US 12,322,476 B2
Methods for detecting and suppressing alignment errors caused by fusion events
Carlo Artieri, Redwood City, CA (US); and Marcin Sikora, Redwood City, CA (US)
Assigned to Guardant Health, Inc., Palo Alto, CA (US)
Filed by GUARDANT HEALTH, INC., Redwood City, CA (US)
Filed on Apr. 12, 2019, as Appl. No. 16/383,349.
Claims priority of provisional application 62/657,200, filed on Apr. 13, 2018.
Prior Publication US 2020/0020416 A1, Jan. 16, 2020
Int. Cl. G16B 20/00 (2019.01); G16B 30/00 (2019.01); G16B 40/00 (2019.01)
CPC G16B 20/00 (2019.02) [G16B 30/00 (2019.02); G16B 40/00 (2019.02)] 11 Claims
 
1. A method for treating a subject having lung cancer, comprising:
(a) providing a biological sample comprising cell-free nucleic acid molecules from the subject and sequencing the cell-free nucleic acid molecules to generate sequence information comprising genetic sequence reads obtained or derived from the cell-free nucleic acid molecules;
(b) aligning the genetic sequence reads to a reference sequence to produce aligned sequence reads, wherein the reference sequence is a human genome;
(c) identifying a set of gene fusion reads that comprise an intragenic fusion breakpoint from the aligned sequence reads;
(d) detecting an alignment error in a subset of one or more of the gene fusion reads by identifying a potential genetic variant as compared to the reference sequence which: (1) is up to 20 nucleotides adjacent to the intragenic fusion breakpoint, and (2) has a mutant allele fraction that is less than or equal to a mutant allele fraction of the intragenic fusion breakpoint in the biological sample;
(e) filtering out the alignment error in the subset of the one or more gene fusion reads to produce filtered sequence reads, thereby removing the alignment error and decreasing detection of false positive variants;
(f) determining filtered sequence reads that include a single nucleotide variant (SNV) or an insertion or deletion (indel) as compared to the reference sequence indicating that the SNV or indel is present in the biological sample of the subject; and
(g) administering an immunotherapeutic agent to the subject based on the determining of one or more SNVs or indels in (f) to treat the lung cancer, wherein the immunotherapeutic agent is selected from the group consisting of pembrolizumab, nivolumab, ipilimumab, atezolizumab, avelumab, and durvalumab.