| CPC G16B 20/20 (2019.02) [G16H 50/20 (2018.01); C12Q 1/6809 (2013.01); C12Q 2600/156 (2013.01)] | 19 Claims |
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1. A method for treating a subject having a cancer associated with homologous recombination deficiency (HRD), the method comprising:
(a) determining that the subject has a somatic homozygous deletion for a BRCA1 gene or BRCA2 gene in a sample of cell-free nucleic acid molecules by:
(i) obtaining the sample of cell-free nucleic acid molecules from the subject;
(ii) performing a diagnostic assay on the sample to detect the somatic homozygous deletion for the BRCA1 gene or BRCA2 gene, wherein the diagnostic assay comprises:
A) generating, via a first probabilistic distribution, a first model of allelic counts based on one or more germline single nucleotide polymorphism (SNP) positions associated with the BRCA1 gene or BRCA2 gene, the first model representing the somatic homozygous deletion;
B) generating, via a second probabilistic distribution, a second model of allelic counts in the sample based on the one or more germline SNP positions, the second model representing the somatic heterozygous deletion;
C) comparing a first output of the first model and a second output of the second model;
D) generating a prediction that the somatic homozygous deletion for the BRCA1 gene or BRCA2 gene exists in the sample based on the comparison; and
(b) administering a therapy comprising a poly ADP ribose polymerase (PARP) inhibitor to the subject to treat the cancer.
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