Compositions and methods for synthesis and use of probes targeting nucleic acid rearrangements

A method of analyzing DNA from a subject, the method comprising:

• a) contacting a first sample or a first subsample thereof comprising DNA from the subject with a plurality of primers that do not comprise a capture moiety, wherein the DNA comprises a rearranged sequence comprising a rearrangement breakpoint, the plurality of primers comprises a first primer that anneals upstream of the rearrangement breakpoint and a second primer that anneals downstream of the rearrangement breakpoint, and the first and second primers anneal in an anti-parallel orientation, thereby producing primer-annealed DNA;
• b) amplifying the primer-annealed DNA, wherein the amplification comprises contacting the primer-annealed DNA with a DNA polymerase and deoxynucleoside triphosphates, wherein the deoxynucleoside triphosphates comprise a modified deoxynucleoside triphosphate comprising a capture moiety, thereby producing one or more capture probes;
• c) contacting DNA from the subject with the one or more capture probes;
• d) capturing the capture probes and any DNA that anneals to the one or more capture probes;
• and
• e) detecting the presence of DNA molecules that annealed to the one or more capture probes.