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US 12,614,609 B2Granted
Systems and methods to identify mutations in mitochondrial genomes
AssigneeQuest Diagnostics Investments Incorporated
InventorAnindya Bhattacharya
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Abstract
The present disclosure describes a sequencing system configured to identify structural variants in mitochondrial DNA. Variant callers configured to identify variants in linear genomes (e.g., those found in chromosomes) can fail to properly identify structural variants in mitochondrial DNA. The system and methods can identify structural variants in next generation sequencing data collected from circular, mitochondrial DNA.
Claims17
A method to identify variants in mitochondrial sequencing data, comprising:
- receiving a plurality of sequence reads comprising an indication of sequenced DNA samples;
- identifying a subset of the plurality of sequence reads, wherein each sequence read of the subset of the plurality of sequence reads is partially mapped or not mapped to a target mitochondrial DNA sample;
- generating a plurality of query sequences from the subset of the plurality of sequence reads that are partially mapped to the target mitochondrial DNA sample or inverted versions of the subset of the plurality of sequence reads;
- calculating a score for each of the subset of the plurality of sequence reads based on an alignment of the plurality of query sequences with the target mitochondrial DNA sample, wherein the score is an e-value indicating a probability of the alignment of each plurality of query sequences occurring by chance;
- selecting a plurality of test reads, wherein the plurality of test reads comprises the subset of the plurality of sequence reads having a score below a predetermined threshold;
- identifying a breakpoint for each of the plurality of test reads;
- determining a count of the plurality of test reads having the breakpoint at a predetermined location of the target mitochondrial DNA sample;
- identifying a sequence variant based on the count of the plurality of test reads having the breakpoint at the predetermined location, wherein the sequence variant is one of a deletion, insertion, duplication, or inversion;
- and
- generating a report identifying the sequence variant from the sequenced DNA samples.
7 more elements
A system to identify variants in mitochondrial sequencing data, comprising one or more processors to:
- receive a plurality of sequence reads comprising an indication of sequenced DNA samples;
- identify a subset of the plurality of sequence reads, wherein each sequence read of the subset of the plurality of sequence reads is partially mapped to a target mitochondrial DNA sample;
- generate a plurality of query sequences from the subset of the plurality of sequence reads that are partially mapped to the target mitochondrial DNA sample or inverted versions of the subset of the plurality of sequence reads;
- calculate a score for each of the subset of the plurality of sequence reads based on an alignment of the plurality of query sequences with the target mitochondrial DNA sample;
- wherein the score is an e-value indicating a probability of the alignment of each plurality of query sequences occurring by chance;
- select a plurality of test reads, wherein the plurality of test reads comprises the subset of the plurality of sequence reads having a score below a predetermined threshold;
- identify a breakpoint for each of the plurality of test reads;
- determine a count of the plurality of test reads having the breakpoint at a predetermined location of the target mitochondrial DNA sample;
- identify a sequence variant based on the count of the plurality of test reads having the breakpoint at the predetermined location, wherein the sequence variant is one of a deletion, insertion, duplication, or inversion;
- and generate a report identifying the sequence variant from the sequenced DNA samples.
7 more elements
Dependencies are inferred from the claim text.