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Chunk #15 — Methods — DNA preparation and assessment of allelic frequencies

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Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples.
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We have compared the patterns of human brain expression for the genes identified herein to those identified using a novel tool based on the distribution of expressed sequence tags (ESTs) contained in an annotated set of brain cDNA libraries (CYL, GRU et al, in preparation). Briefly, we identified 846 human cDNA libraries with cDNAs represented in dbEST. These libraries were constructed from regions of brains that appeared to display modest or no pathology. We based the analyses on two sets of criteria: 1) all entries in these libraries and 2) "more reliable" entries that display i) correct genomic orientation and either ii a) evidence for polyA tail or ii b) spliced structure (CYL, GRU et al, in preparation). For each brain region, we assessed the p-value for over-representation of expression of the dependence-associated genes using hypergeometric distribution tests with false discovery rate (FDR) corrections. Q-values < 0.05 were considered statistically significant.