Data Release 2012
GEFOS stands for the GEnetic Factors for OSteoporosis Consortium. It is a large international collaboration involving various prominent research groups.Osteoporosis is a common age-related complex disease with a strong genetic component. Osteoporotic fractures account for considerable disease burden and costs. The genes responsible, however, are poorly defined. The GEFOS project used meta-analysis of Genome Wide Association (GWA) studies with high density SNP arrays, to identify common risk gene variants for osteoporosis. Two DXA-derived traits are included in this data release: Femoral Neck BMD (FN-BMD) and Lumbar Spine BMD (LS-BMD). So far, the GEFOS consortium has identified common genetic variants at 56 loci that are associated with BMD and 16 of them with increase risk of fracture. A map of GEFOS and GENOMOS studies can be found here.
This release includes the summary data from our 2012 meta-analyses of GWA data. These files include p-values and direction of effect at over 2 million SNPs. To prevent identification of individuals from summary results, effect sizes and allele frequencies are not included.
Data file description
Each file contains the following information for each SNP and its association to the specified trait based on the GEFOS2 meta-analysis. SNPs missing in more than 3 studies were excluded.The dbSNP name of the genetic marker The first allele (hg18 + strand) The second allele (hg18 + strand) P value after meta-analysis using regression coefficients (beta and standard error), and after correction for inflation of test statistics using genomic control both at the individual study level and again after meta-analysis Direction of the effect of Allele1 (increasing/decreasing BMD from beta coefficient) The allele frequency of Allele1 in the HapMap CEU population
Estrada K, Styrkarsdottir U, Evangelou E, Hsu YH, Duncan EL, Ntzani EE, Oei L et al,(2012). Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet 44, 491-501
A list of collaborators from the GEFOS Consortium for this data release can be found here: GEFOS COLLABORATORS