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Xiao X, Wu Q. Ethnic disparities in fracture risk assessment using polygenic scores. Osteoporos Int 2023; 34:943-953. [PMID: 36840773 PMCID: PMC11225529 DOI: 10.1007/s00198-023-06712-y] [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: 06/21/2022] [Accepted: 02/17/2023] [Indexed: 02/26/2023]
Abstract
Whether the PGS developed using data from European ancestry is predictive of fracture risk for minorities remains unclear. This study demonstrated that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry. PURPOSE Large-scale genome-wide association studies (GWAS) on bone mineral density (BMD) have been conducted predominantly in European cohorts. Genetic models based on common variants associated with BMD have been evaluated using almost exclusively European data, which could potentially exacerbate health disparities due to different linkage disequilibrium among different ethnic groups. METHODS UK Biobank (UKB) is a large-scale population-based observational study starting in 2006 that recruited 502,617 individuals aged between 40 and 69 years with genotypic and phenotypic data available. Based on the summary statistics of two GWAS studies of femoral neck BMD and total body BMD, we derived four PGSs and assessed the association between each PGS and prevalent/incident fractures within each ethnic group separately using Multivariate logistic regressions and Cox proportional hazard models. All models were adjusted for age, sex, and the first four principal components. RESULTS We assessed four PGSs derived from European cohorts. Significant associations were observed between PGSs and fracture in European and Asian cohorts but not in the African cohort. Of all four PGSs, [Formula: see text] performed the best. A standard deviation decreases in [Formula: see text] were associated with an increased hazard ratio (HR) of 1.24 (1.22-1.27), 1.28 (0.83-1.99), and 1.34 (1.10-1.64) in European, African, and Asian ancestry, respectively. A low BMD-related PGS is associated with up to 2.35- and 4.31-fold increased fracture risk in European and Asian populations. CONCLUSIONS These results showed that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry.
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Affiliation(s)
- Xiangxue Xiao
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, NV, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Qing Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320K Lincoln Tower, 1800 Cannon Dr., Columbus, OH, 43210, USA.
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Xiao X, Wu Q. Multiple polygenic scores improve bone mineral density prediction in an independent sample of Caucasian women. Postgrad Med J 2022; 98:670-674. [PMID: 34810269 DOI: 10.1136/postgradmedj-2021-139722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE OF THE STUDY To determine if multiple Genetic Risk Scores (GRSs) improve bone mineral density (BMD) prediction over single GRS in an independent sample of Caucasian women. STUDY DESIGN Based on summary statistics of four genome-wide association studies related to two osteoporosis-associated traits, namely BMD and heel quantitative ultrasound derived estimated BMD (eBMD), four GRSs were derived for 1205 individuals in the Genome-Wide Scan for Female Osteoporosis Gene Study. The effect of each GRS on BMD variation was assessed using multivariable linear regression, with conventional risk factors adjusted for. Next, the eBMD-related GRS that explained the most variance in BMD was selected to be entered into a multi-score model, along with the BMD-related GRS. Elastic net regularised regression was used to develop the multiscore model, which estimated the joint effect of two GRSs (GRS_BMD and GRS_eBMD) on BMD variation, after being adjusted for conventional risk factors. RESULTS With the same clinical risk factors having been adjusted for, the model that included GRS_BMD performed best by explaining 32.53% of the variance in BMD; the single-score model that included GRS_eBMD explained 34.03% of BMD variance. The model that includes both GRS_BMD and GRS_ eBMD, as well as the clinical risk factors, aggregately explained 35.05% in BMD variation. Compared with the single GRS models, the multiscore model explained significantly more variance in BMD. CONCLUSIONS The multipolygenic score model explained a considerable amount of BMD variation. Compared with single score models, multipolygenic score model provided significant improvement in explaining BMD variation.
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Affiliation(s)
- Xiangxue Xiao
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada Las Vegas, Las Vegas, Nevada, USA.,Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Qing Wu
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada Las Vegas, Las Vegas, Nevada, USA .,Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, Nevada, USA
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Yau MS, Kuipers AL, Price R, Nicolas A, Tajuddin SM, Handelman SK, Arbeeva L, Chesi A, Hsu YH, Liu CT, Karasik D, Zemel BS, Grant SFA, Jordan JM, Jackson RD, Evans MK, Harris TB, Zmuda JM, Kiel DP. A Meta-Analysis of the Transferability of Bone Mineral Density Genetic Loci Associations From European to African Ancestry Populations. J Bone Miner Res 2021; 36:469-479. [PMID: 33249669 PMCID: PMC8353846 DOI: 10.1002/jbmr.4220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022]
Abstract
Genetic studies of bone mineral density (BMD) largely have been conducted in European populations. We therefore conducted a meta-analysis of six independent African ancestry cohorts to determine whether previously reported BMD loci identified in European populations were transferable to African ancestry populations. We included nearly 5000 individuals with both genetic data and assessments of BMD. Genotype imputation was conducted using the 1000G reference panel. We assessed single-nucleotide polymorphism (SNP) associations with femoral neck and lumbar spine BMD in each cohort separately, then combined results in fixed effects (or random effects if study heterogeneity was high, I2 index >60) inverse variance weighted meta-analyses. In secondary analyses, we conducted locus-based analyses of rare variants using SKAT-O. Mean age ranged from 12 to 68 years. One cohort included only men and another cohort included only women; the proportion of women in the other four cohorts ranged from 52% to 63%. Of 56 BMD loci tested, one locus, 6q25 (C6orf97, p = 8.87 × 10-4 ), was associated with lumbar spine BMD and two loci, 7q21 (SLC25A13, p = 2.84 × 10-4 ) and 7q31 (WNT16, p = 2.96 × 10-5 ), were associated with femoral neck BMD. Effects were in the same direction as previously reported in European ancestry studies and met a Bonferroni-adjusted p value threshold, the criteria for transferability to African ancestry populations. We also found associations that met locus-specific Bonferroni-adjusted p value thresholds in 11q13 (LRP5, p < 2.23 × 10-4 ), 11q14 (DCDC5, p < 5.35 × 10-5 ), and 17p13 (SMG6, p < 6.78 × 10-5 ) that were not tagged by European ancestry index SNPs. Rare single-nucleotide variants in AKAP11 (p = 2.32 × 10-2 ), MBL2 (p = 4.09 × 10-2 ), MEPE (p = 3.15 × 10-2 ), SLC25A13 (p = 3.03 × 10-2 ), STARD3NL (p = 3.35 × 10-2 ), and TNFRSF11A (p = 3.18 × 10-3 ) were also associated with BMD. The majority of known BMD loci were not transferable. Larger genetic studies of BMD in African ancestry populations will be needed to overcome limitations in statistical power and to identify both other loci that are transferable across populations and novel population-specific variants. © 2020 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Michelle S Yau
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Allison L Kuipers
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan Price
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Baltimore, MD, USA
| | - Samuel K Handelman
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Liubov Arbeeva
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alessandra Chesi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi-Hsiang Hsu
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - David Karasik
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Babette S Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Struan FA Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joanne M Jordan
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca D Jackson
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Baltimore, MD, USA
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Baltimore, MD, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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