SYSTEMS AND METHODS FOR ANALYSIS AND INTERPRETATION OF NUCLEIC ACID SEQUENCE DATA

• US 20130091126A1
• Filed: 10/10/2012
• Published: 04/11/2013
• Est. Priority Date: 10/11/2011
• Status: Abandoned Application

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: BREU, Heinz, HYLAND, Fiona, JANDHYALA, Srikanth, LOU, Yuandan, KUHLMANN, Karl, ALTUN, Gulsah, DHAPULKAR, Ameet, THOMAS, Daryl, SHUKLA, Amitabh, KRISHNASWAMI, Brijesh, AGATE, Mrunal, SIDDIQUI, Asim
• Application Number:
  US13/648,998
• Publication Number:
  US 20130091126A1
• Time in Patent Office: Days
• US Class Current: 707/722
• CPC Class Codes: G06F 16/9038 Presentation of query results
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations

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.

Claims

1. 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;

an annotations component communicatively connected with the first data store and the second data store, comprising;

a functional annotations engine configured to;

receive the called variants from the first data store, and

associate functional type annotations from the second data store with the called variants, and

an interpretive annotations engine configured to;

receive the called variants from the first data store, and

associate interpretive type annotations from the second data store with the called variants;

a reporting module communicatively connected with the first data store and the second data store and configured to generate a report of the called variants, the functional annotations, and the interpretive annotations.

2. A system of claim 1, wherein the functional type annotation includes an indication of a change in an amino acid sequence, an indication of a change in an expression level of a protein, an indication of a change in the splicing of a transcript, or any combination thereof.

3. A system of claim 1, wherein the functional-type annotations includes a listing of transcripts impacted by the called variant.

4. A system of claim 3, wherein the functional-type annotations includes a protein function impact score for the called variant.

5. A system of claim 4, wherein the functional-type annotations includes base information for codons with the called variant.

6. A system of claim 1, wherein the interpretive type annotation includes an association of a variant with a disease, an correlation between a variant and a response to a treatment, metabolic pathways impacted by the called variant, biological signaling pathway impacted by the called variant, regulation pathway impacted by the called variant, a match to a list of annotated variants, or a combination thereof.

7. A system of claim 1, wherein the interpretive type annotation includes a metabolic pathways impacted by the called variant, a biological signaling pathway impacted by the called variant, a regulation pathway impacted by the called variant, or a combination thereof.

8. A system of claim 1, wherein the called variants that fall within blocks of overlapping transcripts are annotated at the same time.

9. A system of claim 1, further comprising a filtering component in communications with the first data source and configured to query the first data store based a set of variant filter conditions and wherein the report summarizes results of the query.

10. The system of claim 1, further comprising:

an annotations importer component in communications with the second data store and configured to convert annotations information received from external annotations sources to a format that can be stored on the second data store.

11. A computer implemented method, comprising:

receiving the called variants from a first data store configured to store genetic sequence information comprising called variants, and

associating the called variants with functional type annotations from the second data store configured to store sequence annotation data, and

associating the called variants with interpretive type annotations from the second data store;

generating a report of the called variants, the functional annotations, and the interpretive annotations; and

providing the report to a first user

12. The computer implemented method of claim 11, further including:

selecting variant report filter conditions;

querying the first data store based on the selected variant report filter conditions; and

wherein the report summarizes the results of the query.

13. The method of claim 11, further comprising receiving instructions from the first user to modify the report.

14. The method of claim 13, wherein a second user is restricted from modifying the report.

15. The method of claim 11, further comprising receiving instructions from the first user to publish the report.

16. The method of claim 14, wherein a second user is restricted from publishing the report.

17. The method of claim 11, further comprising receiving instructions from a second user to associate the called variants with the functional type annotations or to associate the called variants with the interpretive type annotations.

18. The method of claim 17, wherein the first user is of a first class of users and the second user is of a second class of users.

19. 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;

an annotations component communicatively connected with the first data store and the second data store, comprising;

an annotations engine configured to;

receive the called variants from the first data store, and

associate annotations from the second data store with the called variants, and

a reporter module communicatively connected with the first data store and the second data store and configured to;

select sentence templates corresponding to associated annotations;

generate report paragraphs based on the annotations and the selected sentence templates; and

provide a report including the report paragraphs for the called variants and the associated annotations.