Addiction biology snp array

DNA was genotyped using the Illumina Addiction biology SNP array using the Illumina GoldenGate platform (Hodgkinson et al., 2008 (link)). GABRA2 SNP rs279858 (exon 5, K132K) was examined given prior work demonstrating associations between the minor allele and problem behavior and maladaptive personality (Trucco et al., 2014 (link); Villafuerte et al., 2013 (link)). All MLS participants (n=1139) were also genotyped for 150 ancestry informative markers (Hodgkinson et al., 2008 (link)), and ethnic factor scores were calculated using principal component analysis in SAS 9.3 as in prior work (Glaser et al., 2014 (link)). The four scores explaining the highest variance (~96%) were examined to control for population stratification.

Three GABRA2 SNPs were selected for this study (rs279827, rs279826, and rs279858) to correspond to previous work (e.g., Dick et al., 2009 (link)). For simplicity and clarity, findings focus on SNP rs279827 given previous haplotype analyses conducted on this sample demonstrates high linkage disequilibrium across these SNPs (r² = .80–.92; Villafuerte et al., 2013 (link)). As expected when SNPs are highly correlated, findings were largely consistent across SNPs. SNP rs279827 was chosen for its potential as a functional SNP. It is located next to an acceptor splice site (Tian, Chen, Cross, & Edenberg, 2005 (link)). SNP rs279827 was included in the Illumina Addiction biology SNP array designed by Hodgkinson and colleagues (2008) (link), a panel genotyped in the MLS sample using the Illumina GoldenGate platform (Illumina Inc., San Diego, CA). SNPs rs279826 (intron 4) and rs279858 (exon 5, K132K) were genotyped by Taqman (Villafuerte et al., 2012 (link)). We included duplicates (78 for the array and 12 for the Taqman assay) and no discrepancies were observed. All SNPs were in Hardy–Weinberg equilibrium.

DNA was genotyped using the Illumina Addiction biology SNP array (Hodgkinson et al., 2008 (link)) a panel genotyped in the MLS sample using the Illumina GoldenGate platform (Ilumina Inc,. San Diego, CA). Three SNPs were examined in this study (rs279858, rs279826, and rs279827) as they represent a haplotype block associated with alcohol dependence (Edenberg et al., 2004 (link); Villafuerte et al., 2012 (link)), they represent potential functional SNPs (exonic and splice), and they correspond with previous work on GxE interactions (e.g., Dick et al., 2009 (link); Heitzeg et al., 2014 (link)). SNPs rs279858 and rs279826 are in strong LD (r2 > 0.77) with rs279827. Duplicates were included and no discrepancies were observed. All SNPs were in Hardy-Weinberg equilibrium. Findings focus on SNP rs279858 (exon 5, K132K; AA 31.0% [n=93], AG 51.0% [n=153], and GG 18.0% [n = 54]) for simplicity and clarity, although findings were consistent across SNPs and the haplotype block.