MEGA chip subject genotype for PMDBS samples. ASAP CRN - Team Scherzer

Genotype of subjects contributing PMDBS samples. This dataset details the genotype for subjects contributing samples to our snRNAseq PMDBS datasets (e.g. scherzer-sn-rnaseq-mtg and scherzer-sn-rnaseq-mtg-hybsel) as a tar.gz archive of PLINK outputs (.bed, .bim, .fam, .log, and .nosex files). Methods Summary: All subjects were genotyped by Multi-Ethnic Genotyping Array (MEGA) using the Infinium Multi-Ethnic Global-8 v1 kit (Illumina, #WG-316-1001) following manufacturer’s instructions and using the DNA extracted from brain tissue. Additional information about this chip, pls see: https://support.illumina.com/downloads/infinium-multi-ethnic-global-8-v1-support-files.html. PLINK (v1.9beta) were applied to perform rigorous subject and SNP quality control (QC) for each dataset in the following order (Extended Data Fig.1): (1) remove variants with GenCall score (GC) < 0.15; (2) remove subjects with call rate < 95%; (3) remove subjects with gender misidentification; (4) remove SNPs with genotype call rate < 95%; (6) remove SNPs with Hardy-Weinberg Equilibrium testing P value < 1e-6; (6) remove SNPs with informative missingness test (Test-mishap) P value < 1e-9; (7) remove SNPs with minor allele frequency (MAF) < 0.01; (8) remove subjects with outlying heterozygosity rate based on heterozygosity F score (beyond 4-fold sd from the mean F score); (9) IBS/IBD filtering: pairwise identity-by-state probabilities were computed for removing both individuals in each pair with IBD>0.9 and one subject of each pair with IBD > 0.1875; (10) Subjects were integrated with 1000 Genomes phase3 individuals and tested for population substructure by performing principal components analysis (PCA) using PLINK. Based on first and second principal components, significant genotypic outliers (non-European individuals) were excluded.