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gbb12043-sup-0001-FigureS1.docxWord 2007 document451KFigure S1: Flowchart of the two-stage, genome-wide scoring approach.
gbb12043-sup-0002-FigureS2.docxWord 2007 document183KFigure S2: Plot of first and second PC scores estimated from COGA genome-wide genotype data. Assignment of samples to AA and EA populations is based on their respective placement or lack thereof within the two major population clusters observable in the PC plot.
gbb12043-sup-0003-FigureS3.docxWord 2007 document155KFigure S3: Plot of first and second PC scores estimated from SAGE genome-wide genotype data. Assignment of samples to AA and EA populations is based on their respective placement or lack thereof within the two major population clusters observable in the PC plot.
gbb12043-sup-0004-FigureS4.docxWord 2007 document187KFigure S4: Quantile–quantile plots of genome-wide association results for AD in the COGA and SAGE datasets (covariates age and sex). The negative logarithmic P-values (y axes) of each tested SNP are plotted against the expected negative logarithmic P-values (x axes) under the null distribution for no association. The genomic control lambda values (λGC) are listed for each plot.
gbb12043-sup-0005-FigureS5.docxWord 2007 document219KFigure S5: Variance explained by genome-wide scoring routines for observed and simulated disease phenotypes according to MAF class. The variances explained, derived from MAF bins comprised of different score alleles, are presented for nine disease models for each study population. The models represent either 100, 1000 or 5000 causal variants, which were randomly drawn from SNP data excluded from the original design of scoring routines, representing either rare/uncommon markers (<5% MAF), common markers (>5% MAF), or spanning the entire MAF spectrum. Each model was replicated 100 times. Disease heritability was set at 0.65, with causal effect sizes fixed for all loci. Observed R2 results for AD are given as black, dotted lines.
gbb12043-sup-0006-FigureS6.docxWord 2007 document349KFigure S6: Five biological ontologies and signaling pathways that exhibit concordant empirical P-value distributions for permuted (1000×) Fisher's exact tests of gene enrichment in EA and AA samples. Allele bins, delineated by genome-wide association P-values at cumulative increments of 0.05, were annotated for gene location using UCSC hg18 coordinates.
gbb12043-sup-0007-FigureS7.docxWord 2007 document350KFigure S7: Seven biological ontologies and signaling pathways that exhibit significant empirical P-values (<0.01) for permuted (1000×) Fisher's exact tests of gene enrichment in AA samples. Allele bins, delineated by genome-wide association P-values at cumulative increments of 0.05, were annotated for gene location using UCSC hg18 coordinates.
gbb12043-sup-0008-FigureS8.docxWord 2007 document315KFigure S8: Six biological ontologies and signaling pathways that exhibit significant empirical P-values (<0.01) for permuted (1000×) Fisher's exact tests of gene enrichment in EA samples. Allele bins, delineated by genome-wide association P-values at cumulative increments of 0.05, were annotated for gene location using UCSC hg18 coordinates.
gbb12043-sup-0009-TableS1.docxWord 2007 document17KTable S1: Logistic regression results for population-matched GWAS scores as predictors of AD in SAGE target samples
gbb12043-sup-0010-TableS2.docxWord 2007 document15KTable S2: Estimation of variance in AD liability explained from pairwise genetic correlations by REML
gbb12043-sup-0011-TableS3.docxWord 2007 document17KTable S3: Logistic regression results for population-mismatched genome-wide scores as predictors of AD in SAGE target samples
gbb12043-sup-0012-TableS4.docxWord 2007 document18KTable S4: Logistic regression results for population-matched genome-wide scores of non-overlapping P-value bins as predictors of AD in SAGE target samples
gbb12043-sup-0013-TableS5.docxWord 2007 document15KTable S5: Logistic regression results for population-matched genome-wide scores of five MAF bins as predictors of AD in SAGE target samples
gbb12043-sup-0014-TableS6.docxWord 2007 document16KTable S6: Results from permuted gene enrichment analysis of annotated bins drawn from different GWAS P-value thresholds
gbb12043-sup-0015-TableS7.docxWord 2007 document15KTable S7: Shared genes from ontologies exhibiting significant evidence of gene enrichment for both AA and EA annotated bins
gbb12043-sup-0016-TableS8.docxWord 2007 document14KTable S8: Shared genes from ontologies presented in Fig. 4 for both AA and EA annotated bins

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