A robust method for the rapid detection of microsatellite instability in colorectal cancer

Although several computational tools using next-generation sequencing (NGS) data have been proposed to detect microsatellite instability (MSI) status, they still have limitations and need improvement. We developed a NovoPM-MSI method to detect MSI status based on NGS data. This method evaluated target mononucleotide microsatellite loci that were sequenced during targeted gene enrichment analysis and reported sample instability score as the fraction of unstable loci within the target set after assessing locus instability by comparing length distribution in paired tumor-normal samples. We validated this method against the conventional MSI-PCR method in 113 paired colorectal cancer (CRC) specimens and compared the performance of NovoPM-MSI to that of mSINGS and MANTIS in accuracy and runtime efficiency. By using the MSI status from MSI-PCR as the gold standard, the three computational methods showed the same sensitivity of 88.9% but different specificities (NovoPM-MSI 97.1%, MANTIS 86.5% and mSINGS 99.0%). Only NovoPM-MSI could greatly improve both the sensitivity and specificity by setting an ambiguous interval. MANTIS had the shortest average runtime (16.3 sec), followed by NovoPM-MSI (18.3 sec) and mSINGS (109.0 sec). In short, the NovoPM-MSI method provides a fast and reliable MSI detection method with accuracy comparable to MSI-PCR in paired CRC samples.