Abstract: A genomic data processing system can be configured to process next-generation sequencing information. The genomic data processing system described herein can accurately detect mutations in nucleic acid (e.g., cell free DNA (cfDNA) sequence reads associated with plasma nucleic acid samples. The genomic data processing system of the present disclosure also detects microsatellite instability in nucleic acid sequence reads with a higher degree of sensitivity compared to existing genomic data processing systems.