Helix tree

Adherence to Hardy-Weinberg equilibrium was determined using the chi-square test in Haploview version 4 (Barrett et al. 2005 (link)). Analyses of SCZ cases with history of suicide attempt versus SCZ cases without were done using Fisher’s Exact Tests both in terms of allele frequencies and genotype frequencies. Haplotype analyses were done using UNPHASED version 3.1.5 (Dudbridge 2008 (link)) for the analysis of history of suicide attempt. Haplotypes with frequencies of less than 5% were excluded from the analyses. For multiple-testing correction, our study of nineteen single-nucleotide polymorphisms was equivalent to testing twelve independent markers (Nyholt et al. 2004 (link); Li and Ji 2005 (link)). Thus, the significance threshold was adjusted to 0.0042. Gene-gene interaction analyses were performed using HELIXTREE (GoldenHelix; e.g., (Zai et al. 2008 (link))), and the significant analyses (after Bonferroni correction) were validated with the R package Model-Based Multifactor Dimensionality Reduction version 2.6 (MB-MDR) (Calle et al. 2010 (link)) as well as SPSS version 15 (IBM). The significance of the model was determined by running 1000 permutations. The meta-analysis, which incorporated replication samples, was carried out in STATA version 8.

Plasma HIV RNA levels were measured using the NASBA/NuciSens HIV RNA assay (BioMerieux, Durham, NC, USA), in laboratories certified by the NIH National Institute of Allergy and Infectious Diseases Virology Quality Assurance Certification Program. HCV and HBV serological markers were performed using standard commercial assays and included hepatitis C antibody by EIA 3.0 (Ortho-Clinical Diagnostics, Raritan, NJ, USA) and hepatitis B surface antigen (HBsAg) (Abbott Laboratories, Abbott Park, IL, USA). HCV RNA levels were measured by the COBAS Amplicor Monitor 2.0 assay (Roche Diagnostics, Branchburg, NJ, USA) with a linear range of 600–700 000 IU/mL, or COBAS TaqMan (Roche Diagnostics), with a linear range of 10–2.0 × 10⁸ IU/mL. Genotyping for rs368234815 (ss469415590) was performed at the Laboratory of Translational Genomics National Cancer Institute with custom TaqMan allelic discrimination genotyping assays, as previously described [14 (link)]. IFNL3/IFNL4 SNPs were genotyped as part of the WIHS genomewide association study using the IlluminaOmni2.5-quad beadchip (Illumina Inc, San Diego, CA, USA). Ancestry informative marker SNPs were selected using Helix Tree (Golden Helix, Bozeman, MT, USA).