US 12,270,083 B2
Methods for using mosaicism in nucleic acids sampled distal to their origin
John West, Cupertino, CA (US)
Assigned to Personalis, Inc., Fremont, CA (US)
Filed by Personalis, Inc., Fremont, CA (US)
Filed on Mar. 22, 2024, as Appl. No. 18/613,618.
Application 17/494,513 is a division of application No. 16/132,123, filed on Sep. 14, 2018, granted, now 11,142,802, issued on Oct. 12, 2021.
Application 18/613,618 is a continuation of application No. 17/828,572, filed on May 31, 2022, granted, now 11,965,214.
Application 17/828,572 is a continuation of application No. 17/748,200, filed on May 19, 2022, granted, now 11,649,507, issued on May 16, 2023.
Application 17/748,200 is a continuation of application No. 17/494,513, filed on Oct. 5, 2021, granted, now 11,584,968, issued on Feb. 21, 2023.
Application 16/132,123 is a continuation of application No. 14/929,075, filed on Oct. 30, 2015, granted, now 10,125,399, issued on Nov. 13, 2018.
Claims priority of provisional application 62/072,936, filed on Oct. 30, 2014.
Prior Publication US 2024/0229160 A1, Jul. 11, 2024
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); A61K 31/7068 (2006.01); C12Q 1/6809 (2018.01); C12Q 1/6827 (2018.01); G16B 45/00 (2019.01)
CPC C12Q 1/6886 (2013.01) [A61K 31/7068 (2013.01); G16B 45/00 (2019.02); C12Q 1/6809 (2013.01); C12Q 1/6827 (2013.01); C12Q 2600/156 (2013.01)] 30 Claims
 
1. A method for detecting a presence or recurrence of a solid tumor, comprising:
(a) generating a first set of sequence reads and a second set of sequence reads by independently performing whole genome sequencing on: (i) nucleic acid molecules extracted from a tissue sample of a subject, wherein the tissue sample comprises a benign tissue, a malignant tissue, or a mixed tissue sample, and (ii) nucleic acid molecules extracted from leukocytes from a first blood sample, wherein the leukocytes are a normal sample;
(b) comparing with a programmed computer processor the first set of sequence reads and the second set of sequence reads to identify mosaic variants, wherein the mosaic variants are present in the first set of sequence reads and are not present in the second set of sequence reads;
(c) creating a first report based on an identification of the mosaic variants;
(d) obtaining one or more blood samples from the subject at a later time point than the first tissue sample and the first blood sample;
(e) extracting non-amplified nucleic acid molecules from the one or more blood samples obtained in step (d) using a plurality of biotin-labeled capture probes in solution, wherein individual instances of the plurality of biotin-labeled capture probes are configured to hybridize to individual instances of the mosaic variants identified in step (b);
(f) performing a sequencing assay on nucleic acid molecules extracted from the one or more blood samples obtained in step (d) to identify the presence or absence of individual instances of the mosaic variants identified in step (b) one or more times over the life of the subject; and
(g) providing a second report based on the presence or absence of the individual instances of mosaic variants in the one or more blood samples, thereby detecting the presence or recurrence of the solid tumor in the subject.