A method for targeted genetic analysis of cell-free DNA (cfDNA) comprising: (a) treating the cfDNA with one or more end-repair enzymes to generate end-repaired cfDNA and ligating an adaptor module to each end of the end-repaired cfDNA to generate a cfDNA library; (b) amplifying the cfDNA library to generate cfDNA library clones and determining the number of genome equivalents in the cfDNA clone library; and (c) performing a quantitative genetic analysis of a target genetic locus in the cfDNA library clones comprising: (i) hybridizing one or more capture probe modules to a target genetic locus in the cfDNA clone library to form one or more capture probe module-cfDNA clone complexes, wherein the target genetic locus is a region of a gene, wherein the capture probe modules comprise capture probes that are 25 to 45 nucleotides in length and hybridize comparably, as well as, or better than capture probes that are 60 nucleotides in length; (ii) isolating the one or more isolated capture probe module-cfDNA clone complexes from (i); (iii) enzymatically processing the one or more isolated capture probe module cfDNA clone complexes from (ii), wherein the enzymatic processing comprises performing 5'-3' DNA polymerase extension of the capture probe using the isolated cfDNA clone in the complex as a template; (iv) performing PCR on the enzymatically processed complex of (iii) to generate amplified hybrid nucleic acid molecules, wherein the amplified hybrid nucleic acid molecules comprise a target sequence capable of hybridizing to the capture probe and the complement of the capture probe module tail sequence; and (v) sequencing the amplified hybrid nucleic acid molecules of (iv) to generate a plurality of sequencing reads and performing bioinformatics analysis on the plurality of sequencing reads. (a) treating the cfDNA with one or more end-repair enzymes to generate end-repaired cfDNA and ligating an adaptor module to each end of the end-repaired cfDNA to generate a cfDNA library; (b) amplifying the cfDNA library to generate cfDNA library clones and determining the number of genome equivalents in the cfDNA clone library; and (c) performing a quantitative genetic analysis of a target genetic locus in the cfDNA library clones comprising: (i) hybridizing one or more capture probe modules to a target genetic locus in the cfDNA clone library to form one or more capture probe module-cfDNA clone complexes, wherein the target genetic locus is a region of a gene, wherein the capture probe modules comprise capture probes that are 25 to 45 nucleotides in length and hybridize comparably, as well as, or better than capture probes that are 60 nucleotides in length; (ii) isolating the one or more isolated capture probe module-cfDNA clone complexes from (i); (iii) enzymatically processing the one or more isolated capture probe module cfDNA clone complexes from (ii), wherein the enzymatic processing comprises performing 5'-3' DNA polymerase extension of the capture probe using the isolated cfDNA clone in the complex as a template; (iv) performing PCR on the enzymatically processed complex of (iii) to generate amplified hybrid nucleic acid molecules, wherein the amplified hybrid nucleic acid molecules comprise a target sequence capable of hybridizing to the capture probe and the complement of the capture probe module tail sequence; and (v) sequencing the amplified hybrid nucleic acid molecules of (iv) to generate a plurality of sequencing reads and performing bioinformatics analysis on the plurality of sequencing reads. (i) hybridizing one or more capture probe modules to a target genetic locus in the cfDNA clone library to form one or more capture probe module-cfDNA clone complexes, wherein the target genetic locus is a region of a gene, wherein the capture probe modules comprise capture probes that are 25 to 45 nucleotides in length and hybridize comparably, as well as, or better than capture probes that are 60 nucleotides in length; (ii) isolating the one or more isolated capture probe module-cfDNA clone complexes from (i); (iii) enzymatically processing the one or more isolated capture probe module cfDNA clone complexes from (ii), wherein the enzymatic processing comprises performing 5'-3' DNA polymerase extension of the capture probe using the isolated cfDNA clone in the complex as a template; (iv) performing PCR on the enzymatically processed complex of (iii) to generate amplified hybrid nucleic acid molecules, wherein the amplified hybrid nucleic acid molecules comprise a target sequence capable of hybridizing to the capture probe and the complement of the capture probe module tail sequence; and (v) sequencing the amplified hybrid nucleic acid molecules of (iv) to generate a plurality of sequencing reads and performing bioinformatics analysis on the plurality of sequencing reads.