Abstract MP79: Identification of Novel Loci Associated with Anthropometric Traits in African Ancestry Populations
Authors: Maggie C Ng, Mariaelisa Graff, Anne Justice, Ying Chang Lu, Poorva Mudgal, Ching-Ti Liu, Kristin Rand, Qing Duan, Brian Cade, Jennifer Brody, Mary K Wojczynski, Mary F Feitosa, Lisa R Yanek, Jennifer A Smith, Michael A Nalls, Guanjie Chen, Jin Sha, Leslie Lange, Sailaja Vedantam, Xiuqing Guo, Wei-Min Chen, Alessandra Chesi, Christopher Haiman, Ruth Loos, Kari North
Journal: Circulation (2016)

Introduction: African Americans have the highest prevalence of obesity in the U.S. Our prior work on HapMap imputed genome-wide association studies (GWAS) from the African Ancestry Anthropometry Genetics Consortium (AAAGC) revealed seven genome-wide significant loci for body mass index (BMI). Hypothesis: In this study, we extended to use genome-wide imputation to the cosmopolitan 1000 Genomes Phase 1 reference panel to examine individuals of African ancestry for association with BMI (N=53,493), waist-to-hip ratio adjusted for BMI (WHRadjBMI) (N=23,692) and height (N=53,362) in the discovery and replication stages. Methods: In each study, traits were stratified by gender and transformed to normality and adjusted for age, study specific covariates and principal components for single variant association test under an additive model. In the discovery stage, meta-analyses using fixed-effects inverse variance weighted method were performed to combine association results in all and sex-stratified samples. Variants with P&lt;1E-4 were selected for subsequent replications in both individuals of African ancestry and European ancestry, the latter results were obtained by imputation of summary statistics from the GIANT consortium (N=322,154 for BMI, 210,062 for WHRadjBMI, and 253,252 for height). Results: For BMI, we observed genome-wide significant associations (P&lt;5E-8) at seven established loci (near SEC16B, TMEM18, GNPDA2, GALNT10, KLHL32, FTO and MC4R) in meta-analysis of all African ancestry individuals from the discovery and replication stages. Sex-stratified meta-analysis revealed two novel loci near IRX4-IRX2 in women, and near MLC1 in men, respectively. Meta-analysis of all individuals from African and European ancestry revealed an additional novel locus near ARAP1. For WHRadjBMI, we observed genome-wide significant associations at one established locus (ADAMTS9) in all African ancestry individuals, and three novel loci (near SSX2IP, RREB1 and PDE3B) in women. For height, we observed 29 established loci and three novel loci (near NCOA2, P4HA1 and TGFB3) in all African ancestry individuals, and three novel loci (near CRB1, MIR4268 and LINC00704) in women. Among 12 lead variants at novel loci associated with anthropometry traits, four variants are low frequencies in our African ancestry populations (0.005&lt;MAF &lt;0.05). On the contrary, all but one of the lead variants at established loci were common. Conclusions: We identified 12 novel loci associated with anthropometry traits in sex-combined and sex-stratified analyses of African ancestry populations and additional European populations. Our findings support that imputation to higher density reference panels such as 1000 Genomes improves the power to detect associations at low frequency variants, which is particularly useful for African ancestry populations with a low degree of linkage disequilibrium.