A method for quantifying DNA gene fusion molecules in a sample, comprising: (a) combining a test sample comprising cell-free DNA (cfDNA) obtained from the bloodstream of a human subject with a set of primers and a polymerase to produce a reaction mix, wherein the set of primers comprises: i. at least 20 fusion-specific forward primers, wherein the fusion-specific forward primers tile across the same strand of a first region in a reference human genome, ii. at least 20 fusion-specific reverse primers, wherein the fusion-specific reverse primers tile across the same strand in a second region of the reference human genome; wherein the first and second regions are on different chromosomes or are on the same chromosome but spaced apart by at least 10 kb; and iii. a reference primer pair, wherein the reference primer pair amplifies a different region of the reference human genome, wherein the region amplified by the reference primer pair is in the range of 40 bp to 160 bp; (b) thermocycling the reaction mix to produce PCR products that comprise: i. a reference amplicon that is produced by the reference primer pair, and ii. one or more fusion amplicons that are produced using the fusion-specific primers from fusion molecules in the cfDNA, wherein the fusion molecules correspond to a genomic rearrangement that fuses the first region with the second region in at least some cells of the subject; and (c) sequencing the PCR products of (b) or amplification products thereof to produce sequence reads; and (d) quantifying the relative abundance of the fusion molecules in the test sample by comparing the number of sequence reads corresponding to fusion molecules with of the number of sequence reads corresponding to the reference region, to produce a ratio. (a) combining a test sample comprising cell-free DNA (cfDNA) obtained from the bloodstream of a human subject with a set of primers and a polymerase to produce a reaction mix, wherein the set of primers comprises: i. at least 20 fusion-specific forward primers, wherein the fusion-specific forward primers tile across the same strand of a first region in a reference human genome, ii. at least 20 fusion-specific reverse primers, wherein the fusion-specific reverse primers tile across the same strand in a second region of the reference human genome; wherein the first and second regions are on different chromosomes or are on the same chromosome but spaced apart by at least 10 kb; and iii. a reference primer pair, wherein the reference primer pair amplifies a different region of the reference human genome, wherein the region amplified by the reference primer pair is in the range of 40 bp to 160 bp; i. at least 20 fusion-specific forward primers, wherein the fusion-specific forward primers tile across the same strand of a first region in a reference human genome, ii. at least 20 fusion-specific reverse primers, wherein the fusion-specific reverse primers tile across the same strand in a second region of the reference human genome; wherein the first and second regions are on different chromosomes or are on the same chromosome but spaced apart by at least 10 kb; and iii. a reference primer pair, wherein the reference primer pair amplifies a different region of the reference human genome, wherein the region amplified by the reference primer pair is in the range of 40 bp to 160 bp; (b) thermocycling the reaction mix to produce PCR products that comprise: i. a reference amplicon that is produced by the reference primer pair, and ii. one or more fusion amplicons that are produced using the fusion-specific primers from fusion molecules in the cfDNA, wherein the fusion molecules correspond to a genomic rearrangement that fuses the first region with the second region in at least some cells of the subject; and i. a reference amplicon that is produced by the reference primer pair, and ii. one or more fusion amplicons that are produced using the fusion-specific primers from fusion molecules in the cfDNA, wherein the fusion molecules correspond to a genomic rearrangement that fuses the first region with the second region in at least some cells of the subject; and (c) sequencing the PCR products of (b) or amplification products thereof to produce sequence reads; and (d) quantifying the relative abundance of the fusion molecules in the test sample by comparing the number of sequence reads corresponding to fusion molecules with of the number of sequence reads corresponding to the reference region, to produce a ratio.