Variant database

• US 9,298,804 B2
• Filed: 07/11/2014
• Issued: 03/29/2016
• Est. Priority Date: 04/09/2012
• Status: Active Grant

• Current Assignee: Invitae Corporation
• Original Assignee: Good Start Genetics, Inc. (Invitae Corporation)
• Inventors: Nizzari, Marcia M., Breton, Benjamin H., Tefft, David L., Haurie, Xavier S.
• Primary Examiner(s): Chaki, Kakali
• Assistant Examiner(s): Figueroa, Kevin W
• Application Number:
  US14/329,243
• Publication Number:
  US 20140324869A1
• Time in Patent Office: 627 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: G06F 16/285 Clustering or classification
• CPC Class Codes: G06N 5/02 Knowledge representation; Symbolic representation
• 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

The invention provides a system and method for describing polymorphisms or genetic variants based on information about mutations and relationships among them. The invention uses object-oriented concepts to describe variants as variant objects and relations among those variants as variant relation object, each object being an instance of an abstract class of genomic feature and able to contain any number of other objects. Information about genetic disorders is stored in association with the object that represents the pathogenic variant. Genetic test results are used to access corresponding objects to provide a report based on variants or polymorphisms in a patient'"'"'s genetic material.

Claims

1. A method of describing mutations in a patient genome, the method comprising using a computer system comprising a memory coupled to a processor for:

receiving data representing a first mutation and a second mutation in the patient genome;

creating a first instance of an abstract class of genomic feature and storing in the first instance a number representing a start position in a reference human genome and at least one IUPAC character representing a nucleotide found in the patient genome at the start position and not found in the reference human genome;

creating a second instance of the abstract class and storing in the second instance a second number representing a second start position, different from the first start position, in the reference human genome and at least one second IUPAC character representing a nucleotide found in the patient genome at the second start position and not found in the reference human genome;

creating a third instance of the abstract class and storing in the third instance;

the first instance, the second instance, and a description of a relationship between the first instance and the second instance; and

describing the mutations in the patient genome based on the third instance.

2. The method of claim 1, further comprising:

receiving data identifying a genomic region; and

creating a fourth instance of the abstract class, the fourth instance comprising a description of a relationship between the genomic region and the first mutation and the second mutation.

3. The method of claim 2, wherein the genomic region is identified as one selected from the list consisting of:

exon, intron, gene, and ORF.

4. The method of claim 2, wherein the genomic region is identified as one selected from the list consisting of:

regulatory region, promoter, splice site, and non-coding region.

5. The method of claim 2, wherein the genomic region is identified as one selected from the list consisting of:

epigenetically modified region and methylated sequence.

6. The method of claim 2, wherein the genomic region is identified as one selected from the list consisting of:

protein motif and protein secondary structure.

7. The method of claim 1, wherein the first mutation is not already stored within the computer system.

8. The method of claim 7, further comprising storing the first instance in one or more computer storage devices.

9. A system for providing a description of a variant in a patient'"'"'s genome, the system comprising:

a processor; and

a computer-readable storage device containing instructions which when executed by the processor cause the system to

receive data representing a first mutation and a second mutation in the patient'"'"'s genome;

create a first instance of an abstract class of genomic feature and store in the first instance a number representing a start position in a reference human genome and at least one IUPAC character representing a nucleotide found in the patient genome at the start position and not found in the reference human genome;

create a second instance of the abstract class and store in the second instance a second number representing a second start position—

different from the first start position—

in the reference human genome and at least one second IUPAC character representing a nucleotide found in the patient genome at the second start position and not found in the reference human genome comprising a description of the second mutation as a variant of the reference;

create a third instance of the abstract class and store in the third instance;

the first instance, the second instance, and a description of a relationship between the first instance and the second instance; and

provide a description of the genome based on the third instance.

10. The system of claim 9, further operable to:

receive data identifying a genomic region; and

create a fourth instance of the abstract class, the fourth instance comprising a description of a relationship between the genomic region and the first mutation and the second mutation.

11. The system of claim 10, wherein the genomic region is identified as one selected from the list consisting of:

exon, intron, gene, and ORF.

12. The system of claim 10, wherein the genomic region is identified as one selected from the list consisting of:

regulatory region, promoter, splice site, and non-coding region.

13. The system of claim 10, wherein the genomic region is identified as one selected from the list consisting of:

epigenetically modified region and methylated sequence.

14. The system of claim 10, wherein the genomic region is identified as one selected from the list consisting of:

protein motif and protein secondary structure.

15. The system of claim 9, wherein the first mutation is not already stored within the system.

16. The system of claim 15, further operable to store the first instance in one or more computer storage devices.