Genotyping for the ExomeChip WashU dataset was performed on the Illumina HumanExome BeadChip v1.0 at WashU. One variant rs75932628 (p.R47H) in TREM2 clustered poorly across all ADGC cohorts, and was therefore re-genotyped using a Taqman assay. Data on all samples underwent standard quality control procedures applied to genome-wide association studies (GWAS), including excluding variants with call rates <95%, and then filtering samples with call rate <95%.
Variants with MAF>0.01 were evaluated for departure from HWE and any variants for PHWE<10-6 were excluded.
Population substructure within each of the five ExomeChip ADGC subsets (NorthShore, Miami, WashU, CHOP, and ADC7) was examined using PC analysis in EIGENSTRAT4, and population outliers (>6 SD) were excluded from further analyses; the first three PCs were adjusted for as covariates in association testing.
Prior to analysis, the alternate and reference alleles were harmonized over all datasets. All sample genotyping and quality control was performed blind to participant’s disease status.
The exome chip data was first reported in the Sims et al. publication.
Detailed information about the dataset is provided in the following document: NG00085_ExomeChip_WashU_README.txt