Methods for quantitative genetic analysis of cell free dna

A method for targeted genetic analysis of circulating cell-free DNA (cfDNA), said method comprising:

• (a) hybridizing one or more capture probe modules to a target genetic locus in a tagged cfDNA library to form one or more tagged cfDNA-capture probe module complexes,
• wherein the one or more capture probe modules are not immobilized to a surface,
• wherein each capture probe module comprises a capture probe sequence at a 3′ end of the capture probe module and a tail sequence at a 5′ end of the capture probe module,
• wherein the capture probe sequence is about 25 nucleotides to about 45 nucleotides in length and hybridizes to a specific DNA target region, and
• wherein the tail sequence is capable of hybridizing to a partner oligonucleotide comprising at its 3′ end a first member of a binding pair to allow for isolation and/or purification of a tagged cfDNA-capture probe module complex;
• (b) isolating one or more of the tagged cfDNA-capture probe module complexes from (a) to form one or more isolated tagged cfDNA capture probe module complexes, each isolated tagged cfDNA-capture probe module complex comprising a tagged cfDNA molecule and a capture probe module, wherein the isolating comprises binding the first member of the binding pair of a partner oligonucleotide hybridized to a tagged cfDNA capture probe module complex to a second member of the binding pair;
• and
• (c) for at least one of the one or more isolated tagged cfDNA-capture probe module complexes from (b), performing 5′ to 3′ DNA polymerase extension of the capture probe module using the isolated tagged cfDNA molecule as a template.