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Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel.

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Cell-free DNA (cfDNA) sequencing accurately detects microsatellite instability (MSI) in pan-cancer patients, showing high concordance with tissue tests. This advances immunotherapy access for advanced cancers.

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Area of Science:

  • Oncology
  • Genomics
  • Molecular Diagnostics

Background:

  • Microsatellite instability (MSI) is a key biomarker for immunotherapy response.
  • Current tissue-based MSI testing can be limited in accessibility and application.
  • Cell-free DNA (cfDNA) offers a minimally invasive alternative for molecular profiling.

Purpose of the Study:

  • To analytically and clinically validate MSI detection using cfDNA sequencing.
  • To assess the performance of Guardant360 for pan-cancer MSI detection.
  • To investigate the clinical utility of cfDNA-based MSI in advanced cancers.

Main Methods:

  • Analytical validation of Guardant360 for MSI detection according to guidelines.
  • Clinical validation using 1,145 cfDNA samples with matched tissue MSI status.
  • Pan-cancer MSI landscape analysis in 28,459 plasma samples.
  • Evaluation of immunotherapy outcomes in 16 cfDNA MSI-H gastric cancer patients.

Main Results:

  • cfDNA MSI detection demonstrated high specificity, precision, and sensitivity (0.1% limit of detection).
  • Overall accuracy for cfDNA MSI detection was 98.4% compared to tissue testing (87% MSI-H, 99.5% MSS).
  • Concordance of cfDNA MSI with tissue PCR and NGS was superior to IHC.
  • Significant clinical activity of immunotherapy was observed in cfDNA MSI-H advanced gastric cancer patients (63% remission).

Conclusions:

  • cfDNA-based MSI detection using Guardant360 is highly accurate and concordant with tissue testing.
  • This method enables concurrent comprehensive genomic profiling and expands immunotherapy access.
  • cfDNA MSI testing addresses limitations of current practices for advanced cancer patients.