US 12,297,508 B2
Customized assays for personalized cancer monitoring
John West, Menlo Park, CA (US); Laurie Goodman, Menlo Park, CA (US); and Richard Chen, Menlo Park, CA (US)
Assigned to Personalis, Inc., Fremont, CA (US)
Filed by Personalis, Inc., Menlo Park, CA (US)
Filed on Oct. 4, 2022, as Appl. No. 17/960,026.
Claims priority of provisional application 63/365,054, filed on May 20, 2022.
Claims priority of provisional application 63/252,412, filed on Oct. 5, 2021.
Prior Publication US 2023/0103464 A1, Apr. 6, 2023
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6827 (2018.01); C12Q 1/6874 (2018.01); G16B 30/10 (2019.01); G16H 10/40 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6827 (2013.01); C12Q 1/6874 (2013.01); G16B 30/10 (2019.02); G16H 10/40 (2018.01); C12Q 2600/118 (2013.01); C12Q 2600/156 (2013.01)] 25 Claims
 
1. A method for informing therapy decisions in a subject, said method comprising:
(a) generating nucleic acid sequencing data from nucleic acid molecules derived from a first biological sample from a subject, wherein:
(i) generating nucleic acid sequencing data comprises using a first sequencing assay to sequence nucleic molecules derived from said first biological sample from the subject,
(ii) said first sequencing assay comprises whole genome sequencing or whole exome sequencing,
(iii) said nucleic acid molecules derived from said first biological sample from said subject comprises a first quantity of nucleic acid molecules to be used as an input for said first sequencing assay,
(iv) said first quantity of nucleic acid molecules to be used as an input for said first sequencing assay comprises about 5 nanograms (ng) to about 20 ng of nucleic acids, and
(v) sequencing depth of said first sequencing assay is about 10.0× or higher;
(b) processing said nucleic acid sequencing data to identify a plurality of nucleic acid sequences having a plurality of genetic characteristics, wherein:
(i) said plurality of genetic characteristics include a set of genetic variants,
(ii) said set of genetic variants are identified with respect to a reference,
(iii) said set of genetic variants comprises one or more multiple nucleotide polymorphisms,
(iv) at least a subset of individual polymorphisms comprising said one or more multiple nucleotide polymorphisms are not in phase, and
(v) said set of genetic variants are combined to generate a signature of said subject;
(c) enriching or amplifying sequences from nucleic acid molecules derived from a second biological sample from said subject using a probe set configured to selectively enrich or amplify said set of genetic variants comprising said signature of said subject over other sequences in said second biological sample to generate a sequencing library, wherein:
(i) said probe set configured to selectively enrich or amplify said set of genetic variants over other sequences comprises a plurality of nucleic acid probe molecules, and
(ii) said set of genetic variants that are selectively enriched or amplified comprise one or more out of phase multiple nucleotide polymorphisms identified in step (b); and
(d) subjecting said sequencing library to a personalized sequencing assay to identify at least a subset of said set of genetic variants in said second biological sample from said subject,
(e) wherein a presence of said at least a subset of said set of genetic variants from said sequencing library informs therapy decisions for said subject.