The International Genomics of Alzheimer's Project (IGAP) is releasing the summary results data from the Alzheimer’s disease GWAS of Kunkle et al. , Nat Genet, 2019 analysis in order to enable other researchers to examine particular variants or loci for their evidence of association.
Please note that these summary data should not be used for research into the genetics of intelligence, education, social outcomes such as income, or potentially sensitive behavioral traits such as alcohol or drug addictions. The files include p-values and direction of effect at over 11 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). Due to the possibility of identification of individuals from these summary results, allele frequency data are accessible through the application process.
Two dataset are provided. The first one corresponds to the meta-analysis results obtained in stage 1 including genotyped and imputed data (11,480,632 variants, phase 1 integrated release 3, March 2012) of 21,982 Alzheimer’s disease cases and 41,944 cognitively normal controls. The second one corresponds to the meta-analysis results of the 11,632 variants that were genotyped on the I-select chip and tested for association in an independent set of 8,362 Alzheimer's disease cases and 10,483 controls with the combined stage1/stage2 P-values. 11,540 of the I-select chip variants were available for meta-analysis with the stage 1 dataset. The Stage 3A (n = 11,666) and Stage 3B (n = 30,511) (for variants in regions not well captured on the I-select chip) results are available in the manuscript. The final sample was 35,274 clinical and autopsy-documented Alzheimer’s disease cases and 59,163 controls.
Although the individual datasets examined excluded any SNPs with call rates <95%, IGAP meta-analysis only analyzed SNPs either genotyped or successfully imputed in at least 30% of the AD cases and 30 %of the control samples across all datasets.
P-value data is generally available to all users using the link below. However, gaining access to allele frequencies and beta values requires a formal data request.
For detailed information and instructions on how to cite IGAP data for publication, please see this document: NG00075_Kunkle_IGAP_SummaryStats_README.docx
For details on how to cite IGAP data for publication, please see this document (also attached to the data file): NG00075_Kunkle_IGAP_SummaryStats_README.docx
We thank the International Genomics of Alzheimer's Project (IGAP) for providing summary results data for these analyses. The investigators within IGAP contributed to the design and implementation of IGAP and/or provided data but did not participate in analysis or writing of this report. IGAP was made possible by the generous participation of the control subjects, the patients, and their families. The i–Select chips was funded by the French National Foundation on Alzheimer's disease and related disorders. EADI was supported by the LABEX (laboratory of excellence program investment for the future) DISTALZ grant, Inserm, Institut Pasteur de Lille, Université de Lille 2 and the Lille University Hospital. GERAD/PERADES was supported by the Medical Research Council (Grant n° 503480), Alzheimer's Research UK (Grant n° 503176), the Wellcome Trust (Grant n° 082604/2/07/Z) and German Federal Ministry of Education and Research (BMBF): Competence Network Dementia (CND) grant n° 01GI0102, 01GI0711, 01GI0420. CHARGE was partly supported by the NIH/NIA grant R01 AG033193 and the NIA AG081220 and AGES contract N01–AG–12100, the NHLBI grant R01 HL105756, the Icelandic Heart Association, and the Erasmus Medical Center and Erasmus University. ADGC was supported by the NIH/NIA grants: U01 AG032984, U24 AG021886, U01 AG016976, and the Alzheimer's Association grant ADGC–10–196728.