Polymorphisms in known genes associated with human disease, methods of detection and uses thereof

• US 20070037165A1
• Filed: 09/15/2004
• Published: 02/15/2007
• Est. Priority Date: 09/08/2000
• Status: Abandoned Application

• Current Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Rowe, William, Naik, Ashwinikumar, Zhang, Jinghui, Woodage, Trevor, Kalush, Francis, Subramanian, Gangadharan, Liu, Xiangjun, Venter, J., Cravchik, Anibal
• Application Number:
  US10/940,774
• Publication Number:
  US 20070037165A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention is based on the discovery of novel polymorphisms (SNPs) in the genes known in the art to contribute to human disease. Such polymorphisms can lead to a variety of disorders that are mediated/modulated by a variant human disease associated protein. The present invention provides reagents used for detecting and expressing the variant nucleic acid/protein sequence as well as methods of identifying and using these variants.

Claims

1. A detection reagent capable of detecting one or more single nucleic acid polymorphisms selected from group consisting of the SNPs provided in Table 1.

6. A method of determining whether a trait is linked to one of the human chromosomes, or a sub-region thereof, comprising the steps of determining whether said trait is linked to one or more SNPs using the detection reagents of claim 1.

19. The detection reagent of claim 1, wherein the detection reagent is a nucleic acid array.

20. A kit comprising at least one container, wherein the at least one container contains a detection reagent of claim 1.

2. A detection reagent capable of detecting 100 or more single nucleic acid polymorphisms selected from group consisting of the SNPs provided in Table 1.

7. A method of determining whether a trait is linked to one of the human chromosomes, or a sub-region thereof, comprising the steps of determining whether said trait is linked to one or more SNPs using the detection reagents of claim 2.

3. A detection reagent capable of detecting 500 or more single nucleic acid polymorphisms selected from group consisting of the SNPs provided in Table 1.

8. A method of determining whether a trait is linked to one of the human chromosomes, or a sub-region thereof, comprising the steps of determining whether said trait is linked to one or more SNPs using the detection reagents of claim 3.

4. A detection reagent capable of detecting 1000 or more single nucleic acid polymorphisms selected from group consisting of the SNPs provided in Table 1.

9. A method of determining whether a trait is linked to one of the human chromosomes, or a sub-region thereof, comprising the steps of determining whether said trait is linked to one or more SNPs using the detection reagents of claim 4.

5. A detection reagent capable of detecting 5000 or more single nucleic acid polymorphisms selected from group consisting of the SNPs provided in Table 1.

10. A method of determining whether a trait is linked to one of the human chromosomes, or a sub-region thereof, comprising the steps of determining whether said trait is linked to one or more SNPs using the detection reagents of claim 5.

11. A computer system for studying SNP linkage, said system comprising storage means containing the SNP information in Table 1 or a subset thereof specific for human one of the human chromosomes mapping studies.

12. Computer readable medium having stored therein the SNP relational information provided on Table 1.

13. An isolated nucleic acid molecule for detecting at least one SNP provided in Table 1, wherein the nucleic acid molecule comprises at least about 12 contiguous nucleotides selected from the group consisting of SEQ ID NOS:

17,012 and fragments thereof.

14. The isolated nucleic acid molecule of claim 13, wherein the at least about 12 contiguous nucleotides hybridize to a SNP identified in Table 1.

15. The isolated nucleic acid molecule of claim 13, wherein the at least about 12 contiguous nucleotides are adjacent to the SNP.

16. A method of genotyping at least one SNP position provided in Table 1 in a sample, the method comprising contacting the sample with a detection reagent that differentiates between alternative alleles at at least one SNP position provided in Table 1, and determining which allele is present at the at least one SNP position.

17. A method of identifying an individual having or at risk of developing a disorder, the method comprising the step of genotyping at least one SNP in a nucleic acid sample from said individual, wherein the at least one SNP is selected from the group consisting of the SNPs provided in Table 1.

18. The method of claim 17, wherein the disorder is a human disease identified in Table 1.