	US 12,437,839 B2
	Methods for detecting nucleic acid variants
Gilad Almogy, Palo Alto, CA (US); Mark Pratt, Bozeman, MT (US); Omer Barad, Mazkeret Batya (IL); Simchon Faigler, Bet Izhak (IL); and Florian Oberstrass, Redwood City, CA (US)
Assigned to Ultima Genomics, Inc., Fremont, CA (US)
Filed by Ultima Genomics, Inc., Fremont, CA (US)
Filed on Mar. 26, 2024, as Appl. No. 18/617,448.
Application 18/617,448 is a continuation in part of application No. 18/362,754, filed on Jul. 31, 2023.
Application 18/362,754 is a continuation of application No. 16/864,981, filed on May 1, 2020, granted, now 11,763,915, issued on Sep. 19, 2023.
Application 18/617,448 is a continuation in part of application No. 16/875,645, filed on May 15, 2020, abandoned.
Claims priority of provisional application 62/971,530, filed on Feb. 7, 2020.
Claims priority of provisional application 62/849,414, filed on May 17, 2019.
Claims priority of provisional application 62/842,534, filed on May 3, 2019.
Prior Publication US 2024/0257906 A1, Aug. 1, 2024
Int. Cl. G16B 20/20 (2019.01); C12Q 1/6874 (2018.01); G01N 21/64 (2006.01); G06F 17/00 (2019.01); G16B 20/00 (2019.01); G16B 30/00 (2019.01); G16B 30/10 (2019.01)

CPC G16B 20/20 (2019.02) [C12Q 1/6874 (2013.01); G06F 17/00 (2013.01); G16B 20/00 (2019.02); G16B 30/00 (2019.02); G16B 30/10 (2019.02); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01); G01N 2021/6439 (2013.01)]

17 Claims

1. A method for detecting a disease based on single nucleotide variants identified from sequencing, comprising:

selecting a set of single nucleotide variants (SNV) loci from a disease-associated SNV locus panel, wherein the disease-associated SNV locus panel had been or is generated by sequencing a nucleic acid sample derived from diseased tissue from a subject, and wherein the SNV loci in the selected set of SNV loci are associated with a diseased sequencing data set that differs from a reference sequencing data set associated with a reference sequence across at least one flow cycle when the diseased sequencing data set and the reference sequencing data set are obtained by sequencing using non-terminating nucleotides provided in separate flow positions according to a flow-cycle order;

sequencing a cell-free nucleic acid sample from the subject using non-terminating nucleotides provided in separate flow positions according to a flow-cycle order to obtain a cell-free nucleic acid data set, wherein the mean sequencing depth of the cell-free nucleic acid sequencing data set (D) is less than 10;

determining a fraction value (F) by processing a total number of SNV reads detected at the set of SNV loci in the cell-free nucleic acid sequencing data set (N_total), a number of loci selected in the set of SNV loci (N_var), a mean sequencing depth of the cell-free nucleic acid sequencing data set (D), and a sequencing false positive error rate (E), wherein the fraction value is determined as:

and

calling a presence, absence, progression, or regression of the disease in the subject based on the fraction value or a degree of change in the fraction value from a prior fraction value determined for the subject.