Abstract
Background Associations of several Single Nucleotide Polymorphisms (SNPs) with common diseases like Coronary Artery Disease (CAD), Crohn’s Disease (CD), Hypertension (HT), Bipolar Disorder (BD), Type 1 Diabetes (T1D), Type 2 Diabetes (T2D) and Rheumatoid Arthritis (RA) were identified in a study conducted by the Wellcome Trust Case Control Consortium (WTCCC) (1). WTCCC study compared the effects of genetic variations in 14,000 cases and 3000 shared controls and identified 24 independent associations with the diseases mentioned above using the genotype information of approximately 500,000 directly genotyped SNPs and genotype information simulated at 2.8 million loci studied by the International Hapmap Project(2). We hypothesize that there are more chances of finding association of rare SNPs with diseases by refined analysis of non-synonymous SNPs (nsSNPs) in genome wide association studies. In the present study we analyzed the association of 12,660 nsSNPs using a case control study in the WTCCC population.
Highlights
Associations of several Single Nucleotide Polymorphisms (SNPs) with common diseases like Coronary Artery Disease (CAD), Crohn’s Disease (CD), Hypertension (HT), Bipolar Disorder (BD), Type 1 Diabetes (T1D), Type 2 Diabetes (T2D) and Rheumatoid Arthritis (RA) were identified in a study conducted by the Wellcome Trust Case Control Consortium (WTCCC) (1)
Materials and methods We simulated the genotypes at 10,798 non-synonymous SNPs (nsSNPs) loci studied by the Stage 2 HapMap project using the genotype information from WTCCC for all 14,000 individuals studied for seven diseases and in 3000 controls
We found 2 nsSNPs associated with BD, 2 with Coronary Artery Disease, 7 with CD, 1 with HT, 22 with RA, 17 with T1D and 2 with T2D
Summary
Associations of several Single Nucleotide Polymorphisms (SNPs) with common diseases like Coronary Artery Disease (CAD), Crohn’s Disease (CD), Hypertension (HT), Bipolar Disorder (BD), Type 1 Diabetes (T1D), Type 2 Diabetes (T2D) and Rheumatoid Arthritis (RA) were identified in a study conducted by the Wellcome Trust Case Control Consortium (WTCCC) (1). Materials and methods We simulated the genotypes at 10,798 nsSNP loci studied by the Stage 2 HapMap project using the genotype information from WTCCC for all 14,000 individuals studied for seven diseases and in 3000 controls. These simulations were done using the genetic recombination map of the respective regions obtained from the haplotypes of Hapmap European population.
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