US 12,473,589 B2
Compositions and methods for evaluating genomic alterations
Geoffrey Alan Otto, Cambridge, MA (US); Travis Clark, Winchester, MA (US); Doron Lipson, Cambridge, MA (US); Daniel Lieber, Needham, MA (US); and David Fabrizio, Cambridge, MA (US)
Assigned to Foundation Medicine, Inc., Boston, MA (US)
Filed by Foundation Medicine, Inc., Boston, MA (US)
Filed on Feb. 3, 2025, as Appl. No. 19/044,599.
Application 19/044,599 is a division of application No. 16/437,974, filed on Jun. 11, 2019.
Claims priority of provisional application 62/683,469, filed on Jun. 11, 2018.
Prior Publication US 2025/0171836 A1, May 29, 2025
Int. Cl. C12Q 1/6848 (2018.01); C12N 15/10 (2006.01); C12Q 1/6827 (2018.01); C12Q 1/6853 (2018.01); C12Q 1/6886 (2018.01)
CPC C12Q 1/6848 (2013.01) [C12N 15/1093 (2013.01); C12Q 1/6827 (2013.01); C12Q 1/6853 (2013.01); C12Q 1/6886 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 18 Claims
 
1. A method of analyzing a sample, comprising:
(a) contacting a sample comprising first fragments (F1s) having a first target nucleic acid sequence and second fragments (F2s) having a second target nucleic acid sequence with plurality of target capture reagents, said plurality of target capture reagent comprising first target capture reagents (R1s) and second target capture reagents (R2s) to form a plurality of first fragment/first target capture reagent (F1/R1) hybrids and a plurality of second fragment/second target capture reagent (F1/R2) hybrids,
wherein each R1 comprises an oligonucleotide comprising a first nucleic acid sequence that hybridizes to an F1 from the F1s, the oligonucleotides of the R1s are the same, a first portion of the R1s comprises a first member of a binding pair, and a second portion of the R1s lacks the first member of the binding pair, and
wherein each R2 comprises an oligonucleotide comprising a second nucleic acid sequence that hybridizes to an F2 from the F2s, the oligonucleotides of the R2s are the same, a first portion of the R2s comprises the first member of a binding pair, and a second portion of the R2s lacks the first member of the binding pair;
(b) contacting the F1/R1 hybrids with a substrate comprising a second member of the binding pair that binds to the first member of the binding pair to form F1/R1 hybrid/substrate complexes, and
contacting the F2/R2 hybrids with the substrate to form F2/R2 hybrid/substrate complexes, wherein the proportion of F1/R1 hybrids that bind to the substrate is greater than the proportion of F2/R2 hybrids that bind to the substrate; and
(c) analyzing first fragments from the plurality of F1/R1 hybrids and second fragments from the F2/R2 hybrids.