We’re moving! Datasets in the NIAGADS database are being transitioned to the DSS database, more info coming soon.
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
This dataset is part of the Knight ADRC Collection. Other datasets in this collection can be found at: https://www.niagads.org/knight-adrc-collection
This work was supported by grants from the National Institutes of Health (R01AG044546, P01AG003991, RF1AG053303, R01AG058501, U01AG058922, RF1AG058501 and R01AG057777). The recruitment and clinical characterization of research participants at Washington University were supported by NIH P50 AG05681, P01 AG03991, and P01 AG026276. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, and the Departments of Neurology and Psychiatry at Washington University School of Medicine.
We thank the contributors who collected samples used in this study, as well as patients and their families, whose help and participation made this work possible. This work was supported by access to equipment made possible by the Hope Center for Neurological Disorders, and the Departments of Neurology and Psychiatry at Washington University School of Medicine.