Chunk #145 — IV. Results of tests of clustering within individual samples and tests of convergence between replicate samples for the same phenotypes — E. Success in smoking cessation (Samples 12, 13, 14)
In comparing data from successful vs unsuccessful quitters from samples 12, 13 and 14, we identified 5,411, 4,539 and 4,894 SNPs whose allele frequencies differ between these successful and unsuccessful quitters with nominal p < 0.01 [36]. These nominally-positive SNPs cluster together to extents much greater than expected by chance if their allele frequencies were independent of each other (Monte Carlo p < 0.00001). For Sample 12, 1434 of the 5411 nominally-positive SNPs lay in 308 clusters in which each positive SNP lay within 100 kb of at least two other positive SNPs with representation from SNPs on both array types. For Samples 13 and 14, 2258 of the 4539 nominally-positive SNPs and 2184 of the 4894 nominally-positive SNPs lay in 820 and 861 clusters along with at least one other nominally-positive SNP. We thus observed clustering in each of these independent samples. We would anticipate such clustering if many of these nominally-positive SNPs identified haplotypes that were present in different frequencies in our samples of successful vs unsuccessful quitters, but not if they represented chance independent observations.
