US 11,946,106 B2
Methods and systems to improve the signal to noise ratio of DNA methylation partitioning assays
Andrew Kennedy, San Diego, CA (US); and William J. Greenleaf, Menlo Park, CA (US)
Assigned to Guardant Health, Inc., Palo Alto, CA (US)
Filed by GUARDANT HEALTH, INC., Palo Alto, CA (US)
Filed on Dec. 22, 2022, as Appl. No. 18/087,724.
Application 18/087,724 is a continuation of application No. 17/489,677, filed on Sep. 29, 2021.
Claims priority of provisional application 63/105,183, filed on Oct. 23, 2020.
Claims priority of provisional application 63/086,000, filed on Sep. 30, 2020.
Prior Publication US 2023/0130140 A1, Apr. 27, 2023
Int. Cl. C12Q 1/6886 (2018.01); C12N 9/22 (2006.01); C12N 15/10 (2006.01); C12Q 1/6809 (2018.01); C12Q 1/683 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12N 9/22 (2013.01); C12N 15/1065 (2013.01); C12Q 1/6809 (2013.01); C12Q 1/683 (2013.01); C12N 2800/80 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/154 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/166 (2013.01)] 29 Claims
 
1. A method for analyzing nucleic acid molecules in a biological sample, comprising:
a) physically partitioning at least a subset of the nucleic acid molecules in the biological sample based on methylation status of the nucleic acid molecules into a plurality of partitioned sets, wherein the biological sample comprises methylated nucleic acid molecules and unmethylated nucleic acid molecules; the plurality of partitioned sets comprises a first partitioned set and a second partitioned set and the methylated nucleic acid molecules are overrepresented in the first partitioned set relative to the second partitioned set;
b) digesting the first partitioned set with at least one methylation sensitive restriction enzyme, thereby removing incorrectly partitioned molecules; and
c) sequencing at least a subset of the nucleic acid molecules of the first partitioned set.