Identification of somatic or germline origin for cell-free DNA

A method of identifying a germline origin or a somatic origin of a genetic variant comprising:

• allocating a read budget of sequence reads that specifies a first number of sequence reads directed to a backbone sub-panel that interrogates a plurality of backbone genomic loci and a second number of sequencing reads directed to a hotspot sub-panel that interrogates a plurality of hotspot genomic loci, wherein the second number is selected to achieve a user-defined lower-limit-of-detection;
• a) receiving, from a sequencer, sequence data indicative of a plurality of sequence reads of cfDNA molecules generated in accordance with the allocated read budget, wherein the sequence data comprises sequence data for the plurality of backbone genomic loci and the plurality of hotspot genomic loci;
• b) processing, using a computer, the sequence data to:
• (i) for each of the plurality of backbone genomic loci, obtain an allele fraction (AF) measure and a measure of AF variability,
• (ii) bin the plurality of backbone genomic loci based on a presumed origin, and
• (iii) using the AF measures and the measures of AF variability of the binned plurality of backbone genomic loci, determine an AF variability threshold such that backbone genomic loci of the binned plurality of backbone genomic loci having AF variability above the AF variability threshold are designated high copy number loci and backbone genomic loci of the binned plurality of backbone genomic loci having AF variability below the AF variability threshold are designated low copy number loci and an AF threshold that separates germline from somatic AF distributions associated with the backbone genomic loci of the binned plurality of backbone genomic loci designated as the low copy number loci;
• c) for a variant detected at any hotspot genomic locus of the plurality of hotspot genomic loci, obtaining, using a computer, a variant AF and a variant AF variability, and comparing the variant AF variability against the AF variability threshold to identify the variant with the measure of variant AF variability below the AF variability threshold as having low copy number;
• and
• d) based on the variant having a low copy number, identifying germline origin or somatic origin for the variant by comparing, using a computer, the variant AF against the AF threshold, wherein,
• the variant is germline origin if the variant AF is above the AF threshold, and
• the variant is somatic origin if the variant AF is below the AF threshold.