Methods for detecting nucleic acid variants

A method for detecting a disease based on single nucleotide variants identified from sequencing, comprising:

• selecting a set of single nucleotide variants (SNV) loci from a disease-associated SNV locus panel, wherein the disease-associated SNV locus panel is generated by sequencing a nucleic acid sample derived from diseased tissue from a subject;
• obtaining a cell-free nucleic acid sequencing data set, wherein the cell-free nucleic acid sequencing data set is generated by sequencing a cell-free nucleic acid sample from the subject using non-terminating nucleotides provided in separate flow positions according to a flow-cycle order;
• determining a fraction value by processing a total number of SNV reads detected at the set of SNV loci in the cell-free nucleic acid sequencing data set, a number of loci selected in the set of SNV loci, a mean sequencing depth of the cell-free nucleic acid sequencing data set, and a sequencing false positive error rate;
• and
• calling a presence, absence, progression, or regression of the disease in the subject based on the fraction value or a degree of change in the fraction value from a prior fraction value determined for the subject.