Methods and systems for detecting MSI are provided. Also provided are methods for enriching human
genomic DNA for
microsatellite loci. Additionally, an
oligonucleotide array for detecting MSI is provided. In some embodiments, the method for detecting MSI comprises detecting sequencing reads from a sample for a plurality of
microsatellite loci; determining a metric for repeat
length distribution (RLD) for each
microsatellite locus; comparing the metric to a threshold value for the microsatellite locus; quantifying the number of microsatellite loci having an RLD metric exceeding the threshold value; and comparing the number of microsatellite loci having an RLD metric exceeding the threshold value to a
microsatellite instability (MSI) proportion threshold.