Axiom biobank genotyping array

Genome-wide SNP data were generated using the Affymetrix (Santa Clara, CA) Axiom Biobank Genotyping Array for all Peruvian Andean and Mexican Maya study participants. We performed a PCA using 405,419 variants that were filtered for linkage disequilibrium (r² > 0.8) and genotyping rate (<0.1) in Plink 2.0 (Purcell et al. 2007 (link); Chang et al. 2015 (link)) (fig. 1). PCA included publicly available data from the 1000 Genomes Project for 60 Yorubans (YRI), 45 CHB, 45 Japanese from Tokyo (JPT), and 60 individuals of north-central European ancestry (CEU) from the Human Genome Diversity Project-Centre d’Etude du Polymorphisme Humain (HGDP-CEPH) (1000 Genomes Project Consortium). Participant relatedness was estimated using KING (Manichaikul et al. 2010 (link)) in PLINK 2.0. Three individuals related at the first-degree level and six individuals related at the second-degree level were identified and excluded from genotype–phenotype association testing. Standard linear regression was performed in PLINK using dominant and additive models of inheritance (Purcell et al. 2007 (link)). Regression coefficients were calculated for the minor allele. Participant sex and the first five PCs were included as covariates in the models.

RNA was extracted from the brain tissues using the Qiagen RNeasy kit (Qiagen, Germantown, MD, USA). The RNA-seq samples were prepared using the TruSeq RNA Library Pre Kit v2 (Illumina, Inc., San Diego, CA, USA) and sequenced on the Illumina HiSeq 2000. Paired-end libraries with an average insert size of 180 bp were obtained. Raw reads were aligned to human genome 19 (hg19) using STAR aligner version 2.5.3.a [15 (link)]. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to evaluate RNA sequence quality. The RNA-seq data is available through the NCBI BioProject database (BLA: PRJNA551909, CE: PRJNA551908, NAC: PRJNA551775, SFC: PRJNA530758).
DNA was obtained from the same brain tissues. The Axiom Biobank Genotyping Array (Thermo Fisher Scientific, Waltham, MA, USA) was used for genotyping. Monomorphic variants, variants with call rate ≤0.98 or Hardy–Weinberg equilibrium p < 10⁻⁵, and samples with call rate <0.90 were removed using PLINK [16 (link)]. Phasing was done using SHAPEIT2 [17 (link)]. IMPUTE2 [18 (link)] was used for imputation using the 1000 Genomes Phase 1 integrated panel (excluding singleton variants) as the reference. Variants with imputation score ≥0.8 and estimated minor allele frequency (MAF) ≥0.5 were included in the analysis.