Method and system for providing a polymorphism database

• US 6,484,183 B1
• Filed: 07/24/1998
• Issued: 11/19/2002
• Est. Priority Date: 07/25/1997
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Berno, Anthony, Baid, Joyti, Balaban, David J.
• Primary Examiner(s): Mizrahi, Diane D.
• Application Number:
  US09/122,169
• Time in Patent Office: 1,579 Days
• Field of Search: 707/4, 707/10, 707/100, 707/101, 707/103, 707/104, 435/325
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: H04M 1/006 Call diverting means
• CPC Class Codes: H04M 1/724 User interfaces specially adapted for cordless or mobile telephones
• CPC Class Codes: H04M 2207/206 composed of PSTN and wireless network
• CPC Class Codes: H04M 3/46 Arrangements for calling a number of substations in a predetermined sequence until an answer is obtained
• CPC Class Codes: H04M 3/54 Arrangements for diverting calls for one subscriber to another predetermined subscriber based on the calling party profile H04M3/42059; based on location H04M3/42348; based on presence H04M3/42365; to voice mail H04M3/53308
• CPC Class Codes: Y10S 128/922 including image analysis
• CPC Class Codes: Y10S 707/925 Drafting an application
• CPC Class Codes: Y10S 707/955 Object-oriented
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching
• CPC Class Codes: Y10S 707/99934 Query formulation, input preparation, or translation
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of subjects, samples, experiments, chips, etc.

Claims

1. A computer program embodied on a computer-readable medium comprising:

an item table listing a plurality of item records identifying items, wherein said item records are used in a biological analysis;

an item attribute table listing a plurality of item attribute records identifying attributes of said items; and

wherein an association is defined between a subset of the item records and a plurality of item attribute records.

2. The computer, program of claim 1 wherein said biological analysis comprises a polymorphism analysis.

3. A computer program embodied on a computer-readable storage medium comprising:

an atom result table listing a plurality of atom result records, specifying relative wild-type and mutant sequence concentrations in targets; and

a subject sequence position table listing a plurality of subject sequence position records, specifying combinations of subjects from whom said targets are derived and sequence positions, each said atom result record being associated with one or more atom result records.

4. The computer program of claim 3 wherein said atom result records further specify upper and lower bounds for said concentrations.

5. The computer program of claim 3 further comprising:

one or more instructions for accessing a subject table listing subject records specifying said subjects.

6. A computer program embodied in a computer-readable medium comprising:

one or more instructions for accessing a polymorphism table listing polymorphism sequence records specifying sequences known to contain polymorphisms; and

one or more instructions for accessing a patent application table listing patent application records specifying one or more polymorphisms specified by said. polymorphism sequence records.

7. The computer program of claim 6 wherein said polymorphism sequence records specify for each one of said polymorphisms a polymorphism position, a reference allele, and a base allele.

8. The computer program of claim 7 wherein said polymorphism sequence records further specify for each one of said polymorphisms a measured heterozygocity.

9. A method of creating a database in a computer system, the method comprising:

creating an item table listing a plurality of item records identifying items used in biological analysis; and

creating an item attribute table listing a plurality of item attribute records identifying attributes of said items; and

wherein an association is defined between a subset of the item records and a plurality of item attribute records.

10. The method of claim 9 further comprising the step of:

creating an item attribute item map table defining said association between a subset of the item records and a plurality of item attribute records, said item attribute item map table listing a plurality of map records identifying both a particular item attribute and a particular item.

11. The method of claim 9 comprising:

an item derivation table listing a plurality of item derivation records identifying transformations between said items used in biological analysis.

12. The method of claim 11 further comprising:

creating a protocol table listing a plurality of protocol records specifying parameters of said transformation.

13. The method of claim 9 wherein said biological analysis comprises a polymorphism analysis.

14. A method for creating data relationships in a computer system, the method comprising:

creating an atom result table listing a plurality of atom result records, specifying relative wild-type and mutant sequence concentrations in targets; and

creating a subject sequence position table listing a plurality of subject sequence position records, specifying combinations of subjects from whom said targets are derived and sequence positions, each said atom result record being associated with one or more atom result records.

15. The method of claim 14 wherein said atom result records further specify upper and lower bounds for said concentrations.

16. The method of claim 14 further comprising:

creating a subject table listing subject records specifying said subjects.

17. A method for creating data relationships in a computer system, the method comprising:

creating a polymorphism table listing polymorphism sequence records specifying sequences known to contain polymorphisms; and

creating a patent application table listing patent application records specifying one or more polymorphisms specified by said polymorphism sequence records.

18. The method of claim 17, wherein said polymorphism sequence records specify for each one of said polymorphisms a polymorphism position, a reference allele, and a base allele.

19. The method of claim 18, wherein said polymorphism sequence records further specify for at least one of said polymorphisms a measured heterozygocity.