US 12,258,628 B2
Methods and systems for genetic analysis
John West, Fremont, CA (US); Christian Haudenschild, Fremont, CA (US); and Richard Chen, Fremont, CA (US)
Assigned to Personalis, Inc., Fremont, CA (US)
Filed by Personalis, Inc., Fremont, CA (US)
Filed on Mar. 1, 2024, as Appl. No. 18/593,406.
Application 18/593,406 is a continuation of application No. 18/179,582, filed on Mar. 7, 2023, granted, now 11,952,625.
Application 18/179,582 is a continuation of application No. 17/747,436, filed on May 18, 2022, granted, now 11,643,685, issued on May 9, 2023.
Application 17/747,436 is a continuation of application No. 17/688,072, filed on Mar. 7, 2022.
Application 17/688,072 is a continuation of application No. 17/235,776, filed on Apr. 20, 2021, granted, now 11,299,783, issued on Apr. 12, 2022.
Application 17/235,776 is a continuation in part of application No. 17/065,411, filed on Oct. 7, 2020, abandoned.
Application 17/065,411 is a continuation of application No. 16/843,115, filed on Apr. 8, 2020, abandoned.
Application 16/843,115 is a continuation of application No. 16/547,451, filed on Aug. 21, 2019, abandoned.
Application 16/547,451 is a continuation of application No. 15/793,845, filed on Oct. 25, 2017, granted, now 10,450,611, issued on Oct. 22, 2019.
Application 15/793,845 is a continuation of application No. PCT/US2017/034823, filed on May 26, 2017.
Claims priority of provisional application 62/342,674, filed on May 27, 2016.
Prior Publication US 2024/0200136 A1, Jun. 20, 2024
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6874 (2018.01); C12Q 1/6806 (2018.01); C12Q 1/6869 (2018.01); G16B 20/00 (2019.01); G16B 30/00 (2019.01); G16B 35/00 (2019.01); G16B 99/00 (2019.01); G16C 20/60 (2019.01)
CPC C12Q 1/6874 (2013.01) [C12Q 1/6806 (2013.01); G16B 20/00 (2019.02); G16B 30/00 (2019.02); G16B 99/00 (2019.02); C12Q 1/6869 (2013.01); G16B 35/00 (2019.02); G16C 20/60 (2019.02)] 30 Claims
 
1. A method for personalized genetic testing, comprising:
(a) performing a first assay on nucleic acid molecules extracted from at least one biological sample from a subject to produce a first set of nucleic acid sequence data, wherein:
(i) the at least one biological sample comprises a tumor sample from the subject,
(ii) the first assay comprises whole genome sequencing, and
(iii) the whole genome sequencing comprises sequencing by synthesis;
(b) extracting a set of one or more genetic characteristics from the first set of nucleic acid sequence data by aligning the first set of nucleic acid sequence data to a reference genome;
(c) aggregating the set of one or more genetic characteristics to generate a signature of the subject;
(d) obtaining a personalized probe set for the subject, wherein the personalized probe set comprises the signature of aggregating step (c) or complements thereof;
(e) performing a second assay on nucleic acid molecules extracted from one or more plasma samples from the subject using a microarray to obtain a second set of nucleic acid sequence data, wherein the microarray comprises the personalized probe set; and
(f) outputting biomedical information of the subject based on an analysis comparing results from the first assay with results from the second assay.