Methods and Systems for Analyzing Nucleic Acid Molecules

The method comprises determining a state of the condition based on identification of a set of cell-free nucleic acid molecules from a plurality of said molecules obtained from the subject and comparing that to a second set obtained subsequently; and determining the progress of the condition based on the comparison, wherein the molecules are a plurality of phased variants relative to a reference genomic sequence that are separated by at least one nucleotide, captured by a set of nucleic acid probes that hybridise to genomic regions associated with the condition, as noted in Tables 1 and 3. The condition may be B cell lymphoma. The phased variants may comprise a single nucleotide variant that is at least 2 nucleotides away from an adjacent SNV. The nucleic acid probes may be designed based on the variants that identified by sequencing data from a tumour, lymphoma or healthy subject.