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Chen F, Dong X, Yu Z, Zhang Y, Shi Y. The brain-heart axis: Integrative analysis of the shared genetic etiology between neuropsychiatric disorders and cardiovascular disease. J Affect Disord 2024; 355:147-156. [PMID: 38518856 DOI: 10.1016/j.jad.2024.03.098] [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: 02/09/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
BACKGROUND Multiple observational studies have reported substantial comorbidity between neuropsychiatric disorders and cardiovascular disease (CVD), but the underlying mechanisms remain largely unknown. METHODS Using GWAS summary datasets of 8 neuropsychiatric disorders and 6 cardiovascular diseases, an integrative analysis incorporating linkage-disequilibrium-score-regression (LDSC), Mendelian randomization (MR), functional mapping and annotation (FUMA), and functional enrichment analysis, was conducted to investigate shared genetic etiology of the brain-heart axis from the whole genome level, single-nucleotide polymorphism (SNP) level, gene level, and biological pathway level. RESULTS In LDSC analysis, 18 pairwise traits between neuropsychiatric disorders and CVD were identified with significant genetic overlaps, revealing extensive genome-wide genetic correlations. In bidirectional MR analysis, 19 pairwise traits were identified with significant causal relationships. Genetic liabilities to neuropsychiatric disorders, particularly attention-deficit hyperactivity disorder and major depressive disorder, conferred extensive significant causal effects on the risk of CVD, while hypertension seemed to be a risk factor for multiple neuropsychiatric disorders, with no significant heterogeneity or pleiotropy. In FUMA analysis, 13 shared independent significant SNPs and 887 overlapping protein-coding genes were detected between neuropsychiatric disorders and CVD. With GO and KEEG functional enrichment analysis, biological pathways of the brain-heart axis were highly concentrated in neurotransmitter synaptic transmission, lipid metabolism, aldosterone synthesis and secretion, glutathione metabolism, and MAPK signaling pathway. CONCLUSION Extensive genetic correlations and genetic overlaps between neuropsychiatric disorders and CVD were identified in this study, which might provide some new insights into the brain-heart axis and the therapeutic targets in clinical practice.
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Affiliation(s)
- Feifan Chen
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
| | - Xinyu Dong
- Department of Neurosurgery, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.
| | - Zhiwei Yu
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Chongqing 400014, China.
| | - Yihan Zhang
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
| | - Yuan Shi
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
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2
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Lu Q, Zhou Y, Qian Q, Chen Z, Tan Q, Chen H, Yin F, Wang Y, Liu Z, Tian P, Sun D. Whole-exome sequencing identifies high-confidence genes for tic disorders in a Chinese Han population. Clin Chim Acta 2024:119759. [PMID: 38880274 DOI: 10.1016/j.cca.2024.119759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Tic disorder (TD) is a polygenic neurodevelopmental disorder with high susceptibility. However, identifying high-confidence risk genes has been challenging due to poor replication across multiple studies. METHODS Whole-exome sequencing was performed on 390 TD patients and 372 unaffected individuals in a Chinese Han population. Analysis of variance, burden analysis and in silico prediction were used to identify candidate genes for TD. To facilitate data analysis and to focus on high-confidence genes, we defined a panel of 160 genes as known causal or candidate TD genes from previous studies. Gene enrichment and protein-protein interaction analysis were utilized to detect potential novel TD risk genes. RESULTS Totally, 14 variants across 12 known TD candidate genes were considered potential susceptibility variants. Ten variants across 10 known TD candidate genes were identified as potential disease-causing variants. Burden analysis identified variants of 28 known genes were significantly excess in TD patients. In addition, 354 previously unproven TD genes are over-represented in patients. Genes enriched in the PI3K-Akt signaling, sphingolipid metabolism and serotonergic synaptic pathways, as well as those interacting with FN1, were considered potential new candidate genes for TD. CONCLUSIONS This is the largest WES study focusing on TD patients in a Chinese Han population. Several variants recurring in our cohort were identified as high-confidence risk loci for TD. Moreover, we provided potential new risk genes that may be prioritized for further investigation.
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Affiliation(s)
- Qing Lu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yong Zhou
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Qiaoqiao Qian
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Haiyun Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Yue Wang
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Peichao Tian
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
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3
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Chen LG, Tubbs JD, Liu Z, Thach TQ, Sham PC. Mendelian randomization: causal inference leveraging genetic data. Psychol Med 2024; 54:1461-1474. [PMID: 38639006 DOI: 10.1017/s0033291724000321] [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] [Indexed: 04/20/2024]
Abstract
Mendelian randomization (MR) leverages genetic information to examine the causal relationship between phenotypes allowing for the presence of unmeasured confounders. MR has been widely applied to unresolved questions in epidemiology, making use of summary statistics from genome-wide association studies on an increasing number of human traits. However, an understanding of essential concepts is necessary for the appropriate application and interpretation of MR. This review aims to provide a non-technical overview of MR and demonstrate its relevance to psychiatric research. We begin with the origins of MR and the reasons for its recent expansion, followed by an overview of its statistical methodology. We then describe the limitations of MR, and how these are being addressed by recent methodological advances. We showcase the practical use of MR in psychiatry through three illustrative examples - the connection between cannabis use and psychosis, the link between intelligence and schizophrenia, and the search for modifiable risk factors for depression. The review concludes with a discussion of the prospects of MR, focusing on the integration of multi-omics data and its extension to delineating complex causal networks.
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Affiliation(s)
- Lane G Chen
- Department of Psychiatry, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Justin D Tubbs
- Department of Psychiatry, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zipeng Liu
- Department of Psychiatry, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Thuan-Quoc Thach
- Department of Psychiatry, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Department of Psychiatry, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China
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4
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Trejo S. Exploring the Fetal Origins Hypothesis Using Genetic Data. SOCIAL FORCES; A SCIENTIFIC MEDIUM OF SOCIAL STUDY AND INTERPRETATION 2024; 102:1555-1581. [PMID: 38638179 PMCID: PMC11021852 DOI: 10.1093/sf/soae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/12/2023] [Accepted: 11/23/2023] [Indexed: 04/20/2024]
Abstract
Birth weight is a robust predictor of valued life course outcomes, emphasizing the importance of prenatal development. But does birth weight act as a proxy for environmental conditions in utero, or do biological processes surrounding birth weight themselves play a role in healthy development? To answer this question, we leverage variation in birth weight that is, within families, orthogonal to prenatal environmental conditions: one's genes. We construct polygenic scores in two longitudinal studies (Born in Bradford, N = 2008; Wisconsin Longitudinal Study, N = 8488) to empirically explore the molecular genetic correlates of birth weight. A 1 standard deviation increase in the polygenic score is associated with an ~100-grams increase in birth weight and a 1.4 pp (22 percent) decrease in low birth weight probability. Sibling comparisons illustrate that this association largely represents a causal effect. The polygenic score-birth weight association is increased for children who spend longer in the womb and whose mothers have higher body mass index, though we find no differences across maternal socioeconomic status. Finally, the polygenic score affects social and cognitive outcomes, suggesting that birth weight is itself related to healthy prenatal development.
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Affiliation(s)
- Sam Trejo
- Princeton University, Department of Sociology and Office of Population Research, United States
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Patel A, DiTraglia FJ, Zuber V, Burgess S. Selecting Invalid Instruments to Improve Mendelian Randomization with Two-Sample Summary Data. Ann Appl Stat 2024; 18:23-aoas1856. [PMID: 38737575 PMCID: PMC7615940 DOI: 10.1214/23-aoas1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Mendelian randomization (MR) is a widely-used method to estimate the causal relationship between a risk factor and disease. A fundamental part of any MR analysis is to choose appropriate genetic variants as instrumental variables. Genome-wide association studies often reveal that hundreds of genetic variants may be robustly associated with a risk factor, but in some situations investigators may have greater confidence in the instrument validity of only a smaller subset of variants. Nevertheless, the use of additional instruments may be optimal from the perspective of mean squared error even if they are slightly invalid; a small bias in estimation may be a price worth paying for a larger reduction in variance. For this purpose, we consider a method for "focused" instrument selection whereby genetic variants are selected to minimise the estimated asymptotic mean squared error of causal effect estimates. In a setting of many weak and locally invalid instruments, we propose a novel strategy to construct confidence intervals for post-selection focused estimators that guards against the worst case loss in asymptotic coverage. In empirical applications to: (i) validate lipid drug targets; and (ii) investigate vitamin D effects on a wide range of outcomes, our findings suggest that the optimal selection of instruments does not involve only a small number of biologically-justified instruments, but also many potentially invalid instruments.
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Affiliation(s)
| | | | - Verena Zuber
- Department of Biostatistics and Epidemiology, Imperial College London
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge
- Cardiovascular Epidemiology Unit, University of Cambridge
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6
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Deng Q, Song C, Lin S. An adaptive and robust method for multi-trait analysis of genome-wide association studies using summary statistics. Eur J Hum Genet 2024; 32:681-690. [PMID: 37237036 PMCID: PMC11153499 DOI: 10.1038/s41431-023-01389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human traits or diseases in the past decade. Nevertheless, much of the heritability of many traits is still unaccounted for. Commonly used single-trait analysis methods are conservative, while multi-trait methods improve statistical power by integrating association evidence across multiple traits. In contrast to individual-level data, GWAS summary statistics are usually publicly available, and thus methods using only summary statistics have greater usage. Although many methods have been developed for joint analysis of multiple traits using summary statistics, there are many issues, including inconsistent performance, computational inefficiency, and numerical problems when considering lots of traits. To address these challenges, we propose a multi-trait adaptive Fisher method for summary statistics (MTAFS), a computationally efficient method with robust power performance. We applied MTAFS to two sets of brain imaging derived phenotypes (IDPs) from the UK Biobank, including a set of 58 Volumetric IDPs and a set of 212 Area IDPs. Through annotation analysis, the underlying genes of the SNPs identified by MTAFS were found to exhibit higher expression and are significantly enriched in brain-related tissues. Together with results from a simulation study, MTAFS shows its advantage over existing multi-trait methods, with robust performance across a range of underlying settings. It controls type 1 error well and can efficiently handle a large number of traits.
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Affiliation(s)
- Qiaolan Deng
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
- Department of Statistics, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Shili Lin
- Department of Statistics, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA.
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7
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Peña E, Mas-Bermejo P, Lecube A, Ciudin A, Arenas C, Simó R, Rigla M, Caixàs A, Rosa A. Use of polygenic risk scores to assess weight loss after bariatric surgery: a five-year follow-up study. J Gastrointest Surg 2024:S1091-255X(24)00485-2. [PMID: 38821212 DOI: 10.1016/j.gassur.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Bariatric surgery is currently the most effective long-term treatment for severe obesity. However, the interindividual variability observed in surgical outcomes suggests a moderating effect of several factors, including individual genetic background. Our goal was to investigate the contribution of the genetic architecture of BMI to the variability in weight loss outcomes after bariatric surgery. METHODS A total of 106 patients with severe obesity who underwent Roux-en-Y gastric bypass or sleeve gastrectomy were followed up for five years. Changes in body mass index (BMIchange) and percentage of total weight loss (%TWL) were evaluated during the postoperative period. Polygenic risk scores including 50 genetic variants were calculated for each participant to determine their individual genetic risk for high BMI based on a previous GWAS. Generalized estimating equation models were used to study the role of the individual's polygenic score, as well as other factors, on BMIchange and %TWL in the long term after surgery. RESULTS We found an effect of the polygenic score on %TWL and BMIchange, where subjects with lower scores had better outcomes after surgery than those with higher scores. Furthermore, when analyzing only patients who underwent Roux-en-Y gastric bypass, these results were replicated showing greater weight loss after surgery for those with lower polygenic scores. DISCUSSION These results indicate that genetic background assessed with polygenic risk scores, along with other individual factors such as sex, age, and preoperative BMI, has an impact on bariatric surgery outcomes and could represent a useful tool for estimating surgical outcomes in advance.
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Affiliation(s)
- Elionora Peña
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Patricia Mas-Bermejo
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Albert Lecube
- Endocrinology and Nutrition Department, Arnau de Vilanova University Hospital, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Andreea Ciudin
- Endocrinology and Nutrition Department, Hospital Universitari Vall d'Hebron, Diabetes and Metabolism Research Unit, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Concepción Arenas
- Statistics Section of the Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), Barcelona, Spain
| | - Rafael Simó
- Endocrinology and Nutrition Department, Hospital Universitari Vall d'Hebron, Diabetes and Metabolism Research Unit, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mercedes Rigla
- Endocrinology and Nutrition Department, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació (I3PT-CERCA), Departament de Medicina, Universitat Autònoma de Barcelona (UAB), Sabadell, Spain
| | - Assumpta Caixàs
- Endocrinology and Nutrition Department, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació (I3PT-CERCA), Departament de Medicina, Universitat Autònoma de Barcelona (UAB), Sabadell, Spain.
| | - Araceli Rosa
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain; CIBER de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain.
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8
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Liu Y, Yuan M, He J, Cai L, Leng A. The Impact of Non-alcohol Fatty Liver Disease on Bone Mineral Density is Mediated by Sclerostin by Mendelian Randomization Study. Calcif Tissue Int 2024; 114:502-512. [PMID: 38555554 DOI: 10.1007/s00223-024-01204-5] [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: 05/30/2023] [Accepted: 02/19/2024] [Indexed: 04/02/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has been found to be associated with osteoporosis (OP) in observational studies. However, the precise causal relationship between NAFLD and OP remains unclear. Here, we used Mendelian randomization (MR) to explore the causal relationship. We selected NAFLD-related single-nucleotide polymorphisms from a genome-wide meta-analysis (8434 cases and 434,770 controls) as instrumental variants. We used inverse variance weighted analysis for the primary MR analysis. Furthermore, we used similar methodologies in parallel investigations of other chronic liver diseases (CLDs). We performed sensitivity analyses to ensure the reliability of the results. We observed a causality between NAFLD and forearm bone mineral density (FABMD) (beta-estimate [β]: - 0.212; p-value: 0.034). We also found that sclerostin can act as a mediator to influence the NAFLD and FABMD pathways to form a mediated MR network (mediated proportion = 8.8%). We also identified indications of causal relationships between other CLDs and OP. However, we were unable to establish any associated mediators. Notably, our analyses did not yield any evidence of pleiotropy. Our findings have implications in the development of preventive and interventional measures aimed at managing low bone mineral density in patients with NAFLD.
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Affiliation(s)
- Yuan Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, No.88 Xiangya Road, Kaifu District, Changsha, 410000, Hunan Province, China
| | - Mengqin Yuan
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jian He
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Longjiao Cai
- Department of Gastroenterology, Xiangya Hospital, Central South University, No.88 Xiangya Road, Kaifu District, Changsha, 410000, Hunan Province, China
| | - Aimin Leng
- Department of Gastroenterology, Xiangya Hospital, Central South University, No.88 Xiangya Road, Kaifu District, Changsha, 410000, Hunan Province, China.
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9
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Cao X, Zhang S, Sha Q. A novel method for multiple phenotype association studies based on genotype and phenotype network. PLoS Genet 2024; 20:e1011245. [PMID: 38728360 PMCID: PMC11111089 DOI: 10.1371/journal.pgen.1011245] [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: 08/18/2023] [Revised: 05/22/2024] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
Joint analysis of multiple correlated phenotypes for genome-wide association studies (GWAS) can identify and interpret pleiotropic loci which are essential to understand pleiotropy in diseases and complex traits. Meanwhile, constructing a network based on associations between phenotypes and genotypes provides a new insight to analyze multiple phenotypes, which can explore whether phenotypes and genotypes might be related to each other at a higher level of cellular and organismal organization. In this paper, we first develop a bipartite signed network by linking phenotypes and genotypes into a Genotype and Phenotype Network (GPN). The GPN can be constructed by a mixture of quantitative and qualitative phenotypes and is applicable to binary phenotypes with extremely unbalanced case-control ratios in large-scale biobank datasets. We then apply a powerful community detection method to partition phenotypes into disjoint network modules based on GPN. Finally, we jointly test the association between multiple phenotypes in a network module and a single nucleotide polymorphism (SNP). Simulations and analyses of 72 complex traits in the UK Biobank show that multiple phenotype association tests based on network modules detected by GPN are much more powerful than those without considering network modules. The newly proposed GPN provides a new insight to investigate the genetic architecture among different types of phenotypes. Multiple phenotypes association studies based on GPN are improved by incorporating the genetic information into the phenotype clustering. Notably, it might broaden the understanding of genetic architecture that exists between diagnoses, genes, and pleiotropy.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
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10
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Fang Z, Jia S, Mou X, Li Z, Hu T, Tu Y, Zhao J, Zhang T, Lin W, Lu Y, Feng C, Xia S. Shared genetic architecture and causal relationship between liver and heart disease. iScience 2024; 27:109431. [PMID: 38523778 PMCID: PMC10959668 DOI: 10.1016/j.isci.2024.109431] [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: 10/13/2023] [Revised: 01/08/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
This study investigates the relationship and genetic mechanisms of liver and heart diseases, focusing on the liver-heart axis (LHA) as a fundamental biological basis. Through genome-wide association study analysis, we explore shared genes and pathways related to LHA. Shared genetic factors are found in 8 out of 20 pairs, indicating genetic correlations. The analysis reveals 53 loci with pleiotropic effects, including 8 loci exhibiting shared causality across multiple traits. Based on SNP-p level tissue-specific multi-marker analysis of genomic annotation (MAGMA) analysis demonstrates significant enrichment of pleiotropy in liver and heart diseases within different cardiovascular tissues and female reproductive appendages. Gene-specific MAGMA analysis identifies 343 pleiotropic genes associated with various traits; these genes show tissue-specific enrichment primarily in the liver, cardiovascular system, and other tissues. Shared risk loci between immune cells and both liver and cardiovascular diseases are also discovered. Mendelian randomization analyses provide support for causal relationships among the investigated trait pairs.
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Affiliation(s)
- Ziyi Fang
- Department of Gastroenterology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Sixiang Jia
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Xuanting Mou
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Zhe Li
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Tianli Hu
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Yiting Tu
- Department of Orthopedics, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianqiang Zhao
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Tianlong Zhang
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Wenting Lin
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Yile Lu
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Chao Feng
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
| | - Shudong Xia
- Department of Cardiology, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
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11
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Luo L, Mehrotra DV, Shen J, Tang ZZ. Multi-trait analysis of gene-by-environment interactions in large-scale genetic studies. Biostatistics 2024; 25:504-520. [PMID: 36897773 DOI: 10.1093/biostatistics/kxad004] [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: 11/03/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
Identifying genotype-by-environment interaction (GEI) is challenging because the GEI analysis generally has low power. Large-scale consortium-based studies are ultimately needed to achieve adequate power for identifying GEI. We introduce Multi-Trait Analysis of Gene-Environment Interactions (MTAGEI), a powerful, robust, and computationally efficient framework to test gene-environment interactions on multiple traits in large data sets, such as the UK Biobank (UKB). To facilitate the meta-analysis of GEI studies in a consortium, MTAGEI efficiently generates summary statistics of genetic associations for multiple traits under different environmental conditions and integrates the summary statistics for GEI analysis. MTAGEI enhances the power of GEI analysis by aggregating GEI signals across multiple traits and variants that would otherwise be difficult to detect individually. MTAGEI achieves robustness by combining complementary tests under a wide spectrum of genetic architectures. We demonstrate the advantages of MTAGEI over existing single-trait-based GEI tests through extensive simulation studies and the analysis of the whole exome sequencing data from the UKB.
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Affiliation(s)
- Lan Luo
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Devan V Mehrotra
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., North Wales, PA 19454, USA
| | - Judong Shen
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 330 N Orchard St, Madison, WI 53715, USA
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12
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Bridges EC, Torsney C, Bates TC, Luciano M. Childhood Reading Ability and Pain in Childhood Through to Midlife. THE JOURNAL OF PAIN 2024:104518. [PMID: 38580099 DOI: 10.1016/j.jpain.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
Dyslexia and pain have recently been shown to correlate on a genetic level, but there has been little exploration of this association on the phenotypic level despite reports of increased pain in Attention Deficit Hyperactivity Disorder, which commonly co-occurs with dyslexia. In this study we test for an association between reading ability, which is the primary feature of dyslexia, and pain both in childhood and adulthood. Logistic regression modeling was used to test associations between reading ability in childhood and pain from childhood to midlife in a large UK birth cohort; the 1958 National Child Development Study. Associations were found between poor childhood reading ability and increased headache and abdominal pain in childhood, and between poor childhood reading ability and headache, eye pain, back pain, and rheumatism in adulthood. Mediation analyses indicated that socioeconomic status (defined by employment) fully mediated the association between poor reading ability in childhood and back pain at age 42. By contrast, the association between reading ability and eye pain acted independently of socioeconomic status. Different mechanisms were thus indicated for the association of reading with different pain types, including manual labor and a potential shared biological pathway. PERSPECTIVE: This study found a relationship between poor reading ability in childhood and pain in childhood and adulthood. Those with reading difficulties should be monitored for pain symptoms. Future research may uncover shared biological mechanisms, increasing our understanding of pain and potential treatments.
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Affiliation(s)
- Elinor C Bridges
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | - Carole Torsney
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Timothy C Bates
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | - Michelle Luciano
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
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13
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024:10.1038/s41576-024-00711-3. [PMID: 38565962 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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14
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Liu R, Shang X, Fu Y, Wang Y, Wang P, Yan S. Shared genetic architecture between hypothyroidism and rheumatoid arthritis: A large-scale cross-trait analysis. Mol Immunol 2024; 168:17-24. [PMID: 38368726 DOI: 10.1016/j.molimm.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND In recent years, mounting evidence has indicated a co-morbid relationship between hypothyroidism and rheumatoid arthritis (RA), however, the shared genetic factors underlying this association remain unclear. This study aims to investigate the common genetic architecture between hypothyroidism and RA. METHODS Genome-wide association study (GWAS) summary statistics from recently published studies were utilized to examine the genetic correlation, shared genetic loci, and potential causal relationship between hypothyroidism and RA. Statistical methods included linkage disequilibrium score regression (LDSC), high-definition likelihood (HDL), cross-trait meta-analyses, colocalization analysis, multi-marker analysis of genomic annotation (MAGMA), tissue-specific enrichment analysis (TSEA), functional enrichment analysis, and latent causal variable method (LCV). RESULTS Our study demonstrated a significant genetic correlation between hypothyroidism and RA(LDSC:rg=0.3803,p=7.23e-11;HDL:rg=0.3849,p=1.02e-21). Through cross-trait meta-analysis, we identified 1035 loci, including 43 novel genetic loci. By integrating colocalization analysis and the MAGMA algorithm, we found a substantial number of genes, such as PTPN22, TYK2, and CTLA-4, shared between the two diseases, which showed significant enrichment across 14 tissues. These genes were primarily associated with the regulation of alpha-beta T cell proliferation, positive regulation of T cell activation, positive regulation of leukocyte cell-cell adhesion, T cell receptor signaling pathway, and JAK-STAT signaling pathway. However, our study did not reveal a significant causal association between the two diseases using the LCV approach. CONCLUSION Based on these findings, there is a significant genetic correlation between hypothyroidism and RA, suggesting a shared genetic basis for these conditions.
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Affiliation(s)
- Ruiyan Liu
- Endocrine Ward II, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Xin Shang
- Endocrine Ward II, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Yu Fu
- Endocrine Ward II, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Ying Wang
- Department of Geriatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Ping Wang
- Endocrine Ward II, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China.
| | - Shuxun Yan
- Endocrine Ward II, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China.
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15
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Tissink EP, Shadrin AA, van der Meer D, Parker N, Hindley G, Roelfs D, Frei O, Fan CC, Nagel M, Nærland T, Budisteanu M, Djurovic S, Westlye LT, van den Heuvel MP, Posthuma D, Kaufmann T, Dale AM, Andreassen OA. Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study. Nat Commun 2024; 15:2655. [PMID: 38531894 DOI: 10.1038/s41467-024-46817-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Genetic pleiotropy is abundant across spatially distributed brain characteristics derived from one neuroimaging modality (e.g. structural, functional or diffusion magnetic resonance imaging [MRI]). A better understanding of pleiotropy across modalities could inform us on the integration of brain function, micro- and macrostructure. Here we show extensive genetic overlap across neuroimaging modalities at a locus and gene level in the UK Biobank (N = 34,029) and ABCD Study (N = 8607). When jointly analysing phenotypes derived from structural, functional and diffusion MRI in a genome-wide association study (GWAS) with the Multivariate Omnibus Statistical Test (MOSTest), we boost the discovery of loci and genes beyond previously identified effects for each modality individually. Cross-modality genes are involved in fundamental biological processes and predominantly expressed during prenatal brain development. We additionally boost prediction of psychiatric disorders by conditioning independent GWAS on our multimodal multivariate GWAS. These findings shed light on the shared genetic mechanisms underlying variation in brain morphology, functional connectivity, and tissue composition.
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Affiliation(s)
- E P Tissink
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands.
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
| | - A A Shadrin
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
| | - D van der Meer
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - N Parker
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
| | - G Hindley
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
- Psychosis Studies, Institute of Psychiatry, Psychology and Neurosciences, King's College London, 16 De Crespigny Park, London, SE5 8AB, United Kingdom
| | - D Roelfs
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
| | - O Frei
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
| | - C C Fan
- Laureate Institute for Brain Research, Tulsa, OK, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92037, USA
| | - M Nagel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands
| | - T Nærland
- K.G. Jebsen Centre for Neurodevelopmental disorders, Division of Paediatric Medicine, Institute of Clinical Medicine, University of Oslo, Building 31, Oslo, Norway
| | - M Budisteanu
- Prof. Dr. Alex Obregia Clinical Hospital of Psychiatry, Bucharest, Romania
- "Victor Babes" National Institute of Pathology, Bucharest, Romania
| | - S Djurovic
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, Division of Paediatric Medicine, Institute of Clinical Medicine, University of Oslo, Building 31, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - L T Westlye
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, Division of Paediatric Medicine, Institute of Clinical Medicine, University of Oslo, Building 31, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - M P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychology and Psychiatry, section Complex Trait Genetics, Amsterdam Neuroscience, VU University Medical Centre, Amsterdam, The Netherlands
| | - D Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HV, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychology and Psychiatry, section Complex Trait Genetics, Amsterdam Neuroscience, VU University Medical Centre, Amsterdam, The Netherlands
| | - T Kaufmann
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany
| | - A M Dale
- Department of Radiology, University of California San Diego, La Jolla, CA, 92037, USA
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA, 92037, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
| | - O A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Building 48, Oslo, Norway.
- K.G. Jebsen Centre for Neurodevelopmental disorders, Division of Paediatric Medicine, Institute of Clinical Medicine, University of Oslo, Building 31, Oslo, Norway.
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16
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Mota LFM, Arikawa LM, Santos SWB, Fernandes Júnior GA, Alves AAC, Rosa GJM, Mercadante MEZ, Cyrillo JNSG, Carvalheiro R, Albuquerque LG. Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle. Sci Rep 2024; 14:6404. [PMID: 38493207 PMCID: PMC10944497 DOI: 10.1038/s41598-024-57234-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control. Prediction accuracy (Acc) was evaluated using a forward validation splitting the dataset based on birth year, considering the phenotypes adjusted for the fixed effects and covariates as pseudo-phenotypes. The MLNN and SVR approaches were trained by randomly splitting the training population into fivefold to select the best hyperparameters. The results show that the machine learning methods (MLNN and SVR) and MTGBLUP outperformed STGBLUP and the Bayesian regression approaches, increasing the Acc by approximately 8.9%, 14.6%, and 13.7% using MLNN, SVR, and MTGBLUP, respectively. Acc for SVR and MTGBLUP were slightly different, ranging from 0.62 to 0.69 and 0.62 to 0.68, respectively, with empirically unbiased for both models (0.97 and 1.09). Our results indicated that SVR and MTGBLUBP approaches were more accurate in predicting FE-related traits than Bayesian regression and STGBLUP and seemed competitive for GS of complex phenotypes with various degrees of inheritance.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Leonardo M Arikawa
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Anderson A C Alves
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil.
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17
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Guo J, Luo Q, Li C, Liang H, Cao Q, Li Z, Chen G, Yu X. Evidence for the gut-skin axis: Common genetic structures in inflammatory bowel disease and psoriasis. Skin Res Technol 2024; 30:e13611. [PMID: 38348734 PMCID: PMC10862160 DOI: 10.1111/srt.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) and psoriasis (Ps) are common immune-mediated diseases that exhibit clinical comorbidity, possibly due to a common genetic structure. However, the exact mechanism remains unknown. METHODS The study population consisted of IBD and Ps genome-wide association study (GWAS) data. Genetic correlations were first evaluated. Then, the overall evaluation employed LD score regression (LDSC), while the local assessment utilized heritability estimation from summary statistics (HESS). Causality assessment was conducted through two-sample Mendelian randomization (2SMR), and genetic overlap analysis utilized the conditional false discovery rate/conjunctional FDR (cond/conjFDR) method. Finally, LDSC applied to specifically expressed genes (LDSC-SEG) was performed at the tissue level. For IBD and Ps-specific expressed genes, genetic correlation, causality, shared genetics, and trait-specific associated tissues were methodically examined. RESULTS At the genomic level, both overall and local genetic correlations were found between IBD and Ps. MR analysis indicated a positive causal relationship between Ps and IBD. The conjFDR analysis with a threshold of < 0.01 identified 43 loci shared between IBD and Ps. Subsequent investigations into disease-associated tissues indicated a close association of IBD and Ps with whole blood, lung, spleen, and EBV-transformed lymphocytes. CONCLUSION The current research offers a novel perspective on the association between IBD and Ps. It contributes to an enhanced comprehension of the genetic structure and mechanisms of comorbidities in both diseases.
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Affiliation(s)
- Jinyan Guo
- Department of Anorectal SurgeryJiangmen Wuyi Hospital of Traditional Chinese MedicineJiangmenChina
| | - Qinghua Luo
- Clinical Medical CollegeJiangxi University of Chinese MedicineNanchangChina
| | - Chunsheng Li
- Department of Anorectal SurgeryJiangmen Wuyi Hospital of Traditional Chinese MedicineJiangmenChina
| | - Hong Liang
- Department of Anorectal SurgeryJiangmen Wuyi Hospital of Traditional Chinese MedicineJiangmenChina
| | - Qiurui Cao
- Department of Anorectal SurgeryJiangmen Wuyi Hospital of Traditional Chinese MedicineJiangmenChina
| | - Zihao Li
- Department of Anorectal SurgeryJiangmen Wuyi Hospital of Traditional Chinese MedicineJiangmenChina
| | - Guanghua Chen
- Department of Anorectal SurgeryAffiliated Hospital of Jiangxi University of Chinese MedicineNanchangChina
| | - Xuchao Yu
- Department of Anorectal SurgeryAffiliated Hospital of Jiangxi University of Chinese MedicineNanchangChina
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18
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Li LJ, Zhong XX, Tan GZ, Song MX, Li P, Liu ZX, Xiong SC, Yang DQ, Liang ZJ. Investigation of causal relationships between cortical structure and osteoporosis using two-sample Mendelian randomization. Cereb Cortex 2024; 34:bhad529. [PMID: 38216542 DOI: 10.1093/cercor/bhad529] [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: 11/12/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/14/2024] Open
Abstract
The mutual interaction between bone characteristics and brain had been reported previously, yet whether the cortical structure has any relevance to osteoporosis is questionable. Therefore, we applied a two-sample bidirectional Mendelian randomization analysis to investigate this relationship. We utilized the bone mineral density measurements of femoral neck (n = 32,735) and lumbar spine (n = 28,498) and data on osteoporosis (7300 cases and 358,014 controls). The global surficial area and thickness and 34 specific functional regions of 51,665 patients were screened by magnetic resonance imaging. For the primary estimate, we utilized the inverse-variance weighted method. The Mendelian randomization-Egger intercept test, MR-PRESSO, Cochran's Q test, and "leave-one-out" sensitivity analysis were conducted to assess heterogeneity and pleiotropy. We observed suggestive associations between decreased thickness in the precentral region (OR = 0.034, P = 0.003) and increased chance of having osteoporosis. The results also revealed suggestive causality of decreased bone mineral density in femoral neck to declined total cortical surface area (β = 1400.230 mm2, P = 0.003), as well as the vulnerability to osteoporosis and reduced thickness in the Parstriangularis region (β = -0.006 mm, P = 0.002). Our study supports that the brain and skeleton exhibit bidirectional crosstalk, indicating the presence of a mutual brain-bone interaction.
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Affiliation(s)
- Long-Jun Li
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Xian-Xing Zhong
- Guangdong Research Institute for Orthopedics and Traumatology of Chinese Medicine, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510378, PR China
| | - Guo-Zhi Tan
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Ming-Xi Song
- Department of Education and Research, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510378, PR China
| | - Pian Li
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Zhen-Xin Liu
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Si-Cheng Xiong
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Da-Qi Yang
- The Third Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Zu-Jian Liang
- Department of Preventive Medicine, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510378, PR China
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19
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Gong H, Zhou Z, Bu C, Zhang D, Fang Q, Zhang XY, Song Y. Computational dissection of genetic variation modulating the response of multiple photosynthetic phenotypes to the light environment. BMC Genomics 2024; 25:81. [PMID: 38243219 PMCID: PMC10799405 DOI: 10.1186/s12864-024-09968-8] [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: 06/30/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The expression of biological traits is modulated by genetics as well as the environment, and the level of influence exerted by the latter may vary across characteristics. Photosynthetic traits in plants are complex quantitative traits that are regulated by both endogenous genetic factors and external environmental factors such as light intensity and CO2 concentration. The specific processes impacted occur dynamically and continuously as the growth of plants changes. Although studies have been conducted to explore the genetic regulatory mechanisms of individual photosynthetic traits or to evaluate the effects of certain environmental variables on photosynthetic traits, the systematic impact of environmental variables on the dynamic process of integrated plant growth and development has not been fully elucidated. RESULTS In this paper, we proposed a research framework to investigate the genetic mechanism of high-dimensional complex photosynthetic traits in response to the light environment at the genome level. We established a set of high-dimensional equations incorporating environmental regulators to integrate functional mapping and dynamic screening of gene‒environment complex systems to elucidate the process and pattern of intrinsic genetic regulatory mechanisms of three types of photosynthetic phenotypes of Populus simonii that varied with light intensity. Furthermore, a network structure was established to elucidate the crosstalk among significant QTLs that regulate photosynthetic phenotypic systems. Additionally, the detection of key QTLs governing the response of multiple phenotypes to the light environment, coupled with the intrinsic differences in genotype expression, provides valuable insights into the regulatory mechanisms that drive the transition of photosynthetic activity and photoprotection in the face of varying light intensity gradients. CONCLUSIONS This paper offers a comprehensive approach to unraveling the genetic architecture of multidimensional variations in photosynthetic phenotypes, considering the combined impact of integrated environmental factors from multiple perspectives.
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Affiliation(s)
- Huiying Gong
- College of Science, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Ziyang Zhou
- College of Science, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Chenhao Bu
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Deqiang Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Qing Fang
- Faculty of Science, Yamagata University, Yamagata, 990, Japan
| | - Xiao-Yu Zhang
- College of Science, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
| | - Yuepeng Song
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
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20
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Li R, Benz L, Duan R, Denny JC, Hakonarson H, Mosley JD, Smoller JW, Wei WQ, Ritchie MD, Moore JH, Chen Y. mixWAS: An efficient distributed algorithm for mixed-outcomes genome-wide association studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.09.24301073. [PMID: 38260403 PMCID: PMC10802662 DOI: 10.1101/2024.01.09.24301073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Genome-wide association studies (GWAS) have been instrumental in identifying genetic associations for various diseases and traits. However, uncovering genetic underpinnings among traits beyond univariate phenotype associations remains a challenge. Multi-phenotype associations (MPA), or genetic pleiotropy, offer important insights into shared genes and pathways among traits, enhancing our understanding of genetic architectures of complex diseases. GWAS of biobank-linked electronic health record (EHR) data are increasingly being utilized to identify MPA among various traits and diseases. However, methodologies that can efficiently take advantage of distributed EHR to detect MPA are still lacking. Here, we introduce mixWAS, a novel algorithm that efficiently and losslessly integrates multiple EHRs via summary statistics, allowing the detection of MPA among mixed phenotypes while accounting for heterogeneities across EHRs. Simulations demonstrate that mixWAS outperforms the widely used MPA detection method, Phenome-wide association study (PheWAS), across diverse scenarios. Applying mixWAS to data from seven EHRs in the US, we identified 4,534 MPA among blood lipids, BMI, and circulatory diseases. Validation in an independent EHR data from UK confirmed 97.7% of the associations. mixWAS fundamentally improves the detection of MPA and is available as a free, open-source software.
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Affiliation(s)
- Ruowang Li
- Department of Computational Biomedicine, Cedars-Sinai Medical Center
| | - Luke Benz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health
| | - Rui Duan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia
- Center for Applied Genomics, Children's Hospital of Philadelphia
- Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center
- Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Marylyn D Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center
| | - Yong Chen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania
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21
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Wang M, Li X, Wang C, Zou M, Yang J, Li XD, Guo B. Asymmetric and parallel subgenome selection co-shape common carp domestication. BMC Biol 2024; 22:4. [PMID: 38166816 PMCID: PMC10762839 DOI: 10.1186/s12915-023-01806-9] [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: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. RESULTS We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. CONCLUSIONS In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.
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Affiliation(s)
- Min Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yang
- Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
| | - Xiang-Dong Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810008, China.
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22
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Roy DG, Singh L, Chaturvedi HK, Chinnaswamy S. Gender-dependent multiple cross-phenotype association of interferon lambda genetic variants with peripheral blood profiles in healthy individuals. Mol Genet Genomic Med 2024; 12:e2292. [PMID: 37795763 PMCID: PMC10767428 DOI: 10.1002/mgg3.2292] [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] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Type III interferons (IFN), also called as lambda IFNs (IFN-λs), are antiviral and immunomodulatory cytokines that are evolutionarily important in humans. Given their central roles in innate immunity, they could be influencing other aspects of human biology. This study aimed to examine the association of genetic variants that control the expression and/or activity of IFN-λ3 and IFN-λ4 with multiple phenotypes in blood profiles of healthy individuals. METHODS In a cohort of about 550 self-declared healthy individuals, after applying several exclusion criteria to determine their health status, we measured 30 blood parameters, including cellular, biochemical, and metabolic profiles. We genotyped them at rs12979860 and rs28416813 using competitive allele-specific PCR assays and tested their association with the blood profiles under dominant and recessive models for the minor allele. IFN-λ4 variants rs368234815 and rs117648444 were also genotyped or inferred. RESULTS We saw no association in the combined cohort under either of the models for any of the phenotypes. When we stratified the cohort based on gender, we saw a significant association only in males with monocyte (p = 1 × 10-3 ) and SGOT (p = 7 × 10-3 ) levels under the dominant model and with uric acid levels (p = 0.01) under the recessive model. When we tested the IFN-λ4 activity modifying variant within groupings based on absence or presence of one or two copies of IFN-λ4 and on different activity levels of IFN-λ4, we found significant (p < 0.05) association with several phenotypes like monocyte, triglyceride, VLDL, ALP, and uric acid levels, only in males. All the above significant associations did not show any confounding when we tested for the same with up to ten different demographic and lifestyle variables. CONCLUSIONS These results show that lambda interferons can have pleiotropic effects. However, gender seems to be an effect modifier, with males being more sensitive than females to the effect.
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Affiliation(s)
- Debarati Guha Roy
- Infectious Disease GeneticsNational Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
| | - Lucky Singh
- ICMR‐National Institute of Medical StatisticsNew DelhiIndia
| | | | - Sreedhar Chinnaswamy
- Infectious Disease GeneticsNational Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
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23
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Xie H, Cao X, Zhang S, Sha Q. Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies using multi-layer network. Bioinformatics 2023; 39:btad707. [PMID: 37991852 PMCID: PMC10697735 DOI: 10.1093/bioinformatics/btad707] [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: 03/04/2023] [Revised: 09/29/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
MOTIVATION Genome-wide association studies is an essential tool for analyzing associations between phenotypes and single nucleotide polymorphisms (SNPs). Most of binary phenotypes in large biobanks are extremely unbalanced, which leads to inflated type I error rates for many widely used association tests for joint analysis of multiple phenotypes. In this article, we first propose a novel method to construct a Multi-Layer Network (MLN) using individuals with at least one case status among all phenotypes. Then, we introduce a computationally efficient community detection method to group phenotypes into disjoint clusters based on the MLN. Finally, we propose a novel approach, MLN with Omnibus (MLN-O), to jointly analyse the association between phenotypes and a SNP. MLN-O uses the score test to test the association of each merged phenotype in a cluster and a SNP, then uses the Omnibus test to obtain an overall test statistic to test the association between all phenotypes and a SNP. RESULTS We conduct extensive simulation studies to reveal that the proposed approach can control type I error rates and is more powerful than some existing methods. Meanwhile, we apply the proposed method to a real data set in the UK Biobank. Using phenotypes in Chapter XIII (Diseases of the musculoskeletal system and connective tissue) in the UK Biobank, we find that MLN-O identifies more significant SNPs than other methods we compare with. AVAILABILITY AND IMPLEMENTATION https://github.com/Hongjing-Xie/Multi-Layer-Network-with-Omnibus-MLN-O.
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Affiliation(s)
- Hongjing Xie
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, United States
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24
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Ma Z, Chang Y, Brito LF, Li Y, Yang T, Wang Y, Yang N. Multitrait meta-analyses identify potential candidate genes for growth-related traits in Holstein heifers. J Dairy Sci 2023; 106:9055-9070. [PMID: 37641329 DOI: 10.3168/jds.2023-23462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/20/2023] [Indexed: 08/31/2023]
Abstract
Understanding the underlying pleiotropic relationships among growth and body size traits is important for refining breeding strategies in dairy cattle for optimal body size and growth rate. Therefore, we performed single-trait GWAS for monthly-recorded body weight (BW), hip height, body length, and chest girth from birth to 12 mo of age in Holstein animals, followed by stepwise multiple regression of independent or lowly-linked markers from GWAS loci using conditional and joint association analyses (COJO). Subsequently, we conducted a multitrait meta-analysis to detect pleiotropic markers. Based on the single-trait GWAS, we identified 170 significant SNPs, in which 59 of them remained significant after the COJO analyses. The most significant SNP, located at BTA7:3,676,741, explained 2.93% of the total phenotypic variance for BW6 (BW at 6 mo of age). We identified 17 SNPs with potential pleiotropic effects based on the multitrait meta-analyses, which resulted in 3 additional SNPs in comparison to those detected based on the single-trait GWAS. The identified quantitative trait loci regions overlap with genes known to influence human growth-related traits. According to positional and functional analyses, we proposed HMGA2, HNF4G, MED13L, BHLHE40, FRZB, DMP1, TRIB3, and GATAD2A as important candidate genes influencing the studied traits. The combination of single-trait GWAS and meta-analyses of GWAS results improved the efficiency of detecting associated SNPs, and provided new insights into the genetic mechanisms of growth and development in Holstein cattle.
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Affiliation(s)
- Z Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China; Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - Y Chang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Y Li
- Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - T Yang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Y Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - N Yang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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25
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Jaholkowski P, Hindley GFL, Shadrin AA, Tesfaye M, Bahrami S, Nerhus M, Rahman Z, O’Connell KS, Holen B, Parker N, Cheng W, Lin A, Rødevand L, Karadag N, Frei O, Djurovic S, Dale AM, Smeland OB, Andreassen OA. Genome-wide Association Analysis of Schizophrenia and Vitamin D Levels Shows Shared Genetic Architecture and Identifies Novel Risk Loci. Schizophr Bull 2023; 49:1654-1664. [PMID: 37163672 PMCID: PMC10686370 DOI: 10.1093/schbul/sbad063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Low vitamin D (vitD) levels have been consistently reported in schizophrenia (SCZ) suggesting a role in the etiopathology. However, little is known about the role of underlying shared genetic mechanisms. We applied a conditional/conjunctional false discovery rate approach (FDR) on large, nonoverlapping genome-wide association studies for SCZ (N cases = 53 386, N controls = 77 258) and vitD serum concentration (N = 417 580) to evaluate shared common genetic variants. The identified genomic loci were characterized using functional analyses and biological repositories. We observed cross-trait SNP enrichment in SCZ conditioned on vitD and vice versa, demonstrating shared genetic architecture. Applying the conjunctional FDR approach, we identified 72 loci jointly associated with SCZ and vitD at conjunctional FDR < 0.05. Among the 72 shared loci, 40 loci have not previously been reported for vitD, and 9 were novel for SCZ. Further, 64% had discordant effects on SCZ-risk and vitD levels. A mixture of shared variants with concordant and discordant effects with a predominance of discordant effects was in line with weak negative genetic correlation (rg = -0.085). Our results displayed shared genetic architecture between SCZ and vitD with mixed effect directions, suggesting overlapping biological pathways. Shared genetic variants with complex overlapping mechanisms may contribute to the coexistence of SCZ and vitD deficiency and influence the clinical picture.
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Affiliation(s)
- Piotr Jaholkowski
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Guy F L Hindley
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King’s College
London, London, UK
| | - Alexey A Shadrin
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and
Oslo University Hospital, Oslo, Norway
| | - Markos Tesfaye
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- Department of Psychiatry, St. Paul’s Hospital Millennium Medical
College, Addis Ababa, Ethiopia
| | - Shahram Bahrami
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Mari Nerhus
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- Department of Special Psychiatry, Akershus University
Hospital, Lørenskog, Norway
- Division of Health Services Research and Psychiatry,
Institute of Clinical Medicine, Campus Ahus, University of Oslo,
Oslo, Norway
| | - Zillur Rahman
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Kevin S O’Connell
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Børge Holen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Nadine Parker
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Weiqiu Cheng
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Aihua Lin
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Linn Rødevand
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Naz Karadag
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- Center for Bioinformatics, Department of Informatics, University of
Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital,
Oslo, Norway
- NORMENT Centre, Department of Clinical Science, University of
Bergen, Bergen, Norway
| | - Anders M Dale
- Department of Radiology, University of California, San Diego,
La Jolla, CA
- Multimodal Imaging Laboratory, University of California San
Diego, La Jolla, CA
- Department of Psychiatry, University of California, San
Diego, La Jolla, CA
- Department of Neurosciences, University of California San
Diego, La Jolla, CA
| | - Olav B Smeland
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health
and Addiction, Oslo University Hospital, and Institute of Clinical Medicine,
University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and
Oslo University Hospital, Oslo, Norway
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26
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Wang S, Peng H, Chen F, Liu C, Zheng Q, Wang M, Wang J, Yu H, Xue E, Chen X, Wang X, Fan M, Qin X, Wu Y, Li J, Ye Y, Chen D, Hu Y, Wu T. Identification of genetic loci jointly influencing COVID-19 and coronary heart diseases. Hum Genomics 2023; 17:101. [PMID: 37964352 PMCID: PMC10647050 DOI: 10.1186/s40246-023-00547-8] [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: 06/28/2023] [Accepted: 10/29/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Comorbidities of coronavirus disease 2019 (COVID-19)/coronary heart disease (CHD) pose great threats to disease outcomes, yet little is known about their shared pathology. The study aimed to examine whether comorbidities of COVID-19/CHD involved shared genetic pathology, as well as to clarify the shared genetic variants predisposing risks common to COVID-19 severity and CHD risks. METHODS By leveraging publicly available summary statistics, we assessed the genetically determined causality between COVID-19 and CHD with bidirectional Mendelian randomization. To further quantify the causality contributed by shared genetic variants, we interrogated their genetic correlation with the linkage disequilibrium score regression method. Bayesian colocalization analysis coupled with conditional/conjunctional false discovery rate analysis was applied to decipher the shared causal single nucleotide polymorphisms (SNPs). FINDINGS Briefly, we observed that the incident CHD risks post COVID-19 infection were partially determined by shared genetic variants. The shared genetic variants contributed to the causality at a proportion of 0.18 (95% CI 0.18-0.19) to 0.23 (95% CI 0.23-0.24). The SNP (rs10490770) located near LZTFL1 suggested direct causality (SNPs → COVID-19 → CHD), and SNPs in ABO (rs579459, rs495828), ILRUN(rs2744961), and CACFD1(rs4962153, rs3094379) may simultaneously influence COVID-19 severity and CHD risks. INTERPRETATION Five SNPs located near LZTFL1 (rs10490770), ABO (rs579459, rs495828), ILRUN (rs2744961), and CACFD1 (rs4962153, rs3094379) may simultaneously influence their risks. The current study suggested that there may be shared mechanisms predisposing to both COVID-19 severity and CHD risks. Genetic predisposition to COVID-19 is a causal risk factor for CHD, supporting that reducing the COVID-19 infection risk or alleviating COVID-19 severity among those with specific genotypes might reduce their subsequent CHD adverse outcomes. Meanwhile, the shared genetic variants identified may be of clinical implications for identifying the target population who are more vulnerable to adverse CHD outcomes post COVID-19 and may also advance treatments of 'Long COVID-19.'
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Affiliation(s)
- Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Hexiang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Feng Chen
- Department of Intensive Care Unit, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Chunfang Liu
- School of Public Health, Baotou Medical College, Baotou, 014040, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jiating Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Huan Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Enci Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xi Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xueheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Meng Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Xueying Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Yiqun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Ying Ye
- Department of Local Diseases Control and Prevention, Fujian Provincial Center for Disease Control and Prevention, Fuzhou, 350001, China
| | - Dafang Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
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27
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Liang Q, Jiang Y, Shieh AW, Zhou D, Chen R, Wang F, Xu M, Niu M, Wang X, Pinto D, Wang Y, Cheng L, Vadukapuram R, Zhang C, Grennan K, Giase G, White KP, Peng J, Li B, Liu C, Chen C, Wang SH. The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543603. [PMID: 37873195 PMCID: PMC10592607 DOI: 10.1101/2023.06.04.543603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The impact of genetic variants on gene expression has been intensely studied at the transcription level, yielding in valuable insights into the association between genes and the risk of complex disorders, such as schizophrenia (SCZ). However, the downstream impact of these variants and the molecular mechanisms connecting transcription variation to disease risk are not well understood. Results We quantitated ribosome occupancy in prefrontal cortex samples of the BrainGVEX cohort. Together with transcriptomics and proteomics data from the same cohort, we performed cis-Quantitative Trait Locus (QTL) mapping and identified 3,253 expression QTLs (eQTLs), 1,344 ribosome occupancy QTLs (rQTLs), and 657 protein QTLs (pQTLs) out of 7,458 genes quantitated in all three omics types from 185 samples. Of the eQTLs identified, only 34% have their effects propagated to the protein level. Further analysis on the effect size of prefrontal cortex eQTLs identified from an independent dataset showed clear post-transcriptional attenuation of eQTL effects. To investigate the biological relevance of the attenuated eQTLs, we identified 70 expression-specific QTLs (esQTLs), 51 ribosome-occupancy-specific QTLs (rsQTLs), and 107 protein-specific QTLs (psQTLs). Five of these omics-specific QTLs showed strong colocalization with SCZ GWAS signals, three of them are esQTLs. The limited number of GWAS colocalization discoveries from omics-specific QTLs and the apparent prevalence of eQTL attenuation prompted us to take a complementary approach to investigate the functional relevance of attenuated eQTLs. Using S-PrediXcan we identified 74 SCZ risk genes, 34% of which were novel, and 67% of these risk genes were replicated in a MR-Egger test. Notably, 52 out of 74 risk genes were identified using eQTL data and 70% of these SCZ-risk-gene-driving eQTLs show little to no evidence of driving corresponding variations at the protein level. Conclusion The effect of eQTLs on gene expression in the prefrontal cortex is commonly attenuated post-transcriptionally. Many of the attenuated eQTLs still correlate with SCZ GWAS signal. Further investigation is needed to elucidate a mechanistic link between attenuated eQTLs and SCZ disease risk.
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Affiliation(s)
- Qiuman Liang
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yi Jiang
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430000, China
| | - Annie W. Shieh
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dan Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Feiran Wang
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Meng Xu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Mingming Niu
- Department of Structural Biology, Department of Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xusheng Wang
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Dalila Pinto
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Lijun Cheng
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ramu Vadukapuram
- Department of Psychiatry, The University of Texas Rio Grande Valley, Harlingen, TX 78550, USA
| | - Chunling Zhang
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Kay Grennan
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Gina Giase
- The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Kevin P White
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Chunyu Liu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- School of Psychology, Shaanxi Normal University, Xi’an, Shaanxi 710062, China
| | - Chao Chen
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- Furong Laboratory, Changsha, Hunan 410000, China
- National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410000, China
| | - Sidney H. Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Li X, Chen H, Selvaraj MS, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen YDI, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung YJ, Irvin MR, Kaplan RC, Kardia SL, Kelly T, Konigsberg I, Kooperberg C, Kral BG, Li C, Loos RJ, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari H, Vasan RS, Wang Z, Yanek LR, Yu B, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564764. [PMID: 37961350 PMCID: PMC10634938 DOI: 10.1101/2023.10.30.564764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.
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Affiliation(s)
- Xihao Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Eric Van Buren
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary R. McCaw
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Yu
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Donna K. Arnett
- Provost Office, University of South Carolina, Columbia, SC, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jenna C. Carlson
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Charles Gu
- Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Yi-Jen Hung
- Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Medicine, Division of Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Iain Konigsberg
- Department of Biomedical Informatics, University of Colorado, Aurora, CO, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G. Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael C. Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Lisa W. Martin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - May E. Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ramachandran S. Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Quantitative and Qualitative Health Sciences, UT Health San Antonio School of Public Health, San Antonia, TX, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhonghua Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
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29
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Zhang Z, Jung J, Kim A, Suboc N, Gazal S, Mancuso N. A scalable approach to characterize pleiotropy across thousands of human diseases and complex traits using GWAS summary statistics. Am J Hum Genet 2023; 110:1863-1874. [PMID: 37879338 PMCID: PMC10645558 DOI: 10.1016/j.ajhg.2023.09.015] [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: 03/27/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
Genome-wide association studies (GWASs) across thousands of traits have revealed the pervasive pleiotropy of trait-associated genetic variants. While methods have been proposed to characterize pleiotropic components across groups of phenotypes, scaling these approaches to ultra-large-scale biobanks has been challenging. Here, we propose FactorGo, a scalable variational factor analysis model to identify and characterize pleiotropic components using biobank GWAS summary data. In extensive simulations, we observe that FactorGo outperforms the state-of-the-art (model-free) approach tSVD in capturing latent pleiotropic factors across phenotypes while maintaining a similar computational cost. We apply FactorGo to estimate 100 latent pleiotropic factors from GWAS summary data of 2,483 phenotypes measured in European-ancestry Pan-UK BioBank individuals (N = 420,531). Next, we find that factors from FactorGo are more enriched with relevant tissue-specific annotations than those identified by tSVD (p = 2.58E-10) and validate our approach by recapitulating brain-specific enrichment for BMI and the height-related connection between reproductive system and muscular-skeletal growth. Finally, our analyses suggest shared etiologies between rheumatoid arthritis and periodontal condition in addition to alkaline phosphatase as a candidate prognostic biomarker for prostate cancer. Overall, FactorGo improves our biological understanding of shared etiologies across thousands of GWASs.
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Affiliation(s)
- Zixuan Zhang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Junghyun Jung
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Artem Kim
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Noah Suboc
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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30
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Schmengler H, Oldehinkel AJ, Vollebergh WAM, Pasman JA, Hartman CA, Stevens GWJM, Nolte IM, Peeters M. Disentangling the interplay between genes, cognitive skills, and educational level in adolescent and young adult smoking - The TRAILS study. Soc Sci Med 2023; 336:116254. [PMID: 37751630 DOI: 10.1016/j.socscimed.2023.116254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/17/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]
Abstract
Recent studies suggest that smoking and lower educational attainment may have genetic influences in common. However, little is known about the mechanisms through which genetics contributes to educational inequalities in adolescent and young adult smoking. Common genetic liabilities may underlie cognitive skills associated with both smoking and education, such as IQ and effortful control, in line with indirect health-related selection explanations. Additionally, by affecting cognitive skills, genes may predict educational trajectories and hereby adolescents' social context, which may be associated with smoking, consistent with social causation explanations. Using data from the Dutch TRAILS Study (N = 1581), we estimated the extent to which polygenic scores (PGSs) for ever smoking regularly (PGSSMOK) and years of education (PGSEDU) predict IQ and effortful control, measured around age 11, and whether these cognitive skills then act as shared predictors of smoking and educational level around age 16, 19, 22, and 26. Second, we assessed if educational level mediated associations between PGSs and smoking. Both PGSs were associated with lower effortful control, and PGSEDU also with lower IQ. Lower IQ and effortful control, in turn, predicted having a lower educational level. However, neither of these cognitive skills were directly associated with smoking behaviour after controlling for covariates and PGSs. This suggests that IQ and effortful control are not shared predictors of smoking and education (i.e., no indirect health-related selection related to cognitive skills). Instead, PGSSMOK and PGSEDU, partly through their associations with lower cognitive skills, predicted selection into a lower educational track, which in turn was associated with more smoking, in line with social causation explanations. Our findings suggest that educational differences in the social context contribute to associations between genetic liabilities and educational inequalities in smoking.
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Affiliation(s)
- Heiko Schmengler
- Department of Interdisciplinary Social Science, Utrecht University, the Netherlands.
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, Department of Psychiatry, University Medical Center of Groningen, University of Groningen, the Netherlands
| | - Wilma A M Vollebergh
- Department of Interdisciplinary Social Science, Utrecht University, the Netherlands
| | - Joëlle A Pasman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Sweden
| | - Catharina A Hartman
- Interdisciplinary Center Psychopathology and Emotion Regulation, Department of Psychiatry, University Medical Center of Groningen, University of Groningen, the Netherlands
| | | | - Ilja M Nolte
- Department of Epidemiology, University Medical Center of Groningen, University of Groningen, the Netherlands
| | - Margot Peeters
- Department of Interdisciplinary Social Science, Utrecht University, the Netherlands
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31
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Qu Y, Xiao C, Wu X, Zhu J, Qin C, He L, Cui H, Zhang L, Zhang W, Yang C, Yao Y, Li J, Liu Z, Zhang B, Wang W, Jiang X. Genetic Correlation, Shared Loci, and Causal Association Between Sex Hormone-Binding Globulin and Bone Mineral Density: Insights From a Large-Scale Genomewide Cross-Trait Analysis. J Bone Miner Res 2023; 38:1635-1644. [PMID: 37615194 DOI: 10.1002/jbmr.4904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/20/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Although the impact of sex hormones on bone metabolism is well-documented, effect of their primary modulator, sex hormone-binding globulin (SHBG), remains inconclusive. This study aims to elucidate the genetic overlap between SHBG and heel estimated bone mineral density (eBMD), a widely-accepted tool for osteoporosis management and fracture risk assessment. Using summary statistics from large-scale genomewide association studies conducted for SHBG (N = 370,125), SHBG adjusted for body mass index (SHBGa, N = 368,929), and eBMD (N = 426,824), a comprehensive genomewide cross-trait approach was performed to quantify global and local genetic correlations, identify pleiotropic loci, and infer causal associations. A significant overall inverse genetic correlation was found for SHBG and eBMD (rg = -0.11, p = 3.34 × 10-10 ), which was further supported by the significant local genetic correlations observed in 11 genomic regions. Cross-trait meta-analysis revealed 219 shared loci, of which seven were novel. Notably, four novel loci (rs6542680, rs8178616, rs147110934, and rs815625) were further demonstrated to colocalize. Mendelian randomization identified a robust causal effect of SHBG on eBMD (beta = -0.22, p = 3.04 × 10-13 ), with comparable effect sizes observed in both men (beta = -0.16, p = 1.99 × 10-6 ) and women (beta = -0.19, p = 2.73 × 10-9 ). Replacing SHBG with SHBGa, the observed genetic correlations, pleiotropic loci and causal associations did not change substantially. Our work reveals a shared genetic basis between SHBG and eBMD, substantiated by multiple pleiotropic loci and a robust causal relationship. Although SHBG has been implicated in preventing and screening aging-related diseases, our findings support its etiological role in osteoporosis. © 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)
- Yang Qu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Changfeng Xiao
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenjiarui Qin
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lin He
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenzhi Wang
- Department of Osteoporosis/Rheumatology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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32
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St-Pierre J, Oualkacha K. A copula-based set-variant association test for bivariate continuous, binary or mixed phenotypes. Int J Biostat 2023; 19:369-387. [PMID: 36279152 PMCID: PMC10644254 DOI: 10.1515/ijb-2022-0010] [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: 01/20/2022] [Revised: 05/26/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022]
Abstract
In genome wide association studies (GWAS), researchers are often dealing with dichotomous and non-normally distributed traits, or a mixture of discrete-continuous traits. However, most of the current region-based methods rely on multivariate linear mixed models (mvLMMs) and assume a multivariate normal distribution for the phenotypes of interest. Hence, these methods are not applicable to disease or non-normally distributed traits. Therefore, there is a need to develop unified and flexible methods to study association between a set of (possibly rare) genetic variants and non-normal multivariate phenotypes. Copulas are multivariate distribution functions with uniform margins on the [0, 1] interval and they provide suitable models to deal with non-normality of errors in multivariate association studies. We propose a novel unified and flexible copula-based multivariate association test (CBMAT) for discovering association between a genetic region and a bivariate continuous, binary or mixed phenotype. We also derive a data-driven analytic p-value procedure of the proposed region-based score-type test. Through simulation studies, we demonstrate that CBMAT has well controlled type I error rates and higher power to detect associations compared with other existing methods, for discrete and non-normally distributed traits. At last, we apply CBMAT to detect the association between two genes located on chromosome 11 and several lipid levels measured on 1477 subjects from the ASLPAC study.
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Affiliation(s)
- Julien St-Pierre
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Karim Oualkacha
- Département de Mathématiques, Université du Québec à Montréal, Montreal, QC, Canada
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Zuo H, Li MM. Ankylosing spondylitis and psychiatric disorders in European population: a Mendelian randomization study. Front Immunol 2023; 14:1277959. [PMID: 37954601 PMCID: PMC10637577 DOI: 10.3389/fimmu.2023.1277959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/13/2023] [Indexed: 11/14/2023] Open
Abstract
Background Epidemiologic evidence has demonstrated a correlation between ankylosing spondylitis and psychiatric disorders. However, little is known about the common genetics and causality of this association. This study aimed to investigate the common genetics and causality between ankylosing spondylitis (AS) and psychiatric disorders. Methods A two-sample Mendelian Randomization (MR) analysis was carried out to confirm causal relationships between ankylosing spondylitis and five mental health conditions including major depressive disorder (MDD), anxiety disorder (AXD), schizophrenia (SCZ), bipolar disorder (BIP), and anorexia nervosa (AN). Genetic instrumental variables associated with exposures and outcomes were derived from the largest available summary statistics of genome-wide association studies (GWAS). Bidirectional causal estimation of MR was primarily obtained using the inverse variance weighting (IVW) method. Other MR methods include MR-Egger regression, Weighted Median Estimator (WME), Weighted Mode, Simple Mode, and Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO). Sensitivity analyses are conducted to estimate the robustness of MR results. Results The findings suggest that AS may be causally responsible for the risk of developing SCZ (OR = 1.18, 95% confidence interval = (1.06, 1.31), P = 2.58 × 10-3) and AN (OR = 1.32, 95% confidence interval = (1.07, 1.64), P = 9.43 × 10-3). In addition, MDD, AXD, SCZ, AN, and BIP were not inversely causally related to AS (all p > 0.05). Conclusion Our study provides fresh insights into the relationship between AS and psychiatric disorders (SCZ and AN). Furthermore, it may provide new clues for risk management and preventive interventions for mental disorders in patients with AS.
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Affiliation(s)
| | - Min-Min Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Vorstman JAS, Scherer SW. Contemplating syndromic autism. Genet Med 2023; 25:100919. [PMID: 37330697 DOI: 10.1016/j.gim.2023.100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Jin X, Shi G. Cauchy combination methods for the detection of gene-environment interactions for rare variants related to quantitative phenotypes. Heredity (Edinb) 2023; 131:241-252. [PMID: 37481617 PMCID: PMC10539363 DOI: 10.1038/s41437-023-00640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
The characterization of gene-environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an extremely small proportion of causal rare variants in a gene or a region. By extending the aggregated Cauchy association test (ACAT), we propose three GEI tests to address this issue: a Cauchy combination GEI test with fixed main effects (CCGEI-F), a Cauchy combination GEI test with random main effects (CCGEI-R), and an omnibus Cauchy combination GEI test (CCGEI-O). ACAT was applied to combine p values of single-variant GEI analyses to obtain CCGEI-F and CCGEI-R and p values of multiple GEI tests were combined in CCGEI-O. Through numerical simulations, for small numbers of causal variants, CCGEI-F, CCGEI-R and CCGEI-O provided approximately 5% higher power than the existing GEI tests INT-FIX and INT-RAN; however, they had slightly higher power than the existing GEI test TOW-GE. For large numbers of causal variants, although CCGEI-F and CCGEI-R exhibited comparable or slightly lower power values than the competing tests, the results were still satisfactory. Among all simulation conditions evaluated, CCGEI-O provided significantly higher power than that of competing GEI tests. We further applied our GEI tests in genome-wide analyses of systolic blood pressure or diastolic blood pressure to detect gene-body mass index (BMI) interactions, using whole-exome sequencing data from UK Biobank. At a suggestive significance level of 1.0 × 10-4, KCNC4, GAR1, FAM120AOS and NT5C3B showed interactions with BMI by our GEI tests.
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Affiliation(s)
- Xiaoqin Jin
- State Key Laboratory of Integrated Services Networks, Xidian University, 2 South Taibai Road, Xi'an, Shaanxi, 710071, China.
| | - Gang Shi
- State Key Laboratory of Integrated Services Networks, Xidian University, 2 South Taibai Road, Xi'an, Shaanxi, 710071, China
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Liu Z, Ye T, Sun B, Schooling M, Tchetgen ET. Mendelian randomization mixed-scale treatment effect robust identification and estimation for causal inference. Biometrics 2023; 79:2208-2219. [PMID: 35950778 DOI: 10.1111/biom.13735] [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] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Standard Mendelian randomization (MR) analysis can produce biased results if the genetic variant defining an instrumental variable (IV) is confounded and/or has a horizontal pleiotropic effect on the outcome of interest not mediated by the treatment variable. We provide novel identification conditions for the causal effect of a treatment in the presence of unmeasured confounding by leveraging a possibly invalid IV for which both the IV independence and exclusion restriction assumptions may be violated. The proposed Mendelian randomization mixed-scale treatment effect robust identification (MR MiSTERI) approach relies on (i) an assumption that the treatment effect does not vary with the possibly invalid IV on the additive scale; (ii) that the confounding bias does not vary with the possibly invalid IV on the odds ratio scale; and (iii) that the residual variance for the outcome is heteroskedastic with respect to the possibly invalid IV. Although assumptions (i) and (ii) have, respectively, appeared in the IV literature, assumption (iii) has not; we formally establish that their conjunction can identify a causal effect even with an invalid IV. MR MiSTERI is shown to be particularly advantageous in the presence of pervasive heterogeneity of pleiotropic effects on the additive scale. We propose a simple and consistent three-stage estimator that can be used as a preliminary estimator to a carefully constructed efficient one-step-update estimator. In order to incorporate multiple, possibly correlated, and weak invalid IVs, a common challenge in MR studies, we develop a MAny Weak Invalid Instruments (MR MaWII MiSTERI) approach for strengthened identification and improved estimation accuracy. Both simulation studies and UK Biobank data analysis results demonstrate the robustness of the proposed methods.
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Affiliation(s)
- Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Ting Ye
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Baoluo Sun
- Department of Statistics and Data Science, National University of Singapore, Singapore
| | - Mary Schooling
- CUNY Graduate School of Public Health and Health Policy, New York, New York, USA
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Eric Tchetgen Tchetgen
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Asgari Y, Sugier PE, Baghfalaki T, Lucotte E, Karimi M, Sedki M, Ngo A, Liquet B, Truong T. GCPBayes pipeline: a tool for exploring pleiotropy at the gene level. NAR Genom Bioinform 2023; 5:lqad065. [PMID: 37416786 PMCID: PMC10320750 DOI: 10.1093/nargab/lqad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023] Open
Abstract
Cross-phenotype association using gene-set analysis can help to detect pleiotropic genes and inform about common mechanisms between diseases. Although there are an increasing number of statistical methods for exploring pleiotropy, there is a lack of proper pipelines to apply gene-set analysis in this context and using genome-scale data in a reasonable running time. We designed a user-friendly pipeline to perform cross-phenotype gene-set analysis between two traits using GCPBayes, a method developed by our team. All analyses could be performed automatically by calling for different scripts in a simple way (using a Shiny app, Bash or R script). A Shiny application was also developed to create different plots to visualize outputs from GCPBayes. Finally, a comprehensive and step-by-step tutorial on how to use the pipeline is provided in our group's GitHub page. We illustrated the application on publicly available GWAS (genome-wide association studies) summary statistics data to identify breast cancer and ovarian cancer susceptibility genes. We have shown that the GCPBayes pipeline could extract pleiotropic genes previously mentioned in the literature, while it also provided new pleiotropic genes and regions that are worthwhile for further investigation. We have also provided some recommendations about parameter selection for decreasing computational time of GCPBayes on genome-scale data.
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Affiliation(s)
- Yazdan Asgari
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Pierre-Emmanuel Sugier
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
- Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l’Adour, UMR CNRS 5142, E2S-UPPA, 64000 Pau, France
| | | | - Elise Lucotte
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Mojgan Karimi
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Mohammed Sedki
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Psychiatrie du développement et trajectoires, 94807 Villejuif, France
| | - Amélie Ngo
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Benoit Liquet
- Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l’Adour, UMR CNRS 5142, E2S-UPPA, 64000 Pau, France
- School of Mathematical and Physical Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Thérèse Truong
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
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Calderwood A, Siles L, Eastmond PJ, Kurup S, Morris RJ. A causal inference and Bayesian optimisation framework for modelling multi-trait relationships-Proof-of-concept using Brassica napus seed yield under controlled conditions. PLoS One 2023; 18:e0290429. [PMID: 37656702 PMCID: PMC10473526 DOI: 10.1371/journal.pone.0290429] [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: 12/23/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023] Open
Abstract
The improvement of crop yield is a major breeding target and there is a long history of research that has focussed on unravelling the mechanisms and processes that contribute to yield. Quantitative prediction of the interplay between morphological traits, and the effects of these trait-trait relationships on seed production remains, however, a challenge. Consequently, the extent to which crop varieties optimise their morphology for a given environment is largely unknown. This work presents a new combination of existing methodologies by framing crop breeding as an optimisation problem and evaluates the extent to which existing varieties exhibit optimal morphologies under the test conditions. In this proof-of-concept study using spring and winter oilseed rape plants grown under greenhouse conditions, we employ causal inference to model the hierarchically structured effects of 27 morphological yield traits on each other. We perform Bayesian optimisation of seed yield, to identify and quantify the morphologies of ideotype plants, which are expected to be higher yielding than the varieties in the studied panels. Under the tested growth conditions, we find that existing spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant winter varieties. The same approach can be used to evaluate trait (morphology) space for any environment.
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Affiliation(s)
- Alexander Calderwood
- Department of Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Laura Siles
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter J. Eastmond
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Smita Kurup
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
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Gonggrijp BMA, van de Weijer SGA, Bijleveld CCJH, van Dongen J, Boomsma DI. The Co-Twin Control Design: Implementation and Methodological Considerations. Twin Res Hum Genet 2023:1-8. [PMID: 37655521 DOI: 10.1017/thg.2023.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Establishing causal relationships in observational studies is an important step in research and policy decision making. The association between an exposure and an outcome can be confounded by multiple factors, often making it hard to draw causal conclusions. The co-twin control design (CTCD) is a powerful approach that allows for the investigation of causal effects while controlling for genetic and shared environmental confounding factors. This article introduces the CTCD and offers an overview of analysis methods for binary and continuous outcome and exposure variables. Tools for data simulation are provided, along with practical guidance and accompanying scripts for implementing the CTCD in R, SPSS, and Stata. While the CTCD offers valuable insights into causal inference, it depends on several assumptions that are important when interpreting CTCD results. By presenting a broad overview of the CTCD, this article aims to equip researchers with actionable recommendations and a comprehensive understanding of the design's strengths and limitations.
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Affiliation(s)
- Bodine M A Gonggrijp
- Netherlands Institute for the Study of Crime and Law Enforcement (NSCR), Amsterdam, the Netherlands
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Steve G A van de Weijer
- Netherlands Institute for the Study of Crime and Law Enforcement (NSCR), Amsterdam, the Netherlands
| | - Catrien C J H Bijleveld
- Netherlands Institute for the Study of Crime and Law Enforcement (NSCR), Amsterdam, the Netherlands
- Department of Criminal Law and Criminology, VU University Amsterdam, Amsterdam, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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Petti S, Reddy G, Desai MM. Inferring sparse structure in genotype-phenotype maps. Genetics 2023; 225:iyad127. [PMID: 37437111 PMCID: PMC10471201 DOI: 10.1093/genetics/iyad127] [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: 05/24/2023] [Revised: 05/24/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023] Open
Abstract
Correlation among multiple phenotypes across related individuals may reflect some pattern of shared genetic architecture: individual genetic loci affect multiple phenotypes (an effect known as pleiotropy), creating observable relationships between phenotypes. A natural hypothesis is that pleiotropic effects reflect a relatively small set of common "core" cellular processes: each genetic locus affects one or a few core processes, and these core processes in turn determine the observed phenotypes. Here, we propose a method to infer such structure in genotype-phenotype data. Our approach, sparse structure discovery (SSD) is based on a penalized matrix decomposition designed to identify latent structure that is low-dimensional (many fewer core processes than phenotypes and genetic loci), locus-sparse (each locus affects few core processes), and/or phenotype-sparse (each phenotype is influenced by few core processes). Our use of sparsity as a guide in the matrix decomposition is motivated by the results of a novel empirical test indicating evidence of sparse structure in several recent genotype-phenotype datasets. First, we use synthetic data to show that our SSD approach can accurately recover core processes if each genetic locus affects few core processes or if each phenotype is affected by few core processes. Next, we apply the method to three datasets spanning adaptive mutations in yeast, genotoxin robustness assay in human cell lines, and genetic loci identified from a yeast cross, and evaluate the biological plausibility of the core process identified. More generally, we propose sparsity as a guiding prior for resolving latent structure in empirical genotype-phenotype maps.
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Affiliation(s)
- Samantha Petti
- NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gautam Reddy
- NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Physics & Informatics Laboratories, NTT Research, Inc., Sunnyvale, CA 94085, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
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Roth K, Pröll-Cornelissen MJ, Henne H, Appel AK, Schellander K, Tholen E, Große-Brinkhaus C. Multivariate genome-wide associations for immune traits in two maternal pig lines. BMC Genomics 2023; 24:492. [PMID: 37641029 PMCID: PMC10463314 DOI: 10.1186/s12864-023-09594-w] [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: 02/01/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Immune traits are considered to serve as potential biomarkers for pig's health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines. RESULTS In total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified. CONCLUSIONS This study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.
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Affiliation(s)
- Katharina Roth
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | | | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, 21368, Dahlenburg-Ellringen, Germany
| | | | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
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Burgess S, Davey Smith G, Davies NM, Dudbridge F, Gill D, Glymour MM, Hartwig FP, Kutalik Z, Holmes MV, Minelli C, Morrison JV, Pan W, Relton CL, Theodoratou E. Guidelines for performing Mendelian randomization investigations: update for summer 2023. Wellcome Open Res 2023; 4:186. [PMID: 32760811 PMCID: PMC7384151 DOI: 10.12688/wellcomeopenres.15555.3] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
This paper provides guidelines for performing Mendelian randomization investigations. It is aimed at practitioners seeking to undertake analyses and write up their findings, and at journal editors and reviewers seeking to assess Mendelian randomization manuscripts. The guidelines are divided into ten sections: motivation and scope, data sources, choice of genetic variants, variant harmonization, primary analysis, supplementary and sensitivity analyses (one section on robust statistical methods and one on other approaches), extensions and additional analyses, data presentation, and interpretation. These guidelines will be updated based on feedback from the community and advances in the field. Updates will be made periodically as needed, and at least every 24 months.
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Affiliation(s)
- Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Neil M. Davies
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Division of Psychiatry, University College London, London, UK
- Department of Statistical Sciences, University College London, London, WC1E 6BT, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - M. Maria Glymour
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Fernando P. Hartwig
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Michael V. Holmes
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jean V. Morrison
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
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Willis TW, Wallace C. Accurate detection of shared genetic architecture from GWAS summary statistics in the small-sample context. PLoS Genet 2023; 19:e1010852. [PMID: 37585442 PMCID: PMC10461826 DOI: 10.1371/journal.pgen.1010852] [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: 10/12/2022] [Revised: 08/28/2023] [Accepted: 06/30/2023] [Indexed: 08/18/2023] Open
Abstract
Assessment of the genetic similarity between two phenotypes can provide insight into a common genetic aetiology and inform the use of pleiotropy-informed, cross-phenotype analytical methods to identify novel genetic associations. The genetic correlation is a well-known means of quantifying and testing for genetic similarity between traits, but its estimates are subject to comparatively large sampling error. This makes it unsuitable for use in a small-sample context. We discuss the use of a previously published nonparametric test of genetic similarity for application to GWAS summary statistics. We establish that the null distribution of the test statistic is modelled better by an extreme value distribution than a transformation of the standard exponential distribution. We show with simulation studies and real data from GWAS of 18 phenotypes from the UK Biobank that the test is to be preferred for use with small sample sizes, particularly when genetic effects are few and large, outperforming the genetic correlation and another nonparametric statistical test of independence. We find the test suitable for the detection of genetic similarity in the rare disease context.
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Affiliation(s)
- Thomas W. Willis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Chris Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Fazia T, Baldrighi GN, Nova A, Bernardinelli L. A systematic review of Mendelian randomization studies on multiple sclerosis. Eur J Neurosci 2023; 58:3172-3194. [PMID: 37463755 DOI: 10.1111/ejn.16088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/31/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023]
Abstract
Mendelian randomization (MR) is a powerful approach for assessing the causal effect of putative risk factors on an outcome, using genetic variants as instrumental variables. The methodology and application developed in the framework of MR have been dramatically improved, taking advantage of the many public genome-wide association study (GWAS) data. The availability of summary-level data allowed to perform numerous MR studies especially for complex diseases, pinpointing modifiable exposures causally related to increased or decreased disease risk. Multiple sclerosis (MS) is a complex multifactorial disease whose aetiology involves both genetic and non-genetic risk factors and their interplay. Previous observational studies have revealed associations between candidate modifiable exposures and MS risk; although being prone to confounding, and reverse causation, these studies were unable to draw causal conclusions. MR analysis addresses the limitations of observational studies and allows to establish reliable and accurate causal conclusions. Here, we systematically reviewed the studies evaluating the causal effect, through MR, of genetic and non-genetic exposures on MS risk. Among 107 papers found, only 42 were eligible for final evaluation and qualitative synthesis. We found that, above all, low vitamin D levels and high adult body mass index (BMI) appear to be uncontested risk factors for increased MS risk.
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Affiliation(s)
- Teresa Fazia
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | | | - Andrea Nova
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
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Gómez-Vecino A, Corchado-Cobos R, Blanco-Gómez A, García-Sancha N, Castillo-Lluva S, Martín-García A, Mendiburu-Eliçabe M, Prieto C, Ruiz-Pinto S, Pita G, Velasco-Ruiz A, Patino-Alonso C, Galindo-Villardón P, Vera-Pedrosa ML, Jalife J, Mao JH, Macías de Plasencia G, Castellanos-Martín A, Sáez-Freire MDM, Fraile-Martín S, Rodrigues-Teixeira T, García-Macías C, Galvis-Jiménez JM, García-Sánchez A, Isidoro-García M, Fuentes M, García-Cenador MB, García-Criado FJ, García-Hernández JL, Hernández-García MÁ, Cruz-Hernández JJ, Rodríguez-Sánchez CA, García-Sancho AM, Pérez-López E, Pérez-Martínez A, Gutiérrez-Larraya F, Cartón AJ, García-Sáenz JÁ, Patiño-García A, Martín M, Alonso-Gordoa T, Vulsteke C, Croes L, Hatse S, Van Brussel T, Lambrechts D, Wildiers H, Chang H, Holgado-Madruga M, González-Neira A, Sánchez PL, Pérez Losada J. Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk. Cells 2023; 12:1956. [PMID: 37566035 PMCID: PMC10417374 DOI: 10.3390/cells12151956] [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: 04/17/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.
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Affiliation(s)
- Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain;
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 24040 Madrid, Spain
| | - Ana Martín-García
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Carlos Prieto
- Servicio de Bioinformática, Nucleus, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Sara Ruiz-Pinto
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Alejandro Velasco-Ruiz
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Carmen Patino-Alonso
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Estadística, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Purificación Galindo-Villardón
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Estadística, Universidad de Salamanca, 37007 Salamanca, Spain
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Estudios e Investigaciones Estadísticas, Campus Gustavo Galindo, Km. 30.5 Via Perimetral, Guayaquil P.O. Box 09-01-5863, Ecuador
| | | | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, 28029 Madrid, Spain; (M.L.V.-P.); (J.J.)
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 92720, USA
| | - Guillermo Macías de Plasencia
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
| | - Andrés Castellanos-Martín
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - María del Mar Sáez-Freire
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Susana Fraile-Martín
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Telmo Rodrigues-Teixeira
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Carmen García-Macías
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Julie Milena Galvis-Jiménez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Instituto Nacional de Cancerología de Colombia, Bogotá 111511-110411001, Colombia
| | - Asunción García-Sánchez
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - María Isidoro-García
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Manuel Fuentes
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Unidad de Proteómica y Servicio General de Citometría de Flujo, Nucleus, Universidad de Salamanca, 37007 Salamanca, Spain
| | - María Begoña García-Cenador
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Cirugía, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Francisco Javier García-Criado
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Cirugía, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Juan Luis García-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | | | - Juan Jesús Cruz-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - César Augusto Rodríguez-Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Alejandro Martín García-Sancho
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Hematología, Hospital Universitario de Salamanca, CIBERONC, 37007 Salamanca, Spain;
| | - Estefanía Pérez-López
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Hematología, Hospital Universitario de Salamanca, CIBERONC, 37007 Salamanca, Spain;
| | - Antonio Pérez-Martínez
- Department of Paediatric Hemato-Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Federico Gutiérrez-Larraya
- Department of Paediatric Cardiology, Hospital Universitario La Paz, 28046 Madrid, Spain; (F.G.-L.); (A.J.C.)
| | - Antonio J. Cartón
- Department of Paediatric Cardiology, Hospital Universitario La Paz, 28046 Madrid, Spain; (F.G.-L.); (A.J.C.)
| | - José Ángel García-Sáenz
- Medical Oncology Service, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - Ana Patiño-García
- Department of Pediatrics, Solid Tumor Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IdisNA, 31008 Pamplona, Spain;
| | - Miguel Martín
- Department of Medicine, Gregorio Marañón Health Research Institute (IISGM), Centro de Investigación Biomédica en Red Oncológica (CIBERONC), Universidad Complutense, 28007 Madrid, Spain;
| | - Teresa Alonso-Gordoa
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Christof Vulsteke
- Department of Molecular Imaging, Pathology, Radiotherapy and Oncology (MIPRO), Center for Oncological Research (CORE), Antwerp University, 2610 Antwerp, Belgium; (C.V.); (L.C.)
- Department of Oncology, Integrated Cancer Center in Ghent, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Lieselot Croes
- Department of Molecular Imaging, Pathology, Radiotherapy and Oncology (MIPRO), Center for Oncological Research (CORE), Antwerp University, 2610 Antwerp, Belgium; (C.V.); (L.C.)
- Department of Oncology, Integrated Cancer Center in Ghent, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium;
| | - Thomas Van Brussel
- VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; (T.V.B.); (D.L.)
- Laboratory of Translational Genetics, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; (T.V.B.); (D.L.)
- Laboratory of Translational Genetics, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology and Multidisciplinary Breast Unit, Leuven Cancer Institute, and Laboratory of Experimental Oncology (LEO), Department of Oncology, Leuven Cancer Institute and University Hospital Leuven, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium;
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 92720, USA
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Pedro L. Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Jesús Pérez Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
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O'Connell KS, Koch E, Lenk HÇ, Akkouh IA, Hindley G, Jaholkowski P, Smith RL, Holen B, Shadrin AA, Frei O, Smeland OB, Steen NE, Dale AM, Molden E, Djurovic S, Andreassen OA. Polygenic overlap with body-mass index improves prediction of treatment-resistant schizophrenia. Psychiatry Res 2023; 325:115217. [PMID: 37146461 PMCID: PMC10788293 DOI: 10.1016/j.psychres.2023.115217] [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] [Received: 01/23/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
Treatment resistant schizophrenia (TRS) is characterized by repeated treatment failure with antipsychotics. A recent genome-wide association study (GWAS) of TRS showed a polygenic architecture, but no significant loci were identified. Clozapine is shown to be the superior drug in terms of clinical effect in TRS; at the same time it has a serious side effect profile, including weight gain. Here, we sought to increase power for genetic discovery and improve polygenic prediction of TRS, by leveraging genetic overlap with Body Mass Index (BMI). We analysed GWAS summary statistics for TRS and BMI applying the conditional false discovery rate (cFDR) framework. We observed cross-trait polygenic enrichment for TRS conditioned on associations with BMI. Leveraging this cross-trait enrichment, we identified 2 novel loci for TRS at cFDR <0.01, suggesting a role of MAP2K1 and ZDBF2. Further, polygenic prediction based on the cFDR analysis explained more variance in TRS when compared to the standard TRS GWAS. These findings highlight putative molecular pathways which may distinguish TRS patients from treatment responsive patients. Moreover, these findings confirm that shared genetic mechanisms influence both TRS and BMI and provide new insights into the biological underpinnings of metabolic dysfunction and antipsychotic treatment.
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Affiliation(s)
- Kevin S O'Connell
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Elise Koch
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hasan Çağın Lenk
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway; Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ibrahim A Akkouh
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Guy Hindley
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Psychosis Studies, Institute of Psychiatry, Psychology and Neurosciences, King's College London, United Kingdom
| | - Piotr Jaholkowski
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robert Løvsletten Smith
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
| | - Børge Holen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
| | - Olav B Smeland
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nils Eiel Steen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders M Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA; Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway; Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; NORMENT Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A Andreassen
- NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo and Oslo University Hospital, Oslo, Norway.
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Lee S, Yang HK, Lee HJ, Park DJ, Kong SH, Park SK. Cross-phenotype association analysis of gastric cancer: in-silico functional annotation based on the disease-gene network. Gastric Cancer 2023; 26:517-527. [PMID: 36995485 DOI: 10.1007/s10120-023-01380-7] [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: 11/10/2022] [Accepted: 03/02/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND A gene or variant has pleiotropic effects, and genetic variant identification across multiple phenotypes can provide a comprehensive understanding of biological pathways shared among different diseases or phenotypes. Discovery of genetic loci associated with multiple diseases can simultaneously support general interventions. Several meta-analyses have shown genetic associations with gastric cancer (GC); however, no study has identified associations with other phenotypes using this approach. METHODS Here, we applied disease network analysis and gene-based analysis (GBA) to examine genetic variants linked to GC and simultaneously associated with other phenotypes. We conducted a single-nucleotide polymorphism (SNP) level meta-analysis and GBA through a systematic genome-wide association study (GWAS) linked to GC, to integrate published results for the SNP variants and group them into major GC-associated genes. We then performed disease network and expression quantitative trait loci (eQTL) analyses to evaluate cross-phenotype associations and expression levels of GC-related genes. RESULTS Seven genes (MTX1, GBAP1, MUC1, TRIM46, THBS3, PSCA, and ABO) were associated with GC as well as blood urea nitrogen (BUN), glomerular filtration rate (GFR), and uric acid (UA). In addition, 17 SNPs regulated the expression of genes located on 1q22, 24 SNPs regulated the expression of PSCA on 8q24.3, and rs7849820 regulated the expression of ABO on 9q34.2. Furthermore, rs1057941 and rs2294008 had the highest posterior causal probabilities of being a causal candidate SNP in 1q22, and 8q24.3, respectively. CONCLUSIONS These findings identified seven GC-associated genes exhibiting a cross-association with GFR, BUN, and UA.
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Affiliation(s)
- Sangjun Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-Ro, Jongro-Gu, Seoul, 03080, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Han-Kwang Yang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk-Joon Lee
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Do Joong Park
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ho Kong
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-Ro, Jongro-Gu, Seoul, 03080, Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea.
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48
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Kang M, Ang TFA, Devine SA, Sherva R, Mukherjee S, Trittschuh EH, Gibbons LE, Scollard P, Lee M, Choi SE, Klinedinst B, Nakano C, Dumitrescu LC, Durant A, Hohman TJ, Cuccaro ML, Saykin AJ, Kukull WA, Bennett DA, Wang LS, Mayeux RP, Haines JL, Pericak-Vance MA, Schellenberg GD, Crane PK, Au R, Lunetta KL, Mez JB, Farrer LA. A genome-wide search for pleiotropy in more than 100,000 harmonized longitudinal cognitive domain scores. Mol Neurodegener 2023; 18:40. [PMID: 37349795 PMCID: PMC10286470 DOI: 10.1186/s13024-023-00633-4] [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: 02/17/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND More than 75 common variant loci account for only a portion of the heritability for Alzheimer's disease (AD). A more complete understanding of the genetic basis of AD can be deduced by exploring associations with AD-related endophenotypes. METHODS We conducted genome-wide scans for cognitive domain performance using harmonized and co-calibrated scores derived by confirmatory factor analyses for executive function, language, and memory. We analyzed 103,796 longitudinal observations from 23,066 members of community-based (FHS, ACT, and ROSMAP) and clinic-based (ADRCs and ADNI) cohorts using generalized linear mixed models including terms for SNP, age, SNP × age interaction, sex, education, and five ancestry principal components. Significance was determined based on a joint test of the SNP's main effect and interaction with age. Results across datasets were combined using inverse-variance meta-analysis. Genome-wide tests of pleiotropy for each domain pair as the outcome were performed using PLACO software. RESULTS Individual domain and pleiotropy analyses revealed genome-wide significant (GWS) associations with five established loci for AD and AD-related disorders (BIN1, CR1, GRN, MS4A6A, and APOE) and eight novel loci. ULK2 was associated with executive function in the community-based cohorts (rs157405, P = 2.19 × 10-9). GWS associations for language were identified with CDK14 in the clinic-based cohorts (rs705353, P = 1.73 × 10-8) and LINC02712 in the total sample (rs145012974, P = 3.66 × 10-8). GRN (rs5848, P = 4.21 × 10-8) and PURG (rs117523305, P = 1.73 × 10-8) were associated with memory in the total and community-based cohorts, respectively. GWS pleiotropy was observed for language and memory with LOC107984373 (rs73005629, P = 3.12 × 10-8) in the clinic-based cohorts, and with NCALD (rs56162098, P = 1.23 × 10-9) and PTPRD (rs145989094, P = 8.34 × 10-9) in the community-based cohorts. GWS pleiotropy was also found for executive function and memory with OSGIN1 (rs12447050, P = 4.09 × 10-8) and PTPRD (rs145989094, P = 3.85 × 10-8) in the community-based cohorts. Functional studies have previously linked AD to ULK2, NCALD, and PTPRD. CONCLUSION Our results provide some insight into biological pathways underlying processes leading to domain-specific cognitive impairment and AD, as well as a conduit toward a syndrome-specific precision medicine approach to AD. Increasing the number of participants with harmonized cognitive domain scores will enhance the discovery of additional genetic factors of cognitive decline leading to AD and related dementias.
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Affiliation(s)
- Moonil Kang
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
| | - Ting Fang Alvin Ang
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Sherral A. Devine
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
| | - Shubhabrata Mukherjee
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Emily H. Trittschuh
- Geriatric Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA USA
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Laura E. Gibbons
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Phoebe Scollard
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Michael Lee
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Seo-Eun Choi
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Brandon Klinedinst
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Connie Nakano
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Logan C. Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Alaina Durant
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, Miami, FL USA
| | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Services, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Walter A. Kukull
- Department of Epidemiology, University of Washington, Seattle, WA USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Richard P. Mayeux
- Department of Neurology, Columbia University School of Medicine, New York, NY USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH USA
| | | | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Paul K. Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Rhoda Au
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA USA
| | - Kathryn L. Lunetta
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Jesse B. Mez
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
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49
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Lindström S, Wang L, Feng H, Majumdar A, Huo S, Macdonald J, Harrison T, Turman C, Chen H, Mancuso N, Bammler T, Gallinger S, Gruber SB, Gunter MJ, Le Marchand L, Moreno V, Offit K, De Vivo I, O’Mara TA, Spurdle AB, Tomlinson I, Fitzgerald R, Gharahkhani P, Gockel I, Jankowski J, Macgregor S, Schumacher J, Barnholtz-Sloan J, Bondy ML, Houlston RS, Jenkins RB, Melin B, Wrensch M, Brennan P, Christiani DC, Johansson M, Mckay J, Aldrich MC, Amos CI, Landi MT, Tardon A, Bishop DT, Demenais F, Goldstein AM, Iles MM, Kanetsky PA, Law MH, Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM, Klein A, Petersen G, Risch H, Chanock SJ, Purdue MP, Scelo G, Pharoah P, Kar S, Hung RJ, Pasaniuc B, Kraft P. Genome-wide analyses characterize shared heritability among cancers and identify novel cancer susceptibility regions. J Natl Cancer Inst 2023; 115:712-732. [PMID: 36929942 PMCID: PMC10248849 DOI: 10.1093/jnci/djad043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/07/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The shared inherited genetic contribution to risk of different cancers is not fully known. In this study, we leverage results from 12 cancer genome-wide association studies (GWAS) to quantify pairwise genome-wide genetic correlations across cancers and identify novel cancer susceptibility loci. METHODS We collected GWAS summary statistics for 12 solid cancers based on 376 759 participants with cancer and 532 864 participants without cancer of European ancestry. The included cancer types were breast, colorectal, endometrial, esophageal, glioma, head and neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancers. We conducted cross-cancer GWAS and transcriptome-wide association studies to discover novel cancer susceptibility loci. Finally, we assessed the extent of variant-specific pleiotropy among cancers at known and newly identified cancer susceptibility loci. RESULTS We observed widespread but modest genome-wide genetic correlations across cancers. In cross-cancer GWAS and transcriptome-wide association studies, we identified 15 novel cancer susceptibility loci. Additionally, we identified multiple variants at 77 distinct loci with strong evidence of being associated with at least 2 cancer types by testing for pleiotropy at known cancer susceptibility loci. CONCLUSIONS Overall, these results suggest that some genetic risk variants are shared among cancers, though much of cancer heritability is cancer-specific and thus tissue-specific. The increase in statistical power associated with larger sample sizes in cross-disease analysis allows for the identification of novel susceptibility regions. Future studies incorporating data on multiple cancer types are likely to identify additional regions associated with the risk of multiple cancer types.
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Affiliation(s)
- Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Helian Feng
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Arunabha Majumdar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sijia Huo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James Macdonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Tabitha Harrison
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Nicholas Mancuso
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | | | - Steve Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Marc J Gunter
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Radcliffe Institute, Cambridge, MA, USA
| | - Tracy A O’Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ian Tomlinson
- Cancer Research Centre, The University of Edinburgh, Edinburgh, UK
| | | | - Rebecca Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Janusz Jankowski
- Institute for Clinical Trials, University College London, Holborn, UK
- University of the South Pacific, Suva, Fiji
| | - Stuart Macgregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Jill Barnholtz-Sloan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Trans-Divisional Research Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - David C Christiani
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James Mckay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adonina Tardon
- University Institute of Oncology of the Principality of Asturias (IUOPA), University of Oviedo and Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Oviedo, Spain
| | | | - D Timothy Bishop
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Florence Demenais
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Paris, France
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | | | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Alison Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gloria Petersen
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, USA
| | - Harvey Risch
- Yale School of Public Health, Chronic Disease Epidemiology, New Haven, CT, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Peng Q, Wilhelmsen KC, Ehlers CL. Pleiotropic loci for cannabis use disorder severity in multi-ancestry high-risk populations. Mol Cell Neurosci 2023; 125:103852. [PMID: 37061172 PMCID: PMC10247496 DOI: 10.1016/j.mcn.2023.103852] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Cannabis use disorder (CUD) is common and has in part a genetic basis. The risk factors underlying its development likely involve multiple genes that are polygenetic and interact with each other and the environment to ultimately lead to the disorder. Co-morbidity and genetic correlations have been identified between CUD and other disorders and traits in select populations primarily of European descent. If two or more traits, such as CUD and another disorder, are affected by the same genetic locus, they are said to be pleiotropic. The present study aimed to identify specific pleiotropic loci for the severity level of CUD in three high-risk population cohorts: American Indians (AI), Mexican Americans (MA), and European Americans (EA). Using a previously developed computational method based on a machine learning technique, we leveraged the entire GWAS catalog and identified 114, 119, and 165 potentially pleiotropic variants for CUD severity in AI, MA, and EA respectively. Ten pleiotropic loci were shared between the cohorts although the exact variants from each cohort differed. While majority of the pleiotropic genes were distinct in each cohort, they converged on numerous enriched biological pathways. The gene ontology terms associated with the pleiotropic genes were predominately related to synaptic functions and neurodevelopment. Notable pathways included Wnt/β-catenin signaling, lipoprotein assembly, response to UV radiation, and components of the complement system. The pleiotropic genes were the most significantly differentially expressed in frontal cortex and coronary artery, up-regulated in adipose tissue, and down-regulated in testis, prostate, and ovary. They were significantly up-regulated in most brain tissues but were down-regulated in the cerebellum and hypothalamus. Our study is the first to attempt a large-scale pleiotropy detection scan for CUD severity. Our findings suggest that the different population cohorts may have distinct genetic factors for CUD, however they share pleiotropic genes from underlying pathways related to Alzheimer's disease, neuroplasticity, immune response, and reproductive endocrine systems.
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Affiliation(s)
- Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kirk C Wilhelmsen
- Department of Neurology, West Virginia University, Morgantown, WV 26506, USA
| | - Cindy L Ehlers
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
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