Differentiation of coinfection from contamination within genetic samples
AssigneeHelix OpCo, LLC
InventorsShishi Luo, Alexandre Bolze, Hang Dai, Dana Wyman, Andrew Dei Rossi
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Abstract
Various embodiments disclosed relate to a method for detection of coinfection of two or more pathogen variants in an individual. The present disclosure includes methods of receiving a biological sample, selecting a first variant of the pathogen and a second variant of the pathogen, sequencing the biological sample, calculating a composite alternative allele fraction, and if the sample is a mixed sample, searching individual reads to detect a recombinant pathogen.
Claims20
A method of distinguishing between coinfection and contamination for a biological sample, the biological sample including a first variant of a pathogen and a second variant of the pathogen, wherein the first variant corresponds to a first mutation and the second variant corresponds to a second mutation different than the first mutation, the method comprising:
- acquiring sequencing data for the biological sample, the sequencing data including a plurality of reads;
- determining that the biological sample is a mixed sample of the first variant and the second variant based on an alternative allele fraction calculated according to the plurality of reads;
- searching individual reads of the plurality of reads for recombinant reads that include the first mutation and the second mutation;
- and
- determining whether the biological sample is indicative of a coinfection or a contamination, based on an amount of the recombinant reads that each indicate both the first variant and the second variant.
A non-transitory machine-readable medium including instructions that, when executed by a processor of a machine, cause the machine to perform operations comprising:
- acquiring sequencing data for a biological sample, the sequencing data including a plurality of reads;
- identifying a first variant and a second variant of the biological sample, the first variant corresponding to a first mutation and the second variant corresponding to a second mutation different than the first mutation;
- determining that the biological sample is a mixed sample of the first variant and the second variant based on an alternative allele fraction calculated according to the plurality of reads;
- searching individual reads of the plurality of reads for recombinant reads that include the first mutation and the second mutation;
- and
- determining whether the biological sample is indicative of a coinfection or a contamination, based on an amount of the recombinant reads that each indicate both the first variant and the second variant.
Dependencies are inferred from the claim text.