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AssigneeIllumina, Inc.
InventorsEgor Dolzhenko, Michael A. Eberle
Estimating the term…
The disclosed embodiments concern methods, apparatus, systems and computer program products for genotyping repeat sequences such as medically significant short tandem repeats (STRs). The methods involve aligning reads to a repeat sequence represented by a sequence graph, and using the aligned reads to genotype the repeat sequence. The sequence graph is a directed graph each including at least one self-loop representing a repeat sub-sequence. In some implementations, the reads are paired end reads, and both mates of each read pair may be used to genotype the repeat sequences. Some implementations can be used to determine degenerate codon repeats. Some implementations can be used to genotype repeat sequences each including two or more repeat sub-sequences. Some implementations can be used to genotype nucleic acid sequences each including at least one repeat sub-sequence and another genetic variant such as an insertion, deletion, or substitution.
A method, implemented using a computer comprising one or more processors and system memory, for genotyping one or more repeat sequences each including one or more repeat sub-sequences, the method comprising:
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A system comprising:
A computer program product comprising a non-transitory machine readable medium storing program code that, when executed by one or more processors of a computer system, causes the computer system to implement a method for genotyping a repeat sequence in a test sample comprising nucleic acids, said program code comprising:
Dependencies are inferred from the claim text.