MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk
Surakka, Ida; Fritsche, Lars; Zhou, Wei; Backman, Joshua; Kosmicki, Jack A.; Lu, Haocheng; Brumpton, Ben Michael; Nielsen, Jonas B.; Gabrielsen, Maiken Elvestad; Skogholt, Anne Heidi; Wolford, Brooke N.; Graham, Sarah E.; Chen, Y. Eugene; Lee, Seunggeun; Kang, Hyun Min; Langhammer, Arnulf; Forsmo, Siri; Åsvold, Bjørn Olav; Styrkarsdottir, Unnur; Holm, Hilma; Gudbjartsson, Daniel F.; Stefansson, Kari; Baras, Aris; Bai, Xiaodong; Balasubramanian, Suganthi; Barnard, Leland; Blumenfeld, Andrew; Cantor, Michael; Coppola, Giovanni; Economides, Aris; Eom, Gisu; Habegger, Lukas; Hahn, Young; Hawes, Alicia; Jones, Marcus B.; Khalid, Shareef; Lotta, Luca A.; Maxwell, Evan K.; Mitnaul, Lyndon J.; Overton, John D.; Reid, Jeffrey G.; Ferreira, Manuel Allen Revez; Salerno, William; Sharma, Deepika; Shuldiner, Alan R.; Staples, Jeffrey C.; Yadav, Ashish; Abecasis, Goncalo R.; Hveem, Kristian; Willer, Cristen J.
Peer reviewed, Journal article
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Original versionNature Communications. 2020, 11:4093 1-8. 10.1038/s41467-020-17315-0
A major challenge in genetic association studies is that most associated variants fall in the non-coding part of the human genome. We searched for variants associated with bone mineral density (BMD) after enriching the discovery cohort for loss-of-function (LoF) mutations by sequencing a subset of the Nord-Trøndelag Health Study, followed by imputation in the remaining sample (N = 19,705), and identified ten known BMD loci. However, one previously unreported variant, LoF mutation in MEPE, p.(Lys70IlefsTer26, minor allele frequency [MAF] = 0.8%), was associated with decreased ultradistal forearm BMD (P-value = 2.1 × 10−18), and increased osteoporosis (P-value = 4.2 × 10−5) and fracture risk (P-value = 1.6 × 10−5). The MEPE LoF association with BMD and fractures was further evaluated in 279,435 UK (MAF = 0.05%, heel bone estimated BMD P-value = 1.2 × 10−16, any fracture P-value = 0.05) and 375,984 Icelandic samples (MAF = 0.03%, arm BMD P-value = 0.12, forearm fracture P-value = 0.005). Screening for the MEPE LoF mutations before adulthood could potentially prevent osteoporosis and fractures due to the lifelong effect on BMD observed in the study. A key implication for precision medicine is that high-impact functional variants missing from the publicly available cosmopolitan panels could be clinically more relevant than polygenic risk scores.