Dataset updated 12/19/2018
NG00080 - ExomeChip-Miami genotype and covariate files

Genotyping for the ExomeChip Miami dataset was performed on the Illumina HumanExome BeadChip v1.0 at Miami. 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.

Due to consent updates, the following IDs were removed:
MU-DUK269-2023
MU-DUK26099-100
MU-DUK26161-100
MU-DUK26328-1
MU-DUK26333-1
MU-IHG3401-21
MU-IHG33072-1
MU-VAN685-101


The covariate files were generated by ADGC in 2014. The only updates were to remove the IDs listed above.

These files have been divided by consent level: non-profit (ALL) or for-profit.
Subject Consent files: NG00080_ExomeChip_Miami_Consent_ALL.txt and NG00080_ExomeChip_Miami_Consent_forprofit.txt
Genotype files: ExomeChip_Miami.* and ExomeChip_Miami_forprofit.*
Covariate files: ExomeChip_Miami_covar.txt and ExomeChip_Miami_covar_forprofit.txt
Covariate Data Dictionary: ADGC_ExomeChip_Data_Dictionary.xlsx