Supplementary Online Content

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1 Supplementary Online Content Lee JH, Cheng R, Barral S, Reitz C, Medrano M, Lantigua R, Jiménez-Velazquez IZ, Rogaeva E, St. George-Hyslop P, Mayeux R. Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals [published online November 8, 2010]. Arch Neurol. doi: /archneurol eappendix. Supplement methods. efigure 1. Q-Q plots. efigure 2. Candidate SNP regions. efigure 3. Linkage disequilibrium plots for CLU, PICALM, and BIN1 in unaffected, unrelated individuals. This supplementary material has been provided by the authors to give readers additional information about their work American Medical Association. All rights reserved.

2 eappendix. Supplement Methods Population Stratification. We applied two methods, namely STRUCTURE 1 and PLINK 2, to examine population stratification in this Caribbean Hispanic cohort. First, we used a set of 500 unlinked SNPs spread evenly across the autosomal chromosomes for total Caribbean Hispanic 1,093 individuals and then repeated the analysis using unaffected individuals only. The mean of inter-marker distance of the 500 SNPs was 5,454.5kb (SD=±5,501.4kb). To assess admixture in Hispanics, we pooled data from 1,093 Caribbean Hispanics in the current study with 255 subjects from the HapMap website ( which included 60 European Americans, 60 Yorubans and 90 East- Asians. We used the STRUCTURE program version to check underlying population substructure, and estimate ancestry genomic proportions for all individuals. We set the predefined number (k) of populations ranging from four to seven for the pooled data and three to six when we restricted the set to Caribbean Hispanics only. We tested admixture model using 100,000 burn-ins and 100,000 iterations. From this analysis, the best fitting number (k) of underlying populations was three (Figure 1). We then compared the findings from STRUCTURE with the identical-by-state (IBS) based clustering analysis as implemented in the PLINK program version For the IBS based clustering analysis, we used 627,380 genome-wide autosomal SNPs to assign 1,093 Caribbean Hispanic individuals to different clusters. The assignment of cluster from the STRUCTURE algorithm was comparable to that from the PLINK algorithm. For all subsequent association analyses, we used the cluster information obtained from the PLINK analysis. The lambda, genomic inflation factor was not inflated (Supplementary Figure) American Medical Association. All rights reserved.

3 efigure 1: Q-Q Plots The 2 Q-Q plots reveal that after controlling for population structure, the lambdas are within the acceptable range of and efigure 2: Candidate SNP regions Four SNP regions and genes are shown. These four genes are selected because they were strongly associated with LOAD in Caribbean Hispanics and supporting evidence for allelic association was observed in Caucasians in the NIA-LOAD GWAS. efigure 3: Linkage disequilibrium plots for CLU, PICALM, and BIN1 in unaffected, unrelated individuals The linkage disequilibrium patterns for the three candidate genes are shown for the Caribbean Hispanic and NIA-LOAD European American unaffected individuals. Black or dark grey represent strong LD. As the color becomes lighter, there is strong evidence of recombination. Shades of pink represent high LD but not statistically significant at LOD<2. The number in the cell represents D' American Medical Association. All rights reserved.

4 efigure 1. Q-Q PLOTS * clean 2AD.assoc.out Lambda = Data points above lift off: Observed 2Log(e)P Expected 2Log(e)P * cleanK3cmh.out Lambda = Data points above lift off: Observed 2Log(e)P Expected 2Log(e)P

5 Recombination rate (cm/mb) Recombination rate (cm/mb) Recombination rate (cm/mb) efigure 2: Candidate SNPs Candidate regions: 2p25.1, 3q25.2, 7p21.1, and 10q23.1 rs region Observed ( logp) Observed ( logp) Chromosome 2 position (hg18) (kb) rs region rs (CEU) Chromosome 3 position (hg18) (kb) Recombination rate (cm/mb) Observed ( logp) Chromosome 7 position (hg18) (kb) rs Chromosome 10 position (hg18) (kb) Observed ( logp)

6 The figures were generated using SNP ( Each dot represents -log (p-value) for each SNP as shown on the left side bar. The right bar shows recombination rates. The green bar on the x-axis represents the location and the size of genes in the region.

7 efigure 3: Linkage disequilibrium plots for CLU, PICALM, and BIN1 in unaffected and unrelated individuals Caribbean Hispanic cohort NIA-LOAD cohort CLU BIN1

8 PICALM Black or dark grey represent strong LD. As the color becomes lighter, there is strong evidence of recombination. Shades of pink represent high LD but not statistically significant at LOD<2. The number in the cell represents D'.