Microsatellite Instability Status

The DRAGEN microsatellite instability status (MSI) module assesses microsatellite sites for evidence of microsatellite instability, relative to a set of baseline normal samples that are based on Jensen– Shannon (JS) distance (an information entropy metric). In total, there are 2343 selected MSI sites with 6 or 7 single nucleotide repeats in the panel. For MSI sites with 500 or more spanning duplex collapsed reads, JS distance is calculated using a test sample vs baseline normal samples, and then any two baseline normal samples. If the JS distance is significantly higher in the test sample vs baseline normal with p-value ≤ 0.01 and the JS distance difference is ≥ 0.02, the site is considered unstable. The final MSI score aggregates all JS distance across all unstable sites. The input is the BAM file from the DNA alignment and read collapsing step, and the output is an MSI metric file.