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NG00075 - IGAP Rare Variant Summary Statistics- Kunkle et al. (2019)


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

Summary Statistics p-values only

Molecular Data Type


Submission date: 

Stage 1:
Cases: 21,982
Controls: 41,944

Stage 2:
Cases: 8,362
Controls: 10,483

PI Information