US 11,932,899 B2
Methods and systems for characterizing nucleic acid molecules
Kamila Belhocine, Fremont, CA (US); Michael Schnall-Levin, San Francisco, CA (US); and Andrew D. Price, Hayward, CA (US)
Assigned to 10X GENOMICS, INC., Pleasanton, CA (US)
Filed by 10X Genomics, Inc., Pleasanton, CA (US)
Filed on Jun. 6, 2019, as Appl. No. 16/434,068.
Claims priority of provisional application 62/682,119, filed on Jun. 7, 2018.
Prior Publication US 2019/0376118 A1, Dec. 12, 2019
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/68 (2018.01)
CPC C12Q 1/68 (2013.01) [C12Q 2537/164 (2013.01); C12Q 2563/149 (2013.01); C12Q 2563/185 (2013.01)] 21 Claims
 
1. A method for determining an epigenetic characteristic of a nucleic acid molecule from a cell, comprising:
(a) providing a cell bead comprising the cell, the cell comprising the nucleic acid molecule from the cell, wherein the nucleic acid molecule contains or is suspected of containing one or more epigenetic features;
(b) partitioning the cell bead with a nucleic acid barcode molecule comprising a cell barcode sequence in a partition among a plurality of partitions;
(c) in the partition, using the nucleic acid molecule and the nucleic acid barcode molecule to synthesize a barcoded nucleic acid molecule, which barcoded nucleic acid molecule comprises the cell barcode sequence, wherein the cell barcode sequence is indicative of the cell from which the nucleic acid molecule originates;
(d) processing the barcoded nucleic acid molecule or a derivative thereof to identify the one or more epigenetic features and the cell barcode sequence; and
(e) using the one or more epigenetic features and the cell barcode sequence to determine the epigenetic characteristic of the nucleic acid molecule as being associated with the cell,
wherein, subsequent to (a), an enzymatic deamination reaction is performed within the cell bead, and wherein the enzymatic deamination reaction transforms at least a portion of a sequence of the nucleic acid molecule.