The International Genomics of Alzheimer's Project (IGAP) is releasing the summary results data from the 2013 meta-analysis of Genome-wide Association (GWA) data in Alzheimer's disease, in order to enable other researchers to examine particular variants or loci for their evidence of association. The files include p-values and direction of effect at over 7 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). To prevent the possibility of identification of individuals from these summary results, allele frequency data are not released.
Data file description
Two dataset are provided. The first one corresponds to the meta-analysis results obtained in stage 1 including genotyped and imputed data (7,055,881 single nucleotide polymorphisms, 1000G phase 1 alpha imputation, Build 37, Assembly Hg19) of 17,008 Alzheimer's disease cases and 37,154 controls. The second one corresponds to the meta-analysis results of the 11,632 SNPs that were genotyped and tested for association in an independent set of 8,572 Alzheimer's disease cases and 11,312 controls with the combined stage1/stage2 P-values.
Each file consists of the following information for each SNP and its association to Alzheimer's disease based on meta-analysis in the publication mentioned below. 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 40% of the AD cases and 40 % of the control samples across all datasets.
Chromosome: Chromosome of the SNP (Build 37, Assembly Hg19)
Position: Position of the SNP (Build 37, Assembly Hg19)
MarkerName: SNP rsID or chromosome:position if rsID not available
Effect_allele: Reference allele (coded allele)
Non_Effect_allele: Non reference allele (non coded allele)
Beta: Overall estimated effect size for the effect allele
SE: Overall standard error for effect size estimate
Pvalue: Meta-analysis Pvalue using regression coefficients (beta and standard error)
Description lifted from the archived IGAP website on 04/15/22.
Stage 1: 7,055,881
Stage 2: 11,632
Use of IGAP data for publications
If IGAP data are used in publications, IGAP should be cited in acknowledgments, Materials and Methods, and References sections of the manuscript as follows:
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 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.
Material and methods
International Genomics of Alzheimer's Project (IGAP) is a large two-stage study based upon genome-wide association studies (GWAS) on individuals of European ancestry. In stage 1, IGAP used genotyped and imputed data on 7,055,881 single nucleotide polymorphisms (SNPs) to meta-analyse four previously-published GWAS datasets consisting of 17,008 Alzheimer's disease cases and 37,154 controls (The European Alzheimer's disease Initiative – EADI the Alzheimer Disease Genetics Consortium – ADGC The Cohorts for Heart and Aging Research in Genomic Epidemiology consortium – CHARGE The Genetic and Environmental Risk in AD consortium – GERAD). In stage 2, 11,632 SNPs were genotyped and tested for association in an independent set of 8,572 Alzheimer's disease cases and 11,312 controls. Finally, a meta-analysis was performed combining results from stages 1 & 2.
Your manuscript should cite the following reference
Jean-Charles Lambert et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nature Genetics, 2013, 45 : 1452–1458. doi:10.1038/ng.2802 [PubMed ID: 24162737]