US 12,234,518 B2
Compositions and methods for analyzing DNA using partitioning and base conversion
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., Redwood City, CA (US)
Filed on Oct. 21, 2021, as Appl. No. 17/507,697.
Claims priority of provisional application 63/105,184, filed on Oct. 23, 2020.
Prior Publication US 2022/0154286 A1, May 19, 2022
Int. Cl. C12Q 1/6886 (2018.01); C12N 9/22 (2006.01); C12N 15/10 (2006.01)
CPC C12Q 1/6886 (2013.01) [C12N 9/22 (2013.01); C12N 15/1065 (2013.01); C12N 2800/80 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/154 (2013.01); C12Q 2600/156 (2013.01)] 24 Claims
 
1. A method of analyzing DNA in a sample, the method comprising:
a) partitioning the sample into a plurality of subsamples, including a first subsample and a second subsample, wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample;
b) subjecting the second subsample to a base conversion procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the second subsample, wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and the first nucleobase and the second nucleobase have the same base pairing specificity, thereby producing a treated subsample;
c) capturing a target region set comprising epigenetic target regions from the treated subsample; and
d) sequencing DNA in the target region set and DNA from the first subsample, wherein DNA from the second subsample is sequenced in a manner that distinguishes the first nucleobase from the second nucleobase in the DNA of the target region set.