Sequence map-based tools for determining variations in short tandem repeat regions
By aligning the sequence reads with the sequence graph, and using the data structure of the sequence graph to identify and type repeat sequences, the problem of difficult to identify and diagnose genetic diseases in the prior art is solved, and the efficiency and accuracy of genotyping are achieved.
CN119724336APending Publication Date: 2025-03-28ILLUMINA INC
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Patent Information
- Application Number
- CN202411810020.5
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Priority Date
- 2019-03-07
- Filing Date
- 2020-03-06
- Publication Date
- 2025-03-28
AI Technical Summary
Technical Problem
The prior art is difficult to effectively identify and diagnose repeated amplifications associated with hereditary diseases, especially when using short reads.
Method used
By aligning the sequence reads with sequence graphs containing self-loops, the data structure of the sequence graph is used to identify and type repeat sequences, including the use of anchor reads and anchor reads to determine the genotype of the repeat sequence.
Benefits of technology
It realizes efficient genotyping of loci including repeat sequences, which can identify medically-related repetitive amplification, and improves the accuracy and efficiency of diagnosis.
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Abstract
The invention relates to a sequence map-based tool for determining variations in short tandem repeat regions. The present application relates to methods, apparatuses, systems, and computer program products for genotyping repetitive sequences, such as medically significant short tandem repetitive sequences. The method involves aligning reads to repetitive sequences represented by a sequence map, and genotyping the repetitive sequences using the aligned reads. The sequence diagrams are directed diagrams, each of which includes at least one self-loop representing a repetitive sub-sequence. The reads are paired end reads, and the two matches of each read pair are used to genotype the repetitive sequence. Some implementations may be used to determine degenerate codon repetitions. Some implementations are used for genotyping repetitive sequences each comprising two or more repetitive subsequences. Some implementations are useful for genotyping nucleic acid sequences, each comprising at least one repeat sequence and another genetic variation, such as an insertion, deletion or substitution.
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