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US 2019/0172549 A1Published application
Systems and methods for analysis and interpretation of nucliec acid sequence data
AssigneeLife Technologies Corporation
InventorsBrijesh KRISHNASWAMI, Yuandan LOU, Asim SIDDIQUI, Heinz BREU, Amitabh SHUKLA, Karl KUHLMANN
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Abstract
Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.
Claims20
A system, comprising:
- a first data store configured to store genetic sequence information comprising called variants;
- a second data store configured to store sequence annotation data;
- and
- a processor communicatively connected with the first data store and the second data store, the processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to:
- receive the called variants from the first data store,
- receive functional type annotations from the second data store, wherein the functional type annotations include an indication of a change in an amino acid sequence, an indication of a change in an expression level of a protein and an indication of a change in a splicing of a transcript,
- receive interpretive type annotations from the second data store,
- normalize genomic coordinates of the functional type annotations and the interpretive type annotations to form normalized genomic coordinates for the functional type annotations and the interpretive type annotations,
- assign positions to the called variants in accordance with the normalized genomic coordinates,
- associate functional type annotations with the called variants based on the normalized genomic coordinates,
- update the called variants in the first data store with the associated functional type annotations,
- associate interpretive type annotations with the called variants based on the normalized genomic coordinates,
- update the called variants in the first data store with the associated interpretive type annotations, and
- generate a report of the called variants, the functional annotations, and the interpretive annotations.
11 more elements
A method, comprising:
- receiving called variants from a first data store configured to store genetic sequence information comprising the called variants;
- receiving functional type annotations from a second data store, wherein the functional type annotations include an indication of a change in an amino acid sequence, an indication of a change in an expression level of a protein and an indication of a change in a splicing of a transcript;
- receiving interpretive type annotations from the second data store;
- normalizing genomic coordinates of the functional type annotations and the interpretive type annotations to form normalized genomic coordinates for the functional type annotations and the interpretive type annotations;
- assigning positions to the called variants in accordance with the normalized genomic coordinates;
- associating the functional type annotations with the called variants based on the normalized genomic coordinates;
- updating the called variants in the first data store with the associated functional type annotations;
- associating interpretive type annotations with the called variants based on the normalized genomic coordinates;
- updating the called variants in the first data store with the associated interpretive type annotations;
- and
- generating a report of the called variants, the functional annotations, and the interpretive annotations.
8 more elements
Dependencies are inferred from the claim text.