Chunk #11 — Materials and Methods — Subjects, genotyping and assignment of nominal significance of dependent vs control allele frequencies in each sample — 3) Identification of chromosomal regions containing clusters of SNPs with nominally-significant case vs control differences in single or multiple samples
We performed analyses based on previously-defined criteria using datasets of approximately 1 million SNPs [21]. We identified chromosomal regions of interest in individual samples by seeking regions in which at least 4 clustered SNPs displayed case vs control differences with nominal, p<0.05 levels of statistical significance. We defined clustering based on separation of each clustered SNP from the nearest nominally-significant SNP by ≤10 kb. We identified similarities between the results obtained from multiple samples by identifying the chromosomal regions that were tagged by such clustered, nominally positive SNPs in each of the samples of individuals from the same racial/ethnic groups. We identified genes for which these chromosomal intervals lay within the exons of the gene and/or in 10 kb of 5′ or 3′ flanking sequence.
