Method and apparatus for deriving the genome of an individual

• US 20080125978A1
• Filed: 10/11/2002
• Published: 05/29/2008
• Est. Priority Date: 10/11/2002
• Status: Abandoned Application

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Robson, Barry, Mushlin, Richard
• Application Number:
  US10/269,150
• Publication Number:
  US 20080125978A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium

Abstract

A computer-based method is provided for deriving a genome of an individual. The method comprises the steps of accessing a selector for an individual and a reference template for a group genome, the selector comprising a locus value and a base value; and processing the selector and the reference template to derive a sequence representative of the genome of the individual. The reference template preferably comprises data components representing a probability of occurrence of a base value. The probability of occurrence is based on base value occurrences at corresponding locus values in the group genome. The method of the present invention further comprises computing a base value from the data component in the reference template, for base values not in the selector.

Claims

1. A method for deriving a genome of an individual, comprising the steps of:

accessing a selector for an individual and a reference template for a group genome, the selector comprising a locus value and a base value; and

processing the selector and the reference template to derive a sequence representative of the genome of the individual.

2. The method of claim 1, wherein the locus value represents a position in a nucleotide sequence.

3. The method of claim 1, wherein the base value represents a nucleotide base.

4. The method of claim 1, wherein the selector comprises a plurality of locus values and a plurality of base values.

5. The method of claim 1, wherein the reference template comprises data components representing a base value.

6. The method of claim 5, wherein the data components represent a probability of occurrence for the base value.

7. The method of claim 6, wherein the probability of occurrence is based on base value occurrences at corresponding locus values in the group genome.

8. The method of claim 7, further comprising:

computing a base value from the data component in the reference template, for base values not in the selector.

9. The method of claim 8, further comprising the step of:

finding a maximum data component.

10. The method of claim 8, wherein the computed base value comprises a plurality of base values.

11. The method of claim 9, wherein the maximum data component represents a greatest probability of occurrence.

12. The method of claim 9, wherein finding the maximum component includes use of a mixture table.

13. A system comprising:

a memory that stores computer-readable code; and

a processor operatively coupled to the memory, the processor configured to implement the computer-readable code, the computer-readable code configured to;

access a reference template for a group genome and a selector for an individual, the selector comprising a locus value and a base value; and

process the reference template and the selector to derive a sequence representative of the genome of the individual.

14. The system of claim 13, wherein the reference template comprises data components representing a probability of occurrence of a base value.

15. The system of claim 14, wherein the probability of occurrence is based on base value occurrences at corresponding locus values in the group genome.

16. The system of claim 14, wherein the computer-readable code is further configured to:

compute a base value from the data component in the reference template, for base values not in the selector.

17. An article of manufacture comprising:

a computer-readable medium having computer-readable code embodied thereon, the computer-readable code comprising;

a step to access a reference template for a group genome and a selector for an individual, the selector comprising a locus value and a base value; and

a step to process the reference template and the selector to derive a sequence representative of the genome of the individual.

18. The article of manufacture of claim 17, wherein the reference template comprises data components representing a probability of occurrence of a base value.

19. The article of manufacture of claim 18, wherein the probability of occurrence is based on base value occurrences at corresponding locus values in the group genome.

20. The article of manufacture of claim 18, wherein the computer-readable code further comprises:

a step to compute a base value from the data component in the reference template, for base values not in the selector.