Genechip 6

ROS/MAP samples were genotyped on the Affymetrix GeneChip 6.0 platform [8 (link)]. We performed sample and SNP quality control procedures on GWAS data (SNP call rate<95%, Hardy-Weinberg equilibrium test p < 10⁻⁶ in controls, and frequency filtering MAF<1%) were performed. After the standard quality control procedures for genetic markers and subjects, only non-Hispanic Caucasian participants were selected by clustering with CEU (Utah residents with Northern and Western European ancestry from the CEPH collection) + TSI (Toscani in Italia) populations using HapMap 3 genotype data and the multidimensional scaling (MDS) analysis [9 (link)]. Un-genotyped SNPs were imputed using MaCH and the 1000 Genomes Project as a reference panel [10 (link)]. Final SNP data used for the analysis is coded as the number of minor alleles.

SNP data were available from the ROSMAP cohort who had completed a range of personality trait questionnaires. Details on GWAS data generation have been described previously^{43 (link)}. Briefly, DNA for genotyping was collected from blood, lymphocytes or postmortem brain tissue. The majority of samples (N = 1,709) were genotyped on the Affymetrix GeneChip 6.0 platform and additional samples (N = 384) were genotyped on the Illumina OmniQuad Express platform. Imputation was performed by Alzheimer’s Disease Genetics Consortium on Michigan Imputation Server using the Haplotype Reference Consortium (HRC) reference panel (release 1.1). After quality control, the HRC imputed data were available in 2,182 ROSMAP participants. This dataset was used to identify significant SV2A SNPs associated with neuroticism and anxiety, based on a 10-item anxiety questionnaire (N = 1,706).
PLINK^{44 (link)} was used to test the effects of SNPs with minor allele frequency >1%, including imputed SNPs, to perform set-based tests for all SNPs that mapped to SV2A (±20 kilo-bases). The set-based parameters were r² = 0.5, p value = 0.05, maximum number of SNPs = 5, and max (T) permutations = 10,000. SV2A SNPs identified by PLINK were also cross-referenced against published summary statistics^{10 (link)} from the meta-analysis and GWAS for neuroticism and worry, with samples ranging from 340,569 to 390,278 individuals.

The discovery PWAS data were obtained from the dorsolateral prefrontal cortex (dPFC) of postmortem brain tissues from 376 subjects recruited by the Religious Orders Study/Memory and Aging Project (ROS/MAP) [19 (link)]. For proteome sequencing, isobaric tandem mass tag peptide labeling was utilized, and peptides were assessed using liquid chromatography coupled to mass spectrometry (MS) [20 (link)]. Wingo et al. [21 (link)] used Thermo Fisher Scientific’s Proteome Discoverer suite v.2.3 and tandem MS spectra to search against the standard UniProtKB human proteome database, which has 20,338 total sequences, to assign peptide spectral matches. Genotyping was done using whole-genome sequencing or genome-wide genotyping on the Illumina OmniQuad Express or Affymetrix GeneChip 6.0 platforms. Over 8356 proteins having both proteomic and genomic data, among which 1475 protein could find significant cis associations with genetic variation.