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Yuan W, Li X, Wang G, Qu B, Zhao F. Association of autoimmune and allergic diseases with senile cataract: a bidirectional two-sample Mendelian randomization study. Front Immunol 2024; 15:1325868. [PMID: 38585265 PMCID: PMC10995295 DOI: 10.3389/fimmu.2024.1325868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background Many observational studies have been reported that patients with autoimmune or allergic diseases seem to have a higher risk of developing senile cataract, but the views are not consistent. In order to minimize the influence of reverse causality and potential confounding factors, we performed Mendelian Randomization (MR) analysis to investigate the genetic causal associations between autoimmune, allergic diseases and senile cataract. Methods Single nucleotide polymorphisms associated with ten common autoimmune and allergic diseases were obtained from the IEU Open genome-wide association studies (GWAS) database. Summary-level GWAS statistics for clinically diagnosed senile cataract were obtained from the FinnGen research project GWAS, which consisted of 59,522 individuals with senile cataracts and 312,864 control individuals. MR analysis was conducted using mainly inverse variance weighted (IVW) method and further sensitivity analysis was performed to test robustness. Results As for ten diseases, IVW results confirmed that type 1 diabetes (OR = 1.06; 95% CI = 1.05-1.08; p = 2.24×10-12), rheumatoid arthritis (OR = 1.05; 95% CI = 1.02-1.08; p = 1.83×10-4), hypothyroidism (OR = 2.4; 95% CI = 1.42-4.06; p = 1.12×10-3), systemic lupus erythematosus (OR = 1.02; 95% CI = 1.01-1.03; p = 2.27×10-3), asthma (OR = 1.02; 95% CI = 1.01-1.03; p = 1.2×10-3) and allergic rhinitis (OR = 1.07; 95% CI = 1.02-1.11; p = 2.15×10-3) were correlated with the risk of senile cataract. Celiac disease (OR = 1.04; 95% CI = 1.01-1.08; P = 0.0437) and atopic dermatitis (OR = 1.05; 95% CI = 1.01-1.10; P = 0.0426) exhibited a suggestive connection with senile cataract after Bonferroni correction. These associations are consistent across weighted median and MR Egger methods, with similar causal estimates in direction and magnitude. Sensitivity analysis further proved that these associations were reliable. Conclusions The results of the MR analysis showed that there were causal relationships between type 1 diabetes, rheumatoid arthritis, hypothyroidism, systemic lupus erythematosus, asthma, allergic rhinitis and senile cataract. To clarify the possible role of autoimmune and allergy in the pathophysiology of senile cataract, further studies are needed.
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Affiliation(s)
- Weichen Yuan
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Xiangrui Li
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Guan Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Bo Qu
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
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Long J, Yang M, Pang Y, Kang H, Liang S, Wang D. The causal relationship between psoriasis and cancers: a two-sample Mendelian randomization analysis. Front Oncol 2024; 14:1366958. [PMID: 38577332 PMCID: PMC10991695 DOI: 10.3389/fonc.2024.1366958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Background Although observational studies suggest a correlation between psoriasis (PS) and cancers, it is still unknown whether this association can replace causal relationships due to the limitations of observational studies. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis to evaluate the causal relationship between PS and cancers. Methods PS genetic summary data were obtained from two genome-wide association studies (GWAS). We employed MR Base for individuals retrieving tumors from distinct locations. Inverse-variance weighted analysis was the principal method used for MR, supplemented by weighted median, MR Egger, simple mode, and weighted mode. To investigate the possible link between psoriasis and cancers, we performed two independent two-sample MR studies and a meta-analysis based on two independent MR analyses. Results Two independent MR analyses both found no significant causal relationship between PS and overall cancers (OR=1.0000, 95% confidence interval [CI]:0.9999-1.0001, P=0.984; OR=1.0000, 95% CI:0.9999-1.0001, P=0.761), and no significant causal relationship with 17 site-specific cancers. In the meta-analysis conducted by two two-sample MR analyses, there was no significant causal relationship between PS and overall cancers (OR=1.0000, 95% CI: 0.9999-1.0001, P=1.00, I 2 = 0.0%), and there was no significant causal relationship with 17 site-specific cancers. Conclusions Our findings do not support a genetic link between PS and cancers. More population-based and experimental investigations will be required better to understand the complicated relationship between PS and cancers.
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Affiliation(s)
- Jiaye Long
- Department of Interventional Radiology, Inner Mongolia Forestry General Hospital, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, Yakeshi, Inner Mongolia, China
| | - Miyang Yang
- Department of Radiology, The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Yingrong Pang
- Department of Cardiology, Inner Mongolia Forestry General Hospital, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, Yakeshi, Inner Mongolia, China
| | - Hongyan Kang
- Department of Interventional Radiology, Inner Mongolia Forestry General Hospital, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, Yakeshi, Inner Mongolia, China
| | - Shuai Liang
- Department of Cardiology, Inner Mongolia Forestry General Hospital, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, Yakeshi, Inner Mongolia, China
| | - Du Wang
- Department of Interventional Radiology, Inner Mongolia Forestry General Hospital, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, Yakeshi, Inner Mongolia, China
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Zhang ZYO, Jian ZY, Tang Y, Li W. The relationship between blood lipid and risk of psoriasis: univariable and multivariable Mendelian randomization analysis. Front Immunol 2023; 14:1174998. [PMID: 37426655 PMCID: PMC10323678 DOI: 10.3389/fimmu.2023.1174998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Background Psoriasis is a chronic inflammatory skin disease. Dyslipidemia may be a risk factor of psoriasis. But the causal relationship between psoriasis and blood lipid still remains uncertain. Methods The two data of blood lipid were obtained from UK Biobank (UKBB) and Global Lipid Genetics Consortium Results (GLGC). The primary and secondary database were from large publicly available genome-wide association study (GWAS) with more than 400,000 and 170,000 subjects of European ancestry, respectively. The psoriasis from Finnish biobanks of FinnGen research project for psoriasis, consisting of 6,995 cases and 299,128 controls. The single-variable Mendelian randomization (SVMR) and multivariable Mendelian randomization (MVMR) were used to assess the total and direct effects of blood lipid on psoriasis risk. Results SVMR estimates in primary data of blood lipid showed low-density lipoprotein cholesterol (LDL-C) (odds ratio (OR): 1.11, 95%, confidence interval (CI): 0.99-1.25, p = 0.082 in stage 1; OR: 1.15, 95% CI: 1.05-1.26, p = 0.002 in stage 2; OR: 1.15, 95% CI: 1.04-1.26, p = 0.006 in stage 3) and triglycerides (TG) (OR: 1.22, 95% CI: 1.10-1.35, p = 1.17E-04 in stage 1; OR: 1.15, 95% CI: 1.06-1.24, p = 0.001 in stage 2; OR: 1.14, 95% CI: 1.05-1.24, p = 0.002 in stage 3) had a highly robust causal relationship on the risk of psoriasis. However, there were no robust causal associations between HDL-C and psoriasis. The SVMR results in secondary data of blood lipid were consistent with the primary data. Reverse MR analysis showed a causal association between psoriasis and LDL-C (beta: -0.009, 95% CI: -0.016- -0.002, p = 0.009) and HDL-C (beta: -0.011, 95% CI: -0.021- -0.002, p = 0.016). The reverse causation analyses results between psoriasis and TG did not reach significance. In MVMR of primary data of blood lipid, the LDL-C (OR: 1.05, 95% CI: 0.99-1.25, p = 0.396 in stage 1; OR: 1.07, 95% CI: 1.01-1.14, p = 0.017 in stage 2; OR: 1.08, 95% CI: 1.02-1.15, p = 0.012 in stage 3) and TG (OR: 1.11, 95% CI: 1.01-1.22, p = 0.036 in stage 1; OR: 1.09, 95% CI: 1.03-1.15, p = 0.002 in stage 2; OR: 1.07, 95% CI: 1.01-1.13 p = 0.015 in stage 3) positively correlated with psoriasis, and there had no correlation between HDL-C and psoriasis. The results of the secondary analysis were consistent with the results of primary analysis. Conclusions Mendelian randomization (MR) findings provide genetic evidence for causal link between psoriasis and blood lipid. It may be meaningful to monitor and control blood lipid level for a management of psoriasis patients in clinic.
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Affiliation(s)
- Zeng-Yun-Ou Zhang
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhong-Yu Jian
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Yin Tang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Department of Dermatology & Rare Disease Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Nott A, Holtman IR. Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease. Front Immunol 2023; 14:1168539. [PMID: 37359515 PMCID: PMC10285485 DOI: 10.3389/fimmu.2023.1168539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 06/28/2023] Open
Abstract
Microglia, the macrophages of the brain, are vital for brain homeostasis and have been implicated in a broad range of brain disorders. Neuroinflammation has gained traction as a possible therapeutic target for neurodegeneration, however, the precise function of microglia in specific neurodegenerative disorders is an ongoing area of research. Genetic studies offer valuable insights into understanding causality, rather than merely observing a correlation. Genome-wide association studies (GWAS) have identified many genetic loci that are linked to susceptibility to neurodegenerative disorders. (Post)-GWAS studies have determined that microglia likely play an important role in the development of Alzheimer's disease (AD) and Parkinson's disease (PD). The process of understanding how individual GWAS risk loci affect microglia function and mediate susceptibility is complex. A rapidly growing number of publications with genomic datasets and computational tools have formulated new hypotheses that guide the biological interpretation of AD and PD genetic risk. In this review, we discuss the key concepts and challenges in the post-GWAS interpretation of AD and PD GWAS risk alleles. Post-GWAS challenges include the identification of target cell (sub)type(s), causal variants, and target genes. Crucially, the prediction of GWAS-identified disease-risk cell types, variants and genes require validation and functional testing to understand the biological consequences within the pathology of the disorders. Many AD and PD risk genes are highly pleiotropic and perform multiple important functions that might not be equally relevant for the mechanisms by which GWAS risk alleles exert their effect(s). Ultimately, many GWAS risk alleles exert their effect by changing microglia function, thereby altering the pathophysiology of these disorders, and hence, we believe that modelling this context is crucial for a deepened understanding of these disorders.
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Affiliation(s)
- Alexi Nott
- Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Inge R. Holtman
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Gupta P, Li S. Editorial: Methods in genome, pan-genome, pan-transcriptome, and gene regulatory network (GRN) construction and analysis. Front Plant Sci 2023; 14:1152708. [PMID: 36909378 PMCID: PMC9998991 DOI: 10.3389/fpls.2023.1152708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Song Li
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
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Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. Front Plant Sci 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Levina AV, Hoekenga OA, Gordin M, Broeckling C, De Jong WS. Applying network and genetic analysis to the potato metabolome. Front Plant Sci 2023; 14:1108351. [PMID: 37152172 PMCID: PMC10154602 DOI: 10.3389/fpls.2023.1108351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Compositional traits in potato [Solanum tuberosum L.] are economically important but genetically complex, often controlled by many loci of small effect; new methods need to be developed to accelerate analysis and improvement of such traits, like chip quality. In this study, we used network analysis to organize hundreds of metabolic features detected by mass spectrometry into groups, as a precursor to genetic analysis. 981 features were condensed into 44 modules; module eigenvalues were used for genetic mapping and correlation analysis with phenotype data collected by the Solanaceae Coordinated Agricultural Project. Half of the modules were associated with at least one SNP according to GWAS; 11 of those modules were also significantly correlated with chip color. Within those modules features associated with chipping provide potential targets for selection in addition to selection for reduced glucose. Loci associated with module eigenvalues were not evenly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8. Comparison of GWAS on single features and modules of clustered features often identified the same SNPs. However, features with related chemistries (for example, glycoalkaloids with precursor/product relationships) were not found to be near neighbors in the network analysis and did not share common SNPs from GWAS. Instead, the features within modules were often structurally disparate, suggesting that linkage disequilibrium complicates network analyses in potato. This result is consistent with recent genomic studies of potato showing that chromosomal rearrangements that create barriers to recombination are common in cultivated germplasm.
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Affiliation(s)
- Anna V. Levina
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Mikhail Gordin
- Department of Mechanical Engineering, Penn State University, State College, PA, United States
| | - Corey Broeckling
- Bioanalysis and Omics Team, Colorado State University, Fort Collins, CO, United States
| | - Walter S. De Jong
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Walter S. De Jong,
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Kerns S, Owen KA, Kain J, Lipsky PE. Commentary: Systemic lupus erythematosus and cardiovascular disease: A Mendelian randomization study. Front Immunol 2022; 13:1075400. [PMID: 36569872 PMCID: PMC9773385 DOI: 10.3389/fimmu.2022.1075400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sophia Kerns
- AMPEL BioSolutions, LLC, Charlottesville, VA, United States,ReImagined Lupus Investigation, Treatment and Education (RILITE) Research Institute, Charlottesville, VA, United States
| | - Katherine A. Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, United States,ReImagined Lupus Investigation, Treatment and Education (RILITE) Research Institute, Charlottesville, VA, United States,*Correspondence: Katherine A. Owen,
| | - Jessica Kain
- AMPEL BioSolutions, LLC, Charlottesville, VA, United States,ReImagined Lupus Investigation, Treatment and Education (RILITE) Research Institute, Charlottesville, VA, United States
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, United States,ReImagined Lupus Investigation, Treatment and Education (RILITE) Research Institute, Charlottesville, VA, United States
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Chandran AKN, Sandhu J, Irvin L, Paul P, Dhatt BK, Hussain W, Gao T, Staswick P, Yu H, Morota G, Walia H. Rice Chalky Grain 5 regulates natural variation for grain quality under heat stress. Front Plant Sci 2022; 13:1026472. [PMID: 36304400 PMCID: PMC9593041 DOI: 10.3389/fpls.2022.1026472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature grain images to be effective in distinguishing chalky grains from translucent grains derived from control (28/24°C) and heat stressed (36/32°C) plants. Our analysis yielded a novel gene, rice Chalky Grain 5 (OsCG5) that regulates natural variation for grain chalkiness under heat stress. OsCG5 encodes a grain-specific, expressed protein of unknown function. Accessions with lower transcript abundance of OsCG5 exhibit higher chalkiness, which correlates with higher RG values under stress. These findings are supported by increased chalkiness of OsCG5 knock-out (KO) mutants relative to wildtype (WT) under heat stress. Grains from plants overexpressing OsCG5 are less chalky than KOs but comparable to WT under heat stress. Compared to WT and OE, KO mutants exhibit greater heat sensitivity for grain size and weight relative to controls. Collectively, these results show that the natural variation at OsCG5 may contribute towards rice grain quality under heat stress.
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Affiliation(s)
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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Chen M, Lu YL, Chen XF, Wang Z, Ma L. Association of cannabis use disorder with cardiovascular diseases: A two-sample Mendelian randomization study. Front Cardiovasc Med 2022; 9:966707. [PMID: 36277767 PMCID: PMC9582269 DOI: 10.3389/fcvm.2022.966707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background The use of cannabis has increased globally due to more regions decriminalizing marijuana use for therapeutic and recreational aims. Several observational studies have revealed that cannabis use is associated with an increased risk of adverse cardiovascular pathologies and diseases. Nevertheless, the causal associations between cannabis use and cardiovascular diseases remain unclear. Hence, we performed single-variable and multivariable Mendelian randomization (MR) to evaluate the association between cannabis use disorder and various cardiovascular diseases. Materials and methods Summary statistics were collected from the largest-to-date genome-wide association studies (GWAS) of cannabis use disorder. The 12 SNPs for cannabis use disorder were used as instrumental variables in this study. MR estimates were pooled using a random-effects inverse-variance weighted (IVW) method. Simple median and weighted median methods were conducted as sensitivity analyses. Results The genetic liability to cannabis use disorder was associated with an augmented risk of coronary artery disease, myocardial infarction, atrial fibrillation, heart failure, deep venous thrombosis, pulmonary embolism, and stroke. Except for stroke, the results were inconsistent in the sensitivity analyses. The overall patterns for the associations of cannabis use disorder with atrial fibrillation, heart failure, pulmonary embolism and stroke remained in multivariable MR analyses adjusting for potential mediators, including smoking, alcohol, body mass index, blood lipid, type 2 diabetes, hypertension, and depression. However, the association with coronary artery disease, myocardial infarction, and deep venous thrombosis did not persist in multivariable MR analyses. Mediation analysis demonstrated that smoking, body mass index, low-density lipoprotein, hypertension, and depression have more significant mediation effects, which suggests that these factors partly mediate the link from cannabis use disorder to coronary artery disease, myocardial infarction, and deep venous thrombosis. Conclusion The genetic liability to cannabis use disorder was associated with a higher risk of atrial fibrillation, heart failure, pulmonary embolism, and stroke. The evidence for the association between cannabis use disorder, coronary artery disease, myocardial infarction, and deep venous thrombosis was weak. Hence, future use of cannabis for therapeutic and recreational aims should consider its potential impact on cardiovascular diseases.
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Affiliation(s)
- Miao Chen
- Department of Cardiovascular Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Yun-long Lu
- Department of Cardiology, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Xiao-fan Chen
- Department of Cardiovascular Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Zhen Wang
- Department of Cardiovascular Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China,*Correspondence: Zhen Wang,
| | - Liang Ma
- Department of Cardiovascular Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, China,Liang Ma,
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Augustine T, Al-Aghbar MA, Al-Kowari M, Espino-Guarch M, van Panhuys N. Asthma and the Missing Heritability Problem: Necessity for Multiomics Approaches in Determining Accurate Risk Profiles. Front Immunol 2022; 13:822324. [PMID: 35693821 PMCID: PMC9174795 DOI: 10.3389/fimmu.2022.822324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Asthma is ranked among the most common chronic conditions and has become a significant public health issue due to the recent and rapid increase in its prevalence. Investigations into the underlying genetic factors predict a heritable component for its incidence, estimated between 35% and 90% of causation. Despite the application of large-scale genome-wide association studies (GWAS) and admixture mapping approaches, the proportion of variants identified accounts for less than 15% of the observed heritability of the disease. The discrepancy between the predicted heritable component of disease and the proportion of heritability mapped to the currently identified susceptibility loci has been termed the ‘missing heritability problem.’ Here, we examine recent studies involving both the analysis of genetically encoded features that contribute to asthma and also the role of non-encoded heritable characteristics, including epigenetic, environmental, and developmental aspects of disease. The importance of vertical maternal microbiome transfer and the influence of maternal immune factors on fetal conditioning in the inheritance of disease are also discussed. In order to highlight the broad array of biological inputs that contribute to the sum of heritable risk factors associated with allergic disease incidence that, together, contribute to the induction of a pro-atopic state. Currently, there is a need to develop in-depth models of asthma risk factors to overcome the limitations encountered in the interpretation of GWAS results in isolation, which have resulted in the missing heritability problem. Hence, multiomics analyses need to be established considering genetic, epigenetic, and functional data to create a true systems biology-based approach for analyzing the regulatory pathways that underlie the inheritance of asthma and to develop accurate risk profiles for disease.
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Affiliation(s)
- Tracy Augustine
- Laboratory of Immunoregulation, Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Mohammad Ameen Al-Aghbar
- Laboratory of Immunoregulation, Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Moza Al-Kowari
- Laboratory of Immunoregulation, Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Meritxell Espino-Guarch
- Laboratory of Immunoregulation, Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
| | - Nicholas van Panhuys
- Laboratory of Immunoregulation, Systems Biology and Immunology Department, Sidra Medicine, Doha, Qatar
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12
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Zenebe-Gete S, Salowe R, O'Brien JM. Benefits of Cohort Studies in a Consortia-Dominated Landscape. Front Genet 2021; 12:801653. [PMID: 34950194 PMCID: PMC8688987 DOI: 10.3389/fgene.2021.801653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Selam Zenebe-Gete
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Rebecca Salowe
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Joan M O'Brien
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, United States
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Abstract
Uveitis is a generic term for inflammation of the uvea, which includes the iris, ciliary body, and choroid. Prevalence of underlying non-infectious uveitis varies by race and region and is a major cause of legal blindness in developed countries. Although the etiology remains unclear, the involvement of both genetic and environmental factors is considered important for the onset of many forms of non-infectious uveitis. Major histocompatibility complex (MHC) genes, which play a major role in human immune response, have been reported to be strongly associated as genetic risk factors in several forms of non-infectious uveitis. Behçet’s disease, acute anterior uveitis (AAU), and chorioretinopathy are strongly correlated with MHC class I-specific alleles. Moreover, sarcoidosis and Vogt-Koyanagi-Harada (VKH) disease are associated with MHC class II-specific alleles. These correlations can help immunogenetically classify the immune pathway involved in each form of non-infectious uveitis. Genetic studies, including recent genome-wide association studies, have identified several susceptibility genes apart from those in the MHC region. These genetic findings help define the common or specific pathogenesis of ocular inflammatory diseases by comparing the susceptibility genes of each form of non-infectious uveitis. Interestingly, genome-wide association of the interleukin (IL)23R region has been identified in many of the major forms of non-infectious uveitis, such as Behçet’s disease, ocular sarcoidosis, VKH disease, and AAU. The interleukin-23 (IL-23) receptor, encoded by IL23R, is expressed on the cell surface of Th17 cells. IL-23 is involved in the homeostasis of Th17 cells and the production of IL-17, which is an inflammatory cytokine, indicating that a Th17 immune response is a common key in the pathogenesis of non-infectious uveitis. Based on the findings from the immunogenetics of non-infectious uveitis, a personalized treatment approach based on the patient’s genetic make-up is expected.
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Affiliation(s)
- Masaki Takeuchi
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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14
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Gao G, Gao D, Zhao X, Xu S, Zhang K, Wu R, Yin C, Li J, Xie Y, Hu S, Wang Q. Genome-Wide Association Study-Based Identification of SNPs and Haplotypes Associated With Goose Reproductive Performance and Egg Quality. Front Genet 2021; 12:602583. [PMID: 33777090 PMCID: PMC7994508 DOI: 10.3389/fgene.2021.602583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/24/2021] [Indexed: 01/10/2023] Open
Abstract
Geese are one of the most economically important waterfowl. However, the low reproductive performance and egg quality of geese hinder the development of the goose industry. The identification and application of genetic markers may improve the accuracy of beneficial trait selection. To identify the genetic markers associated with goose reproductive performance and egg quality traits, we performed a genome-wide association study (GWAS) for body weight at birth (BBW), the number of eggs at 48 weeks of age (EN48), the number of eggs at 60 weeks of age (EN60) and egg yolk color (EYC). The GWAS acquired 2.896 Tb of raw sequencing data with an average depth of 12.44× and identified 9,279,339 SNPs. The results of GWAS showed that 26 SNPs were significantly associated with BBW, EN48, EN60, and EYC. Moreover, five of these SNPs significantly associated with EN48 and EN60 were in a haplotype block on chromosome 35 from 4,512,855 to 4,541,709 bp, oriented to TMEM161A and another five SNPs significantly correlated to EYC were constructed in haplotype block on chromosome 5 from 21,069,009 to 21,363,580, which annotated by TMEM161A, CALCR, TFPI2, and GLP1R. Those genes were enriched in epidermal growth factor-activated receptor activity, regulation of epidermal growth factor receptor signaling pathway. The SNPs, haplotype markers, and candidate genes identified in this study can be used to improve the accuracy of marker-assisted selection for the reproductive performance and egg quality traits of geese. In addition, the candidate genes significantly associated with these traits may provide a foundation for better understanding the mechanisms underlying reproduction and egg quality in geese.
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Affiliation(s)
- Guangliang Gao
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Dengfeng Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xianzhi Zhao
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | | | - Keshan Zhang
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Rui Wu
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Chunhui Yin
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Jing Li
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Youhui Xie
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qigui Wang
- Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
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15
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Chinchilla-Vargas J, Kramer LM, Tucker JD, Hubbell DS, Powell JG, Lester TD, Backes EA, Anschutz K, Decker JE, Stalder KJ, Rothschild MF, Koltes JE. Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning. Front Genet 2020; 11:717. [PMID: 32719722 PMCID: PMC7350949 DOI: 10.3389/fgene.2020.00717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
The objectives of this study were to explore the usefulness of blood-based traits as indicators of health and performance in beef cattle at weaning and identify the genetic basis underlying the different blood parameters obtained from complete blood counts (CBCs). Disease costs represent one of the main factors determining profitability in animal production. Previous research has observed associations between blood cell counts and an animal’s health status in some species. CBC were recorded from approximately 570 Angus based, crossbred beef calves at weaning born between 2015 and 2016 and raised on toxic or novel tall fescue. The calves (N = ∼600) were genotyped at a density of 50k SNPs and the genotypes (N = 1160) were imputed to a density of 270k SNPs. Genetic parameters were estimated for 15 blood and 4 production. Finally, with the objective of identifying the genetic basis underlying the different blood-based traits, genome-wide association studies (GWAS) were performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were observed among blood-based traits only. Genome-wide association study identified ninety-one 1-Mb windows that accounted for 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping across two or more traits (explaining more than 0.5% of estimated genetic variance for two or more traits). Five candidate genes have been identified in the most interesting overlapping regions related to blood-based traits. Overall, this study represents one of the first efforts represented in scientific literature to identify the genetic basis of blood cell traits in beef cattle. The results presented in this study allow us to conclude that: (1) blood-based traits have weak phenotypic correlations but strong genetic correlations among themselves. (2) Blood-based traits have moderate to high heritability. (3) There is evidence of an important overlap of genetic control among similar blood-based traits which will allow for their use in improvement programs in beef cattle.
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Affiliation(s)
| | - Luke M Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John D Tucker
- Division of Agriculture, Livestock and Forestry Research Station, Batesville, AR, United States
| | - Donald S Hubbell
- Division of Agriculture, Livestock and Forestry Research Station, Batesville, AR, United States
| | - Jeremy G Powell
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Toby D Lester
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth A Backes
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Karen Anschutz
- Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Jared E Decker
- Division of Animal Science, University of Missouri, Columbia, MO, United States
| | - Kenneth J Stalder
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
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16
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Odilbekov F, Armoniené R, Koc A, Svensson J, Chawade A. GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Front Genet 2019; 10:1224. [PMID: 31850073 PMCID: PMC6901976 DOI: 10.3389/fgene.2019.01224] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 11/05/2019] [Indexed: 02/01/2023] Open
Abstract
Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.
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Affiliation(s)
- Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Rita Armoniené
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Akademija, Lithuania
| | - Alexander Koc
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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17
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Zheng J, Frysz M, Kemp JP, Evans DM, Davey Smith G, Tobias JH. Use of Mendelian Randomization to Examine Causal Inference in Osteoporosis. Front Endocrinol (Lausanne) 2019; 10:807. [PMID: 31824424 PMCID: PMC6882110 DOI: 10.3389/fendo.2019.00807] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/04/2019] [Indexed: 12/15/2022] Open
Abstract
Epidemiological studies have identified many risk factors for osteoporosis, however it is unclear whether these observational associations reflect true causal effects, or the effects of latent confounding or reverse causality. Mendelian randomization (MR) enables causal relationships to be evaluated, by examining the relationship between genetic susceptibility to the risk factor in question, and the disease outcome of interest. This has been facilitated by the development of two-sample MR analysis, where the exposure and outcome are measured in different studies, and by exploiting summary result statistics from large well-powered genome-wide association studies that are available for thousands of traits. Though MR has several inherent limitations, the field is rapidly evolving and at least 14 methodological extensions have been developed to overcome these. The present paper aims to discuss some of the limitations in the MR analytical framework, and how this method has been applied to the osteoporosis field, helping to reinforce conclusions about causality, and discovering potential new regulatory pathways, exemplified by our recent MR study of sclerostin.
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Affiliation(s)
- Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Monika Frysz
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - John P. Kemp
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Jonathan H. Tobias
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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18
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Affiliation(s)
- Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China
- *Correspondence: Hui Xia
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Fudan University, Shanghai, China
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