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Lee J, Kim J, Jeong C, Ha J, Lim Y, Baek KH. Predicting fragility fractures based on frailty and bone mineral density among rural community-dwelling older adults. Eur J Endocrinol 2024; 191:75-86. [PMID: 38970525 DOI: 10.1093/ejendo/lvae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
OBJECTIVE We aim to investigate the association between bone mineral density (BMD) measurement and fragility fractures and assess the predictive value of combining BMD measurement and frailty for fracture risk assessment. METHODS This retrospective cohort study analyzed data from 5126 rural Koreans in the Chungju Metabolic Disease Cohort study. Frailty was defined using Fried's frailty phenotype. Fractures were assessed via structured medical interviews. Adjusted odds ratios (ORs) were calculated considering age, sex, body mass index, behavior, BMD, handgrip strength, medications, and comorbidities. RESULTS The study cohort consisted of 5126 participants comprising 1955 (38.1%) males and 3171 (61.9%) females. Osteoporosis significantly increased the fracture risk across all types, except vertebral fracture, with adjusted OR (95% CI) of 1.89 (1.23-3.47) for any fracture, 2.05 (1.37-2.98) for hip fracture, 2.18 (1.06-4.50) for other fracture, and 1.71 (1.03-3.63) for major osteoporotic fracture (MOF). Frail individuals exhibited significantly increased risk for any fracture (OR 2.12; 95% CI, 1.21-3.71), vertebral fracture (2.48; 1.84-3.61), hip fracture (2.52; 1.09-3.21), other fracture (2.82; 1.19-8.53), and MOF (1.87; 1.01-3.47). The combination of frailty and BMD further increased the risks, with frail individuals demonstrating elevated ORs across BMD categories. In subgroup analyses, men showed a significant association between frailty with osteoporosis in hip fracture and MOF. Frail women with osteoporosis exhibited the highest risks for all fractures, particularly vertebral (OR 5.12; 95% CI, 2.07-9.68) and MOF (OR 5.19; 95% CI, 2.07-6.61). Age-specific analysis revealed that individuals aged 70 and older exhibited markedly higher fracture risks compared with those under 70. The combination of frailty and low BMD further elevated the fracture risk. Frailty was applied with BMD and demonstrated superior risk prediction for MOF compared with that with either score alone (area under the curve 0.825; P = .000). CONCLUSIONS Combining frailty with BMD provides a more accurate fracture risk assessment for individuals over 50 years.
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Affiliation(s)
- Jeongmin Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 03312, Republic of Korea
| | - Jinyoung Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Republic of Korea
| | - Chaiho Jeong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu 11765, Republic of Korea
| | - Jeonghoon Ha
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yejee Lim
- Division of General Internal Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Ki-Hyun Baek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Republic of Korea
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Zhang W, Lu T, Sladek R, Li Y, Najafabadi H, Dupuis J. SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. Bioinformatics 2024; 40:btae295. [PMID: 38688586 PMCID: PMC11105950 DOI: 10.1093/bioinformatics/btae295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
MOTIVATION Colocalization analysis is commonly used to assess whether two or more traits share the same genetic signals identified in genome-wide association studies (GWAS), and is important for prioritizing targets for functional follow-up of GWAS results. Existing colocalization methods can have suboptimal performance when there are multiple causal variants in one genomic locus. RESULTS We propose SharePro to extend the COLOC framework for colocalization analysis. SharePro integrates linkage disequilibrium (LD) modeling and colocalization assessment by grouping correlated variants into effect groups. With an efficient variational inference algorithm, posterior colocalization probabilities can be accurately estimated. In simulation studies, SharePro demonstrated increased power with a well-controlled false positive rate at a low computational cost. Compared to existing methods, SharePro provided stronger and more consistent colocalization evidence for known lipid-lowering drug target proteins and their corresponding lipid traits. Through an additional challenging case of the colocalization analysis of the circulating abundance of R-spondin 3 GWAS and estimated bone mineral density GWAS, we demonstrated the utility of SharePro in identifying biologically plausible colocalized signals. AVAILABILITY AND IMPLEMENTATION SharePro for colocalization analysis is written in Python and openly available at https://github.com/zhwm/SharePro_coloc.
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Affiliation(s)
- Wenmin Zhang
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec H1T 1C8, Canada
| | - Tianyuan Lu
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert Sladek
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Yue Li
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada
| | - Hamed Najafabadi
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Josée Dupuis
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, McGill College, QC H3A 1Y7, Canada
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Lu T, Forgetta V, Zhou S, Richards JB, Greenwood CM. Identifying Rare Genetic Determinants for Improved Polygenic Risk Prediction of Bone Mineral Density and Fracture Risk. J Bone Miner Res 2023; 38:1771-1781. [PMID: 37830501 DOI: 10.1002/jbmr.4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Osteoporosis and fractures severely impact the elderly population. Polygenic risk scores for bone mineral density have demonstrated potential clinical utility. However, the value of rare genetic determinants in risk prediction has not been assessed. With whole-exome sequencing data from 436,824 UK Biobank participants, we assigned White British ancestry individuals into a training data set (n = 317,434) and a test data set (n = 74,825). In the training data set, we developed a common variant-based polygenic risk score for heel ultrasound speed of sound (SOS). Next, we performed burden testing to identify genes harboring rare determinants of bone mineral density, targeting influential rare variants with predicted high deleteriousness. We constructed a genetic risk score, called ggSOS, to incorporate influential rare variants in significant gene burden masks into the common variant-based polygenic risk score. We assessed the predictive performance of ggSOS in the White British test data set, as well as in populations of non-White British European (n = 18,885), African (n = 7165), East Asian (n = 2236), South Asian (n = 9829), and other admixed (n = 1481) ancestries. Twelve genes in pivotal regulatory pathways of bone homeostasis harbored influential rare variants associated with SOS (p < 5.5 × 10-7 ), including AHNAK, BMP5, CYP19A1, FAM20A, FBXW5, KDM5B, KREMEN1, LGR4, LRP5, SMAD6, SOST, and WNT1. Among 4013 (5.4%) individuals in the test data set carrying these variants, a one standard deviation decrease in ggSOS was associated with 1.35-fold (95% confidence interval [CI] 1.16-1.57) increased hazard of major osteoporotic fracture. However, compared with a common variant-based polygenic risk score (C-index = 0.641), ggSOS had only marginally improved prediction accuracy in identifying at-risk individuals (C-index = 0.644), with overlapping confidence intervals. Similarly, ggSOS did not demonstrate substantially improved predictive performance in non-European ancestry populations. In summary, modeling the effects of rare genetic determinants may assist polygenic prediction of fracture risk among carriers of influential rare variants. Nonetheless, improved clinical utility is not guaranteed for population-level risk screening. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- 5 Prime Sciences Inc., Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Celia Mt Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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Kaya S, Alliston T, Evans DS. Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research. Curr Osteoporos Rep 2023; 21:637-649. [PMID: 37831357 PMCID: PMC11098148 DOI: 10.1007/s11914-023-00821-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE OF REVIEW The integration of data from multiple genomic assays from humans and non-human model organisms is an effective approach to identify genes involved in skeletal fragility and fracture risk due to osteoporosis and other conditions. This review summarizes genome-wide genetic variation and gene expression data resources relevant to the discovery of genes contributing to skeletal fragility and fracture risk. RECENT FINDINGS Genome-wide association studies (GWAS) of osteoporosis-related traits are summarized, in addition to gene expression in bone tissues in humans and non-human organisms, with a focus on rodent models related to skeletal fragility and fracture risk. Gene discovery approaches using these genomic data resources are described. We also describe the Musculoskeletal Knowledge Portal (MSKKP) that integrates much of the available genomic data relevant to fracture risk. The available genomic resources provide a wealth of knowledge and can be analyzed to identify genes related to fracture risk. Genomic resources that would fill particular scientific gaps are discussed.
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Affiliation(s)
- Serra Kaya
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Tamara Alliston
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Daniel S Evans
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
- California Pacific Medical Center Research Institute, San Francisco, CA, USA.
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Lu T, Silveira PP, Greenwood CMT. Development of risk prediction models for depression combining genetic and early life risk factors. Front Neurosci 2023; 17:1143496. [PMID: 37534032 PMCID: PMC10390723 DOI: 10.3389/fnins.2023.1143496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Background Both genetic and early life risk factors play important roles in the pathogenesis and progression of adult depression. However, the interplay between these risk factors and their added value to risk prediction models have not been fully elucidated. Methods Leveraging a meta-analysis of major depressive disorder genome-wide association studies (N = 45,591 cases and 97,674 controls), we developed and optimized a polygenic risk score for depression using LDpred in a model selection dataset from the UK Biobank (N = 130,092 European ancestry individuals). In a UK Biobank test dataset (N = 278,730 European ancestry individuals), we tested whether the polygenic risk score and early life risk factors were associated with each other and compared their associations with depression phenotypes. Finally, we conducted joint predictive modeling to combine this polygenic risk score with early life risk factors by stepwise regression, and assessed the model performance in identifying individuals at high risk of depression. Results In the UK Biobank test dataset, the polygenic risk score for depression was moderately associated with multiple early life risk factors. For instance, a one standard deviation increase in the polygenic risk score was associated with 1.16-fold increased odds of frequent domestic violence (95% CI: 1.14-1.19) and 1.09-fold increased odds of not having access to medical care as a child (95% CI: 1.05-1.14). However, the polygenic risk score was more strongly associated with depression phenotypes than most early life risk factors. A joint predictive model integrating the polygenic risk score, early life risk factors, age and sex achieved an AUROC of 0.6766 for predicting strictly defined major depressive disorder, while a model without the polygenic risk score and a model without any early life risk factors had an AUROC of 0.6593 and 0.6318, respectively. Conclusion We have developed a polygenic risk score to partly capture the genetic liability to depression. Although genetic and early life risk factors can be correlated, joint predictive models improved risk stratification despite limited improvement in magnitude, and may be explored as tools to better identify individuals at high risk of depression.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Center, McGill University, Montreal, QC, Canada
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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Chen Y, Lu T, Pettersson-Kymmer U, Stewart ID, Butler-Laporte G, Nakanishi T, Cerani A, Liang KYH, Yoshiji S, Willett JDS, Su CY, Raina P, Greenwood CMT, Farjoun Y, Forgetta V, Langenberg C, Zhou S, Ohlsson C, Richards JB. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases. Nat Genet 2023; 55:44-53. [PMID: 36635386 PMCID: PMC7614162 DOI: 10.1038/s41588-022-01270-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/18/2022] [Indexed: 01/14/2023]
Abstract
Metabolic processes can influence disease risk and provide therapeutic targets. By conducting genome-wide association studies of 1,091 blood metabolites and 309 metabolite ratios, we identified associations with 690 metabolites at 248 loci and associations with 143 metabolite ratios at 69 loci. Integrating metabolite-gene and gene expression information identified 94 effector genes for 109 metabolites and 48 metabolite ratios. Using Mendelian randomization (MR), we identified 22 metabolites and 20 metabolite ratios having estimated causal effect on 12 traits and diseases, including orotate for estimated bone mineral density, α-hydroxyisovalerate for body mass index and ergothioneine for inflammatory bowel disease and asthma. We further measured the orotate level in a separate cohort and demonstrated that, consistent with MR, orotate levels were positively associated with incident hip fractures. This study provides a valuable resource describing the genetic architecture of metabolites and delivers insights into their roles in common diseases, thereby offering opportunities for therapeutic targets.
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Affiliation(s)
- Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | | | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Agustin Cerani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Julian Daniel Sunday Willett
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Computer Science, McGill University, Montreal, Quebec, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- McMaster Institute for Research on Aging, McMaster University, Hamilton, Ontario, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Fulcrum Genomics, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre of Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- 5 Prime Sciences Inc, Montreal, Quebec, Canada.
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada.
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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