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Chunk #36 — Materials and Methods — Resequencing of nAChR Genes, SNP Selection, and Genotyping

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A candidate gene approach identifies the CHRNA5-A3-B4 region as a risk factor for age-dependent nicotine addiction.
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DNA samples were obtained from all subjects. The resequencing sample comprised 144 smokers identified by a multiple predictor model with unit weighting as being either high or low on a broad range of dependence measures (e.g., relapse likelihood, withdrawal severity; N = 144) and an additional group of lifetime nonsmokers (N = 48). The University of California Santa Cruz genome browser was used to extract positions of proximal promoters and RefSeq exons for CHRNA2, CHRNA3, CHRNA4, CHRNA5, CHRNA6, CHRNA7 (unique 5′ only), CHRNA9, CHRNA10, CHRNB2, CHRNB3 and CHRNB4. Exons, genomic sequences conserved in mouse, and ∼1 kb of 5′ and 3′ flanking regions were targeted by DNA sequencing, as previously described [65]. The resequencing scan surveyed a total range of 56,620 nts. in each of 192 individuals of Northern European descent; survey coordinates from NCBI Build 35 for genomic ranges surveyed with a Phrap quality score of >30 are: CHRNA2 [Chr. 8] 27374096::27375538, 27376211::27377643, 27380318::27381167, 27382561::27383658, 27384018::27384835, 27392219::27392738 nts.; CHRNA5-CHRNA3-CHRNB4 [Chr. 15] 76644811::76645440, 76651089::76651811, 76659985::76660542, 76665576::76666420, 76667214::76668294, 76668898::76670309, 76672128::76676199, 76680573::76681761, 76696115::76696969, 76697824::76698624, 76700082::76700676, 76703348::76704858, 76708170::76709554, 76710234::76710990, 76713688::76715398, 76720101::76721040 nts.; CHRNA4