A method for determining the presence of DNA molecules from an origin of interest in a population of DNA molecules present in a cell-free bodily fluid sample, said method comprising: a) obtaining a DNA sample isolated from a cell-free bodily fluid sample from the subj ect; b) determining, by sequencing, a plurality of protein binding site sequences and their 5' and 3' flanking region sequences for each of one or more proteins, wherein said proteins are transcription factors and the protein binding site sequences are transcription factor binding site sequences, and wherein at least one of the one or more proteins differentially binds to DNA molecules of the origin of interest and DNA molecules of differing origins; c) aligning at least 500 of the determined protein binding site sequences for each of the one or more proteins; d) counting the number of sequencing reads starting at each nucleotide position within each 5' and 3' flanking region sequence of the aligned protein binding site sequences, wherein the 5' and 3' flanking region sequences are at least 500 base pairs; e) generating a coverage map based on the number of counts of step d); f) filtering the coverage map to identify at least one periodic component within the coverage map, wherein the filtering comprises computing a spectral frequency transform of the coverage map and identifying a power of the spectral frequency transform within a frequency band, wherein the frequency band includes frequencies corresponding to spacings of 130to 250 base pairs; g) obtaining a computed metric, wherein said computed metric is percentage spectral power computed as a ratio between the power of the spectral frequency transform within the frequency band computed by integrating the spectral frequency transform within the frequency band and an overall power of the spectral frequency transform computed by integrating the spectral frequency transform over all frequencies; according to the expression: ∫ a b F ω dω ∫ F ω dω where F(ω) corresponds to the Fourier coefficient for frequency ω, a corresponds to a first edge of the frequency band, and b correspond to a second edge of the frequency band; wherein a computed metric that is statistically different from a predetermined set of values is indicative of the presence of DNA molecules from the origin of interest. a) obtaining a DNA sample isolated from a cell-free bodily fluid sample from the subj ect; b) determining, by sequencing, a plurality of protein binding site sequences and their 5' and 3' flanking region sequences for each of one or more proteins, wherein said proteins are transcription factors and the protein binding site sequences are transcription factor binding site sequences, and wherein at least one of the one or more proteins differentially binds to DNA molecules of the origin of interest and DNA molecules of differing origins; c) aligning at least 500 of the determined protein binding site sequences for each of the one or more proteins; d) counting the number of sequencing reads starting at each nucleotide position within each 5' and 3' flanking region sequence of the aligned protein binding site sequences, wherein the 5' and 3' flanking region sequences are at least 500 base pairs; e) generating a coverage map based on the number of counts of step d); f) filtering the coverage map to identify at least one periodic component within the coverage map, wherein the filtering comprises computing a spectral frequency transform of the coverage map and identifying a power of the spectral frequency transform within a frequency band, wherein the frequency band includes frequencies corresponding to spacings of 130to 250 base pairs; g) obtaining a computed metric, wherein said computed metric is percentage spectral power computed as a ratio between the power of the spectral frequency transform within the frequency band computed by integrating the spectral frequency transform within the frequency band and an overall power of the spectral frequency transform computed by integrating the spectral frequency transform over all frequencies; according to the expression: ∫ a b F ω dω ∫ F ω dω where F(ω) corresponds to the Fourier coefficient for frequency ω, a corresponds to a first edge of the frequency band, and b correspond to a second edge of the frequency band; wherein a computed metric that is statistically different from a predetermined set of values is indicative of the presence of DNA molecules from the origin of interest.