Dataset updated 12/19/2018 NG00081 - ExomeChip-CHOP genotype and covariate files Genotyping for the ExomeChip CHOP dataset was performed 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. Due to consent updates as well as not having GDS for NIMH subjects, the following IDs were removed: ACT-ACT150402 ACT-ACT150544 ACT-ACT90088 ACT-ACT90159 ACT-ACT90167 ACT-ACT90188 ACT-ACT90207 ACT-ACT90210 ACT-ACT90269 ACT-ACT90285 ACT-ACT90295 ACT-ACT90307 ACT-ACT90332 ACT-ACT90348 ACT-ACT90419 ACT-ACT90422 ACT-ACT90456 ACT-ACT90466 ACT-ACT90510 ACT-ACT90536 ACT-ACT90591 ACT-ACT90596 ACT-ACT90608 ACT-ACT90619 ACT-ACT90690 ACT-ACT90697 ACT-ACT90709 ACT-ACT90717 ACT-ACT90767 ACT-ACT90797 ACT-ACT90844 ACT-ACT90858 ACT-ACT90861 ACT-ACT90906 ACT-ACT90915 ACT-ACT90917 ACT-ACT90993 ACT-ACT91058 ACT-ACT91107 ACT-ACT91196 ACT-ACT91209 ACT-ACT91225 ACT-ACT91239 ACT-ACT91302 ACT-ACT91310 ACT-ACT91393 ACT-ACT91427 ACT-ACT91428 ACT-ACT91432 ACT-ACT91444 ACT-ACT91447 ACT-ACT91456 ACT-ACT91489 ACT-ACT91516 ACT-ACT91521 ACT-ACT91538 ACT-ACT91549 ACT-ACT91590 ACT-ACT91627 ACT-ACT91635 ACT-ACT91672 ACT-ACT91720 ACT-ACT91731 ACT-ACT91733 ACT-ACT91746 ACT-ACT91776 ACT-ACT91800 ACT-ACT91807 ACT-ACT91887 ACT-ACT91924 ACT-ACT91929 ACT-ACT91950 ACT-ACT91955 ACT-ACT91994 ACT-ACT92021 ACT-ACT92038 ACT-ACT92085 ACT-ACT92086 ACT-ACT92093 ACT-ACT92116 ACT-ACT92130 ACT-ACT92147 ACT-ACT92154 ACT-ACT92156 ACT-ACT92198 ACT-ACT92212 ACT-ACT92222 ACT-ACT92225 ACT-ACT92242 ACT-ACT92321 ACT-ACT92362 ACT-ACT92378 ACT-ACT92380 ACT-ACT92433 ACT-ACT92437 ACT-ACT92441 ACT-ACT92465 ACT-ACT92489 ACT-ACT92496 ACT-ACT92613 ACT-ACT92665 ACT-ACT92734 ACT-ACT92755 ACT-ACT92756 ACT-ACT92791 ACT-ACT92850 ACT-ACT92870 ACT-ACT92929 ACT-ACT92930 ACT-ACT92964 ACT-ACT92992 ACT-ACT93065 ACT-ACT93068 ACT-ACT93091 ACT-ACT93173 ACT-ACT93180 ACT-ACT93243 ACT-ACT93277 ACT-ACT93307 ACT-ACT93332 ACT-ACT93341 ACT-ACT93361 ACT-ACT93371 ACT-ACT93375 ACT-ACT93388 ACT-ACT93435 ACT-ACT93446 ACT-ACT93500 ACT-ACT93523 ACT-ACT93577 ACT-ACT93603 ACT-ACT93615 ACT-ACT93711 ACT-ACT93734 ACT-ACT93736 ACT-ACT93740 ACT-ACT93748 ACT-ACT93755 ACT-ACT93797 ACT-ACT93844 ACT-ACT93890 ACT-ACT93910 ACT-ACT93971 ACT-ACT93994 ACT-ACT94058 ACT-ACT94065 ACT-ACT94158 ACT-ACT94173 ACT-ACT94207 ACT-ACT94218 ACT-ACT94249 ACT-ACT94272 ACT-ACT94310 ACT-ACT94407 ACT-ACT94460 ACT-ACT94472 ACT-ACT94519 ACT-ACT94534 ACT-ACT94663 ACT-ACT94756 ACT-ACT94830 ACT-ACT94870 ACT-ACT94889 ACT-ACT94925 ACT-ACT94973 ACT-ACT94977 ACT-ACT95088 ACT-ACT95123 ACT-ACT95140 ACT-ACT95206 ACT-ACT95231 ACT-ACT95300 ACT-ACT95313 ACT-ACT95334 ACT-ACT95348 ACT-ACT95386 ACT-ACT95410 ACT-ACT95414 ACT-ACT95439 ACT-ACT95468 ACT-ACT95668 ACT-ACT95670 ACT-ACT95810 ACT-ACT95821 ACT-ACT96093 ACT-ACT96114 ACT-ACT96207 ACT-ACT96252 ACT-ACT96259 ACT-ACT96286 ACT-ACT96312 ACT-ACT96438 ACT-ACT96605 ACT-ACT96649 ACT-ACT96813 ACT-ACT96934 ACT-ACT96969 ACT-ACT94109 ACT-ACT90838 ACT-ACT92709 ACT-ACT92373 NIM-90C00073 NIM-90C00076 NIM-90C00112 NIM-90C00117 NIM-90C00123 NIM-90C00150 NIM-90C00174 NIM-90C00183 NIM-90C00184 NIM-90C00190 NIM-90C00195 NIM-90C00199 NIM-90C00204 NIM-90C00269 NIM-90C00308 NIM-90C00425 NIM-90C00433 NIM-90C00444 NIM-90C00497 NIM-90C00501 NIM-90C00584 NIM-90C00637 NIM-90C00668 NIM-90C00669 NIM-90C00689 NIM-90C00738 NIM-90C00982 NIM-90C00984 NIM-90C01012 NIM-90C01110 NIM-90C01180 NIM-90C01192 NIM-90C01229 NIM-90C01243 NIM-90C01244 NIM-90C01263 NIM-90C01283 NIM-90C01311 NIM-90C01315 NIM-90C01330 NIM-90C01391 NIM-90C01458 NIM-90C01498 NIM-90C01520 NIM-90C01531 NIM-90C01552 NIM-90C01573 NIM-90C01606 NIM-90C01686 NIM-90C01687 NIM-90C01694 NIM-90C01729 NIM-90C01730 NIM-90C01765 NIM-90C01768 NIM-90C01806 NIM-90C01809 NIM-90C01854 NIM-90C01899 NIM-90C01942 NIM-90C02112 NIM-90C02125 NIM-90C02148 NIM-90C02149 NIM-90C02151 NIM-90C02157 NIM-90C02216 NIM-90C02217 NIM-90C02219 NIM-90C02222 NIM-90C02245 NIM-90C02264 NIM-90C02268 NIM-90C02287 NIM-90C02294 NIM-90C02332 NIM-90C02357 NIM-90C02528 NIM-90C02554 NIM-90C02559 NIM-90C02660 NIM-90C02674 NIM-90C02809 NIM-90C02811 NIM-90C02829 NIM-90C03079 NIM-90C03115 NIM-90C03184 NIM-90C03201 NIM-90C03214 NIM-90C03246 NIM-90C03302 NIM-90C03480 NIM-90C03503 NIM-90C03511 NIM-90C03518 NIM-90C03524 NIM-90C03569 NIM-90C03591 NIM-90C03637 NIM-90C03673 NIM-90C03685 NIM-90C03691 NIM-90C03869 NIM-90C03956 NIM-90C04052 NIM-90C04120 NIM-90C04148 NIM-90C04314 NIM-90C04462 NIM-90C04482 NIM-90C04518 NIM-90C04540 NIM-90C04548 NIM-90C04576 NIM-90C04671 NIM-90C00618 NIM-90C02736 NIM-90C01021 NIM-90C01209 NIM-90C02339 NIM-90C02321 NIM-90C03236 NIM-90C01868 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: NG00079_ExomeChip_CHOP_Consent_ALL.txt and NG00079_ExomeChip_CHOP_Consent_forprofit.txt Genotype files: ExomeChip_CHOP.* and ExomeChip_CHOP_forprofit.* Covariate files: ExomeChip_CHOP_covar.txt and ExomeChip_CHOP_covar_forprofit.txt Covariate Data Dictionary: ADGC_ExomeChip_Data_Dictionary.xlsx