A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women

Bone Rep. 2016 Aug 27:5:233-242. doi: 10.1016/j.bonr.2016.08.005. eCollection 2016 Dec.


Background: Osteoporosis is a major public health problem associated with excess disability and mortality. It is estimated that 50-70% of the variation in osteoporotic fracture risk is attributable to genetic factors. The purpose of this hypothesis-generating study was to identify possible genetic determinants of fracture among African American (AA) women in a GWAS meta-analysis.

Methods: Data on clinical fractures (all fractures except fingers, toes, face, skull or sternum) were analyzed among AA female participants in the Women's Health Initiative (WHI) (N = 8155), Cardiovascular Health Study (CHS) (N = 504), BioVU (N = 704), Health ABC (N = 651), and the Johnston County Osteoarthritis Project (JoCoOA) (N = 291). Affymetrix (WHI) and Illumina (Health ABC, JoCoOA, BioVU, CHS) GWAS panels were used for genotyping, and a 1:1 ratio of YRI:CEU HapMap haplotypes was used as an imputation reference panel. We used Cox proportional hazard models or logistic regression to evaluate the association of ~ 2.5 million SNPs with fracture risk, adjusting for ancestry, age, and geographic region where applicable. We conducted a fixed-effects, inverse variance-weighted meta-analysis. Genome-wide significance was set at P < 5 × 10- 8.

Results: One SNP, rs12775980 in an intron of SVIL on chromosome 10p11.2, reached genome-wide significance (P = 4.0 × 10- 8). Although this SNP has a low minor allele frequency (0.03), there was no evidence for heterogeneity of effects across the studies (I2 = 0). This locus was not reported in any previous osteoporosis-related GWA studies. We also interrogated previously reported GWA-significant loci associated with fracture or bone mineral density in our data. One locus (SMOC1) generalized, but overall there was not substantial evidence of generalization. Possible reasons for the lack of generalization are discussed.

Conclusion: This GWAS meta-analysis of fractures in African American women identified a potentially novel locus in the supervillin gene, which encodes a platelet-associated factor and was previously associated with platelet thrombus formation in African Americans. If validated in other populations of African descent, these findings suggest potential new mechanisms involved in fracture that may be particularly important among African Americans.

Keywords: AA, African American; ASW, African ancestry individuals from Southwest USA; African American; BMD, bone mineral density; BMI, body mass index; BMP, bone morphogenetic protein; CES-D, Center for Epidemiological Studies-Depression scale; CEU, CEPH-Utah (Utah residents with ancestors from central and western Europe); CHS, Cardiovascular Health Study; DNA, deoxyribonucleic acid; EAF, effect allele frequency; Fracture; GEFOS, Genetic Factors of Osteoporosis; GPGE, genetically predicted gene expression; GTEx Project, Genotype-Tissue Expression project; GWAS, genome-wide association study; Genetic association study; Genome-wide association study (GWAS); JoCoOA, Johnston County Osteoarthritis Project; MAC, minor allele count; MAF, minor allele frequency; Meta-analysis; OF, osteoporotic fracture; Osteoporosis; RNA, ribonucleic acid; SD, standard deviation; SHARe, SNP Health Association Resource; SNP, single nucleotide polymorphism; WHI, Women's Health Initiative; YRI, Yoruban (Nigeria).