Chunk #16 — Materials and Methods — Subjects, genotyping and assignment of nominal significance of dependent vs control allele frequencies in each sample — 4) Monte Carlo methods for assignment of levels of significance to: a) the extent of clustering in each sample and b) the degree to which clustered nominally-positive SNPs from multiple independent samples identify the same chromosomal regions

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Genomic regions identified by overlapping clusters of nominally-positive SNPs from genome-wide studies of alcohol and illegal substance dependence.

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Secondary analysis of dbGAP data used permutation approaches as implemented in PLINK (v1.06) (http://pngu.mgh.harvard.edu/purcell/plink/) [25]. We randomized assignment of the phenotypes to data derived from the current SNPs and analyzed the data from 3,000 permutation trials that addressed each of several null hypotheses (see below).