Microsatellite instability (MSI) is a powerful predictor for the efficacy of immune checkpoint inhibitor (ICI) therapy across tumor types. Although conventional MSI testing strategies are widely used, NGS represents a promising tool for MSI detection. We have developed and validated the NGS test system for MSI detection in solid tumors.
The following sample types were selected for validation of our test system: G1 - archive FFPE tumor samples collected from patients with known MSI status; G2 - archive paired (FFPE/ctDNA) samples collected from patients with tumors where MSI is uncommon (<1%); G3 - paired (FFPE/ctDNA) MSI+ samples. All FFPE samples were tested using the gold standard (5-loci PCR, 4-antibody IHC). Samples were considered MSI+ if PCR or IHC were positive; MSI- when both were negative. Detection of MSI was performed using k-mer distributions of 28 loci.
A total of 123 samples for 109 patients were analyzed - 77 (62.6%) FFPE, 46 (37.4%) ctDNA; 6 patients had paired samples. A total of 30 (FFPE, 83% CRC), 72 (41 FFPE, 31 ctDNA; 62.3% NSCLC) and 21 (6 patients; 6 FFPE, 15 ctDNA; 66.7% CRC) were selected for G1, G2 and G3, respectively. Rate of agreement (κ) between NGS and gold standard in G1 was 0.8 (95% CI, 0.58-1) [κ for NGS/PCR 0.93 (95% CI, 0.8-1)], and 1 in G3. In G2, 100% of samples were MSS following NGS. In G3, for all 6 samples there were no disagreements between NGS and gold standard. Across all analyzed FFPE samples, κ between NGS and gold standard was 0.9 (95% CI 0.88-0.92). When comparing results of PCR and IHC (FFPE samples), low concordance was noted (κ=0.5, 95% CI, 0.22-0.78). High concordance was observed between PCR and NGS (κ=0.94, 95% CI, 0.83-1). Concordance of IHC and NGS was low (κ=0.55, 95% CI, 0.28-0.83). Sensitivity / specificity of NGS vs IHC in detecting MSI were 76.2% / 80%. Sensitivity / specificity of NGS vs PCR were 95.5% / 100%. Sensitivity / specificity of NGS in detecting MSI using ctDNA vs FFPE were 100% / 100%.
Low concordance was observed between IHC and PCR for MSI detection (κ=0.5, 95% CI, 0.22-0.78). Concordance of PCR and NGS was high (κ=0.94, 95% CI, 0.83-1); concordance between IHC and NGS was lower (κ=0.55, 95% CI, 0.28-0.83). Sensitivity of MSI detection using ctDNA was 100%.
Clinical trial identification
Legal entity responsible for the study
This study was supported by Russian Science Foundation (grant № 22-75-10154).
All authors have declared no conflicts of interest.