Patent ID: 11959130
Assignee: 10X GENOMICS, INC.
Field: Biotechnology (Chemistry)
Classification: CPC C | IPC C

Claim 0:
1. A method of determining presence of a genetic variant in a nucleic acid at a spatial location in a biological sample, the method comprising:
(a) contacting the biological sample with a first probe and a second probe, wherein:
(i) the first probe comprises a sequence substantially complementary to a sequence 3′ of a target sequence in the nucleic acid,
(ii) the second probe comprises:
a sequence of non-complementary nucleotides;
a sequence substantially complementary to a sequence 5′ of the target sequence in the nucleic acid; and
a capture probe binding domain, and

(iii) the target sequence is at least one nucleotide;

(b) hybridizing the first probe and the second probe to the nucleic acid;
(c) extending the first probe to generate an extended first probe;
(d) cleaving the sequence of non-complementary nucleotides of the second probe when the genetic variant is present;
(e) ligating the extended first probe and the second probe, thereby creating a ligated probe;
(f) releasing the ligated probe from the nucleic acid;
(g) hybridizing the ligated probe to a capture probe on a substrate comprising a plurality of capture probes, wherein the capture probe is included in the plurality of capture probes, and wherein the capture probe comprises a spatial barcode and a capture domain; and
(h) determining (i) all or a part of the sequence of the ligated probe hybridized to the capture domain, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequences of (i) and (ii) to determine the presence of the genetic variant in the nucleic acid in the biological sample.