Data Release 2015

The GEnetic Factors for OSteoporosis (GEFOS) Consortium is a large international collaboration comprising numerous 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 GEFOS.seq project used meta-analysis of whole genome sequencing, whole exome sequencing and deep imputation of genotype data to identify low-frequency and rare variants associated with risk of osteoporosis. Three (3) DXA-derived traits are included in this data release: Femoral Neck bone mineral density (BMD) (FN-BMD), Lumbar Spine BMD (LS-BMD), and Forearm BMD (FA-BMD).

Release

This release includes the summary data from our 2015 meta-analyses of whole-genome sequencing, whole-exome sequencing, and deep imputation of genotype data. These files include summary statistics for approximately 10 million SNPs.

Data file description

Each file contains the following information:

chromosomeMarker chromosome position Marker position (bp) rs_number Marker ID reference Effect allele other_allele Non effect allele eaf effect allele frequency beta Overall beta value for meta-analysis se standard error beta_95L Lower 95% CI for BETA beta_95U Upper 95% CL for BETA z Z-score p-value Meta-analysis p-value log10_p-value Absolute value of logarithm of meta-analysis p-value to the base of 10 q_statistic Cochran's heterogeneity statistic q_p-value Cochran's heterogeneity statistic's p-value i2 Heterogeneity index I2 by Higgins et al 2003 n_studies Number of studies with marker present n_samples Number of samples with marker present (will be NA if marker is present in any input file where N column is not present) effects Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data)

For further information on this format please refer to GWAMA by visiting http://www.well.ox.ac.uk/gwama/

Publications

Zheng HF, et al. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature 2015.

Terms of Use

The UK10K, AOGC and GEFOS-seq Consortia require appropriate attribution for use of data in a product, service, or publication by citing the article generating this set of results (Zheng et al, Nature 2015) and acknowledging its use.