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Sequence-graph based tool for determining variation in short tandem repeat regions

A technology of repetitive sequences and sequence diagrams, which can be used in sequence analysis, genomics, instruments, etc., and can solve problems such as difficulty in determining repetitive sequences.

Pending Publication Date: 2021-06-11
ILLUMINA INC
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  • Abstract
  • Description
  • Claims
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Problems solved by technology

However, repeat sequence determination is difficult using short reads that do not completely pass through the repeat sequence

Method used

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  • Sequence-graph based tool for determining variation in short tandem repeat regions
  • Sequence-graph based tool for determining variation in short tandem repeat regions
  • Sequence-graph based tool for determining variation in short tandem repeat regions

Examples

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Embodiment Construction

[0042] The present disclosure relates to methods, apparatus, systems and computer program products for identifying repeat expansions of interest, such as expansions of medically significant repeat sequences. Examples of repeat expansions include, but are not limited to, those associated with genetic disorders such as fragile X syndrome, ALS, Huntington's disease, Friedrich's ataxia, spinocerebellar ataxia, spinobulbar muscular atrophy, myotonic Amplifications associated with dystrophy, Machado-Joseph disease, and dentatoerythropallidal Lewy body atrophy).

[0043] Unless otherwise indicated, the practice of the methods and systems disclosed herein involves conventional techniques and apparatus commonly used in the fields of molecular biology, microbiology, protein purification, protein engineering, protein and DNA sequencing, and recombinant DNA, which are described herein within the technical scope of the field. Such techniques and devices are known to those skilled in the a...

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Abstract

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.

Description

[0001] citation merge [0002] The PCT application form is filed simultaneously with this specification as part of this application. Each application to which this application claims the benefit or priority identified in the concurrently filed PCT Application Forms is hereby incorporated by reference in its entirety for all purposes. Background technique [0003] Repeat expansions are a specific class of microsatellite and minisatellite variants involving short tandem repeat (STR) polymorphisms. Repeat expansions are also known as dynamic mutations due to instability when short tandem repeats expand beyond a certain size. Genetic disorders caused by unstable repeat expansions include fragile X syndrome (FXS), Huntington's disease, and amyotrophic lateral sclerosis (ALS). [0004] Identifying repeat expansions is critical in the diagnosis and treatment of certain genetic disorders. However, it is difficult to determine repeat sequences using short reads that do not completel...

Claims

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Application Information

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IPC IPC(8): G16B20/00G16B20/20
CPCG16B20/00G16B20/20G16B5/20G16B30/10G16B40/00G06N7/01
Inventor 伊戈尔·多尔曾科迈克尔·A·埃伯利
Owner ILLUMINA INC
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