Single nucleotide polymorphisms in genes

Abstract

The invention provides nucleic acid segments of the human genome, particularly nucleic acid segments from a gene, including polymorphic sites. Allele-specific primers and probes hybridizing to regions flanking or containing these sites are also provided. The nucleic acids, primers and probes are used in applications such as phenotype correlations, forensics, paternity testing, medicine and genetic analysis. A role for the thrombospondin gene(s) in vascular disease is also disclosed. Use of single nucleotide polymorphisms in the thrombospondin gene(s) for diagnosis, prediction of clinical course and treatment response, development of therapeutics and development of cell-culture-based and animal models for research and treatment are disclosed.

1 . A method of diagnosing or aiding in the diagnosis of a vascular disease in an individual comprising 
 a) obtaining a nucleic acid sample from the individual; and    b) determining the nucleotide present at nucleotide position 2210 of the thrombospondin-1 gene,    wherein presence of a G at nucleotide position 2210 is indicative of increased likelihood of a vascular disease in the individual as compared with an individual having an A at nucleotide position 2210, and wherein presence of an A at nucleotide position 2210 is indicative of decreased likelihood of a vascular disease in the individual as compared with an individual having a G at nucleotide position 2210.    
     
     
         2 . The method of  claim 1 , wherein the thrombospondin-1 gene has the nucleotide sequence of SEQ ID NO: 1.  
     
     
         3 . The method of  claim 1 , wherein the vascular disease is selected from the group consisting of atherosclerosis, coronary heart disease, myocardial infarction, stroke, peripheral vascular diseases, venous thromboembolism and pulmonary embolism.  
     
     
         4 . A method for predicting the likelihood that an individual will have a vascular disease, comprising the steps of: 
 a) obtaining a DNA sample from an individual to be assessed; and    b) determining the nucleotide present at nucleotide position 2210 of the thrombospondin-1 gene,    wherein presence of a G at nucleotide position 2210 is indicative of increased likelihood of a vascular disease in the individual as compared with an individual having an A at nucleotide position 2210.    
     
     
         5 . The method according to  claim 4 , wherein the thrombospondin-I gene has the nucleotide sequence of SEQ ID NO: 1.  
     
     
         6 . The method according to  claim 4 , wherein the individual is an individual at risk for development of a vascular disease.  
     
     
         7 . The method according to  claim 4 , wherein the vascular disease is selected from the group consisting of atherosclerosis, coronary heart disease, myocardial infarction, stroke, peripheral vascular diseases, venous thromboembolism and pulmonary embolism.  
     
     
         8 . A nucleic acid molecule comprising all or a portion of the nucleic acid sequence of SEQ ID NO: 1 wherein said nucleic acid molecule is at least 10 nucleotides in length and wherein the nucleic acid sequence comprises a polymorphic site at nucleotide position 2210 of SEQ ID NO: 1.  
     
     
         9 . The nucleic acid molecule according to  claim 8 , wherein the nucleotide at the polymorphic site is different from a nucleotide at the polymorphic site in a corresponding reference allele.  
     
     
         10 . An allele-specific oligonucleotide that hybridizes to the nucleic acid molecule of  claim 8 .  
     
     
         11 . A peptide of SEQ ID NO: 2 which is at least ten contiguous amino acids, wherein the peptide comprises the serine at amino acid position 700 of SEQ ID NO: 2.  
     
     
         12 . A method of diagnosing or aiding in the diagnosis of a vascular disease in an individual comprising 
 a) obtaining a biological sample comprising thrombospondin-1 protein or relevant portion thereof from the individual; and    b) determining the amino acid present at amino acid position 700 of the thrombospondin-1 protein,    wherein presence of an asparagine at amino acid position 700 is indicative of increased likelihood of a vascular disease in the individual as compared with an individual having a serine at amino acid position 700, and wherein presence of a serine at amino acid position 700 is indicative of reduced likelihood of a vascular disease in the individual as compared with an individual having an asparagine at amino acid position 700.    
     
     
         13 . The method of  claim 12 , wherein the thrombospondin-1 protein has the amino acid sequence of SEQ ID NO: 2.  
     
     
         14 . The method of  claim 12 , wherein the vascular disease is selected from the group consisting of atherosclerosis, coronary heart disease, myocardial infarction, stroke, peripheral vascular diseases, venous thromboembolism and pulmonary embolism.  
     
     
         15 . A nucleic acid molecule comprising all or a portion of the nucleic acid sequence of SEQ ID NO: 3 wherein said nucleic acid molecule is at least 10 nucleotides in length and wherein the nucleic acid sequence comprises a polymorphic site at nucleotide position 1186 of SEQ ID NO: 3.  
     
     
         16 . The nucleic acid molecule according to  claim 15 , wherein the nucleotide at the polymorphic site is different from a nucleotide at the polymorphic site in a corresponding reference allele.  
     
     
         17 . An allele-specific oligonucleotide that hybridizes to the nucleic acid molecule of  claim 15 .  
     
     
         18 . A peptide of SEQ ID NO: 4 which is at least ten contiguous amino acids, wherein the peptide comprises the proline at amino acid position 387 of SEQ ID NO: 4.  
     
     
         19 . A method of diagnosing or aiding in the diagnosis of a vascular disease in an individual comprising 
 a) obtaining a biological sample comprising thrombospondin-4 protein or relevant portion thereof from the individual; and    b) determining the amino acid present at amino acid position 387 of the thrombospondin-4 protein,    wherein presence of an alanine at amino acid position 387 is indicative of increased likelihood of a vascular disease in the individual as compared with an individual having a proline at amino acid position 387, and wherein presence of a proline at amino acid position 387 is indicative of reduced likelihood of a vascular disease in the individual as compared with an individual having an alanine at amino acid position 387.    
     
     
         20 . The method of  claim 19 , wherein the thrombospondin-4 protein has the amino acid sequence of SEQ ID NO: 4.  
     
     
         21 . The method of  claim 19 , wherein the vascular disease is selected from the group consisting of atherosclerosis, coronary heart disease, myocardial infarction, stroke, peripheral vascular diseases, venous thromboembolism and pulmonary embolism.  
     
     
         22 . A nucleic acid molecule selected from the group consisting of the genes listed in the Table, wherein said nucleic acid molecule is at least 10 nucleotides in length and comprises a polymorphic site identified in the Table, wherein a nucleotide at the polymorphic site is different from a nucleotide at the polymorphic site in a corresponding reference allele.  
     
     
         23 . A nucleic acid molecule according to  claim 22 , wherein said nucleic acid molecule is at least 15 nucleotides in length.  
     
     
         24 . A nucleic acid molecule according to  claim 22 , wherein said nucleic acid molecule is at least 20 nucleotides in length.  
     
     
         25 . A nucleic acid molecule according to  claim 22 , wherein the nucleotide at the polymorphic site is the variant nucleotide for the gene listed in the Table.  
     
     
         26 . An allele-specific oligonucleotide that hybridizes to a portion of a gene selected from the group consisting of the genes listed in the Table, wherein said portion is at least 10 nucleotides in length and comprises a polymorphic site identified in the Table, wherein a nucleotide at the polymorphic site is different from a nucleotide at the polymorphic site in a corresponding reference allele.  
     
     
         27 . An allele-specific oligonucleotide according to  claim 26  that is a probe.  
     
     
         28 . An allele-specific oligonucleotide according to  claim 26 , wherein a central position of the probe aligns with the polymorphic site of the portion.  
     
     
         29 . An allele-specific oligonucleotide according to  claim 26  that is a primer.  
     
     
         30 . An allele-specific oligonucleotide according to  claim 29 , wherein the 3′ end of the primer aligns with the polymorphic site of the portion.  
     
     
         31 . An isolated gene product encoded by a nucleic acid molecule according to  claim 22 .  
     
     
         32 . A method of analyzing a nucleic acid sample, comprising obtaining the nucleic acid sample from an individual; and determining a base occupying any one of the polymorphic sites shown in the Table.  
     
     
         33 . A method according to  claim 32 , wherein the nucleic acid sample is obtained from a plurality of individuals, and a base occupying one of the polymorphic positions is determined in each of the individuals, and wherein the method further comprising testing each individual for the presence of a disease phenotype, and correlating the presence of the disease phenotype with the base.