US 12,344,902 B2
Microsatellite instability detection in cell-free DNA
Aliaksandr Artsiomenka, Mountain View, CA (US); Marcin Pawel Sikora, Burlingame, CA (US); Catalin Barbacioru, Fremont, CA (US); Darya Chudova, San Jose, CA (US); and Martina I. Lefterova, Redwood City, CA (US)
Assigned to GUARDANT HEALTH, INC., Palo Alto, CA (US)
Filed by GUARDANT HEALTH, INC., Palo Alto, CA (US)
Filed on Nov. 2, 2023, as Appl. No. 18/500,890.
Application 18/500,890 is a continuation of application No. 18/456,362, filed on Aug. 25, 2023.
Application 18/456,362 is a continuation of application No. 16/907,034, filed on Jun. 19, 2020, granted, now 11,773,451, issued on Oct. 3, 2023.
Application 16/907,034 is a continuation of application No. PCT/US2019/048999, filed on Aug. 30, 2019.
Claims priority of provisional application 62/857,048, filed on Jun. 4, 2019.
Claims priority of provisional application 62/823,578, filed on Mar. 25, 2019.
Claims priority of provisional application 62/726,182, filed on Aug. 31, 2018.
Prior Publication US 2024/0247319 A1, Jul. 25, 2024
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); G16B 20/20 (2019.01); G16B 30/10 (2019.01); G16B 40/20 (2019.01)
CPC C12Q 1/6886 (2013.01) [G16B 20/20 (2019.02); G16B 30/10 (2019.02); G16B 40/20 (2019.02)] 19 Claims
 
1. A method of treatment, comprising:
(a) selecting a human subject having cancer characterized by microsatellite instability, comprising:
(i) generating a site score (SS) by quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information for each of the plurality of the microsatellite loci in each of a plurality of human subjects having cancer characterized by microsatellite instability (MSI),
wherein the sequence information is from a sample comprising cell-free deoxyribonucleic acids (cfDNA) molecules obtained from the human subject,
wherein the site scores of the plurality of the microsatellite loci comprise likelihood scores that comprise probabilistic log likelihood-based scores for an individual microsatellite locus determined using at least a first parameter comprising observed allele frequencies of the different repeat lengths and at least a second parameter comprising noise in the sequence information;
(ii) comparing the SS of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus in each of the plurality of human subjects, wherein the site specific trained threshold is the maximum value of a site score for a microsatellite locus to be classified as stable, for each of the plurality of the microsatellite loci;
(iii) calling the given microsatellite locus as being unstable if the SS of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus in each of the plurality of human subjects, to further generate a microsatellite instability (MI) score comprising at least one unstable microsatellite loci from the plurality of the microsatellite loci;
(iv) classifying microsatellite instability status (MSI-S) of the sample as being unstable in each of the plurality of human subjects, if the MI score exceeds a population trained threshold for the population of microsatellite loci in the sample to identify an unstable sample; and
(b) administering at least one immunotherapy to at least one of the plurality of human subjects whose MSI status is classified as unstable in step (iv) to the human subject, wherein the at least one immunotherapy comprises at least one of:
an immune checkpoint molecule,
an antibody specific for an antigen selected from the group consisting of: PD-1, PD-2, PD-L1, PD-L2, CTLA-4, OX40, B7.1, B7He, LAG3, CD137, KIR, CCR5, CD27, CD40, and CD47,
proinflammatory cytokine selected from the group consisting of: IL-1β, IL-6, and TNF-α, and
activated T-cells, thereby treating the cancer in the human subject.