The ExomeChip CHOP dataset was genotyped on the Illumina HumanExome BeadChip v1.0 at CHOP.
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 ADGC ExomeChip 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: NG00081_ExomeChip_CHOP_README.txt
The US National Institutes of Health, National Institute on Aging (NIH-NIA) supported this work through the following grants: ADGC, U01 AG032984, and RC2 AG036528. Samples from the National Cell Repository for Alzheimer's Disease (NCRAD), which receives government support under a cooperative agreement grant (U24 AG21886) awarded by the National Institute on Aging (NIA), were used in this study. We thank the contributors who collected samples used in this study, as well as the patients and their families, whose help and participation made this work possible. Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer's Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689-01). Data samples are provided through NACC (U01 AG016976), NIA LOAD (Columbia University) (U24 AG026395, R01AG041797), Banner Sun Health Research Institute (P30 AG019610), Boston University (P30 AG013846, U01 AG10483, R01 CA129769, R01 MH080295, R01 AG017173, R01 AG025259, R01 AG048927, R01AG33193), Columbia University (P50 AG008702, R37 AG015473), Duke University (P30 AG028377, AG05128), Emory University (AG025688), Group Health Research Institute (UO1 AG006781, UO1 HG004610, UO1 HG006375), Indiana University (P30 AG10133), Johns Hopkins University (P50 AG005146, R01 AG020688), Massachusetts General Hospital (P50 AG005134), Mayo Clinic (P50 AG016574), Mount Sinai School of Medicine (P50 AG005138, P01 AG002219), New York University (P30 AG08051, UL1 RR029893, 5R01AG012101, 5R01AG022374, 5R01AG013616, 1RC2AG036502, 1R01AG035137), Northwestern University (P30 AG013854), Oregon Health & Science University (P30 AG008017, R01 AG026916), Rush University (P30 AG010161, R01 AG019085, R01 AG15819, R01 AG17917, R01 AG30146), TGen (R01 NS059873), University of Alabama at Birmingham (P50 AG016582), University of Arizona (R01 AG031581), University of California, Davis (P30 AG010129), University of California, Irvine (P50 AG016573), University of California, Los Angeles (P50 AG016570), University of California, San Diego (P50 AG005131), University of California, San Francisco (P50 AG023501, P01 AG019724), University of Kentucky (P30 AG028383, AG05144), University of Michigan (P50 AG008671), University of Pennsylvania (P30 AG010124), University of Pittsburgh (P50 AG005133, AG030653, AG041718, AG07562, AG02365), University of Southern California (P50 AG005142), University of Texas Southwestern (P30 AG012300), University of Miami (R01 AG027944, AG010491, AG027944, AG021547, AG019757), University of Washington (P50 AG005136), University of Wisconsin (P50 AG033514), Vanderbilt University (R01 AG019085), and Washington University (P50 AG005681, P01 AG03991). The Kathleen Price Bryan Brain Bank at Duke University Medical Center is funded by NINDS grant NS39764, NIMH MH60451, and by GlaxoSmithKline. Support was also provided by the Alzheimer's Association (L.A.F., IIRG-08-89720; M.P.-V., IIRG-05-14147), the US Department of Veterans Affairs Administration, the Office of Research and Development, the Biomedical Laboratory Research Program, and the BrightFocus Foundation (M.P.-V., A2111048). P.S.G.-H. is supported by the Wellcome Trust, the Howard Hughes Medical Institute, and the Canadian Institutes of Health Research. We thank D.S. Snyder and M. Miller from the NIA who are ex-officio ADGC members.