PROCESS FOR ALIGNING TARGETED NUCLEIC ACID SEQUENCING DATA
First Claim
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1. A computer-implemented method of aligning RNA comprising:
- receiving onto a data storage unit a plurality of primer sequences and a plurality of transcript sequences from a reference genome, the transcript sequences being transcribable from the reference genome based on a gene model;
generating, using a microprocessor, a plurality of target sequences to be amplified from a combination of the plurality of primer sequences and the plurality of transcript sequences;
generating, using a microprocessor, a modified reference genome based on the plurality of target sequences;
aligning, using a microprocessor, sequence reads generated from a test sample comprising RNA amplicon molecules to the modified reference genome; and
generating an alignment profile for the test sample based on the aligning.
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Abstract
Provided is a computer-implemented method of aligning RNA including receiving onto a data storage unit primer sequences and transcript sequences transcribable from a reference genome based on a gene model, generating target sequences to be amplified from a combination of the primer sequences and the transcript sequences, generating a modified reference genome based on the plurality of target sequences, aligning sequence reads generated from a test sample comprising RNA amplicon molecules to the of target sequences, and generating an alignment profile for the test sample based on the aligning. Also provided is a computer system for performing the foregoing method.
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Citations
24 Claims
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1. A computer-implemented method of aligning RNA comprising:
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receiving onto a data storage unit a plurality of primer sequences and a plurality of transcript sequences from a reference genome, the transcript sequences being transcribable from the reference genome based on a gene model; generating, using a microprocessor, a plurality of target sequences to be amplified from a combination of the plurality of primer sequences and the plurality of transcript sequences; generating, using a microprocessor, a modified reference genome based on the plurality of target sequences; aligning, using a microprocessor, sequence reads generated from a test sample comprising RNA amplicon molecules to the modified reference genome; and generating an alignment profile for the test sample based on the aligning. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A computer-implemented method of aligning RNA comprising:
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receiving onto a data storage unit a plurality of primer sequences and a plurality of transcript sequences from a reference genome, the transcript sequences being transcribable from the reference genome using a gene model comprising identification of splice junctions, fusion junctions, or both, in the reference genome; assigning primer sequences individual loci corresponding to loci of respective transcript sequences; generating, using a microprocessor, a plurality of target sequences to be amplified from a combination of the plurality of transcript sequences and the plurality of primer sequences; generating, using a microprocessor, a modified reference genome based on the plurality of target sequences; aligning, using a microprocessor, sequence reads generated from a test sample comprising RNA amplicon molecules to the modified reference genome; generating an alignment profile wherein the alignment profile includes at least one of placement, a quality score, and sequence integrity for the sequence reads of the test sample; and translating the sequence reads from the test sample to a whole reference genome using the mapped target sequences and the modified reference genome.
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15. A computer system of aligning RNA comprising:
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one or more microprocessors, one or more memories storing a plurality of primer sequences and a plurality of transcript sequences from a reference genome, and a gene model, the transcript sequences being transcribable from the reference genome based on the gene model; the one or more memories storing instructions that, when executed by the one or more microprocessors, cause the computer system to; generate a plurality of target sequences to be amplified from a combination of the plurality of primer sequences and the plurality of transcript sequences; generate a modified reference genome based on the plurality of target sequences; align sequence reads generated from a test sample comprising RNA amplicon molecules to the modified reference genome; and generate an alignment profile for the test sample based on the aligning. - View Dependent Claims (16, 17, 18, 19, 20, 21, 22, 23, 24)
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Specification