US 11,773,451 B2
Microsatellite instability detection in cell-free DNA
Aliaksandr Artsiomenka, Mountain View, CA (US); Marcin Sikora, Redwood City, CA (US); Catalin Barbacioru, Redwood City, 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., Redwood City, CA (US)
Filed on Jun. 19, 2020, as Appl. No. 16/907,034.
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 2021/0363586 A1, Nov. 25, 2021
Int. Cl. C12Q 1/6886 (2018.01); G16B 30/10 (2019.01); G16B 20/20 (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)] 17 Claims
 
1. A method of treating a human subject having cancer characterized by microsatellite instability, the method comprising:
a) in each of a plurality of human subjects having cancer characterized by microsatellite instability (MSI), quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score (SS) for each of the plurality of the microsatellite loci,
wherein the sequence information is from a population of microsatellite loci in 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 that are 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;
b) in each of the plurality of human subjects, comparing the SS of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus, which 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;
c) in each of the plurality of human subjects, 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 to further generate a microsatellite instability (MI) score comprising at least one unstable microsatellite loci from the plurality of the microsatellite loci or not calling the given microsatellite locus as being unstable if the SS of the given microsatellite locus does not exceed the site specific trained threshold for the given microsatellite locus;
d) in each of the plurality of human subjects, classifying microsatellite instability status (MSI-S) of the sample as being unstable if the MI score exceeds a population trained threshold for the population of microsatellite loci in the sample to identify an unstable sample; and,
e) administering at least one immunotherapy to at least one of the plurality of human subjects whose MSI status is classified as unstable in step (d) to the subject, thereby treating the cancer in the human subject, wherein the at least one immunotherapy comprises at least one of: 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, or a proinflammatory cytokine selected from the group consisting of: IL-13, IL-6, and TNF-a or activated T-cells.