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Pagoni P, Higgins JPT, Lawlor DA, Stergiakouli E, Warrington NM, Morris TT, Tilling K. Meta-regression of genome-wide association studies to estimate age-varying genetic effects. Eur J Epidemiol 2024; 39:257-270. [PMID: 38183607 PMCID: PMC10995067 DOI: 10.1007/s10654-023-01086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 11/15/2023] [Indexed: 01/08/2024]
Abstract
Fixed-effect meta-analysis has been used to summarize genetic effects on a phenotype across multiple Genome-Wide Association Studies (GWAS) assuming a common underlying genetic effect. Genetic effects may vary with age (or other characteristics), and not allowing for this in a GWAS might lead to bias. Meta-regression models between study heterogeneity and allows effect modification of the genetic effects to be explored. The aim of this study was to explore the use of meta-analysis and meta-regression for estimating age-varying genetic effects on phenotypes. With simulations we compared the performance of meta-regression to fixed-effect and random -effects meta-analyses in estimating (i) main genetic effects and (ii) age-varying genetic effects (SNP by age interactions) from multiple GWAS studies under a range of scenarios. We applied meta-regression on publicly available summary data to estimate the main and age-varying genetic effects of the FTO SNP rs9939609 on Body Mass Index (BMI). Fixed-effect and random-effects meta-analyses accurately estimated genetic effects when these did not change with age. Meta-regression accurately estimated both main genetic effects and age-varying genetic effects. When the number of studies or the age-diversity between studies was low, meta-regression had limited power. In the applied example, each additional minor allele (A) of rs9939609 was inversely associated with BMI at ages 0 to 3, and positively associated at ages 5.5 to 13. Our findings challenge the assumption that genetic effects are consistent across all ages and provide a method for exploring this. GWAS consortia should be encouraged to use meta-regression to explore age-varying genetic effects.
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Affiliation(s)
- Panagiota Pagoni
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Julian P T Higgins
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicole M Warrington
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, University of Queensland, Brisbane, QLD, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tim T Morris
- Centre for Longitudinal Studies, Social Research Institute, University College London, London, UK
| | - Kate Tilling
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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Zhao YX, Gao GX, Zhou Y, Guo CX, Li B, El-Ashram S, Li ZL. Genome-wide association studies uncover genes associated with litter traits in the pig. Animal 2022; 16:100672. [PMID: 36410176 DOI: 10.1016/j.animal.2022.100672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods-pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)-and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits.
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Affiliation(s)
- Y X Zhao
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China; Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - G X Gao
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Y Zhou
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - C X Guo
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - B Li
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - S El-Ashram
- Faculty of Science, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Z L Li
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China.
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Moazzam-Jazi M, Najd-Hassan-Bonab L, Masjoudi S, Tohidi M, Hedayati M, Azizi F, Daneshpour MS. Risk of type 2 diabetes and KCNJ11 gene polymorphisms: a nested case-control study and meta-analysis. Sci Rep 2022; 12:20709. [PMID: 36456687 PMCID: PMC9715540 DOI: 10.1038/s41598-022-24931-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Due to the central role in insulin secretion, the potassium inwardly-rectifying channel subfamily J member 11 (KCNJ11) gene is one of the essential genes for type 2 diabetes (T2D) predisposition. However, the relevance of this gene to T2D development is not consistent among diverse populations. In the current study, we aim to capture the possible association of common KCNJ11 variants across Iranian adults, followed by a meta-analysis. We found that the tested variants of KCNJ11 have not contributed to T2D incidence in Iranian adults, consistent with similar insulin secretion levels among individuals with different genotypes. The integration of our results with 72 eligible published case-control studies (41,372 cases and 47,570 controls) as a meta-analysis demonstrated rs5219 and rs5215 are significantly associated with the increased T2D susceptibility under different genetic models. Nevertheless, the stratified analysis according to ethnicity showed rs5219 is involved in the T2D risk among disparate populations, including American, East Asian, European, and Greater Middle Eastern, but not South Asian. Additionally, the meta-regression analysis demonstrated that the sample size of both case and control groups was significantly associated with the magnitude of pooled genetic effect size. The present study can expand our knowledge about the KCNJ11 common variant's contributions to T2D incidence, which is valuable for designing SNP-based panels for potential clinical applications in precision medicine. It also highlights the importance of similar sample sizes for avoiding high heterogeneity and conducting a more precise meta-analysis.
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Affiliation(s)
- Maryam Moazzam-Jazi
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Najd-Hassan-Bonab
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sajedeh Masjoudi
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Tohidi
- Prevention of Metabolic Disorder Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Hedayati
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam S Daneshpour
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wu X, Lin X, Li Q, Wang Z, Zhang N, Tian M, Wang X, Deng H, Tan H. Identification of novel SNPs associated with coronary artery disease and birth weight using a pleiotropic cFDR method. Aging (Albany NY) 2020; 13:3618-3644. [PMID: 33411684 PMCID: PMC7906162 DOI: 10.18632/aging.202322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/11/2020] [Indexed: 11/30/2022]
Abstract
Objectives: Clinical and epidemiological findings indicate an association between coronary artery disease (CAD) and low birth weight (BW). However, the mechanisms underlying this relationship are largely unknown. Here, we aimed to identify novel single-nucleotide polymorphisms (SNPs) associated with CAD, BW, and their shared pleiotropic loci, and to detect the potential causal relationship between CAD and BW. Methods: We first applied a genetic pleiotropic conditional false discovery rate (cFDR) method to two independent genome-wide association studies (GWAS) summary statistics of CAD and BW to estimate the pleiotropic enrichment between them. Then, bi-directional Mendelian randomization (MR) analyses were performed to clarify the causal association between these two traits. Results: By incorporating related traits into a conditional analysis framework, we observed the significant pleiotropic enrichment between CAD and BW. By applying the cFDR level of 0.05, 109 variants were detected for CAD, 203 for BW, and 26 pleiotropic variants for both traits. We identified 11 CAD- and/or BW-associated SNPs that showed more than three of the metabolic quantitative trait loci (metaQTL), protein QTL (pQTL), methylation QTL (meQTL), or expression QTL (eQTL) effects. The pleiotropic SNP rs10774625, located at ATXN2, showed metaQTL, pQTL, meQTL, and eQTL effects simultaneously. Using the bi-directional MR approach, we found a negative association from BW to CAD (odds ratio [OR] = 0.68, 95% confidence interval [CI]: 0.59 to 0.80, p = 1.57× 10-6). Conclusion: We identified several pleiotropic loci between CAD and BW by leveraging GWAS results of related phenotypes and identified a potential causal relationship from BW to CAD. Our findings provide novel insights into the shared biological mechanisms and overlapping genetic heritability between CAD and BW.
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Affiliation(s)
- Xinrui Wu
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Qi Li
- Xiangxi Center for Disease Prevention and Control, Jishou 416000, China
| | - Zun Wang
- Xiangya Nursing School, Central South University, Changsha 410013, China
| | - Na Zhang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Mengyuan Tian
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Xiaolei Wang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Hongwen Deng
- School of Basic Medical Science, Central South University, Changsha 410013, China.,Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hongzhuan Tan
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha 410078, China
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Liu Y, Ran S, Lin Y, Zhang YX, Yang XL, Wei XT, Jiang ZX, He X, Zhang H, Feng GJ, Shen H, Tian Q, Deng HW, Zhang L, Pei YF. Four pleiotropic loci associated with fat mass and lean mass. Int J Obes (Lond) 2020; 44:2113-2123. [PMID: 32719433 PMCID: PMC7912634 DOI: 10.1038/s41366-020-0645-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Fat mass and lean mass are two biggest components of body mass. Both fat mass and lean mass are under strong genetic determinants and are correlated. METHODS We performed a bivariate genome-wide association meta-analysis of (lean adjusted) leg fat mass and (fat adjusted) leg lean mass in 12,517 subjects from 6 samples, and followed by in silico replication in large-scale UK biobank cohort sample (N = 370 097). RESULTS We identified four loci that were significant at the genome-wide significance (GWS, α = 5.0 × 10-8) level at the discovery meta-analysis, and successfully replicated in the replication sample: 2q36.3 (rs1024137, pdiscovery = 3.32 × 10-8, preplication = 4.07 × 10-13), 5q13.1 (rs4976033, pdiscovery = 1.93 × 10-9, preplication = 6.35 × 10-7), 12q24.31 (rs4765528, pdiscovery = 7.19 × 10-12, preplication = 1.88 × 10-11) and 18q21.32 (rs371326986, pdiscovery = 9.04 × 10-9, preplication = 2.35 × 10-95). The above four pleiotropic loci may play a pleiotropic role for fat mass and lean mass development. CONCLUSIONS Our findings further enhance the understanding of the genetic association between fat mass and lean mass and provide a new theoretical basis for their understanding.
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Affiliation(s)
- Yu Liu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Shu Ran
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Yong Lin
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Yu-Xue Zhang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Xiao-Lin Yang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China
| | - Xin-Tong Wei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China
- Department of Epidemiology and Health Statistics, Medical College of Soochow University, Jiangsu, PR China
| | - Zi-Xuan Jiang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Xiao He
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Hong Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China
| | - Gui-Juan Feng
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China
- Department of Epidemiology and Health Statistics, Medical College of Soochow University, Jiangsu, PR China
| | - Hui Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Hong-Wen Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China.
| | - Yu-Fang Pei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, PR China.
- Department of Epidemiology and Health Statistics, Medical College of Soochow University, Jiangsu, PR China.
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He P, Meng XH, Zhang X, Lin X, Zhang Q, Jiang RL, Schiller MR, Deng FY, Deng HW. Identifying Pleiotropic SNPs Associated With Femoral Neck and Heel Bone Mineral Density. Front Genet 2020; 11:772. [PMID: 32774344 PMCID: PMC7388689 DOI: 10.3389/fgene.2020.00772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Background Genome-wide association studies (GWASs) routinely identify loci associated with risk factors for osteoporosis. However, GWASs with relatively small sample sizes still lack sufficient power to ascertain the majority of genetic variants with small to modest effect size, which may together truly influence the phenotype. The loci identified only account for a small percentage of the heritability of osteoporosis. This study aims to identify novel genetic loci associated with DXA-derived femoral neck (FNK) bone mineral density (BMD) and quantitative ultrasound of the heel calcaneus estimated BMD (eBMD), and to detect shared/causal variants for the two traits, to assess whether the SNPs or putative causal SNPs associated with eBMD were also associated with FNK-BMD. Methods Novel loci associated with eBMD and FNK-BMD were identified by the genetic pleiotropic conditional false discovery rate (cFDR) method. Shared putative causal variants between eBMD and FNK-BMD and putative causal SNPs for each trait were identified by the colocalization method. Mendelian randomization analysis addresses the causal relationship between eBMD/FNK-BMD and fracture. Results We identified 9,500 (cFDR < 9.8E-6), 137 (cFDR < 8.9E-4) and 124 SNPs associated with eBMD, FNK-BMD, and both eBMD and FNK-BMD, respectively, with 37 genomic regions where there was a SNP that influences both eBMD and FNK-BMD. Most genomic regions only contained putative causal SNPs associated with eBMD and 3 regions contained two distinct putative causal SNPs influenced both traits, respectively. We demonstrated a causal effect of FNK-BMD/eBMD on fracture. Conclusion Most of SNPs or putative causal SNPs associated with FNK-BMD were also associated with eBMD. However, most of SNPs or putative causal SNPs associated with eBMD were not associated with FNK-BMD. The novel variants we identified may help to account for the additional proportion of variance of each trait and advance our understanding of the genetic mechanisms underlying osteoporotic fracture.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiang-He Meng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Center of Reproductive Health, System Biology and Data Information, School of Basic Medical Science, Central South University, Changsha, China.,Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiao Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xu Lin
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Qiang Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ri-Li Jiang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine, School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Center of Reproductive Health, System Biology and Data Information, School of Basic Medical Science, Central South University, Changsha, China.,Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
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Shafquat A, Crystal RG, Mezey JG. Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes. BMC Bioinformatics 2020; 21:178. [PMID: 32381021 PMCID: PMC7204256 DOI: 10.1186/s12859-020-3387-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of disease loci. While well appreciated, almost all analyses of GWAS data consider reported disease phenotype values as is without accounting for potential misclassification. Results Here, we introduce Phenotype Latent variable Extraction of disease misdiagnosis (PheLEx), a GWAS analysis framework that learns and corrects misclassified phenotypes using structured genotype associations within a dataset. PheLEx consists of a hierarchical Bayesian latent variable model, where inference of differential misclassification is accomplished using filtered genotypes while implementing a full mixed model to account for population structure and genetic relatedness in study populations. Through simulations, we show that the PheLEx framework dramatically improves recovery of the correct disease state when considering realistic allele effect sizes compared to existing methodologies designed for Bayesian recovery of disease phenotypes. We also demonstrate the potential of PheLEx for extracting new potential loci from existing GWAS data by analyzing bipolar disorder and epilepsy phenotypes available from the UK Biobank. From the PheLEx analysis of these data, we identified new candidate disease loci not previously reported for these datasets that have value for supplemental hypothesis generation. Conclusion PheLEx shows promise in reanalyzing GWAS datasets to provide supplemental candidate loci that are ignored by traditional GWAS analysis methodologies.
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Affiliation(s)
- Afrah Shafquat
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason G Mezey
- Department of Computational Biology, Cornell University, Ithaca, NY, USA. .,Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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Identification of novel functional CpG-SNPs associated with type 2 diabetes and coronary artery disease. Mol Genet Genomics 2020; 295:607-619. [PMID: 32162118 DOI: 10.1007/s00438-020-01651-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D) and coronary artery disease (CAD), respectively. Nevertheless, these studies were generally performed for single-trait/disease and failed to assess the pleiotropic role of the identified variants. To identify novel functional loci and the pleiotropic relationship between CAD and T2D, the targeted cFDR analysis on CpG-SNPs was performed by integrating two independent large and multi-centered GWASs with summary statistics of T2D (26,676 cases and 132,532 controls) and CAD (60,801 cases and 123,504 controls). Applying the cFDR significance threshold of 0.05, we observed a pleiotropic enrichment between T2D and CAD by incorporating pleiotropic effects into a conditional analysis framework. We identified 79 novel CpG-SNPs for T2D, 61 novel CpG-SNPs for CAD, and 18 novel pleiotropic loci for both traits. Among these novel CpG-SNPs, 33 of them were annotated as methylation quantitative trait locus (meQTL) in whole blood, and ten of them showed expression QTL (eQTL), meQTL, and metabolic QTL (metaQTL) effects simultaneously. To the best of our knowledge, we performed the first targeted cFDR analysis on CpG-SNPs, and our findings provided novel insights into the shared biological mechanisms and overlapped genetic heritability between T2D and CAD.
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Qin H, Niu T, Zhao J. Identifying Multi-Omics Causers and Causal Pathways for Complex Traits. Front Genet 2019; 10:110. [PMID: 30847004 PMCID: PMC6393387 DOI: 10.3389/fgene.2019.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
The central dogma of molecular biology delineates a unidirectional causal flow, i.e., DNA → RNA → protein → trait. Genome-wide association studies, next-generation sequencing association studies, and their meta-analyses have successfully identified ~12,000 susceptibility genetic variants that are associated with a broad array of human physiological traits. However, such conventional association studies ignore the mediate causers (i.e., RNA, protein) and the unidirectional causal pathway. Such studies may not be ideally powerful; and the genetic variants identified may not necessarily be genuine causal variants. In this article, we model the central dogma by a mediate causal model and analytically prove that the more remote an omics level is from a physiological trait, the smaller the magnitude of their correlation is. Under both random and extreme sampling schemes, we numerically demonstrate that the proteome-trait correlation test is more powerful than the transcriptome-trait correlation test, which in turn is more powerful than the genotype-trait association test. In conclusion, integrating RNA and protein expressions with DNA data and causal inference are necessary to gain a full understanding of how genetic causal variants contribute to phenotype variations.
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Affiliation(s)
- Huaizhen Qin
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, United States
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, United States
| | - Tianhua Niu
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University School Medicine, New Orleans, LA, United States
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, United States
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Zhu W, Xu C, Zhang JG, He H, Wu KH, Zhang L, Zeng Y, Zhou Y, Su KJ, Deng HW. Gene-based GWAS analysis for consecutive studies of GEFOS. Osteoporos Int 2018; 29:2645-2658. [PMID: 30306226 PMCID: PMC6279247 DOI: 10.1007/s00198-018-4654-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/03/2018] [Indexed: 10/28/2022]
Abstract
UNLABELLED By integrating the multilevel biological evidence and bioinformatics analyses, the present study represents a systemic endeavor to identify BMD-associated genes and their roles in skeletal metabolism. INTRODUCTION Single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) have already identified about 100 loci associated with bone mineral density (BMD), but these loci only explain a small proportion of heritability to osteoporosis risk. In the present study, we performed a gene-based analysis of the largest GWASs in the bone field to identify additional BMD-associated genes. METHODS BMD-associated genes were identified by combining the summary statistic P values of SNPs across individual genes in the two consecutive meta-analyses of GWASs from the Genetic Factors for Osteoporosis (GEFOS) studies. The potential functionality of these genes to bone was partially assessed by differential gene expression analysis. Additionally, the consistency of the identification of potential bone mineral density (BMD)-associated variants were evaluated by estimating the correlation of the P values of the same single-nucleotide polymorphisms (SNPs)/genes between the two consecutive Genetic Factors for Osteoporosis Studies (GEFOS) with largely overlapping samples. RESULTS Compared to the SNP-based analysis, the gene-based strategy identified additional BMD-associated genes with genome-wide significance and increased their mutual replication between the two GEFOS datasets. Among these BMD-associated genes, three novel genes (UBTF, AAAS, and C11orf58) were partially validated at the gene expression level. The correlation analysis presented a moderately high between-study consistency of potential BMD-associated variants. CONCLUSIONS Gene-based analysis as a supplementary strategy to SNP-based genome-wide association studies, when applied here, is shown that it helped identify some novel BMD-associated genes. In addition to its empirically increased statistical power, gene-based analysis also provides a higher testing stability for identification of BMD genes.
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Affiliation(s)
- W Zhu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - C Xu
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - J-G Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - H He
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - K-H Wu
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - L Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - Y Zeng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Y Zhou
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - K-J Su
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - H-W Deng
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA.
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11
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Taylor S. Association between COMT Val158Met and psychiatric disorders: A comprehensive meta-analysis. Am J Med Genet B Neuropsychiatr Genet 2018; 177:199-210. [PMID: 28608575 DOI: 10.1002/ajmg.b.32556] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/08/2017] [Accepted: 05/05/2017] [Indexed: 01/26/2023]
Abstract
Catechol-O-methyltransferase (COMT) Val158Met is widely regarded as potentially important for understanding the genetic etiology of many different psychiatric disorders. The present study appears to be the first comprehensive meta-analysis of COMT genetic association studies to cover all psychiatric disorders for which there were available data, published in any language, and with an emphasis on investigating disorder subtypes (defined clinically or by demographic or other variables). Studies were included if they reported one or more datasets (i.e., some studies examined more than one clinical group) in which there were sufficient information to compute effect sizes. A total of 363 datasets were included, consisting of 56,998 cases and 74,668 healthy controls from case control studies, and 2,547 trios from family based studies. Fifteen disorders were included. Attention-deficit hyperactivity disorder and panic disorder were associated with the Val allele for Caucasian samples. Substance-use disorder, defined by DSM-IV criteria, was associated with the Val allele for Asian samples. Bipolar disorder was associated with the Met allele in Asian samples. Obsessive-compulsive disorder tended to be associated with the Met allele only for males. There was suggestive evidence that the Met allele is associated with an earlier age of onset of schizophrenia. Results suggest pleiotropy and underscore the importance of examining subgroups-defined by variables such as age of onset, sex, ethnicity, and diagnostic system-rather than examining disorders as monolithic constructs.
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Affiliation(s)
- Steven Taylor
- University of British Columbia, British Columbia, Canada
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12
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Liu HM, He JY, Zhang Q, Lv WQ, Xia X, Sun CQ, Zhang WD, Deng HW. Improved detection of genetic loci in estimated glomerular filtration rate and type 2 diabetes using a pleiotropic cFDR method. Mol Genet Genomics 2018; 293:225-235. [PMID: 29038864 PMCID: PMC5819009 DOI: 10.1007/s00438-017-1381-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/06/2017] [Indexed: 01/19/2023]
Abstract
Genome-wide association studies (GWAS) have been shown to have the potential of explaining more of the "missing heritability" of complex human phenotypes by improving statistical approaches. Here, we applied a genetic-pleiotropy-informed conditional false discovery rate (cFDR) to capture additional polygenic effects associated with estimated glomerular filtration rate (creatinine) (eGFRcrea) and type 2 diabetes (T2D). The cFDR analysis improves the identification of pleiotropic variants by incorporating potentially shared genetic mechanisms between two related traits. The Q-Q and fold-enrichment plots were used to assess the enrichment of SNPs associated with eGFRcrea or T2D, and Manhattan plots were used for showing chromosomal locations of the significant loci detected. By applying the cFDR method, we newly identified 74 loci for eGFRcrea and 3 loci for T2D with the cFDR criterion of 0.05 compared with previous related GWAS studies. Four shared SNPs were detected to be associated with both eGFRcrea and T2D at the significant conjunction cFDR level of 0.05, and these shared SNPs had not been reported in previous studies. In addition, we used DAVID analysis to perform functional analysis of the shared SNPs' annotated genes and found their potential hidden associations with eGFRcrea and T2D. In this study, the cFDR method shows the feasibility to detect more genetic variants underlying the heritability of eGFRcrea and T2D, and the overlapping SNPs identified could be regarded as candidate loci that provide a thread of genetic mechanisms between eGFRcrea and T2D in future research.
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Affiliation(s)
- Hui-Min Liu
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Jing-Yang He
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Qiang Zhang
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Wan-Qiang Lv
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Xin Xia
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Chang-Qing Sun
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China
| | - Wei-Dong Zhang
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China.
| | - Hong-Wen Deng
- College of Public Health Zhengzhou University, No.100 Kexue Road, High-Tech Development Zone of States, Zhengzhou, People's Republic of China.
- Department of Biostatistics and Data Science, Tulane Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
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13
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Identification of novel genetic loci for osteoporosis and/or rheumatoid arthritis using cFDR approach. PLoS One 2017; 12:e0183842. [PMID: 28854271 PMCID: PMC5576737 DOI: 10.1371/journal.pone.0183842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/12/2017] [Indexed: 12/19/2022] Open
Abstract
There are co-morbidity between osteoporosis (OP) and rheumatoid arthritis (RA). Some genetic risk factors have been identified for these two phenotypes respectively in previous research; however, they accounted for only a small portion of the underlying total genetic variances. Here, we sought to identify additional common genetic loci associated with OP and/or RA. The conditional false discovery rate (cFDR) approach allows detection of additional genetic factors (those respective ones as well as common pleiotropic ones) for the two associated phenotypes. We collected and analyzed summary statistics provided by large, multi-center GWAS studies of FNK (femoral neck) BMD (a major risk factor for osteoporosis) (n = 53,236) and RA (n = 80,799). The conditional quantile-quantile (Q-Q) plots can assess the enrichment of SNPs related to FNK BMD and RA, respectively. Furthermore, we identified shared loci between FNK BMD and RA using conjunction cFDR (ccFDR). We found strong enrichment of p-values in FNK BMD when conditional Q-Q was done on RA and vice versa. We identified 30 novel OP-RA associated pleiotropic loci that have not been reported in previous OP or RA GWAS, 18 of which located in the MHC (major histocompatibility complex) region previously reported to play an important role in immune system and bone health. We identified some specific novel polygenic factors for OP and RA respectively, and identified 30 novel OP-RA associated pleiotropic loci. These discovery findings may offer novel pathobiological insights, and suggest new targets and pathways for drug development in OP and RA patients.
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14
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Greenbaum J, Wu K, Zhang L, Shen H, Zhang J, Deng HW. Increased detection of genetic loci associated with risk predictors of osteoporotic fracture using a pleiotropic cFDR method. Bone 2017; 99:62-68. [PMID: 28373146 PMCID: PMC5488332 DOI: 10.1016/j.bone.2017.03.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/26/2017] [Accepted: 03/30/2017] [Indexed: 11/28/2022]
Abstract
Although GWAS have been successful in identifying some osteoporosis associated loci, the findings explain only a small fraction of the total genetic variance. In this study we use a recently developed novel pleiotropic conditional false discovery rate (cFDR) method to identify novel genetic loci associated with two risk traits for osteoporotic fracture (the clinical outcome and end result of osteoporosis), Height (HT) and Femoral Neck (FNK) BMD. The cFDR method allows us to improve the detection of associated variants by incorporating any potentially shared genetic mechanisms between the two associated traits. We analyzed the summary statistics from two GWAS meta-analyses for single nucleotide polymorphisms (SNPs) that are associated with HT and FNK BMD. Using the cFDR method, we show enrichment in the identification of SNPs associated with each trait conditioned on their strength of association with the second trait. The findings revealed 18 SNPs that are associated with both HT and FNK BMD, 4 of which had not previously been reported to play a role in bone health. The novel SNPs located at KIF1B and the intergenic region between FERD3L and TWISTNB are noteworthy as these genes may be associated with processes that are functionally important in bone metabolism. By leveraging GWAS results from related phenotypes we identified several novel loci that may contribute to the proportion of variability explained for each trait, although we cannot speculate about these potential contributions to heritability based on this analysis alone.
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Affiliation(s)
- Jonathan Greenbaum
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Kehao Wu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Lan Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Jigang Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA.
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Athanasiu L, Giddaluru S, Fernandes C, Christoforou A, Reinvang I, Lundervold AJ, Nilsson LG, Kauppi K, Adolfsson R, Eriksson E, Sundet K, Djurovic S, Espeseth T, Nyberg L, Steen VM, Andreassen OA, Le Hellard S. A genetic association study of CSMD1 and CSMD2 with cognitive function. Brain Behav Immun 2017; 61:209-216. [PMID: 27890662 DOI: 10.1016/j.bbi.2016.11.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 01/05/2023] Open
Abstract
The complement cascade plays a role in synaptic pruning and synaptic plasticity, which seem to be involved in cognitive functions and psychiatric disorders. Genetic variants in the closely related CSMD1 and CSMD2 genes, which are implicated in complement regulation, are associated with schizophrenia. Since patients with schizophrenia often show cognitive impairments, we tested whether variants in CSMD1 and CSMD2 are also associated with cognitive functions per se. We took a discovery-replication approach, using well-characterized Scandinavian cohorts. A total of 1637 SNPs in CSMD1 and 206 SNPs in CSMD2 were tested for association with cognitive functions in the NCNG sample (Norwegian Cognitive NeuroGenetics; n=670). Replication testing of SNPs with p-value<0.001 (7 in CSMD1 and 3 in CSMD2) was carried out in the TOP sample (Thematically Organized Psychosis; n=1025) and the BETULA sample (Betula Longitudinal Study on aging, memory and dementia; n=1742). Finally, we conducted a meta-analysis of these SNPs using all three samples. The previously identified schizophrenia marker in CSMD1 (SNP rs10503253) was also included. The strongest association was observed between the CSMD1 SNP rs2740931 and performance in immediate episodic memory (p-value=5×10-6, minor allele A, MAF 0.48-0.49, negative direction of effect). This association reached the study-wide significance level (p⩽1.2×10-5). SNP rs10503253 was not significantly associated with cognitive functions in our samples. In conclusion, we studied n=3437 individuals and found evidence that a variant in CSMD1 is associated with cognitive function. Additional studies of larger samples with cognitive phenotypes will be needed to further clarify the role of CSMD1 in cognitive phenotypes in health and disease.
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Affiliation(s)
- Lavinia Athanasiu
- NORMENT - K.G. Jebsen Center for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway; NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sudheer Giddaluru
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Carla Fernandes
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Andrea Christoforou
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ivar Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Astri J Lundervold
- Department of Biological and Medical Psychology, Jonas Lies vei 91, Bergen, Norway; K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Bergen 5009, Norway
| | - Lars-Göran Nilsson
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187 Umeå, Sweden; Aging Research Center, Karolinska Institutet, Stockholm, Sweden
| | - Karolina Kauppi
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187 Umeå, Sweden; Department of Integrative Medical Biology, Umea University, 90187 Umeå, Sweden
| | - Rolf Adolfsson
- Department of Clinical Sciences, Psychiatry, Umea University, SE 901 85 Umeå, Sweden
| | - Elias Eriksson
- Department of Pharmacology, Institute of Physiology and Neuroscience, Sahlgrenska Academy, Göteborg University, SE 405 30 Göteborg, Sweden
| | - Kjetil Sundet
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Thomas Espeseth
- NORMENT - K.G. Jebsen Center for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway
| | - Lars Nyberg
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187 Umeå, Sweden; Department of Integrative Medical Biology, Umea University, 90187 Umeå, Sweden; Department of Radiation Sciences, Umeå University, 90187 Umeå, Sweden
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway.
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16
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Pei YF, Xie ZG, Wang XY, Hu WZ, Li LB, Ran S, Lin Y, Hai R, Shen H, Tian Q, Zhang YH, Lei SF, Papasian CJ, Deng HW, Zhang L. Association of 3q13.32 variants with hip trochanter and intertrochanter bone mineral density identified by a genome-wide association study. Osteoporos Int 2016; 27:3343-3354. [PMID: 27311723 DOI: 10.1007/s00198-016-3663-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/08/2016] [Indexed: 02/01/2023]
Abstract
UNLABELLED We performed a GWAS of trochanter and intertrochanter bone mineral density (BMD) in the Framingham Heart Study and replicated in three independent studies. Our results identified one novel locus around the associated variations at chromosomal region 3q13.32 and replicated two loci at chromosomal regions 3p21 and 8q24. Our findings provide useful insights that enhance our understanding of bone development, osteoporosis, and fracture pathogenesis. INTRODUCTION Hip trochanter (TRO) and intertrochanter (INT) subregions have important clinical relevance to subtrochanteric and intertrochanteric fractures but have rarely been studied by genome-wide association studies (GWASs). METHODS Aiming to identify genomic loci associated with BMD variation at TRO and INT regions, we performed a GWAS utilizing the Framingham Heart Study (FHS, N = 6,912) as discovery sample and utilized the Women's Health Initiative (WHI) African-American subsample (N = 845), WHI Hispanic subsample (N = 446), and Omaha osteoporosis study (N = 971), for replication. RESULTS Combining the evidence from both the discovery and the replication samples, we identified one novel locus around the associated variations at chromosomal region 3q13.32 (rs1949542, discovery p = 6.16 × 10-8, replication p = 2.86 × 10-4 for INT-BMD; discovery p = 1.35 × 10-7, replication p = 4.16 × 10-4 for TRO-BMD, closest gene RP11-384F7.1). We also replicated two loci at chromosomal regions 3p21 (rs148725943, discovery p = 6.61 × 10-7, replication p = 5.22 × 10-4 for TRO-BMD, closest gene CTNNB1) and 8q24 (rs7839059, discovery p = 2.28 × 10-7, replication p = 1.55 × 10-3 for TRO-BMD, closest gene TNFRSF11B) that were reported previously. We demonstrated that the effects at both 3q13.32 and 3p21 were specific to the TRO, but not to the femoral neck and spine. In contrast, the effect at 8q24 was common to all the sites. CONCLUSION Our findings provide useful insights that enhance our understanding of bone development, osteoporosis, and fracture pathogenesis.
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Affiliation(s)
- Y-F Pei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - Z-G Xie
- The Second Affiliated Hospital of Soochow University, Jiangsu, People's Republic of China
| | - X-Y Wang
- Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, People's Republic of China
| | - W-Z Hu
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Ren-ai Rd., Suzhou City, Jiangsu Province, 215123, People's Republic of China
| | - L-B Li
- The Second Affiliated Hospital of Soochow University, Jiangsu, People's Republic of China
| | - S Ran
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - Y Lin
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - R Hai
- Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia, People's Republic of China
| | - H Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Q Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Y-H Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - S-F Lei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Ren-ai Rd., Suzhou City, Jiangsu Province, 215123, People's Republic of China
| | - C J Papasian
- Department of Basic Medical Science, University of Missouri-Kansas City, Kansas City, MO, USA
| | - H-W Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA.
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, LA, 70112, USA.
| | - L Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China.
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Ren-ai Rd., Suzhou City, Jiangsu Province, 215123, People's Republic of China.
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Giddaluru S, Espeseth T, Salami A, Westlye LT, Lundquist A, Christoforou A, Cichon S, Adolfsson R, Steen VM, Reinvang I, Nilsson LG, Le Hellard S, Nyberg L. Genetics of structural connectivity and information processing in the brain. Brain Struct Funct 2016; 221:4643-4661. [PMID: 26852023 PMCID: PMC5102980 DOI: 10.1007/s00429-016-1194-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/22/2016] [Indexed: 12/20/2022]
Abstract
Understanding the genetic factors underlying brain structural connectivity is a major challenge in imaging genetics. Here, we present results from genome-wide association studies (GWASs) of whole-brain white matter (WM) fractional anisotropy (FA), an index of microstructural coherence measured using diffusion tensor imaging. Data from independent GWASs of 355 Swedish and 250 Norwegian healthy adults were integrated by meta-analysis to enhance power. Complementary GWASs on behavioral data reflecting processing speed, which is related to microstructural properties of WM pathways, were performed and integrated with WM FA results via multimodal analysis to identify shared genetic associations. One locus on chromosome 17 (rs145994492) showed genome-wide significant association with WM FA (meta P value = 1.87 × 10-08). Suggestive associations (Meta P value <1 × 10-06) were observed for 12 loci, including one containing ZFPM2 (lowest meta P value = 7.44 × 10-08). This locus was also implicated in multimodal analysis of WM FA and processing speed (lowest Fisher P value = 8.56 × 10-07). ZFPM2 is relevant in specification of corticothalamic neurons during brain development. Analysis of SNPs associated with processing speed revealed association with a locus that included SSPO (lowest meta P value = 4.37 × 10-08), which has been linked to commissural axon growth. An intergenic SNP (rs183854424) 14 kb downstream of CSMD1, which is implicated in schizophrenia, showed suggestive evidence of association in the WM FA meta-analysis (meta P value = 1.43 × 10-07) and the multimodal analysis (Fisher P value = 1 × 10-07). These findings provide novel data on the genetics of WM pathways and processing speed, and highlight a role of ZFPM2 and CSMD1 in information processing in the brain.
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Affiliation(s)
- Sudheer Giddaluru
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021, Bergen, Norway.,K.G.Jebsen Center for Psychosis Research and the Norwegian Center for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Thomas Espeseth
- K.G. Jebsen Center for Psychosis Research, Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, 0424, Oslo, Norway.,Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Alireza Salami
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187, Umeå, Sweden.,Aging Research Center, Karolinska Institutet and Stockholm University, 11330, Stockholm, Sweden
| | - Lars T Westlye
- K.G. Jebsen Center for Psychosis Research, Norwegian Center for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, 0424, Oslo, Norway.,Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Anders Lundquist
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187, Umeå, Sweden.,Department of Statistics, USBF, Umeå University, 90187, Umeå, Sweden
| | - Andrea Christoforou
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021, Bergen, Norway.,K.G.Jebsen Center for Psychosis Research and the Norwegian Center for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Sven Cichon
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4058, Basel, Switzerland.,Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, 52425, Juelich, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, 53127, Bonn, Germany
| | - Rolf Adolfsson
- Department of Clinical Sciences, Psychiatry, Umeå University, 90187, Umeå, Sweden
| | - Vidar M Steen
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021, Bergen, Norway.,K.G.Jebsen Center for Psychosis Research and the Norwegian Center for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ivar Reinvang
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Lars Göran Nilsson
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187, Umeå, Sweden.,ARC, Karolinska Institutet, Stockholm, Sweden
| | - Stéphanie Le Hellard
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021, Bergen, Norway.,K.G.Jebsen Center for Psychosis Research and the Norwegian Center for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Lars Nyberg
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, 90187, Umeå, Sweden. .,Department of Radiation Sciences, Umeå University, 90187, Umeå, Sweden. .,Department of Integrative Medical Biology, Umeå University, 90187, Umeå, Sweden.
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18
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Pei YF, Tian Q, Zhang L, Deng HW. Exploring the Major Sources and Extent of Heterogeneity in a Genome-Wide Association Meta-Analysis. Ann Hum Genet 2015; 80:113-22. [PMID: 26686198 DOI: 10.1111/ahg.12143] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/27/2015] [Indexed: 11/28/2022]
Abstract
Genome-wide association (GWA) meta-analysis has become a popular approach for discovering genetic variants responsible for complex diseases. The between-study heterogeneity effect is a severe issue that may complicate the interpretation of results. Aiming to improve the interpretation of meta-analysis results, we empirically explored the extent and source of heterogeneity effect. We analyzed a previously reported GWA meta-analysis of obesity, in which over 21,000 subjects from seven individual samples were meta-analyzed. We first evaluated the extent and distribution of heterogeneity across the entire genome. We then studied the effects of several potentially confounding factors, including age, ethnicity, gender composition, study type, and genotype imputation on heterogeneity with a random-effects meta-regression model. Of the total 4,325,550 SNPs being tested, heterogeneity was moderate to very large for 25.4% of the total SNPs. Heterogeneity was more severe in SNPs with stronger association signals. Ethnicity, average age, and genotype imputation accuracy had significant effects on the heterogeneity. Exploring the effects of ethnicity can provide clues to the potential ethnic-specific effects for two loci known to affect obesity, MC4R, and MTCH2. Our analysis can help to clarify understanding of the obesity mechanism and may provide guidance for an effective design of future GWA meta-analysis.
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Affiliation(s)
- Yu-Fang Pei
- Department of Epidemiology and Medical Statistics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, P. R. China
| | - Qing Tian
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, USA
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, P. R. China.,Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, USA
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19
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Liu YJ, Zhang L, Papasian CJ, Deng HW. Genome-wide Association Studies for Osteoporosis: A 2013 Update. J Bone Metab 2014; 21:99-116. [PMID: 25006567 PMCID: PMC4075273 DOI: 10.11005/jbm.2014.21.2.99] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 12/16/2022] Open
Abstract
In the past few years, the bone field has witnessed great advances in genome-wide association studies (GWASs) of osteoporosis, with a number of promising genes identified. In particular, meta-analysis of GWASs, aimed at increasing the power of studies by combining the results from different study populations, have led to the identification of novel associations that would not otherwise have been identified in individual GWASs. Recently, the first whole genome sequencing study for osteoporosis and fractures was published, reporting a novel rare nonsense mutation. This review summarizes the important and representative findings published by December 2013. Comments are made on the notable findings and representative studies for their potential influence and implications on our present understanding of the genetics of osteoporosis. Potential limitations of GWASs and their meta-analyses are evaluated, with an emphasis on understanding the reasons for inconsistent results between different studies and clarification of misinterpretation of GWAS meta-analysis results. Implications and challenges of GWAS are also discussed, including the need for multi- and inter-disciplinary studies.
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Affiliation(s)
- Yong-Jun Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Lei Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA. ; Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, PR, China
| | | | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA. ; Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, PR, China
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20
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Zhang L, Choi HJ, Estrada K, Leo PJ, Li J, Pei YF, Zhang Y, Lin Y, Shen H, Liu YZ, Liu Y, Zhao Y, Zhang JG, Tian Q, Wang YP, Han Y, Ran S, Hai R, Zhu XZ, Wu S, Yan H, Liu X, Yang TL, Guo Y, Zhang F, Guo YF, Chen Y, Chen X, Tan L, Zhang L, Deng FY, Deng H, Rivadeneira F, Duncan EL, Lee JY, Han BG, Cho NH, Nicholson GC, McCloskey E, Eastell R, Prince RL, Eisman JA, Jones G, Reid IR, Sambrook PN, Dennison EM, Danoy P, Yerges-Armstrong LM, Streeten EA, Hu T, Xiang S, Papasian CJ, Brown MA, Shin CS, Uitterlinden AG, Deng HW. Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. Hum Mol Genet 2013; 23:1923-33. [PMID: 24249740 DOI: 10.1093/hmg/ddt575] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aiming to identify novel genetic variants and to confirm previously identified genetic variants associated with bone mineral density (BMD), we conducted a three-stage genome-wide association (GWA) meta-analysis in 27 061 study subjects. Stage 1 meta-analyzed seven GWA samples and 11 140 subjects for BMDs at the lumbar spine, hip and femoral neck, followed by a Stage 2 in silico replication of 33 SNPs in 9258 subjects, and by a Stage 3 de novo validation of three SNPs in 6663 subjects. Combining evidence from all the stages, we have identified two novel loci that have not been reported previously at the genome-wide significance (GWS; 5.0 × 10(-8)) level: 14q24.2 (rs227425, P-value 3.98 × 10(-13), SMOC1) in the combined sample of males and females and 21q22.13 (rs170183, P-value 4.15 × 10(-9), CLDN14) in the female-specific sample. The two newly identified SNPs were also significant in the GEnetic Factors for OSteoporosis consortium (GEFOS, n = 32 960) summary results. We have also independently confirmed 13 previously reported loci at the GWS level: 1p36.12 (ZBTB40), 1p31.3 (GPR177), 4p16.3 (FGFRL1), 4q22.1 (MEPE), 5q14.3 (MEF2C), 6q25.1 (C6orf97, ESR1), 7q21.3 (FLJ42280, SHFM1), 7q31.31 (FAM3C, WNT16), 8q24.12 (TNFRSF11B), 11p15.3 (SOX6), 11q13.4 (LRP5), 13q14.11 (AKAP11) and 16q24 (FOXL1). Gene expression analysis in osteogenic cells implied potential functional association of the two candidate genes (SMOC1 and CLDN14) in bone metabolism. Our findings independently confirm previously identified biological pathways underlying bone metabolism and contribute to the discovery of novel pathways, thus providing valuable insights into the intervention and treatment of osteoporosis.
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Affiliation(s)
- Lei Zhang
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, China
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