Genotyping was conducted with a modified single-nucleotide extension reaction, with allele detection by mass spectrometry (Sequenom MassArray system; Sequenom, San Diego, California). Polymerase chain reaction and extension primers (available on request) were designed using MassArray Assay Design Version 3.1.2.5 (Sequenom). All studies of GABRA2 and alcohol dependence, along with data from The International HapMap Project, have identified 2 linkage disequilibrium blocks in GABRA2.39 Moreover, all significant associations with alcohol dependence have been described with single-nucleotide polymorphisms (SNPs) in the larger haplotype block that extends downstream from intron 3. In the CDP sample, we genotyped 10 SNPs in GABRA2, selected based on evidence of association with alcohol dependence in the COGA sample. All SNPs genotyped in the CDP were located in the previously associated haplotype block. The overall genotyping success rate was 98.4%. A total of 24 biological and 12 technical replicates were genotyped and produced a concordance rate of 100%. All 10 SNPs were successfully genotyped for 96% of the samples. Because allele frequencies and linkage disequilibrium structures often differ across populations, we limited all analyses and data in this
