Methods and systems for evaluating microsatellite instability status

A computer-readable media comprising machine-readable instructions that, when loaded in a machine-readable memory and executed by a processor, are configured to cause a system to perform a method for detecting microsatellite instability (MSI) in a sample, said method comprising:

• receiving a plurality of nucleic acid sequence reads corresponding to a plurality of marker regions for MSI, wherein each of the sequence reads includes a left flank sequence, right flank sequence and a repeat region of bases positioned between a rightmost base of the left flank sequence and a leftmost base of the right flank sequence, wherein the repeat region includes a number of repeats of a repeated sequence of bases corresponding to a particular marker region of the plurality of marker regions;
• for each sequence read corresponding to the plurality of marker regions for MSI, aligning at least a portion the left flank sequence with a reference left flank, wherein the reference left flank borders a reference repeat region of a reference nucleic acid sequence corresponding to the particular marker region;
• for the repeat region corresponding to a target homopolymer in the sequence reads, calculating a histogram of homopolymer signal values based on signal measurements for the target homopolymer, wherein at least a portion of the marker regions corresponds to target homopolymers;
• determining a score per marker by calculating a weighted sum of features of the histogram of homopolymer signal values for each marker region corresponding to the target homopolymers to produce a plurality of scores;
• applying a threshold score to the score per marker;
• and
• combining the plurality of scores to form a total MSI score for the sample.