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US 2026/0226532 A1Published application
Compositions and methods for evaluating genomic alterations
AssigneeFoundation Medicine, Inc.
InventorsGeoffrey Alan OTTO, Travis CLARK, Doron LIPSON, Daniel LIEBER, David FABRIZIO
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Abstract
Compositions and methods of evaluating genomic alterations in a sample are disclosed.
Claims20
A method comprising:
- (a) combining a sample comprising a plurality of nucleic acid molecules with a plurality of target capture reagents comprising a first target capture reagent and a second target capture reagent to form a plurality of hybrids, wherein:
- the first target capture reagent and the second target capture reagent each comprise an oligonucleotide comprising the same sequence that hybridizes to a nucleic acid molecule from the plurality of nucleic acid molecules,
- the first target capture reagent comprises a first member of a binding pair, and
- the second target capture reagent lacks the first member of the binding pair;
- (b) contacting the plurality of hybrids with a substrate comprising a second member of the binding pair that binds to the first member of the binding pair to bind a portion of the plurality of hybrids to the substate;
- and
- (c) sequencing nucleic acid molecules of hybrids that bind to the substrate.
4 more elements
A method comprising:
- providing a sample comprising a plurality of nucleic acid molecules from a subject;
- isolating the plurality of nucleic acid molecules;
- amplifying one or more of the plurality of nucleic acid molecules;
- contacting the plurality of amplified nucleic acid molecules with a plurality of target capture reagents to form a plurality of hybrids,
- wherein the plurality of target capture reagents are designed to capture more targets associated with a first genomic region than a second genomic region by optimizing biotinylation within the plurality of target capture reagents, and
- two or more reagents of the plurality of reagents target the same genomic region but at least one of the two or more reagents lacks a binding pair that binds the plurality of hybrids to a substate, the first genomic region associated with somatic mutations and the second genomic region is associated with germline alterations or SNPs;
- and
- sequencing the plurality of hybrids, wherein the first genomic region has greater sequencing depth than the second genomic region.
5 more elements
Dependencies are inferred from the claim text.