Process for microsatellite instability detection

A method of detecting microsatellite instability (MSI), the method comprising:

• obtaining a sample comprising fragments of cell-free DNA (cfDNA) from a patient;
• attaching barcodes to the fragments, wherein at least some of the barcodes are not unique;
• sequencing the barcodes to obtain sequences of a plurality of markers in the DNA;
• determining a distribution of lengths of the plurality of markers;
• providing a report describing MSI in the patient when peaks in the distribution deviate from expected peaks in a modeled healthy or reference distribution.

A method of detecting micro satellite instability (MSI), the method comprising:

• obtaining fragments cell-free DNA (cfDNA) from a sample of plasma from a patient;
• sequencing portions of the cfDNA to obtain sequences of a plurality of tracts of nucleotide repeats in the cfDNA;
• assembling the sequences using information from endogenous barcodes at the starts and ends of the fragments;
• and
• providing a report describing an MSI status in the patient when a distribution of lengths of the plurality of tracts has peaks that deviate significantly from peaks in a reference distribution.