Systems and methods for identifying sequence variation
AssigneeLife Technologies Corporation
InventorsFiona Hyland, Eric TSUNG, Vasisht TADIGOTLA, Zheng ZHANG, Dumitru BRINZA, Onur SAKARYA, Xing XU
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Abstract
Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.
Claims18
A system to identify variants in nucleic acid sequence data provided by a nucleic acid sequence analysis device, comprising:
- a processor in communication with the nucleic acid sequence analysis device, the processor configured to execute machine-readable instructions, said instructions which when executed cause the processor to perform the following steps:
- map a plurality of nucleic acid sequence reads to a reference sequence to form mapped reads,
- align flow space information for the mapped reads to a flow space representation of the reference sequence to form aligned flow space information,
- identify sequence deviations between the aligned flow space information and the flow space representation of the reference sequence,
- group the sequence deviations identified for multiple reads by position,
- calculate a read score for each of the sequence deviations for a position on a per-read and per-variant basis using characteristics of the aligned flow space information and based on a location of the sequence deviation within the read,
- calculate a variant score for the sequence deviations at the position on a per-variant basis based on the read scores spanning the position, and
- identify a variant at the position if there is sufficient evidence of the variant at the position.
A computer implemented method for identifying variants in nucleic acid sequence data provided by a nucleic acid sequence analysis device, comprising:
- receiving, at a processor in communication with the nucleic acid sequence analysis device, a plurality of nucleic acid sequence reads;
- mapping the plurality of nucleic acid sequence reads to a reference sequence to form mapped reads;
- aligning flow space information for the mapped reads to a flow space representation of the reference sequence to form aligned flow space information;
- identifying sequence deviations between the aligned flow space information and the flow space representation of the reference sequence;
- grouping the sequence deviations identified for multiple reads by position;
- calculating a read score for each of the sequence deviations for a position on a per-read and per-variant basis using characteristics of the aligned flow space information and based on a location of the sequence deviation within the read;
- calculating a variant score for the sequence deviations at the position on a per-variant basis based on the read scores spanning the position;
- and
- identifying a variant at the position if there is sufficient evidence of the variant at the position.
Dependencies are inferred from the claim text.