Genome-wide analyses were performed within each cohort according to a uniform analysis plan. We fit additive genetic models using linear regression on natural-log transformed 25-hydroxyvitamin D, and adjusted the models for month of sample collection (12 categories), age, sex, and body mass index, and principal components capturing genetic ancestry. Further adjustments included cohort-specific variables, such as geographical location and assay batch, where relevant. For participating studies with a case-control design, we analyzed cases and controls separately. We performed a fixed-effects inverse variance weighted meta-analysis across the contributing cohorts, as implemented in the software METAL
26 (link), with control for population structure within each cohort and quality control thresholds of minor allele frequency (MAF) > 0.05, imputation info score > 0.8, Hardy-Weinberg equilibrium (HWE) > 1×10
−6, and a minimum of two studies and 10,000 individuals contributing to each reported SNP-phenotype association. We regarded
P-values < 5×10
−8 as genome-wide significant.
Jiang X., O’Reilly P.F., Aschard H., Hsu Y.H., Richards J.B., Dupuis J., Ingelsson E., Karasik D., Pilz S., Berry D., Kestenbaum B., Zheng J., Luan J., Sofianopoulou E., Streeten E.A., Albanes D., Lutsey P.L., Yao L., Tang W., Econs M.J., Wallaschofski H., Völzke H., Zhou A., Power C., McCarthy M.I., Michos E.D., Boerwinkle E., Weinstein S.J., Freedman N.D., Huang W.Y., Van Schoor N.M., van der Velde N., Groot L.C., Enneman A., Cupples L.A., Booth S.L., Vasan R.S., Liu C.T., Zhou Y., Ripatti S., Ohlsson C., Vandenput L., Lorentzon M., Eriksson J.G., Shea M.K., Houston D.K., Kritchevsky S.B., Liu Y., Lohman K.K., Ferrucci L., Peacock M., Gieger C., Beekman M., Slagboom E., Deelen J., Heemst D.V., Kleber M.E., März W., de Boer I.H., Wood A.C., Rotter J.I., Rich S.S., Robinson-Cohen C., den Heijer M., Jarvelin M.R., Cavadino A., Joshi P.K., Wilson J.F., Hayward C., Lind L., Michaëlsson K., Trompet S., Zillikens M.C., Uitterlinden A.G., Rivadeneira F., Broer L., Zgaga L., Campbell H., Theodoratou E., Farrington S.M., Timofeeva M., Dunlop M.G., Valdes A.M., Tikkanen E., Lehtimäki T., Lyytikäinen L.P., Kähönen M., Raitakari O.T., Mikkilä V., Ikram M.A., Sattar N., Jukema J.W., Wareham N.J., Langenberg C., Forouhi N.G., Gundersen T.E., Khaw K.T., Butterworth A.S., Danesh J., Spector T., Wang T.J., Hyppönen E., Kraft P, & Kiel D.P. (2018). Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels. Nature Communications, 9, 260.