The assay detected high MSI (MSI-H) with 97% accuracy down to 10% tumor.
  • Analytical studies showed a 5% variant allele frequency limit of detection and 0.5 ng input limit.

Conclusions:

  • VarTrace is a swift, accurate, and economical assay for MSI detection, even in samples with low tumor content.
  • The assay does not require matching normal DNA, simplifying the workflow.
  • VarTrace enhances MSI analysis sensitivity, potentially improving clinical workflow efficiency and test accessibility.