Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.
Zheng H-F., Forgetta V., Hsu Y-H., Estrada K., Rosello-Diez A., Leo PJ., Dahia CL., Park-Min KH., Tobias JH., Kooperberg C., Kleinman A., Styrkarsdottir U., Liu C-T., Uggla C., Evans DS., Nielson CM., Walter K., Pettersson-Kymmer U., McCarthy S., Eriksson J., Kwan T., Jhamai M., Trajanoska K., Memari Y., Min J., Huang J., Danecek P., Wilmot B., Li R., Chou W-C., Mokry LE., Moayyeri A., Claussnitzer M., Cheng C-H., Cheung W., Medina-Gómez C., Ge B., Chen S-H., Choi K., Oei L., Fraser J., Kraaij R., Hibbs MA., Gregson CL., Paquette D., Hofman A., Wibom C., Tranah GJ., Marshall M., Gardiner BB., Cremin K., Auer P., Hsu L., Ring S., Tung JY., Thorleifsson G., Enneman AW., van Schoor NM., de Groot LCPGM., van der Velde N., Melin B., Kemp JP., Christiansen C., Sayers A., Zhou Y., Calderari S., van Rooij J., Carlson C., Peters U., Berlivet S., Dostie J., Uitterlinden AG., Williams SR., Farber C., Grinberg D., LaCroix AZ., Haessler J., Chasman DI., Giulianini F., Rose LM., Ridker PM., Eisman JA., Nguyen TV., Center JR., Nogues X., Garcia-Giralt N., Launer LL., Gudnason V., Mellström D., Vandenput L., Amin N., van Duijn CM., Karlsson MK., Ljunggren Ö., Svensson O., Hallmans G., Rousseau F., Giroux S., Bussière J., Arp PP., Koromani F., Prince RL., Lewis JR., Langdahl BL., Hermann AP., Jensen J-EB., Kaptoge S., Khaw K-T., Reeve J., Formosa MM., Xuereb-Anastasi A., Åkesson K., McGuigan FE., Garg G., Olmos JM., Zarrabeitia MT., Riancho JA., Ralston SH., Alonso N., Jiang X., Goltzman D., Pastinen T., Grundberg E., Gauguier D., Orwoll ES., Karasik D., Davey-Smith G., AOGC Consortium None., Smith AV., Siggeirsdottir K., Harris TB., Zillikens MC., van Meurs JBJ., Thorsteinsdottir U., Maurano MT., Timpson NJ., Soranzo N., Durbin R., Wilson SG., Ntzani EE., Brown MA., Stefansson K., Hinds DA., Spector T., Cupples LA., Ohlsson C., Greenwood CMT., UK10K Consortium None., Jackson RD., Rowe DW., Loomis CA., Evans DM., Ackert-Bicknell CL., Joyner AL., Duncan EL., Kiel DP., Rivadeneira F., Richards JB.
The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants, as well as rare, population-specific, coding variants. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 × 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 × 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 × 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.