#-------------------------------------------------------------------------------------------- #--- GWAS Summary Statistics for the IGAP APOE-Stratified Analysis #-------------------------------------------------------------------------------------------- Title: A novel Alzheimer disease locus located near the gene encoding tau protein. Jun et al. Mol Psychiatry. 2016 Jan;21(1):108-17. doi: 10.1038/mp.2015.23. Epub 2015 Mar 17. https://www.ncbi.nlm.nih.gov/pubmed/25778476 PMID: 25778476 PMCID: PMC4573764 These files contain the genome-wide association study (GWAS) meta-analysis results for the discovery (stage 1) presented in the paper above (Jun et al. 2015). A set of GWAS meta-analyses for AD status was performed in four models: 1) using all sample; 2) using APOE e4 carriers; 3) using APOE e4 non-carriers; and 4) interaction test with APOE e4 status. The total of 53,711 subjects for the meta-analysis at the stage 1 were assembled by International Genomics Alzheimer 's Project (IGAP) from the Alzheimer’s Disease Genetic Consortium (ADGC), the Cohorts for Heart and Ageing Research in Genomic Epidemiology (CHARGE) consortium, the European Alzheimer's Disease Initiative (EADI) and the Genetic and Environmental Risk in Alzheimer’s Disease (GERAD) consortium. The detail information for sample recruitment, genotyping, imputation, QC, etc. has been reported previously (Jun et al. 2015). GWAS was performed separately in each study. The additive genetic effect of each SNP after imputation was estimated using regression analysis adjusting for age, sex, and principal components for population structures. SNP effect estimates and their SEs were combined by a fixed effect model with inverse variance weighted method using the METAL software for each model. After the meta-analysis, the SNPs with avaiable estimates at least half number of data sets are reported. Only the SNPs that attained suggestively significant association level (P<1e-5) were tested in the stage 2 using additional ADGC datasets, which have been reported in the Supplementary Table of the paper above (Jun et al. 2015). #-------------------------------------------------------------------------------------------- #--- File Name and the Model #-------------------------------------------------------------------------------------------- Model File_name 1) GWAS using all sample META_IGAP.7.ADGC.15_MODEL_All.Sample.txt.gz 2) GWAS using APOE e4 carriers META_IGAP.7.ADGC.15_MODEL_APOE.e4.Carriers.txt.gz 3) GWAS using APOE e4 non-carriers META_IGAP.7.ADGC.15_MODEL_APOE.e4.Noncarriers.txt.gz 4) Genome-wide interaction test between SNP and APOE e4 status META_IGAP.7.ADGC.15_MODEL_INT.wt.APOE.txt.gz #-------------------------------------------------------------------------------------------- #--- Column Information #-------------------------------------------------------------------------------------------- Column Number Column Name 1 #CHR Chromosome 2 BP Base Position 3 SNP rsid 4 MarkerName chr-baseposition 5 Allele1 Effect Allele 6 Allele2 Non-Effect Allele 7 P-value statistical significance of the effect estimate