GEFOS

The GEFOS consortium is an international network involving various prominent research groups around the world with a general objective to identify the genetic determinants of musculoskeletal and aging-related traits. The GEFOS consortium was initially established in XXX with a goal to:

  • Identify genetic risk factors for osteoporosis related traits and fracture risk.
  • Seek replications and explore the generalizibility of the associations by prospective meta-analysis.
  • Explore the genetic basis of more novel bone phenotypes such as quantative ultrasound, bone geometry, and biochemical markers and gene-environment interactions.
  • Seek clinical translation of the results by evaluating identified risk alleles for their predictive power in prospective cohorts with documented classical risk factors for osteooporosis.
  • Summarize the data from the project in the context of the whole field by publishing datasynopses at regular intervals.
  • Genetic discoveries of bone-related phenotypes

Published work: So far our grop have have contributed to numerous genomic discoveries in the musculoskeletal field, achieved together with researchers from > 30 countries brought together by GEFOS consortium. In the early 2008 Richards, Rivadeneira et al [ref] identified two variants associated with lumbar spine and femoral neck bone mineral density (BMD) mapping to LRP5 and TNFRSF11B (OPG) in only 8,557 individuals; genes implicated in well-established bone metabolism pathways. Nevertheless, the largest yield in discoveries has been facilitated by the rise of GEFOS collaborative network giving way to large-scale GWAS meta-analyses that identified novel bone regions and pathways. The first meta-analysis of the GEFOS consortium (Ntotal=19,195) identified 13 novel loci associated with BMD [ref] followed by a second GEFOS meta-analysis (Ndiscovery=32,961) which replicated the majority of known BMD loci and identified additional 32 novel loci (Ntotal=83,894) [ref]. Fourteen of the BMD-associated loci were also associated with osteoporotic fractures, with those mapping to FAM210A, SLC25A13, LRP5, MEPE, SPTBN1 and DKK1 showing strongest association. This study was followed by additional large meta-analysis by Zheng et al [ref] which have provided evidence that low-frequency non-coding variants also have large effects on BMD and fracture. Next, in 2018 Medina et al. [ref] in a meta-analysis of 30 GWASs (Ntotal=66,628) identified 80 loci associated with total body BMD, of which 36 had not been previously identified. Moreover, in the age-stratified analyses only two loci displayed evidence for age-specific effects, including variants in ESR1 and in close proximity to RANKL. These findings suggest that most of the genes identified throughout the life-course, exert an effect on peak BMD acquisition and this effect can still be observed decades later [ref]. In 2018, Trajanoska et al. [ref] conducted the largest GWAS on osteoporotic fractures to date comprising 37,857 cases and 227,116 non-cases with replication in up to 300,000 individuals (147,200 cases). Altogether, the effort identified 15 fracture loci with modest effects. Interestingly, all identified loci were known BMD loci.
Ongoing work: Currently there are several ongoing efforts within the GEFOS to further expand the genetic determinants influencing DXA-derived bone parameters including femoral neck and lumbar spine BMD and a novel endophenotypes such as the trabecular bone score led by XXX and XXX.
Genetic discoveries muscle-related phenotypes
Osteoporosis (i.e., low bone mass) and sarcopenia (i.e., low lean mass) are common and costly comorbid diseases of aging, and there is an urgent need to prevent and treat both to reduce their associated morbidity and mortality and their consequences fractures and falls. Therefore, the work of the GEFOS consortium have expanded to evaluate the genetic determinants of muscle-related phenotypes.
Published work In 2015, collaborators from the GEFOS consortium identified five loci (HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO) associated with lean mass (total and/or appendicular) [ref], which constitutes a good proxy for skeletal muscle mass. In a follow-up study TNRV6B as identified as additional lean mass locus after more stringent adjustment for fat [ref]. A grip strength GWAS, a proxy for muscular function, have been more fruitful, yielding up to 30 loci associated with continuous measures of grip strength or binary muscle weakness [refs].
Genetics of bone and muscle interactions


Ongoing work: Bone mineral density (BMD) and lean mass (LM) are highly heritable traits with shared heritability estimate ranging between 30 and 70% in adults. This covariation can be result of developmental, homeostatic, mechanical and ageing processes, some of which may be due to pleiotropy. Currently we have ongoing efforts to Identify pleotropic regions associated with lean mass and bone mass measured by DXA using bivariate GWA analysis.

Publications

Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies

Fernando Rivadeneira 1Unnur StyrkársdottirKarol EstradaBjarni V HalldórssonYi-Hsiang HsuJ Brent RichardsM Carola ZillikensFotini K KavvouraNajaf AminYurii S AulchenkoL Adrienne CupplesPanagiotis DeloukasSerkalem DemissieElin GrundbergAlbert HofmanAugustine KongDavid KarasikJoyce B van MeursBen OostraTomi PastinenHuibert A P PolsGunnar SigurdssonNicole SoranzoGudmar ThorleifssonUnnur ThorsteinsdottirFrances M K WilliamsScott G WilsonYanhua ZhouStuart H RalstonCornelia M van DuijnTimothy SpectorDouglas P KielKari StefanssonJohn P A IoannidisAndré G UitterlindenGenetic Factors for Osteoporosis (GEFOS) Consortium

Affiliations

1 Department of Internal Medicine, Rotterdam, The Netherlands.

Abstract

Bone mineral density (BMD) is a heritable complex trait used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. We performed meta-analysis of five genome-wide association studies of femoral neck and lumbar spine BMD in 19,195 subjects of Northern European descent. We identified 20 BMD loci that reached genome-wide significance (GWS; P < 5 x 10(-8)), of which 13 map to regions not previously associated with this trait: 1p31.3 (GPR177), 2p21 (SPTBN1), 3p22 (CTNNB1), 4q21.1 (MEPE), 5q14 (MEF2C), 7p14 (STARD3NL), 7q21.3 (FLJ42280), 11p11.2 (LRP4, ARHGAP1, F2), 11p14.1 (DCDC5), 11p15 (SOX6), 16q24 (FOXL1), 17q21 (HDAC5) and 17q12 (CRHR1). The meta-analysis also confirmed at GWS level seven known BMD loci on 1p36 (ZBTB40), 6q25 (ESR1), 8q24 (TNFRSF11B), 11q13.4 (LRP5), 12q13 (SP7), 13q14 (TNFSF11) and 18q21 (TNFRSF11A). The many SNPs associated with BMD map to genes in signaling pathways with relevance to bone metabolism and highlight the complex genetic architecture that underlies osteoporosis and variation in BMD.

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Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture

J Brent Richards 1Fotini K KavvouraFernando RivadeneiraUnnur StyrkársdóttirKarol EstradaBjarni V HalldórssonYi-Hsiang HsuM Carola ZillikensScott G WilsonBenjamin H MullinNajaf AminYurii S AulchenkoL Adrienne CupplesPanagiotis DeloukasSerkalem DemissieAlbert HofmanAugustine KongDavid KarasikJoyce B van MeursBen A OostraHuibert A P PolsGunnar SigurdssonUnnur ThorsteinsdottirNicole SoranzoFrances M K WilliamsYanhua ZhouStuart H RalstonGudmar ThorleifssonCornelia M van DuijnDouglas P KielKari StefanssonAndré G UitterlindenJohn P A IoannidisTim D SpectorGenetic Factors for Osteoporosis Consortium

Affiliations

1 McGill University, Montreal, Quebec, Canada.

Abstract

Background: Osteoporosis is a highly heritable trait. Many candidate genes have been proposed as being involved in regulating bone mineral density (BMD). Few of these findings have been replicated in independent studies.

Objective: To assess the relationship between BMD and fracture and all common single-nucleotide polymorphisms (SNPs) in previously proposed osteoporosis candidate genes.

Design: Large-scale meta-analysis of genome-wide association data.

Setting: 5 international, multicenter, population-based studies.

Participants: Data on BMD were obtained from 19 195 participants (14 277 women) from 5 populations of European origin. Data on fracture were obtained from a prospective cohort (n = 5974) from the Netherlands.

Measurements: Systematic literature review using the Human Genome Epidemiology Navigator identified autosomal genes previously evaluated for association with osteoporosis. We explored the common SNPs arising from the haplotype map of the human genome (HapMap) across all these genes. BMD at the femoral neck and lumbar spine was measured by dual-energy x-ray absorptiometry. Fractures were defined as clinically apparent, site-specific, validated nonvertebral and vertebral low-energy fractures.

Results: 150 candidate genes were identified and 36 016 SNPs in these loci were assessed. SNPs from 9 gene loci (ESR1, LRP4, ITGA1, LRP5, SOST, SPP1, TNFRSF11A, TNFRSF11B, and TNFSF11) were associated with BMD at either site. For most genes, no SNP was statistically significant. For statistically significant SNPs (n = 241), effect sizes ranged from 0.04 to 0.18 SD per allele. SNPs from the LRP5, SOST, SPP1, and TNFRSF11A loci were significantly associated with fracture risk; odds ratios ranged from 1.13 to 1.43 per allele. These effects on fracture were partially independent of BMD at SPP1 and SOST.

Limitation: Only common polymorphisms in linkage disequilibrium with SNPs in HapMap could be assessed, and previously reported associations for SNPs in some candidate genes could not be excluded.

Conclusion: In this large-scale collaborative genome-wide meta-analysis, 9 of 150 candidate genes were associated with regulation of BMD, 4 of which also significantly affected risk for fracture. However, most candidate genes had no consistent association with BMD.

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A genome-wide copy number association study of osteoporotic fractures points to the 6p25.1 locus

Ling Oei 1Yi-Hsiang HsuUnnur StyrkarsdottirBert H EussenAnnelies de KleinMarjolein J PetersBjarni HalldorssonChing-Ti LiuNerea AlonsoStephen K KaptogeGudmar ThorleifssonGöran HallmansLynne J HockingLise Bjerre HustedKaren A JamesonMarcin KrukJoshua R LewisMillan S PatelSerena ScollenOlle SvenssonStella TrompetNatasja M van SchoorKun ZhuBrendan M BuckleyCyrus CooperIan FordDavid GoltzmanJesús González-MacíasBente Lomholt LangdahlWilliam D LesliePaul LipsRoman S LorencJosé M OlmosUlrika Pettersson-KymmerDavid M ReidJosé A RianchoP Eline SlagboomCarmen Garcia-IbarbiaThorvaldur IngvarssonHrefna JohannsdottirRobert LubenCarolina Medina-GómezPascal ArpKannabiran NandakumarStefan Th PalssonGunnar SigurdssonJoyce B J van MeursYanhua ZhouAlbert HofmanJ Wouter JukemaHuibert A P PolsRichard L PrinceL Adrienne CupplesChristian R MarshallDalila PintoDaisuke SatoStephen W SchererJonathan ReeveUnnur ThorsteinsdottirDavid KarasikJ Brent RichardsKari StefanssonAndré G UitterlindenStuart H RalstonJohn P A IoannidisDouglas P KielFernando RivadeneiraKarol Estrada
Affiliations

1 Department of Internal Medicine, Rotterdam, The Netherlands.

Abstract

Background: Osteoporosis is a systemic skeletal disease characterised by reduced bone mineral density and increased susceptibility to fracture; these traits are highly heritable. Both common and rare copy number variants (CNVs) potentially affect the function of genes and may influence disease risk.

Aim: To identify CNVs associated with osteoporotic bone fracture risk.

Method: We performed a genome-wide CNV association study in 5178 individuals from a prospective cohort in the Netherlands, including 809 osteoporotic fracture cases, and performed in silico lookups and de novo genotyping to replicate in several independent studies.

Results: A rare (population prevalence 0.14%, 95% CI 0.03% to 0.24%) 210 kb deletion located on chromosome 6p25.1 was associated with the risk of fracture (OR 32.58, 95% CI 3.95 to 1488.89; p = 8.69 × 10(-5)). We performed an in silico meta-analysis in four studies with CNV microarray data and the association with fracture risk was replicated (OR 3.11, 95% CI 1.01 to 8.22; p = 0.02). The prevalence of this deletion showed geographic diversity, being absent in additional samples from Australia, Canada, Poland, Iceland, Denmark, and Sweden, but present in the Netherlands (0.34%), Spain (0.33%), USA (0.23%), England (0.15%), Scotland (0.10%), and Ireland (0.06%), with insufficient evidence for association with fracture risk.

Conclusions: These results suggest that deletions in the 6p25.1 locus may predispose to higher risk of fracture in a subset of populations of European origin; larger and geographically restricted studies will be needed to confirm this regional association. This is a first step towards the evaluation of the role of rare CNVs in osteoporosis.

Keywords: Calcium and Bone; Copy-Number; Genetic Epidemiology; Genome-Wide; Osteoporosis.

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Team members