A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations Xianyun Mao, Abigail W. Bigham, Rui Mei, Gerardo Gutierrez, Ken M. Weiss, Tom D. Brutsaert, Fabiola Leon-Velarde, Lorna G. Moore, Enrique Vargas, Paul M. McKeigue, Mark D. Shriver, Esteban J. Parra  The American Journal of Human Genetics  Volume 80, Issue 6, Pages 1171-1178 (June 2007) DOI: 10.1086/518564 Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 1 Outline of the screening procedure for identification of AIMs The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 2 Scatterplots showing, for each chromosome, the physical location of the AIMs selected for the genomewide AM panel (X-axis) and the f values indicating the ancestry-information content for each marker (blackened squares). Scale is indicated on the right Y-axis. We also indicate the SNP density of the Affymetrix 500K mapping array (unblackened circles). Scale is indicated on the left Y-axis. The plotted f values are the averages of the f values between Europeans and Mesoamericans and the f values between Europeans and South Americans. The SNP density is measured using a sliding-window method with a 1-Mb window size and 200-kb offset. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 3 A, 3D PCO plot of the seven population samples included in this analysis (Europeans, Nahua from Mexico, Maya from Mexico, Quechua from Peru, Aymara/Quechua from Bolivia, West Africans, and East Asians), based on the allele-sharing distances between individuals estimated using 490,032 autosomal SNPs genotyped with the Affymetrix 500K Mapping Array. B, 3D PCO plot of the European and Native American populations, based on the allele-sharing distances between individuals estimated using 490,032 autosomal SNPs genotyped with the Affymetrix 500K Mapping Array. C, 3D PCO plot of the European and Native American populations, based on the allele-sharing distances between individuals estimated using the 2,120 AIMs selected for the Hispanic/Latino map. The proportion of variance explained by the first axis is indicated in each plot. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 4 Plot showing results of the analysis of the European and Native American samples with use of the program STRUCTURE, based on the genotype data for the 2,120 AIMs selected for the genomewide AM panel. The program was run using the linkage model, with 10,000 iterations for the burn-in phase and 50,000 iterations to collect parameter data. The model with two parental populations is the model that best fits the data. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions

Figure 5 Plot showing the relationship of f values and FIC values for the full panel of markers of the 500K array (A.1 and A.2) and the subset of markers with f values >0.3 (B.1 and B.2). Panels A.1 and B.1 show f values and FIC values with the assumption of a model with 75%:25% Mesoamerican:European ancestry, and panels A.2 and B.2 represent f values and FIC values with the assumption of a model with 25%:75% Mesoamerican:European ancestry. Spearman’s rank correlation coefficients (ρ) are indicated in bold above each panel. eu=European; ms=Mesoamerican. The American Journal of Human Genetics 2007 80, 1171-1178DOI: (10.1086/518564) Copyright © 2007 The American Society of Human Genetics Terms and Conditions