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Allen-Brady K, Chua JWF, Cuffolo R, Koch M, Sorrentino F, Cartwright R. Systematic review and meta-analysis of genetic association studies of pelvic organ prolapse. Int Urogynecol J 2021; 33:67-82. [PMID: 33893823 PMCID: PMC8739292 DOI: 10.1007/s00192-021-04782-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
INTRODUCTION AND HYPOTHESIS Family and twin studies demonstrate that pelvic organ prolapse (POP) is heritable, but the genetic etiology is poorly understood. This review aimed to identify genetic loci and specific polymorphisms associated with POP, while assessing the strength, consistency, and risk of bias among reported associations. METHODS Updating an earlier systematic review, PubMed and HuGE Navigator as well as relevant conference abstracts were searched using genetic and phenotype keywords from 2015 to 2020. Screening and data extraction were performed in duplicate. Fixed and random effects meta-analyses were conducted using co-dominant models of inheritance. We assessed credibility of pooled associations using interim Venice criteria. RESULTS We screened 504 new abstracts and included 46 published and 7 unpublished studies. In pooled analyses we found significant associations for four polymorphisms: rs2228480 at the ESR1 gene (OR 0.67 95% CI 0.46-0.98, I2 = 0.0%, Venice rating BAB), rs12589592 at the FBLN5 gene (OR 1.46 95% CI 1.11-1.82, I2 = 36.3%, Venice rating BBB), rs484389 in the PGR gene (OR 0.61 95% CI 0.39-0.96, I2 = 32.4%, Venice rating CBB), and rs1800012 at the COL1A1 gene (OR 0.80 95% CI 0.66-0.96, I2 = 0.0%, Venice rating BAB). Further credible novel variants have also been recently identified in genome-wide association studies. CONCLUSION The genetic contributions to POP remain poorly understood. Several biologically plausible variants have been identified, but much work is required to establish the role of these genes in the pathogenesis of POP or to establish a role for genetic testing in clinical practice.
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Affiliation(s)
- Kristina Allen-Brady
- Department of Internal Medicine, Genetic Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - John W F Chua
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Romana Cuffolo
- Department of Obstetrics & Gynaecology, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Marianne Koch
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Felice Sorrentino
- Department of Medical and Surgical Sciences, Institute of Obstetrics and Gynecology, University of Foggia, Foggia, Italy
| | - Rufus Cartwright
- Department of Epidemiology & Biostatistics, Imperial College London, Norfolk Place, London, UK. .,Department of Urogynaecology, LNWH NHS Trust, London, UK.
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Association between the combined effects of GSTM1 present/null and CYP1A1 MspI polymorphisms with lung cancer risk: an updated meta-analysis. Biosci Rep 2021; 40:226457. [PMID: 32945337 PMCID: PMC7533282 DOI: 10.1042/bsr20202275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Many studies have been performed to explore the combined effects of glutathione-S-transferase M1 (GSTM1) present/null and cytochrome P4501A1 (CYP1A1) MspI polymorphisms with lung cancer (LC) risk, but the results are contradictory. Two previous meta-analyses have been reported on the issue in 2011 and 2014. However, several new articles since then have been published. In addition, their meta-analyses did not valuate the credibility of significantly positive results. Objectives: We performed an updated meta-analysis to solve the controversy following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Methods: False-positive report probability (FPRP), Bayesian false discovery probability (BFDP), and the Venice criteria were used to verify the credibility of meta-analyses. Results: Twenty-three publications including 5734 LC cases and 7066 controls met the inclusion criteria in the present study. A significantly increased risk of LC was found in overall analysis, Asians and Indians. However, all positive results were considered as ‘less-credible’ when we used the Venice criteria, FPRP, and BFDP test to assess the credibility of the positive results. Conclusion: These positive findings should be interpreted with caution and results indicate that significant associations may be less-credible, there are no significantly increased LC risk between the combined effects of GSTM1 present/null and CYP1A1 MspI polymorphisms.
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Lebrett MB, Crosbie EJ, Smith MJ, Woodward ER, Evans DG, Crosbie PAJ. Targeting lung cancer screening to individuals at greatest risk: the role of genetic factors. J Med Genet 2021; 58:217-226. [PMID: 33514608 PMCID: PMC8005792 DOI: 10.1136/jmedgenet-2020-107399] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer (LC) is the most common global cancer. An individual’s risk of developing LC is mediated by an array of factors, including family history of the disease. Considerable research into genetic risk factors for LC has taken place in recent years, with both low-penetrance and high-penetrance variants implicated in increasing or decreasing a person’s risk of the disease. LC is the leading cause of cancer death worldwide; poor survival is driven by late onset of non-specific symptoms, resulting in late-stage diagnoses. Evidence for the efficacy of screening in detecting cancer earlier, thereby reducing lung-cancer specific mortality, is now well established. To ensure the cost-effectiveness of a screening programme and to limit the potential harms to participants, a risk threshold for screening eligibility is required. Risk prediction models (RPMs), which provide an individual’s personal risk of LC over a particular period based on a large number of risk factors, may improve the selection of high-risk individuals for LC screening when compared with generalised eligibility criteria that only consider smoking history and age. No currently used RPM integrates genetic risk factors into its calculation of risk. This review provides an overview of the evidence for LC screening, screening related harms and the use of RPMs in screening cohort selection. It gives a synopsis of the known genetic risk factors for lung cancer and discusses the evidence for including them in RPMs, focusing in particular on the use of polygenic risk scores to increase the accuracy of targeted lung cancer screening.
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Affiliation(s)
- Mikey B Lebrett
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK.,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - Emma J Crosbie
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Division of Cancer Sciences, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Miriam J Smith
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Emma R Woodward
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Philip A J Crosbie
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK .,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Thoracic Oncology Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
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Koterov AN, Ushenkova LN, Biryukov AP. Hill’s Temporality Criterion: Reverse Causation and Its Radiation Aspect. BIOL BULL+ 2021. [DOI: 10.1134/s1062359020120031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6641429. [PMID: 33511206 PMCID: PMC7825361 DOI: 10.1155/2021/6641429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022]
Abstract
Background Majority of prostate cancer (PCa) deaths are attributed to localized high-grade aggressive tumours which progress rapidly to metastatic disease. A critical unmet need in clinical management of PCa is discovery and characterization of the molecular drivers of aggressive tumours. The development and progression of aggressive PCa involve genetic and epigenetic alterations occurring in the germline, somatic (tumour), and epigenomes. To date, interactions between genes containing germline, somatic, and epigenetic mutations in aggressive PCa have not been characterized. The objective of this investigation was to elucidate the genomic-epigenomic interaction landscape in aggressive PCa to identify potential drivers aggressive PCa and the pathways they control. We hypothesized that aggressive PCa originates from a complex interplay between genomic (both germline and somatic mutations) and epigenomic alterations. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect gene expression, molecular networks, and signaling pathways which in turn drive aggressive PCa. Methods We addressed these hypotheses by performing integrative data analysis combining information on germline mutations from genome-wide association studies with somatic and epigenetic mutations from The Cancer Genome Atlas using gene expression as the intermediate phenotype. Results The investigation revealed signatures of genes containing germline, somatic, and epigenetic mutations associated with aggressive PCa. Aberrant DNA methylation had effect on gene expression. In addition, the investigation revealed molecular networks and signalling pathways enriched for germline, somatic, and epigenetic mutations including the STAT3, PTEN, PCa, ATM, AR, and P53 signalling pathways implicated in aggressive PCa. Conclusions The study demonstrated that integrative analysis combining diverse omics data is a powerful approach for the discovery of potential clinically actionable biomarkers, therapeutic targets, and elucidation of oncogenic interactions between genomic and epigenomic alterations in aggressive PCa.
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Areeshi MY, Mandal RK, Dar SA, Jawed A, Wahid M, Lohani M, Panda AK, Mishra B, Akhter N, Haque S. IFN-γ +874 A>T (rs2430561) gene polymorphism and risk of pulmonary tuberculosis: a meta-analysis. Arch Med Sci 2021; 17:177-188. [PMID: 33488870 PMCID: PMC7811310 DOI: 10.5114/aoms.2019.88481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/15/2017] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION The role of interferon gamma (IFN-γ) +874 A>T (rs2430561) gene polymorphism has been evaluated in different ethnicities with pulmonary tuberculosis (PTB) infection, and inconsistent results have been reported. In this study, a meta-analysis was performed to determine the precise association between IFN-γ +874 A>T gene polymorphism and PTB susceptibility. MATERIAL AND METHODS A total of 21 studies comprising 4281 confirmed PTB cases and 5186 healthy controls were included in this meta-analysis by searching the PubMed (Medline), EMBASE, and Google Scholar web-databases. RESULTS We observed reduced risk of PTB in allelic contrast (T vs. A: p = 0.001; OR = 0.818, 95% CI: 0.723-0.926), homozygous (TT vs. AA: p = 0.017; OR = 0.715, 95% CI: 0.543-0.941), heterozygous (AT vs. AA: p = 0.002; OR = 0.782, 95% CI: 0.667-0.917), dominant (TT+AT vs. AA: p = 0.002; OR = 0.768, 95% CI: 0.652-0.906), and recessive (TT vs. AA+AT: p = 0.042; OR = 0.802, 95% CI: 0.649-0.992) genetic models. In ethnicity-wise subgroup analysis, reduced risk of PTB was found in the Caucasian population. However, we did not find an association with any of the genetic models in the Asian population. CONCLUSIONS In conclusion, the IFN-γ +874 A>T gene polymorphism is significantly associated with reduced risk of PTB, showing a protective effect in the overall and in the Caucasian population. However, this polymorphism is not associated with PTB risk in the Asian population.
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Affiliation(s)
- Mohammed Y. Areeshi
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Raju K. Mandal
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sajad A. Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- The University College of Medical Sciences and GTB Hospital (University of Delhi), Delhi, India
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Aditya K. Panda
- Centre for Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - B.N. Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow, Uttar Pradesh, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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da Silva FRP, Pessoa LDS, Shin JI, Alves EHP, Koga RS, Smith CV, Vasconcelos DFP, Pereira ACTDC. Polymorphisms in the interleukin genes and chronic periodontitis: A field synopsis and revaluation by Bayesian approaches. Cytokine 2020; 138:155361. [PMID: 33223448 DOI: 10.1016/j.cyto.2020.155361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/03/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022]
Abstract
Periodontitis is a high prevalent disease into the clinical dentistry. Genetic variations in interleukins (IL) genes were associated with chronic periodontitis (CP) and were focus of several meta-analyses. This study aimed to assess the noteworthiness in the meta-analyses by means of a Bayesian approach to determinate possible false report associations. A systematic search was performed for meta-analyses with associations between gene polymorphisms in interleukins and CP. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10-3 and 10-6. As results, eight meta-analyses approaching the IL1A/rs1800587, IL1B/rs1143634, IL1RN/rs2234663, IL4/rs2243250, IL6/rs1800795/rs1800796, IL17A/rs2275913 and IL18/rs1946518/rs187238 polymorphisms have been identified. Twenty-two from 270 calculations (8.15%) were noteworthy. Herein, we have identified the IL1A and IL1B polymorphisms as noteworthy biomarkers for CP susceptibility.
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Affiliation(s)
- Felipe Rodolfo Pereira da Silva
- Doctorate in Post-Graduation Program in Basic and Applied Immunology, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Larissa Dos Santos Pessoa
- Laboratory of Histological Analysis and Preparation (LAPHis), Federal University of the Parnaiba Delta (UFDPar), Parnaiba, Piaui, Brazil
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Even Herlany Pereira Alves
- Laboratory of Histological Analysis and Preparation (LAPHis), Federal University of the Parnaiba Delta (UFDPar), Parnaiba, Piaui, Brazil
| | - Reyce Santos Koga
- Doctorate in Post-Graduation Program in Basic and Applied Immunology, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Camila Valente Smith
- Master Student in the Post-Graduation Program in Dentistry, Dentistry College, Federal University of Amazonas, Manaus, Amazonas, Brazil
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Fullana MA, Abramovitch A, Via E, López-Sola C, Goldberg X, Reina N, Fortea L, Solanes A, Buckley MJ, Ramella-Cravaro V, Carvalho AF, Tortella-Feliu M, Vieta E, Soriano-Mas C, Lázaro L, Stein DJ, Fernández de la Cruz L, Mataix-Cols D, Radua J. Diagnostic biomarkers for obsessive-compulsive disorder: A reasonable quest or ignis fatuus? Neurosci Biobehav Rev 2020; 118:504-513. [DOI: 10.1016/j.neubiorev.2020.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/31/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
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Vassos E, Sham P, Kempton M, Trotta A, Stilo SA, Gayer-Anderson C, Di Forti M, Lewis CM, Murray RM, Morgan C. The Maudsley environmental risk score for psychosis. Psychol Med 2020; 50:2213-2220. [PMID: 31535606 PMCID: PMC7557157 DOI: 10.1017/s0033291719002319] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/06/2019] [Accepted: 08/14/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Risk prediction algorithms have long been used in health research and practice (e.g. prediction of cardiovascular disease and diabetes). However, similar tools have not been developed for mental health. For example, for psychotic disorders, attempts to sum environmental risk are rare, unsystematic and dictated by available data. In light of this, we sought to develop a valid, easy to use measure of the aggregate environmental risk score (ERS) for psychotic disorders. METHODS We reviewed the literature to identify well-replicated and validated environmental risk factors for psychosis that combine a significant effect and large-enough prevalence. Pooled estimates of relative risks were taken from the largest available meta-analyses. We devised a method of scoring the level of exposure to each risk factor to estimate ERS. Relative risks were rounded as, due to the heterogeneity of the original studies, risk effects are imprecisely measured. RESULTS Six risk factors (ethnic minority status, urbanicity, high paternal age, obstetric complications, cannabis use and childhood adversity) were used to generate the ERS. A distribution for different levels of risk based on simulated data showed that most of the population would be at low/moderate risk with a small minority at increased environmental risk for psychosis. CONCLUSIONS This is the first systematic approach to develop an aggregate measure of environmental risk for psychoses in asymptomatic individuals. This can be used as a continuous measure of liability to disease; mostly relevant to areas where the original studies took place. Its predictive ability will improve with the collection of additional, population-specific data.
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Affiliation(s)
- Evangelos Vassos
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Pak Sham
- State Key Laboratory of Brain and Cognitive Sciences, Department of Psychiatry and Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Matthew Kempton
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Antonella Trotta
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Tony Hillis Unit, South London & Maudsley NHS Foundation Trust, London, UK
| | - Simona A. Stilo
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Charlotte Gayer-Anderson
- Health Service and Population Research, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Marta Di Forti
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Psychiatry, Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy
| | - Cathryn M. Lewis
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Robin M. Murray
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Psychiatry, Experimental Biomedicine and Clinical Neuroscience (BIONEC), University of Palermo, Palermo, Italy
| | - Craig Morgan
- Health Service and Population Research, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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Montazeri Z, Li X, Nyiraneza C, Ma X, Timofeeva M, Svinti V, Meng X, He Y, Bo Y, Morgan S, Castellví-Bel S, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo Á, Castells A, Bishop T, Buchanan D, Jenkins MA, Keku TO, Lindblom A, van Duijnhoven FJB, Wu A, Farrington SM, Dunlop MG, Campbell H, Theodoratou E, Zheng W, Little J. Systematic meta-analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer. Gut 2020; 69:1460-1471. [PMID: 31818908 PMCID: PMC7398467 DOI: 10.1136/gutjnl-2019-319313] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2). DESIGN We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as 'positive' and 'less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin. RESULTS We initially identified 18 independent variants at 16 loci that were classified as 'positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as 'less-credible positive' SNPs; 72.2% of the 'positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to 'less-credible' positive (reducing the 'positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-analyses found no evidence to support their associations with CRC risk. CONCLUSION The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility.
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Affiliation(s)
- Zahra Montazeri
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xue Li
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Christine Nyiraneza
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, Chongqing, China
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Xiangrui Meng
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yazhou He
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Yacong Bo
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Shenzhen, Hong Kong
| | - Samuel Morgan
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ceres Fernández-Rozadilla
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Daniel Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Genetic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Anna Wu
- University of Southern California, Preventative Medicine, Los Angeles, California, USA
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre and Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julian Little
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Association between vitamin D receptor BsmI, FokI, and Cdx2 polymorphisms and osteoporosis risk: an updated meta-analysis. Biosci Rep 2020; 40:225702. [PMID: 32627819 PMCID: PMC7364509 DOI: 10.1042/bsr20201200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/06/2022] Open
Abstract
Background: Many studies have reported the association between vitamin D receptor (VDR) polymorphism and osteoporosis risk. However, their results were conflicting. Six previous meta-analyses have been published to analyze VDR BsmI, FokI, and Cdx2 polymorphisms on osteoporosis risk. However, they did not evaluate the reliability of statistically significant associations. Furthermore, a lot of new articles have been published on these themes, and therefore an updated meta-analysis was performed to further explore these issues. Objectives: To explore the association between VDR BsmI, FokI, and Cdx2 polymorphisms polymorphisms and osteoporosis risk. Methods: The odds ratios (ORs) and 95% confidence intervals (95% CIs) were pooled to evaluate the association between VDR BsmI, FokI, and Cdx2 polymorphisms and osteoporosis risk. To evaluate the credibility of statistically significant associations, we applied the false-positive report probabilities (FPRPs) test and the Venice criteria. Results: Overall, statistically significantly increased osteoporosis risk was found in Indians and women for VDR FokI polymorphism. Statistically significantly decreased osteoporosis risk was found in West Asians for VDR BsmI polymorphism. However, when we performed a sensitivity analysis after excluding low quality and Hardy–Weinberg Disequilibrium (HWD) studies, significantly decreased osteoporosis risk was only found in overall population for VDR BsmI polymorphism. Further, less-credible positive results were identified when we evaluated the credibility of positive results. Conclusion: These positive findings should be interpreted with caution and indicate that significant association may most likely result from less-credible, rather than from true associations or biological factors on the VDR BsmI and FokI polymorphisms with osteoporosis risk.
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Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer. Int J Genomics 2020; 2020:2641370. [PMID: 32724790 PMCID: PMC7364202 DOI: 10.1155/2020/2641370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/26/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
Background Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions between germline genetic risk variants and somatic mutations in triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC) have not been characterized. Here, we delineated the possible oncogenic interactions between genes containing germline and somatic mutations in TNBC and non-TNBC and investigated whether there are differences in gene expression and mutation burden between the two types of breast cancer. Methods We addressed this problem by integrating germline mutation information from genome-wide association studies with somatic mutation information from next-generation sequencing using gene expression data as the intermediated phenotype. We performed network and pathway analyses to discover molecular networks and signalling pathways enriched for germline and somatic mutations. Results The investigation revealed signatures of differentially expressed and differentially somatic mutated genes between TNBC and non-TNBC. Network and pathway analyses revealed functionally related genes interacting in gene regulatory networks and multiple signalling pathways enriched for germline and somatic mutations for each type of breast cancer. Among the signalling pathways discovered included the DNA repair and Androgen and ATM signalling pathways for TNBC and the DNA damage response, molecular mechanisms of cancer, and ATM and GP6 signalling pathways for non-TNBC. Conclusions The results show that integrative genomics is a powerful approach for delineating oncogenic interactions between genes containing germline and genes containing somatic mutations in TNBC and non-TNBC and establishes putative functional bridges between genetic and somatic alterations and the pathways they control in the two types of breast cancer.
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Bordbar F, Jensen J, Du M, Abied A, Guo W, Xu L, Gao H, Zhang L, Li J. Identification and validation of a novel candidate gene regulating net meat weight in Simmental beef cattle based on imputed next-generation sequencing. Cell Prolif 2020; 53:e12870. [PMID: 32722873 PMCID: PMC7507581 DOI: 10.1111/cpr.12870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 12/19/2022] Open
Abstract
Objectives Genome‐wide association studies (GWAS) represent a powerful approach to detecting candidate genes for economically important traits in livestock. Our aim was to identify promising candidate muscle development genes that affect net meat weight (NMW) and validate these candidate genes in cattle. Materials and methods Using a next‐generation sequencing (NGS) dataset, we applied ~ 12 million imputed single nucleotide polymorphisms (SNPs) from 1,252 Simmental cattle to detect genes influencing net meat yield by way of a linear mixed model method. Haplotype and linkage disequilibrium (LD) blocks were employed to augment support for identified genes. To investigate the role of MTPN in bovine muscle development, we isolated myoblasts from the longissimus dorsi of a bovine foetus and treated the cells during proliferation, differentiation and hypertrophy. Results We identified one SNP (rs100670823) that exceeded our stringent significance threshold (P = 8.58 × 10−8) for a putative NMW‐related quantitative trait locus (QTL). We identified a promising candidate gene, myotrophin (MTPN), in the region around this SNP Myotrophin had a stimulatory effect on six muscle‐related markers that regulate differentiation and myoblast fusion. During hypertrophy, myotrophin promoted myotube hypertrophy and increased myotube diameters. Cell viability assay and flow cytometry showed that myotrophin inhibited myoblast proliferation. Conclusions The present experiments showed that myotrophin increases differentiation and hypertrophy of skeletal muscle cells, while inhibiting their proliferation. Our examination of GWAS results with in vitro biological studies provides new information regarding the potential application of myotrophin to increase meat yields in cattle and helpful information for further studies.
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Affiliation(s)
- Farhad Bordbar
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Min Du
- Department of Animal Sciences, Washington Center for Muscle Biology, Washington State University, Pullman, WA, USA
| | - Adam Abied
- Animal Genetic Breeding and Reproduction, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Guo
- Meat Science and Muscle Biology, Animal and Diary Science, University of Wisconsin-Madison, Madison, USA
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Ho JSY, Tambyah PA, Ho AFW, Chan MYY, Sia CH. Effect of coronavirus infection on the human heart: A scoping review. Eur J Prev Cardiol 2020; 27:1136-1148. [PMID: 32423250 PMCID: PMC7717245 DOI: 10.1177/2047487320925965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/22/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The global coronavirus disease 2019 pandemic has highlighted the importance of understanding the cardiovascular implications of coronavirus infections, with more severe disease in those with cardiovascular co-morbidities, and resulting cardiac manifestations such as myocardial injury, arrhythmias, and heart failure. DESIGN A systematic review of the current knowledge on the effects of coronavirus infection on the cardiovascular system in humans was performed and results were summarized. METHODS Databases such as MEDLINE, EMBASE, CENTRAL, Scopus, Web of Science, ClinicalTrials.gov, Chinese Knowledge Resource Integrated Database and Chinese Clinical Trial Registry were searched on 20 March 2020. RESULTS In total, 135 studies were included, involving severe acute respiratory syndrome, Middle East respiratory syndrome, coronavirus disease 2019 and other coronaviruses. Most were case reports, case series and cohort studies of poor to fair quality. In post-mortem examinations of subjects who died from infection, around half had virus identified in heart tissues in severe acute respiratory syndrome, but none in Middle East respiratory syndrome and coronavirus disease 2019. Cardiac manifestations reported include tachycardia, bradycardia, arrhythmias, and myocardial injury, secondary to both systemic infection and treatment. Cardiac injury and arrhythmias are more prevalent in coronavirus disease 2019, and elevated cardiac markers are associated with intensive care unit admission and death. In severe acute respiratory syndrome, Middle East respiratory syndrome, and coronavirus disease 2019, comorbidities such as hypertension, diabetes mellitus, and heart disease are associated with intensive care unit admission, mechanical ventilation, and mortality. There were cases of misdiagnosis due to overlapping presentations of cardiovascular diseases and coronavirus infections, leading to hospital spread and delayed management of life-threatening conditions. CONCLUSION This review highlighted the ways in which coronaviruses affect cardiovascular function and interacts with pre-existing cardiovascular diseases.
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Affiliation(s)
- Jamie SY Ho
- />School of Clinical Medicine, University of Cambridge, UK
| | - Paul A Tambyah
- />Division of Infectious Diseases, National University Hospital, Singapore
- />Department of Medicine, National University of Singapore, Singapore
| | - Andrew FW Ho
- />SingHealth Duke-NUS Emergency Medicine Academic Clinical Programme, Singapore
- />Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
- />National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
| | - Mark YY Chan
- />Department of Medicine, National University of Singapore, Singapore
- />Department of Cardiology, National University Heart Centre, Singapore
| | - Ching-Hui Sia
- />Department of Medicine, National University of Singapore, Singapore
- />Department of Cardiology, National University Heart Centre, Singapore
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Tong Y, Tang Y, Li S, Zhao F, Ying J, Qu Y, Niu X, Mu D. Cumulative evidence of relationships between multiple variants in 8q24 region and cancer incidence. Medicine (Baltimore) 2020; 99:e20716. [PMID: 32590746 PMCID: PMC7328976 DOI: 10.1097/md.0000000000020716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple independent cancer susceptibility loci at chromosome 8q24. We aimed to evaluate the associations between variants in the 8q24 region and cancer susceptibility. A comprehensive research synopsis and meta-analysis was performed to evaluate associations between 28 variants in 8q24 and risk of 7 cancers using data from 103 eligible articles totaling 146,932 cancer cases and 219,724 controls. Results: 20 variants were significantly associated with risk of prostate cancer, colorectal cancer, thyroid cancer, breast cancer, bladder cancer, stomach cancer, and glioma, including 1 variant associated with prostate cancer, colorectal cancer, and thyroid cancer. Cumulative epidemiological evidence of an association was graded as strong for DG8S737 -8 allele, rs10090154, rs7000448 in prostate cancer, rs10808556 in colorectal cancer, rs55705857 in gliomas, rs9642880 in bladder cancer, moderate for rs16901979, rs1447295, rs6983267, rs7017300, rs7837688, rs1016343, rs620861, rs10086908 associated in prostate cancer, rs10505477, rs6983267 in colorectal cancer, rs6983267 in thyroid cancer, rs13281615 in breast cancer, and rs1447295 in stomach cancer, weak for rs6983561, rs13254738, rs7008482, rs4242384 in prostate cancer. Data from ENCODE suggested that these variants with strong evidence and other correlated variants might fall within putative functional regions. Our study provides summary evidence that common variants in the 8q24 are associated with risk of multiple cancers in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the mechanisms underlying variants in the 8q24 involved in various human cancers.
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Affiliation(s)
- Yu Tong
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Ying Tang
- Department of Pediatrics
- Department of Diagnostic Ultrasound
| | - Shiping Li
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Fengyan Zhao
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Junjie Ying
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Yi Qu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Dezhi Mu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
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Asiimwe IG, Zhang EJ, Osanlou R, Krause A, Dillon C, Suarez-Kurtz G, Zhang H, Perini JA, Renta JY, Duconge J, Cavallari LH, Marcatto LR, Beasly MT, Perera MA, Limdi NA, Santos PCJL, Kimmel SE, Lubitz SA, Scott SA, Kawai VK, Jorgensen AL, Pirmohamed M. Genetic Factors Influencing Warfarin Dose in Black-African Patients: A Systematic Review and Meta-Analysis. Clin Pharmacol Ther 2020; 107:1420-1433. [PMID: 31869433 PMCID: PMC7217737 DOI: 10.1002/cpt.1755] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022]
Abstract
Warfarin is the most commonly used oral anticoagulant in sub-Saharan Africa. Dosing is challenging due to a narrow therapeutic index and high interindividual variability in dose requirements. To evaluate the genetic factors affecting warfarin dosing in black-Africans, we performed a meta-analysis of 48 studies (2,336 patients). Significant predictors for CYP2C9 and stable dose included rs1799853 (CYP2C9*2), rs1057910 (CYP2C9*3), rs28371686 (CYP2C9*5), rs9332131 (CYP2C9*6), and rs28371685 (CYP2C9*11) reducing dose by 6.8, 12.5, 13.4, 8.1, and 5.3 mg/week, respectively. VKORC1 variants rs9923231 (-1639G>A), rs9934438 (1173C>T), rs2359612 (2255C>T), rs8050894 (1542G>C), and rs2884737 (497T>G) decreased dose by 18.1, 21.6, 17.3, 11.7, and 19.6 mg/week, respectively, whereas rs7294 (3730G>A) increased dose by 6.9 mg/week. Finally, rs12777823 (CYP2C gene cluster) was associated with a dose reduction of 12.7 mg/week. Few studies were conducted in Africa, and patient numbers were small, highlighting the need for further work in black-Africans to evaluate genetic factors determining warfarin response.
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Affiliation(s)
- Innocent G. Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Eunice J. Zhang
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Rostam Osanlou
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa
| | - Chrisly Dillon
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | | | - Honghong Zhang
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Jamila A Perini
- Research Laboratory of Pharmaceutical Sciences, West Zone State University-UEZO, Rio de Janeiro, Brazil
| | - Jessicca Y. Renta
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Jorge Duconge
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Larisa H Cavallari
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Leiliane R. Marcatto
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Mark T. Beasly
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Paulo C. J. L. Santos
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-Unifesp, São Paulo, Brazil
| | - Stephen E. Kimmel
- Perelman School of Medicine at the University of Pennsylvania, Department of Biostatistics, Epidemiology, and Informatics
| | - Steven A. Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea L. Jorgensen
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
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Fullana MA, Tortella-Feliu M, Fernández de la Cruz L, Chamorro J, Pérez-Vigil A, Ioannidis JPA, Solanes A, Guardiola M, Almodóvar C, Miranda-Olivos R, Ramella-Cravaro V, Vilar A, Reichenberg A, Mataix-Cols D, Vieta E, Fusar-Poli P, Fatjó-Vilas M, Radua J. Risk and protective factors for anxiety and obsessive-compulsive disorders: an umbrella review of systematic reviews and meta-analyses. Psychol Med 2020; 50:1300-1315. [PMID: 31172897 DOI: 10.1017/s0033291719001247] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND A multitude of risk/protective factors for anxiety and obsessive-compulsive disorders have been proposed. We conducted an umbrella review to summarize the evidence of the associations between risk/protective factors and each of the following disorders: specific phobia, social anxiety disorder, generalized anxiety disorder, panic disorder, and obsessive-compulsive disorder, and to assess the strength of this evidence whilst controlling for several biases. METHODS Publication databases were searched for systematic reviews and meta-analyses examining associations between potential risk/protective factors and each of the disorders investigated. The evidence of the association between each factor and disorder was graded into convincing, highly suggestive, suggestive, weak, or non-significant according to a standardized classification based on: number of cases (>1000), random-effects p-values, 95% prediction intervals, confidence interval of the largest study, heterogeneity between studies, study effects, and excess of significance. RESULTS Nineteen systematic reviews and meta-analyses were included, corresponding to 216 individual studies covering 427 potential risk/protective factors. Only one factor association (early physical trauma as a risk factor for social anxiety disorder, OR 2.59, 95% CI 2.17-3.1) met all the criteria for convincing evidence. When excluding the requirement for more than 1000 cases, five factor associations met the other criteria for convincing evidence and 22 met the remaining criteria for highly suggestive evidence. CONCLUSIONS Although the amount and quality of the evidence for most risk/protective factors for anxiety and obsessive-compulsive disorders is limited, a number of factors significantly increase the risk for these disorders, may have potential prognostic ability and inform prevention.
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Affiliation(s)
- Miquel A Fullana
- Institute of Neurosciences, Hospital Clinic, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Miquel Tortella-Feliu
- University Research Institute on Health Sciences (IUNICS), University of the Balearic Islands, Mallorca, Spain
| | - Lorena Fernández de la Cruz
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - Jacobo Chamorro
- Anxiety Unit, Institute of Neuropsychiatry and Addictions, Parc de Salut Mar, Barcelona, Spain
| | - Ana Pérez-Vigil
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - John P A Ioannidis
- Department of Medicine, Stanford Prevention Research Center, Stanford, CA, USA
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
- Meta-Research Innovation Center at Stanford, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, USA
| | - Aleix Solanes
- FIDMAG Germanes Hospitalaries, CIBERSAM, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | | | | | | | - Valentina Ramella-Cravaro
- Early Psychosis: Interventions and Clinical-detection Lab (EPIC), Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Mental Health, Florence Public Health Center, Florence, Italy
| | - Ana Vilar
- Institut de Neuropsiquiatria i Addiccions, CSMIJ Sant Martí-La Mina, Parc de Salut Mar, Barcelona, Spain
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Abraham Reichenberg
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Mataix-Cols
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
- Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Eduard Vieta
- Barcelona Bipolar Disorders Program, Institute of Neurosciences, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, CIBERSAM, Barcelona, Spain
| | - Paolo Fusar-Poli
- Early Psychosis: Interventions and Clinical-detection Lab (EPIC), Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Mar Fatjó-Vilas
- FIDMAG Germanes Hospitalaries, CIBERSAM, Barcelona, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Joaquim Radua
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
- FIDMAG Germanes Hospitalaries, CIBERSAM, Barcelona, Spain
- Early Psychosis: Interventions and Clinical-detection Lab (EPIC), Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, CIBERSAM, Barcelona, Spain
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Yang T, Li X, Farrington SM, Dunlop MG, Campbell H, Timofeeva M, Theodoratou E. A Systematic Analysis of Interactions between Environmental Risk Factors and Genetic Variation in Susceptibility to Colorectal Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1145-1153. [PMID: 32238408 PMCID: PMC7311198 DOI: 10.1158/1055-9965.epi-19-1328] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The underlying etiology of colorectal cancer includes both genetic variation and environmental exposures. The main aim of this study was to search for interaction effects between well-established environmental risk factors and published common genetic variants exerting main effects on colorectal cancer risk. METHODS We used a two-phase approach: (i) discovery phase (2,652 incident colorectal cancer cases and 10,608 controls from UK Biobank) and (ii) validation phase (1,656 cases and 2,497 controls from the Study of Colorectal Cancer in Scotland). Interactions with nominal P < 0.05 in phase I were taken forward for validation in phase II. Furthermore, we constructed a weighted genetic risk score (GRS) of colorectal cancer risk for each individual and studied interactions between the GRS and the environmental risk factors. RESULTS Seventy of the 1,500 tested interactions were nominally significant in phase I. After testing these 70 interactions in phase II, an interaction between rs11903757 (2q32.3) and body mass index (BMI) was nominally significant (P = 0.02) with the same direction of effect. The rs11903757*BMI interaction was also significant (ratio of ORs = 1.26; 95% confidence interval, 1.10-1.44; P interaction = 6.03 × 10-4; P heterogeneity = 0.63) in a meta-analysis combining results from both phases. No interactions were significant in phase II after accounting for multiple testing. No interactions involving the GRS were found with statistical significance. CONCLUSIONS Limited evidence of gene-environment interactions in colorectal cancer risk was observed. There are potential modifications of the rs11903757 effect by BMI on colorectal cancer risk. IMPACT Our findings might contribute to identifying subpopulations with different susceptibility to the effect of BMI on colorectal cancer risk.
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Affiliation(s)
- Tian Yang
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom.
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom.
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, United Kingdom
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Chen B, Li HZ. Association of IL-6 174G/C (rs1800795) and 572C/G (rs1800796) polymorphisms with risk of osteoporosis: a meta-analysis. BMC Musculoskelet Disord 2020; 21:330. [PMID: 32466786 PMCID: PMC7257244 DOI: 10.1186/s12891-020-03334-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/07/2020] [Indexed: 01/21/2023] Open
Abstract
Background Several studies have been performed to investigate association between IL-6 174G/C (rs1800795) and 572C/G (rs1800796) gene polymorphisms and osteoporosis predisposition. However, the results were conflicting. So, we performed a meta-analysis designed to provide more reliable results for the association between IL-6 gene polymorphisms and osteoporosis. Methods Studies were searched using PubMed, EMBASE, the Cochrane Library and Wanfang electronic databases. The odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the association between IL-6 174G/C (rs1800795) and 572C/G (rs1800796) gene polymorphisms and osteoporosis risk. The false-positive report probabilities (FPRP) test and the venice criteria were used to assess the credibility of statistically significant associations. Results A total of 9 studies with 1891 osteoporosis patients and 2027 healthy controls were included in current meta-analysis. Overall, The IL-6 174G/C (rs1800795) gene polymorphism was insignificantly associated with osteoporosis vulnerability. For IL-6 572C/G (rs1800796), statistically significant elevated osteoporosis vulnerability was found in IL-6 572C/G additive model (OR = 2.25, 95% CI: 1.55–3.26), dominant model (OR = 1.42, 95% CI: 0.78–2.56) and recessive model (OR = 1.96, 95% CI: 1.36–2.83). However, the IL-6 572C/G C allele was found to be associated with reduced susceptibility to osteoporosis (OR = 0.76, 95% CI: 0.56–1.04). When excluding studies that did not conform to HWE, the results did not change significantly. Further, when we evaluated the credibility of the positive results of the current meta-analysis, we identified less credible positive results in IL-6 572C/G recessive and additive model. Conclusion In conclusion, IL-6 572C/G GG genotype may be associated with increased risk of osteoporosis.
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Affiliation(s)
- Bin Chen
- Changzhi Medical College, No. 161, Jiefangdong Street, Changzhi, 046000, Shanxi Province, China
| | - Hong-Zhuo Li
- Department of Orthopaedics, Heping Hospital Affiliated to Changzhi Medical College, Yanannan Road, Changzhi, 046000, Shanxi, China.
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Cargnin S, Galli U, Lee KS, Shin JI, Terrazzino S. Gene polymorphisms and risk of acute renal graft rejection: A field synopsis of meta-analyses and genome-wide association studies. Transplant Rev (Orlando) 2020; 34:100548. [PMID: 32498977 DOI: 10.1016/j.trre.2020.100548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
Abstract
In the present study we systematically re-analyzed results from meta-analyses and genome-wide association studies (GWASs) to assess the credibility of genetic associations with acute rejection risk in renal transplantation. A comprehensive literature search was performed on PubMed, Web of Knowledge, Cochrane library, and Open Grey up to July 2019. Methodological quality of systematic meta-analyses was assessed by the AMSTAR tool. Credibility of genetic associations was assessed by employing the Venice criteria and two Bayesian statistical approaches, the false positive report probability (FPRP) and the Bayesian false discovery probability (BFDP). Sixteen systematic meta-analyses, with a moderate-high quality score (median AMSTAR score: 9, range: 6-11) and 1 GWAS fulfilled the inclusion criteria. Overall, our systematic re-analysis has identified 9 polymorphic variants in 8 genes (ACE, CD28, CTLA-4, CYP3A5, IFNG, TNF-α, PTPRO and CCDC67) as potential risk factors for acute renal graft rejection. At the pre-specified prior probability of 0.001, the 2 SNPs identified by the GWAS (rs7976329 and rs10765602) showed no evidence of noteworthiness under FPRP or BFDP, indicating the possibility of false-positive associations. After applying the Venice criteria in combination with FPRP and BFDP to results from systematic meta-analyses, TT/AT vs AA of IFNG +874 T/A reached moderate epidemiological credibility, while weak evidence of association was found for all the other genetic comparisons. Well-designed GWASs and large replication studies with updated meta-analyses are still needed to identify reliable genetic predictors of acute renal graft rejection.
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Affiliation(s)
- Sarah Cargnin
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics (CRIFF), University of Piemonte Orientale, Largo Donegani 2, Novara 28100, Italy.
| | - Ubaldina Galli
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy.
| | - Kwang Seob Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Salvatore Terrazzino
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics (CRIFF), University of Piemonte Orientale, Largo Donegani 2, Novara 28100, Italy.
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Abstract
BACKGROUND Postoperative nausea and vomiting (PONV) is the most frequent side effect following anaesthesia. Predisposition to developing PONV is multifactorial with patient risk factors and anaesthetic techniques both being contributory. However, there is also a genetic susceptibility to PONV, and several studies have aimed to identify polymorphisms contributing to a genetic PONV risk. OBJECTIVE We summarised previous published studies investigating genetic contribution to PONV risk. DESIGN Systematic review without meta-analysis. DATA SOURCE We searched MEDLINE until June 2019. ELIGIBILITY CRITERIA Articles were chosen for review when PONV and polymorphisms were included. Exclusion criteria were reviews/meta-analysis/comments, articles not in the English language, nonappropriate content (e.g. PONV not as primary aim of the study, study investigated opioid-induced nausea) or if articles were pharmacogenetic studies addressing treatment of PONV. RESULTS A total of 59 studies were screened and 14 articles were reviewed including one genome-wide association study (GWAS). Seven studies were performed in East Asians, and seven in Caucasians. Seventeen polymorphisms have been positively associated with PONV in at least one study. Allele frequency of the investigated polymorphisms differs widely between the ethnicities. Furthermore, the anaesthesia regimen and the postoperative time point at which the association with PONV was reported were quite different. Only two polymorphisms, the CHRM3 rs2165870 and the KCNB2 rs349358 (both first associated with PONV in a GWAS), have been significantly associated with PONV incidence in Caucasians in independent studies. CONCLUSION There is a genetic susceptibility to the development of PONV. Two single nucleotide polymorphisms (SNPs), the CHRM3 rs2165870 and the KCNB2 rs349358 SNP, seem to have a major influence on PONV incidence, at least in Caucasians. Both SNPs were primarily identified in a GWAS and this association may lead to a better understanding of the disease aetiology. Further high-quality studies are needed to reveal more insights in genetic PONV susceptibility, particularly so in non-Caucasian ethnicities.
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Environmental factors, serum biomarkers and risk of atrial fibrillation: an exposure-wide umbrella review of meta-analyses. Eur J Epidemiol 2020; 35:223-239. [PMID: 32180061 DOI: 10.1007/s10654-020-00618-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 02/24/2020] [Indexed: 01/05/2023]
Abstract
Atrial fibrillation (AF) is the most common cardiac arrhythmia. We designed an umbrella review to systematically assess the epidemiological credibility of the associations of non-genetic factors with risk of AF. We searched PubMed and EMBASE from inception to December 31, 2018 to identify systematic reviews and meta-analyses of observational studies for the association of non-genetic factors with risk of AF. For each meta-analysis, we used the random-effects model, and we estimated the 95% confidence and prediction intervals. We also assessed between-study heterogeneity, small-study effects and excess significance bias. We identified 34 eligible papers that examined 51 associations of 42 unique non-genetic factors with risk of AF. Eighteen associations remained statistically significant at P value < 1 × 10-6. Thirty-one associations presented large or very large between-study heterogeneity. Eight associations presented evidence for small-study effects and 13 associations had evidence for excess significance bias. Ten associations, i.e. corrected QT interval, alcohol consumption (highest vs. lowest category, per 1 drink/day increase), body mass index (> 30 units vs. < 30 units, per 5 units increase), waist circumference, body weight, type 2 diabetes mellitus, and smoking (ever vs. never, per 10 cigarettes/day increase) were supported by convincing or highly suggestive evidence in meta-analyses of prospective cohort studies. Type 2 diabetes mellitus, markers of adiposity, alcohol consumption, smoking, and corrected QT interval constitute credible risk factors of AF. Our proposed grading may guide the design of future studies, including Mendelian randomization studies, to assess whether these associations are causal.
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Miao LF, Ye XH, He XF. Individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on breast cancer risk: A meta-analysis and re-analysis of systematic meta-analyses. PLoS One 2020; 15:e0216147. [PMID: 32155154 PMCID: PMC7064184 DOI: 10.1371/journal.pone.0216147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/15/2019] [Indexed: 12/14/2022] Open
Abstract
Background Fourteen previous meta-analyses have been published to analyze the polymorphisms of individual GSTM1 present/null, GSTT1 present/null, and GSTP1 IIe105Val on breast cancer (BC) risk. However, their meta-analyses did not explore the combined effects of the three genetic polymorphisms on BC risk. In addition, they did not evaluate the credibility of statistically significant associations. Furthermore, a multitude of new articles have been published on these themes, and therefore a meta-analysis and re-analysis of systematic previous meta-analyses were performed to further explore these issues. Objectives To determine the association between the individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on breast cancer risk. Methods Crude odds ratios (ORs) and their 95% confidence intervals (CIs) were applied to estimate the association between individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on BC risk. To evaluate the credibility of statistically significant associations in the current and previous meta-analyses, we applied the the false-positive report probabilities (FPRP) test and the Venice criteria. Results 101 publications were selected to evaluate the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms on BC risk. Overall, statistically significant elevated BC risk was found in any individual and combined effects of GSTM1 present/null, GSTT1 present/null, and GSTP1 IIe105Val polymorphisms. However, when we restricted studies only involving with high-quality, matching, HWE, and genotyping examination performed blindly or with quality control, significantly increased BC risk was only found in overall population for GSTM1 null genotype, among all populations, Caucasians, and postmenopausal women for the combined effects of GSTM1 and GSTT1 polymorphisms, and in overall analysis for the combined effects of GSTM1, GSTT1, and GSTP1 IIe105Val polymorphisms. Further, less-credible positive results were identified when we evaluated the credibility of positive results of the current and previous meta-analyses. Conclusions This meta-analysis indicates that the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms may be not associated with increased BC risk.
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Affiliation(s)
- Li-Feng Miao
- Department of Galactophore, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
| | - Xiang-Hua Ye
- Department of Radiotherapy, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi, China
- * E-mail:
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Li G, Song Q, Jiang Y, Cai A, Tang Y, Tang N, Yi D, Zhang R, Wei Z, Liu D, Chen J, Zhang Y, Liu L, Wu Y, Zhang B, Yi D. Cumulative Evidence for Associations between Genetic Variants and Risk of Esophageal Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:838-849. [PMID: 31969372 DOI: 10.1158/1055-9965.epi-19-1281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/06/2019] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND A large number of studies have been conducted to investigate associations between genetic variants and esophageal cancer risk in the past several decades. However, findings from these studies have been generally inconsistent. We aimed to provide a summary of the current understanding of the genetic architecture of esophageal cancer susceptibility. METHODS We performed a comprehensive field synopsis and meta-analysis to evaluate associations between 95 variants in 70 genes or loci and esophageal cancer risk using data from 304 eligible publications, including 104,904 cases and 159,797 controls, through screening a total of 21,328 citations. We graded levels of cumulative epidemiologic evidence of a significant association with esophageal cancer using the Venice criteria and false-positive report probability tests. We constructed functional annotations for these variants using data from the Encyclopedia of DNA Elements Project and other databases. RESULTS Thirty variants were nominally significantly associated with esophageal cancer risk. Cumulative epidemiologic evidence of a significant association with overall esophageal cancer, esophageal squamous cell carcinoma, or esophageal adenocarcinoma was strong for 13 variants in or near 13 genes (ADH1B, BARX1, CDKN1A, CHEK2, CLPTM1L, CRTC1, CYP1A1, EGF, LTA, MIR34BC, PLCE1, PTEN, and PTGS2). Bioinformatics analysis suggested that these variants and others correlated with them might fall in putative functional regions. CONCLUSIONS Our study summarizes the current literature on the genetic architecture of esophageal cancer susceptibility and identifies several potential polymorphisms that could be involved in esophageal cancer susceptibility. IMPACT These findings provide direction for future studies to identify new genetic factors for esophageal cancer.
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Affiliation(s)
- Gaoming Li
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Qiuyue Song
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yuxing Jiang
- Medical Department, The 305 Hospital of Chinese People's Liberation Army, Beijing, China
| | - Angsong Cai
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yong Tang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Ning Tang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Dali Yi
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Rui Zhang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Zeliang Wei
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Dingxin Liu
- Department of Statistics, Chongqing Technology and Business University, Chongqing, China
| | - Jia Chen
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yanqi Zhang
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Ling Liu
- Department of Health Statistics, Army Medical University, Chongqing, China
| | - Yazhou Wu
- Department of Health Statistics, Army Medical University, Chongqing, China.
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China.
| | - Dong Yi
- Department of Health Statistics, Army Medical University, Chongqing, China.
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75
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Liu G, Tian J, Zuo C, Li Y, Fu K, Chen H. Epidemiological evidence for associations between variants in microRNA or biosynthesis genes and lung cancer risk. Cancer Med 2020; 9:1937-1950. [PMID: 31910330 PMCID: PMC7050065 DOI: 10.1002/cam4.2645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/29/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
In the past decade, the studies involving single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) with lung cancer (LC) risk have been performed, however, these results are inconsistent, and a systematic research synopsis has not been performed yet. Therefore, we attempted to perform comprehensive meta‐analyses to assess the relationships between SNPs in miRNAs or biosynthesis genes and LC risk and further evaluate the epidemiological credibility of these significant associations. We used PubMed, Medline, and Web of Science to search for relevant articles published before 30 May 2019 that assessed relationships between SNPs in miRNAs or biosynthesis genes and LC risk. The cumulative epidemiological evidence of statistical relationships was further assessed combining Venice Criteria and a false‐positive report probability test. Based on 20 publications with 15 969 cases and 17 174 controls, we found that six variants in miRNAs or biosynthesis genes that proved significant associations with LC risk, whereas five proved no association. Subgroup analyses by ethnicity and genetic models were performed, suggesting that four associations were rated as demonstrating strong evidence of relationship with LC risk, including miRNA‐146a rs2910164 in all populations under dominant model and in Asians under dominant and recessive models, and AGO1 rs595961 in Asians under allelic model. Three associations were graded as moderate, and seven associations were rated as weak. This study presents the relationships between SNPs in miRNAs or biosynthesis genes and LC risk, subsequently demonstrates the credibility of these significant associations, and highlights the role in the pathogenesis of LC.
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Affiliation(s)
- Guanchu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Tian
- Department of Thoracic Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Chunjian Zuo
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yufu Li
- Department of Cardiothoracic Surgery, The People's Hospital of Chongqing Tongnan, Chongqing, China
| | - Kui Fu
- Department of Cardiothoracic Surgery, Traditional Chinese Medicine Hospital, Dianjiang, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Duggal P, Ladd-Acosta C, Ray D, Beaty TH. The Evolving Field of Genetic Epidemiology: From Familial Aggregation to Genomic Sequencing. Am J Epidemiol 2019; 188:2069-2077. [PMID: 31509181 PMCID: PMC7036654 DOI: 10.1093/aje/kwz193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
The field of genetic epidemiology is relatively young and brings together genetics, epidemiology, and biostatistics to identify and implement the best study designs and statistical analyses for identifying genes controlling risk for complex and heterogeneous diseases (i.e., those where genes and environmental risk factors both contribute to etiology). The field has moved quickly over the past 40 years partly because the technology of genotyping and sequencing has forced it to adapt while adhering to the fundamental principles of genetics. In the last two decades, the available tools for genetic epidemiology have expanded from a genetic focus (considering 1 gene at a time) to a genomic focus (considering the entire genome), and now they must further expand to integrate information from other “-omics” (e.g., epigenomics, transcriptomics as measured by RNA expression) at both the individual and the population levels. Additionally, we can now also evaluate gene and environment interactions across populations to better understand exposure and the heterogeneity in disease risk. The future challenges facing genetic epidemiology are considerable both in scale and techniques, but the importance of the field will not diminish because by design it ties scientific goals with public health applications.
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Affiliation(s)
- Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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van den Berg FF, Kempeneers MA, van Santvoort HC, Zwinderman AH, Issa Y, Boermeester MA. Meta-analysis and field synopsis of genetic variants associated with the risk and severity of acute pancreatitis. BJS Open 2019; 4:3-15. [PMID: 32011822 PMCID: PMC6996643 DOI: 10.1002/bjs5.50231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Background Genetic risk factors can provide insight into susceptibility for acute pancreatitis (AP) and disease progression towards (infected) necrotizing pancreatitis and persistent organ failure. The aim of the study was to undertake a systematic review of the genetic evidence for AP. Methods Online databases (MEDLINE, Embase, BIOSIS, Web of Science, Cochrane Library) were searched to 8 February 2018. Studies that reported on genetic associations with AP susceptibility, severity and/or complications were eligible for inclusion. Meta‐analyses were performed of variants that were reported by at least two data sources. Venice criteria and Bayesian false‐discovery probability were applied to assess credibility. Results Ninety‐six studies reporting on 181 variants in 79 genes were identified. In agreement with previous meta‐analyses, credible associations were established for SPINK1 (odds ratio (OR) 2·87, 95 per cent c.i. 1·89 to 4·34), IL1B (OR 1·23, 1·06 to 1·42) and IL6 (OR 1·64, 1·15 to 2·32) and disease risk. In addition, two novel credible single‐nucleotide polymorphisms were identified in Asian populations: ALDH2 (OR 0·48, 0·36 to 0·64) and IL18 (OR 1·47, 1·18 to 1·82). Associations of variants in TNF, GSTP1 and CXCL8 genes with disease severity were identified, but were of low credibility. Conclusion Genetic risk factors in genes related to trypsin activation and innate immunity appear to be associated with susceptibility to and severity of AP.
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Affiliation(s)
- F F van den Berg
- Department of Surgery, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - M A Kempeneers
- Department of Surgery, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - H C van Santvoort
- Department of Surgery, St Antonius Hospital, Nieuwegein, the Netherlands.,Department of Surgery, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - A H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Y Issa
- Department of Surgery, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - M A Boermeester
- Department of Surgery, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
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Tortella-Feliu M, Fullana MA, Pérez-Vigil A, Torres X, Chamorro J, Littarelli SA, Solanes A, Ramella-Cravaro V, Vilar A, González-Parra JA, Andero R, Reichenberg A, Mataix-Cols D, Vieta E, Fusar-Poli P, Ioannidis JP, Stein MB, Radua J, Fernández de la Cruz L. Risk factors for posttraumatic stress disorder: An umbrella review of systematic reviews and meta-analyses. Neurosci Biobehav Rev 2019; 107:154-165. [DOI: 10.1016/j.neubiorev.2019.09.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
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Mamidi TKK, Wu J, Hicks C. Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers. JOURNAL OF ONCOLOGY 2019; 2019:4168784. [PMID: 31814827 PMCID: PMC6878815 DOI: 10.1155/2019/4168784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/19/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND A majority of prostate cancers (PCas) are indolent and cause no harm even without treatment. However, a significant proportion of patients with PCa have aggressive tumors that progress rapidly to metastatic disease and are often lethal. PCa develops through somatic mutagenesis, but emerging evidence suggests that germline genetic variation can markedly contribute to tumorigenesis. However, the causal association between genetic susceptibility and tumorigenesis has not been well characterized. The objective of this study was to map the germline and somatic mutation interaction landscape in indolent and aggressive tumors and to discover signatures of mutated genes associated with each type and distinguishing the two types of PCa. MATERIALS AND METHODS We integrated germline mutation information from genome-wide association studies (GWAS) with somatic mutation information from The Cancer Genome Atlas (TCGA) using gene expression data from TCGA on indolent and aggressive PCas as the intermediate phenotypes. Germline and somatic mutated genes associated with each type of PCa were functionally characterized using network and pathway analysis. RESULTS We discovered gene signatures containing germline and somatic mutations associated with each type and distinguishing the two types of PCa. We discovered multiple gene regulatory networks and signaling pathways enriched with germline and somatic mutations including axon guidance, RAR, WINT, MSP-RON, STAT3, PI3K, TR/RxR, and molecular mechanisms of cancer, NF-kB, prostate cancer, GP6, androgen, and VEGF signaling pathways for indolent PCa and MSP-RON, axon guidance, RAR, adipogenesis, and molecular mechanisms of cancer and NF-kB signaling pathways for aggressive PCa. CONCLUSION The investigation revealed germline and somatic mutated genes associated with indolent and aggressive PCas and distinguishing the two types of PCa. The study revealed multiple gene regulatory networks and signaling pathways dysregulated by germline and somatic alterations. Integrative analysis combining germline and somatic mutations is a powerful approach to mapping germline and somatic mutation interaction landscape.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Informatics Institute, University of Alabama at Birmingham, School of Medicine, 1720 2nd Avenue South, Birmingham, AL 35294-3412, USA
| | - Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
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Cui H, Tang M, Zhang M, Liu S, Chen S, Zeng Z, Shen Z, Song B, Lu J, Jia H, Gu D, Zhang B. Variants in the PSCA gene associated with risk of cancer and nonneoplastic diseases: systematic research synopsis, meta-analysis and epidemiological evidence. Carcinogenesis 2019; 40:70-83. [PMID: 30407486 DOI: 10.1093/carcin/bgy151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
Variants in the prostate stem cell antigen (PSCA) gene have been linked with risk of multiple cancers and other diseases. But results have been inconclusive and no systematic research synopsis has been available. We did a comprehensive meta-analysis to investigate associations between variants in this gene and risk of nine cancers and four nonneoplastic diseases based on data from 55 publications including 81 961 cases and 442 932 controls. We graded levels of cumulative epidemiological evidence of a significant association using the Venice criteria and false-positive report probability tests. We performed functional annotation for these variants using data from the Encyclopedia of DNA Elements Project and other public databases. We found that six variants were nominally significantly associated with an increased or reduced risk of three cancers and three nonneoplastic diseases (P < 0.05). Cumulative evidence of an association was graded as strong for rs2294008 [odds ratio (OR) = 1.32, P = 5.1 × 10-33], rs2976392 (OR = 1.29, P = 1.8 × 10-8), rs9297976 (OR = 0.75, P = 1.4 × 10-7), rs2976391 (OR = 1.38, P = 6.1 × 10-5) and rs138377917 (OR = 0.53, P = 0.008) with gastric cancer, rs2294008 with bladder cancer (OR = 1.15, P = 8.0 × 10-19), gastritis (OR = 1.35, P = 1.2 × 10-5), duodenal ulcer (OR = 0.68, P = 2.4 × 10-57) and gastric ulcer (OR = 0.88, P = 1.7 × 10-7). Data from the Encyclopedia of DNA Elements Project and other databases showed that these variants and other variants correlated with them might fall in putative functional regions. In conclusion, this study provides summary evidence that variants in the PSCA gene are associated with risk of gastric and bladder cancer, gastritis, as well as duodenal and gastric ulcer and highlights the significant role of this gene in the pathogenesis of these diseases.
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Affiliation(s)
- Huijie Cui
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Min Zhang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Shanshan Liu
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Siyu Chen
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Ziqian Zeng
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zhuozhi Shen
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Bin Song
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Jiachun Lu
- Department of Epidemiology, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Hong Jia
- Department of Epidemiology, School of Public Health, Southwest Medical University, Luzhou, China
| | - Dongqing Gu
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Southwest School of Medicine and First Affiliated Hospital, Army Medical University, Chongqing, China.,Department of Epidemiology, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China.,Department of Epidemiology, School of Public Health, Southwest Medical University, Luzhou, China.,Department of Epidemiology, School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Yang T, Li X, Montazeri Z, Little J, Farrington SM, Ioannidis JP, Dunlop MG, Campbell H, Timofeeva M, Theodoratou E. Gene-environment interactions and colorectal cancer risk: An umbrella review of systematic reviews and meta-analyses of observational studies. Int J Cancer 2019; 145:2315-2329. [PMID: 30536881 PMCID: PMC6767750 DOI: 10.1002/ijc.32057] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
The cause of colorectal cancer (CRC) is multifactorial, involving both genetic variants and environmental risk factors. We systematically searched the MEDLINE, EMBASE, China National Knowledge Infrastructure (CNKI) and Wanfang databases from inception to December 2016, to identify systematic reviews and meta-analyses of observational studies that investigated gene-environment (G×E) interactions in CRC risk. Then, we critically evaluated the cumulative evidence for the G×E interactions using an extension of the Human Genome Epidemiology Network's Venice criteria. Overall, 15 articles reporting systematic reviews of observational studies on 89 G×E interactions, 20 articles reporting meta-analyses of candidate gene- or single-nucleotide polymorphism-based studies on 521 G×E interactions, and 8 articles reporting 33 genome-wide G×E interaction analyses were identified. On the basis of prior and observed scores, only the interaction between rs6983267 (8q24) and aspirin use was found to have a moderate overall credibility score as well as main genetic and environmental effects. Though 5 other interactions were also found to have moderate evidence, these interaction effects were tenuous due to the lack of main genetic effects and/or environmental effects. We did not find highly convincing evidence for any interactions, but several associations were found to have moderate strength of evidence. Our conclusions are based on application of the Venice criteria which were designed to provide a conservative assessment of G×E interactions and thus do not include an evaluation of biological plausibility of an observed joint effect.
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Affiliation(s)
- Tian Yang
- Centre for Global Health Research, Usher Institute of Population Health Sciences and InformaticsThe University of EdinburghEdinburghUnited Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and InformaticsThe University of EdinburghEdinburghUnited Kingdom
| | - Zahra Montazeri
- School of Epidemiology and Public HealthUniversity of OttawaOttawaOntarioCanada
| | - Julian Little
- School of Epidemiology and Public HealthUniversity of OttawaOttawaOntarioCanada
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - John P.A. Ioannidis
- Stanford Prevention Research Center, Departments of Medicine, of Health Research and Policy, and of Biomedical Data Science, Stanford University School of Medicine, and Department of StatisticsStanford University School of Humanities and SciencesStanfordCaliforniaUSA
- Meta‐Research Innovation Center at Stanford (METRICS)Stanford UniversityStanfordCaliforniaUSA
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and InformaticsThe University of EdinburghEdinburghUnited Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and InformaticsThe University of EdinburghEdinburghUnited Kingdom
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular MedicineWestern General Hospital, The University of EdinburghEdinburghUnited Kingdom
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82
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Wu J, Mamidi TKK, Zhang L, Hicks C. Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11111692. [PMID: 31683572 PMCID: PMC6896043 DOI: 10.3390/cancers11111692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/07/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer. Emerging evidenced suggests that both genetics and epigenetic factors play a role in the pathogenesis of TNBC. However, oncogenic interactions and cooperation between genomic and epigenomic variation have not been characterized. The objective of this study was to deconvolute the genomic and epigenomic interaction landscape in TNBC using an integrative genomics approach, which integrates information on germline, somatic, epigenomic and gene expression variation. We hypothesized that TNBC originates from a complex interplay between genomic (both germline and somatic variation) and epigenomic variation. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect entire molecular networks and signaling pathways which, in turn, drive TNBC. We addressed these hypotheses using germline variation from genome-wide association studies and somatic, epigenomic and gene expression variation from The Cancer Genome Atlas (TCGA). The investigation revealed signatures of functionally related genes containing germline, somatic and epigenetic variations. DNA methylation had an effect on gene expression. Network and pathway analysis revealed molecule networks and signaling pathways enriched for germline, somatic and epigenomic variation, among them: Role of BRCA1 in DNA Damage Response, Hereditary Breast Cancer Signaling, Molecular Mechanisms of Cancer, Estrogen-Dependent Breast Cancer, p53, MYC Mediated Apoptosis, and PTEN Signaling pathways. The investigation revealed that integrative genomics is a powerful approach for deconvoluting the genomic-epigenomic interaction landscape in TNBC. Further studies are needed to understand the biological mechanisms underlying oncogenic interactions between genomic and epigenomic factors in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Graduate Biomedical Sciences, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35233, USA.
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, 513 Edwards Hall, Clemson, SC 29634, USA.
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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83
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Li Y, Wang L, Zhou J, Ye J. Multi-task learning based survival analysis for multi-source block-wise missing data. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2019.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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84
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Belbasis L, Bellou V, Evangelou E, Tzoulaki I. Environmental factors and risk of multiple sclerosis: Findings from meta-analyses and Mendelian randomization studies. Mult Scler 2019; 26:397-404. [DOI: 10.1177/1352458519872664] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Multiple sclerosis (MS) is a chronic demyelinating disease that is associated with permanent disability and low quality of life. Development of MS is attributed to a combination of genetic and environmental factors. Genome-wide association studies revealed more than 200 variants that are associated with risk of MS. An umbrella review showed that smoking, history of infectious mononucleosis, and anti-Epstein–Barr virus nuclear antigen (anti-EBNA) immunoglobulin G (IgG) seropositivity are credible risk factors of MS. In the present narrative review, we updated our published umbrella review, showing that body mass index in childhood and adolescence and anti-viral capsid antigen (anti-VCA) IgG seropositivity are additional credible risk factors of MS. In addition, we discuss the findings from Mendelian randomization studies, which present evidence for a potential causal role of serum vitamin D and adulthood body mass index on risk of MS. Finally, we discuss the potential limitations of meta-analyses, umbrella reviews, and Mendelian randomization studies in the search for risk factors of MS.
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Affiliation(s)
- Lazaros Belbasis
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Vanesa Bellou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece/Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece/Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
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85
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Roos E, Soer E, Klompmaker S, Meijer L, Besselink M, Giovannetti E, Heger M, Kazemier G, Klümpen H, Takkenberg R, Wilmink H, Würdinger T, Dijk F, van Gulik T, Verheij J, van de Vijver M. Crossing borders: A systematic review with quantitative analysis of genetic mutations of carcinomas of the biliary tract. Crit Rev Oncol Hematol 2019; 140:8-16. [PMID: 31158800 DOI: 10.1016/j.critrevonc.2019.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/21/2019] [Indexed: 12/11/2022] Open
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86
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Townsend R, Khalil A, Premakumar Y, Allotey J, Snell KIE, Chan C, Chappell LC, Hooper R, Green M, Mol BW, Thilaganathan B, Thangaratinam S. Prediction of pre-eclampsia: review of reviews. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 54:16-27. [PMID: 30267475 DOI: 10.1002/uog.20117] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 08/23/2018] [Accepted: 08/26/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE Primary studies and systematic reviews provide estimates of varying accuracy for different factors in the prediction of pre-eclampsia. The aim of this study was to review published systematic reviews to collate evidence on the ability of available tests to predict pre-eclampsia, to identify high-value avenues for future research and to minimize future research waste in this field. METHODS MEDLINE, EMBASE and The Cochrane Library including DARE (Database of Abstracts of Reviews of Effects) databases, from database inception to March 2017, and bibliographies of relevant articles were searched, without language restrictions, for systematic reviews and meta-analyses on the prediction of pre-eclampsia. The quality of the included reviews was assessed using the AMSTAR tool and a modified version of the QUIPS tool. We evaluated the comprehensiveness of search, sample size, tests and outcomes evaluated, data synthesis methods, predictive ability estimates, risk of bias related to the population studied, measurement of predictors and outcomes, study attrition and adjustment for confounding. RESULTS From 2444 citations identified, 126 reviews were included, reporting on over 90 predictors and 52 prediction models for pre-eclampsia. Around a third (n = 37 (29.4%)) of all reviews investigated solely biochemical markers for predicting pre-eclampsia, 31 (24.6%) investigated genetic associations with pre-eclampsia, 46 (36.5%) reported on clinical characteristics, four (3.2%) evaluated only ultrasound markers and six (4.8%) studied a combination of tests; two (1.6%) additional reviews evaluated primary studies investigating any screening test for pre-eclampsia. Reviews included between two and 265 primary studies, including up to 25 356 688 women in the largest review. Only approximately half (n = 67 (53.2%)) of the reviews assessed the quality of the included studies. There was a high risk of bias in many of the included reviews, particularly in relation to population representativeness and study attrition. Over 80% (n = 106 (84.1%)) summarized the findings using meta-analysis. Thirty-two (25.4%) studies lacked a formal statement on funding. The predictors with the best test performance were body mass index (BMI) > 35 kg/m2 , with a specificity of 92% (95% CI, 89-95%) and a sensitivity of 21% (95% CI, 12-31%); BMI > 25 kg/m2 , with a specificity of 73% (95% CI, 64-83%) and a sensitivity of 47% (95% CI, 33-61%); first-trimester uterine artery pulsatility index or resistance index > 90th centile (specificity 93% (95% CI, 90-96%) and sensitivity 26% (95% CI, 23-31%)); placental growth factor (specificity 89% (95% CI, 89-89%) and sensitivity 65% (95% CI, 63-67%)); and placental protein 13 (specificity 88% (95% CI, 87-89%) and sensitivity 37% (95% CI, 33-41%)). No single marker had a test performance suitable for routine clinical use. Models combining markers showed promise, but none had undergone external validation. CONCLUSIONS This review of reviews calls into question the need for further aggregate meta-analysis in this area given the large number of published reviews subject to the common limitations of primary predictive studies. Prospective, well-designed studies of predictive markers, preferably randomized intervention studies, and combined through individual-patient data meta-analysis are needed to develop and validate new prediction models to facilitate the prediction of pre-eclampsia and minimize further research waste in this field. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R Townsend
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
| | - A Khalil
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
| | - Y Premakumar
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
| | - J Allotey
- Women's Health Research Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - K I E Snell
- Research Institute for Primary Care and Health Sciences, Keele University, Keele, UK
| | - C Chan
- Pragmatic Clinical Trials Unit, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - L C Chappell
- Department of Women and Children's Health, King's College London, London, UK
| | - R Hooper
- Pragmatic Clinical Trials Unit, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - M Green
- Action on Pre-eclampsia (APEC) Charity, Worcestershire, UK
| | - B W Mol
- Department of Obstetrics and Gynaecology, School of Medicine, Monash University, Melbourne, Australia
| | - B Thilaganathan
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
| | - S Thangaratinam
- Women's Health Research Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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Yuanyuan G, Xue Y, Yachao L, Xiao F, Xu C. Association between IL-18 -607 C/A Polymorphism and the Risk of Prostate Cancer: A Meta-Analysis of Case-Control Studies. Asian Pac J Cancer Prev 2019; 20:1595-1602. [PMID: 31244277 PMCID: PMC7021598 DOI: 10.31557/apjcp.2019.20.6.1595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Indexed: 11/25/2022] Open
Abstract
Background: Accumulating evidence shows that cytokines play an important role in the proliferation of prostate
cancer. This research is trying to determine that IL-18 -607 C/A polymorphism confers susceptibility to prostate cancer.
Methods: Meta-analysis was used to collect data. The relevant studies were identified through a comprehensive search
from PubMed, Excerpta Medica Database (EMBASE), Web of Science, and Chinese Biomedical Literature Database
(CBM) to obtain related studies published up to December 6, 2017. The association between interleukin (IL)-18 -607 C/A
polymorphism and prostate cancer risk was assessed by odds ratios (ORs) together with their 95% confidence intervals
(CIs). Results: Nine case-control studies from 6 articles were eventually identified. In the overall population, there is a
significant association between IL-18 -607 C/A polymorphism and prostate cancer risk in recessive (CC versus CA/AA:
OR = 0.20, 95% CI = 0.15-0.27, P = 0.000) or dominant (CC/CA versus AA:OR = 0.42, 95% CI = 0.30–0.57, P = 0.000)
models. In the sub-group analysis according to ethnicity, for Asians, IL-18 -607 C/A polymorphism was significantly
associated with prostate cancer in allele contrast (C versus. A: OR=0.82, 95%CI=0.70-0.97, P=0.019), homozygote
(CC versus. AA: OR=0.68, 95%CI=0.50-0.92, P=0.013), recessive (CC versus. CA/AA: OR=0.19, 95%CI=0.13-0.27,
P=0.000), and dominant (CC/CA versus. AA: OR=0.37, 95%CI=0.28-0.48, P=0.000) models, for Caucasians, IL-18
-607 C/A polymorphism was significantly associated with prostate cancer risk in allele contrast (C versus. A: OR=1.27,
95%CI=1.02-1.58, P=0.033), homozygote (CC versus. AA: OR=1.86, 95%CI=1.19-2.91, P=0.007) and recessive (CC
versus. CA/AA: OR=0.25, 95%CI=0.19-0.33, P=0.000) models. Conclusion: This meta-analysis has shown that IL-18
-607 C/A polymorphism contributes to a decreased risk of prostate cancer risk in the Asian population but an increased
risk in the Caucasian population.
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Affiliation(s)
- Gao Yuanyuan
- Department of Clinical Laboratory, First Affiliated Hospital of Soochow University, Suzhou, China. ,Central Laboratory of Pediatric Research Institute, Affiliated Children's Hospital of Soochow University, Suzhou, China
| | - Yu Xue
- Department of Clinical Laboratory, First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Li Yachao
- Central Laboratory of Pediatric Research Institute, Affiliated Children's Hospital of Soochow University, Suzhou, China
| | - Feng Xiao
- Central Laboratory of Pediatric Research Institute, Affiliated Children's Hospital of Soochow University, Suzhou, China
| | - Chen Xu
- Department of Clinical Laboratory, First Affiliated Hospital of Soochow University, Suzhou, China.
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Chidambaran V, Gang Y, Pilipenko V, Ashton M, Ding L. Systematic Review and Meta-Analysis of Genetic Risk of Developing Chronic Postsurgical Pain. THE JOURNAL OF PAIN 2019; 21:2-24. [PMID: 31129315 DOI: 10.1016/j.jpain.2019.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/06/2019] [Accepted: 05/20/2019] [Indexed: 02/08/2023]
Abstract
Chronic postsurgical pain (CPSP) is a significant detriment to postsurgical recovery and a risk factor for prolonged opioid use. Emerging evidence suggests the estimated heritability for chronic pain is 45% and that genetic factors partially explain individual susceptibility to CPSP. The aim of this study was to systematically review, assess quality, and summarize the studies in humans that have investigated genetic factors associated with CPSP. We also conducted a meta-analysis to derive a single effect size for evaluable genetic associations with CPSP. Our comprehensive literature search included review of 21 full-text articles evaluating variants of 69 genes for association with CPSP. We found significant gene variant associations reported for variants/haplotypes of 26 genes involved in neurotransmission, pain signaling, immune responses and neuroactive ligand-receptor interaction, with CPSP. Six variants of 5 genes (COMT: rs4680 and rs6269, OPRM1: rs1799971, GCH1: rs3783641, KCNS1: rs734784 and TNFA: rs1800629), were evaluated by more than one study and were included in the meta-analysis. At rs734784 (A>G) of KCNS1, presence of G allele marginally increased risk of CPSP (Additive genetic model; Odds ratio: 1.511; 95% CI 1-2.284; P value: .050), while the other variants did not withstand meta-analyses criteria. Our findings demonstrate the role of genetic factors with different functions in CPSP, and also emphasize that single genetic factors have small effect sizes in explaining complex conditions like CPSP. Heterogeneity in surgical cohorts, population structure, and outcome definitions, as well as small number of available studies evaluating same variants, limit the meta-analysis. There is a need for large-scale, homogenous, replication studies to validate candidate genes, and understand the underlying biological networks underpinning CPSP. PERSPECTIVE: Our systematic review comprehensively describes 21 studies evaluating genetic association with CPSP, and limitations thereof. A meta-analysis of 6 variants (5 genes) found marginally increased risk for CPSP associated with rs734784 A>G of the potassium voltage-gated channel gene (KCNS1). Understanding genetic predisposition for CPSP will enable prediction and personalized management.
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Affiliation(s)
- Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio.
| | - Yang Gang
- Division of Biostatistics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Valentina Pilipenko
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Maria Ashton
- Department of Anesthesiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lili Ding
- Division of Biostatistics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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90
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Wu J, Mamidi TKK, Zhang L, Hicks C. Integrating Germline and Somatic Mutation Information for the Discovery of Biomarkers in Triple-Negative Breast Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16061055. [PMID: 30909550 PMCID: PMC6466377 DOI: 10.3390/ijerph16061055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022]
Abstract
Recent advances in high-throughput genotyping and the recent surge of next generation sequencing of the cancer genomes have enabled discovery of germline mutations associated with an increased risk of developing breast cancer and acquired somatic mutations driving the disease. Emerging evidence indicates that germline mutations may interact with somatic mutations to drive carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic alterations in triple-negative breast cancer (TNBC) have not been characterized. The objective of this study was to investigate the possible oncogenic interactions and cooperation between genes containing germline and somatic mutations in TNBC. Our working hypothesis was that genes containing germline mutations associated with an increased risk developing breast cancer also harbor somatic mutations acquired during tumorigenesis, and that these genes are functionally related. We further hypothesized that TNBC originates from a complex interplay among and between genes containing germline and somatic mutations, and that these complex array of interacting genetic factors affect entire molecular networks and biological pathways which in turn drive the disease. We tested this hypothesis by integrating germline mutation information from genome-wide association studies (GWAS) with somatic mutation information on TNBC from The Cancer Genome Atlas (TCGA) using gene expression data from 110 patients with TNBC and 113 controls. We discovered a signature of 237 functionally related genes containing both germline and somatic mutations. We discovered molecular networks and biological pathways enriched for germline and somatic mutations. The top pathways included the hereditary breast cancer and role of BRCA1 in DNA damage response signaling pathways. In conclusion, this is the first large-scale and comprehensive analysis delineating possible oncogenic interactions and cooperation among and between genes containing germline and somatic mutations in TNBC. Genetic and somatic mutations, along with the genes discovered in this study, will require experimental functional validation in different ethnic populations. Functionally validated genetic and somatic variants will have important implications for the development of novel precision prevention strategies and discovery of prognostic markers in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Lu Zhang
- Louisiana Tumor Registry, Louisiana State University Health Sciences Center, School of Public Health, 2020 Gravier Street, New Orleans, LA 70112, USA.
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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91
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Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer. Prostate Cancer 2019; 2019:4047680. [PMID: 31007957 PMCID: PMC6441536 DOI: 10.1155/2019/4047680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/29/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.
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92
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Mamidi TKK, Wu J, Hicks C. Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer. BMC Cancer 2019; 19:229. [PMID: 30871495 PMCID: PMC6417124 DOI: 10.1186/s12885-019-5440-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the United States. High-throughput genotyping has enabled discovery of germline genetic susceptibility variants (herein referred to as germline mutations) associated with an increased risk of developing PCa. However, germline mutation information has not been leveraged and integrated with information on acquired somatic mutations to link genetic susceptibility to tumorigenesis. The objective of this exploratory study was to address this knowledge gap. METHODS Germline mutations and associated gene information were derived from genome-wide association studies (GWAS) reports. Somatic mutation and gene expression data were derived from 495 tumors and 52 normal control samples obtained from The Cancer Genome Atlas (TCGA). We integrated germline and somatic mutation information using gene expression data. We performed enrichment analysis to discover molecular networks and biological pathways enriched for germline and somatic mutations. RESULTS We discovered a signature of 124 genes containing both germline and somatic mutations. Enrichment analysis revealed molecular networks and biological pathways enriched for germline and somatic mutations, including, the PDGF, P53, MYC, IGF-1, PTEN and Androgen receptor signaling pathways. CONCLUSION Integrative genomic analysis links genetic susceptibility to tumorigenesis in PCa and establishes putative functional bridges between the germline and somatic variation, and the biological pathways they control.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA
| | - Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA.
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93
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Mandal RK, Wahid M, Jawed A, Dar SA, Panda AK, Akhter N, Lohani M, Mishra BN, Khan S, Areeshi MY, Haque S. A trial sequential meta-analysis of IFN-γ +874 A>T (rs2430561) gene polymorphism and extrapulmonary tuberculosis risk. Microb Pathog 2019; 130:1-9. [PMID: 30825502 DOI: 10.1016/j.micpath.2018.12.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 12/29/2022]
Abstract
Interferon-γ (IFN-γ) plays a crucial role in immunological responses against Mycobacterium tuberculosis (M.tb) infection. The polymorphism at +874 A > T (rs2430561) influences the levels of IFN-γ, which may further influence the susceptibility to extrapulmonary tuberculosis (EPTB). This polymorphism has been investigated with respect to EPTB occurrence in different populations and provided contradictory and conflicting results. This study was performed to meta-statistically analyze the data and draw a more accurate conclusion regarding the association of IFN-γ +874 A > T gene polymorphism and EPTB susceptibility. A quantitative synthesis was executed for the pertinent studies retrieved from online web-databases viz. Google Scholar, PubMed/Medline and EMBASE. The pooled odds ratios (ORs) and confidence intervals (95% CIs) were estimated for all the genetic models by meta-analysis. A total of eight studies were retrieved which included 762 confirmed EPTB cases and 1341 controls. The meta-analysis results revealed reduced association of EPTB in allelic contrast (T vs. A: p = 0.001; OR = 0.668, 95% CI = 0.524 to 0.850), homozygous (TT vs. AA: p = 0.017; OR = 0.450, 95% CI = 0.234 to 0.868), heterozygous (AT vs. AA: p = 0.004; OR = 0.574, 95% CI = 0.395 to 0.835), dominant (TT + AT vs. AA: p = 0.003; OR = 0.536, 95% CI = 0.354 to 0.810) and recessive (TT vs. AA + AT: p = 0.039; OR = 0.662, 95% CI = 0.448 to 0.980) genetic models. Furthermore, re-sampling statistics also revealed reduced risk of EPTB in overall population and Asian subgroup. This meta-analysis concluded that IFN-γ +874 A > T gene polymorphism is meaningfully related with the reduced EPTB risk in overall and Asian population, and further necessitates larger studies to be conducted on this topic in other races.
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Affiliation(s)
- Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Aditya K Panda
- Centre for Life Sciences, Central University of Jharkhand, Ranchi, 835205, Jharkhand, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, 65431, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - B N Mishra
- Department of Biotechnology, Institute of Engineering & Technology, Lucknow, 226021, Uttar Pradesh, India
| | - Saif Khan
- Department of Basic Sciences, College of Dentistry, University of Ha'il, Hail, 2440, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.
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94
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Tian J, Liu C, Liu G, Zuo C, Chen H. Cumulative evidence for association between genetic polymorphisms and esophageal cancer susceptibility: A review with evidence from meta-analysis and genome-wide association studies. Cancer Med 2019; 8:1289-1305. [PMID: 30793520 PMCID: PMC6434199 DOI: 10.1002/cam4.1972] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/27/2018] [Accepted: 12/21/2018] [Indexed: 12/16/2022] Open
Abstract
An increasing number of publications had reported the association between single‐nucleotide polymorphisms (SNPs) and esophageal cancer (EC) risk in the past decades. Results from these publications were controversial. We used PubMed, Medline, and Web of Science to identify meta‐analysis articles published before 30 July 2018, that summarize a comprehensive investigation for cumulative evidence of genetic polymorphisms of EC and its subtype risk. Two methods, Venice criteria and false‐positive report probability (FPRP) tests, were used to assess cumulative evidence of significant associations. At last, 107 meta‐analyses were considered to be in conformity with the inclusion criteria, yielding 51 variants associated with EC or esophageal squamous cell carcinoma (ESCC). Thirty‐eight variants were considered to be nominally significant associated with risk of EC or ESCC, whereas the rest showed non‐association. In additional, five variants on five genes were rated as strong cumulative epidemiological evidence for a nominally significant association with EC and ESCC risk, including CYP1A1 rs1048943, EGF rs444903, HOTAIR rs920778, MMP2 rs243865, and PLCE1 rs2274223, 10 variants were rated as moderate, and 18 variants were rated as weak. Additionally, 17 SNPs were verified noteworthy in six genomewide association studies (GWAS) using FPRP methods. Collectively, this review offered a comprehensively referenced information with cumulative evidence of associations between genetic polymorphisms and EC and ESCC risk.
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Affiliation(s)
- Jie Tian
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Caiyang Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanchu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjian Zuo
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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95
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Miao LF, Wang XY, Ye XH, Cui MS, He XF. Combined effects of GSTM1 and GSTT1 polymorphisms on breast cancer risk: A MOOSE-compliant meta-analysis and false-positive report probabilities test. Medicine (Baltimore) 2019; 98:e14333. [PMID: 30732156 PMCID: PMC6380837 DOI: 10.1097/md.0000000000014333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many molecular epidemiology studies have reported an association between the combined effects of glutathione S-transferase M1 (GSTM1) and glutathione S-transferase T1 (GSTT1) polymorphisms on breast cancer risk. However, the results have been controversial.A meta-analysis was performed to clarify this issue.Meta-analysis of observational studies in epidemiology guidelines was used. Pooled the crude odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model or fixed-effects model. Several subgroup analyses were conducted by ethnicity, source of control, matching, and menopausal status. In addition, we also performed sensitivity analysis and publication bias. Moreover, a false-positive report probability (FPRP) test was applied to assess positive results.A significantly increased breast cancer risk was observed in overall population (GSTM1 null/GSTT1 present [- +] vs GSTM1 present/GSTT1 present [+ +]: OR = 1.19, 95% CI: 1.03-1.36, GSTM1 null/GSTT1 null [- -] vs + +: OR = 1.63, 95% CI: 1.29-2.06, (- +) + GSTM1 present/GSTT1 null (+ -) vs + +: OR = 1.17, 95% CI: 1.05-1.31, (- +) + (+ -) + (- -) vs + +: OR = 1.27, 95% CI: 1.12-1.44, and - - vs (- +) + (+ -) + (+ +): OR = 1.39, 95% CI: 1.17-1.66) and several subgroup analyses, such as Caucasians, Indians, postmenopausal women, and so on. However, positive results were only considered noteworthy in overall population (- - vs + +: FPRP = 0.150 and (- +) + (+ -) + (- -) vs + +: FPRP = 0.162). Moreover, no significant association was observed when we used the trim and fill method to adjust the pooled data from all populations. Further, none of positive results of sensitivity analysis were considered noteworthy (FPRP >0.2).These positive findings should be interpreted with caution and indicate that an increased breast cancer risk may most likely result from false-positive results, rather than from true associations or biological factors on the combined effects of GSTM1 and GSTT1. Future studies should be based on sample sizes well-powered and attention needs to be paid to study design to further identify this issue.
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Affiliation(s)
- Li-Feng Miao
- Department of Galactophore, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi
| | - Xiao-Yan Wang
- Department of Epidemiology and Health Statistics, Basic Medical College of Zhejiang University of Traditional Chinese Medicine
| | - Xiang-Hua Ye
- Department of Radiotherapy, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Meng-Shen Cui
- Department of Galactophore, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi
| | - Xiao-Feng He
- Department of Science and Education, Affiliated Heping Hospital, Changzhi Medical College, Shanxi, Changzhi, PR China
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96
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Bayesian statistical methods in genetic association studies: Empirical examination of statistically non-significant Genome Wide Association Study (GWAS) meta-analyses in cancers: A systematic review. Gene 2019; 685:170-178. [DOI: 10.1016/j.gene.2018.10.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/19/2018] [Indexed: 01/22/2023]
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97
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A trial sequential meta-analysis of TNF-α -308G>A (rs800629) gene polymorphism and susceptibility to colorectal cancer. Biosci Rep 2019. [PMID: 30509964 DOI: 10.1042/bsr20181052.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Tumor necrosis factor-α (TNF-α), secreted by the activated macrophages, may participate in the onset and progression of colorectal cancer (CRC). The association of TNF-α -308 G>A (rs1800629) single-nucleotide polymorphism (SNP) with CRC risk has been investigated by many studies but the results are inconclusive. A trial sequential meta-analysis was performed for precise estimation of the relationship between TNF-α -308 G>A gene polymorphism with CRC risk. METHODS Medline (PubMed), EMBASE (Excerpta-Medica) and Google Scholar were mined for relevant articles. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the significance of association. RESULTS The pooled analysis indicated no risk associated with TNF-α -308 G>A SNP and overall CRC risk in five genetic comparison models, i.e. allelic (A vs. G: P = 0.524; OR = 1.074, 95% CI = 0.863-1.335), homozygous (AA vs. GG: P = 0.489; OR = 1.227, 95% CI = 0.688-2.188), heterozygous (AG vs. GG: P = 0.811; OR = 1.024, 95% CI = 0.843-1.244), dominant (AA+AG vs. GG: P = 0.630; OR = 1.055, 95% CI = 0.849-1.311) and recessive (AA vs. AG+GG: P = 0.549; OR = 1.181, 95% CI = 0.686-2.033). Subgroup analysis revealed that TNF-α -308 G>A SNP is associated with reduced risk of CRC in Asian ethnicity. The study showed no publication bias. CONCLUSIONS No association of TNF-α -308 G>A SNP with overall CRC risk was found. This SNP is likely to be protective against CRC in Asian population when compared with Caucasian population. Larger prospective-epidemiological studies are warranted to elucidate the roles of TNF-α -308 G>A SNP in the etiology of CRC and to endorse the present findings.
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98
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Lu H, Wen D, Wang X, Gan L, Du J, Sun J, Zeng L, Jiang J, Zhang A. Host genetic variants in sepsis risk: a field synopsis and meta-analysis. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:26. [PMID: 30683156 PMCID: PMC6347778 DOI: 10.1186/s13054-019-2313-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/07/2019] [Indexed: 01/07/2023]
Abstract
Background Published data revealed that host genetic variants have a substantial influence on sepsis susceptibility. However, the results have been inconsistent. We aimed to systematically review the published studies and quantitatively evaluate the effects of these variants on the risk of sepsis. Methods We searched the PubMed, EMBASE, Medline, Web of Knowledge, and HuGE databases to identify studies that investigated the associations between genetic variants and sepsis risk. Then, we conducted meta-analyses of the associations for genetic variants with at least three study populations and applied the Venice criteria to assess the association result credibility. Results A literature search identified 349 eligible articles that investigated 405 variants of 172 distinct genes. We performed 204 primary and 185 subgroup meta-analyses for 76 variants of 44 genes. The results showed that 29 variants of 23 genes were significantly associated with the risk of sepsis, including 8 variants of pattern recognition receptors (PRRs), 14 variants of cytokines, one variant of an immune-related gene and 6 variants of other genes. Furthermore, the cumulative epidemiological evidence of a significant association between each variant and the risk of sepsis was classified as strong or moderate for 18 variants. For the 329 variants with fewer than three study populations, 63 variants of 48 genes have been reported to be significantly associated with the risk of sepsis in a systematic review. Conclusion We identified several genetic variants that could influence the susceptibility to sepsis by systematic review and meta-analysis. This study provides a comprehensive overview of the genetic architecture of variants involved in sepsis susceptibility and novel insight that may affect personalized targeted treatment in the future clinical management of sepsis. Electronic supplementary material The online version of this article (10.1186/s13054-019-2313-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongxiang Lu
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Dalin Wen
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Xu Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.,Department of Emergency Surgery, The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310009, Zhejiang, China
| | - Lebin Gan
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.,Department of Emergency Surgery, The Affiliated Hospital, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Juan Du
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Jianhui Sun
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Jianxin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.
| | - Anqiang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.
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99
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A trial sequential meta-analysis of TNF-α -308G>A (rs800629) gene polymorphism and susceptibility to colorectal cancer. Biosci Rep 2019; 39:BSR20181052. [PMID: 30509964 PMCID: PMC6331670 DOI: 10.1042/bsr20181052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/29/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Purpose: Tumor necrosis factor-α (TNF-α), secreted by the activated macrophages, may participate in the onset and progression of colorectal cancer (CRC). The association of TNF-α –308 G>A (rs1800629) single-nucleotide polymorphism (SNP) with CRC risk has been investigated by many studies but the results are inconclusive. A trial sequential meta-analysis was performed for precise estimation of the relationship between TNF-α –308 G>A gene polymorphism with CRC risk. Methods: Medline (PubMed), EMBASE (Excerpta-Medica) and Google Scholar were mined for relevant articles. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the significance of association. Results: The pooled analysis indicated no risk associated with TNF-α –308 G>A SNP and overall CRC risk in five genetic comparison models, i.e. allelic (A vs. G: P = 0.524; OR = 1.074, 95% CI = 0.863–1.335), homozygous (AA vs. GG: P = 0.489; OR = 1.227, 95% CI = 0.688–2.188), heterozygous (AG vs. GG: P = 0.811; OR = 1.024, 95% CI = 0.843–1.244), dominant (AA+AG vs. GG: P = 0.630; OR = 1.055, 95% CI = 0.849–1.311) and recessive (AA vs. AG+GG: P = 0.549; OR = 1.181, 95% CI = 0.686–2.033). Subgroup analysis revealed that TNF-α –308 G>A SNP is associated with reduced risk of CRC in Asian ethnicity. The study showed no publication bias. Conclusions: No association of TNF-α –308 G>A SNP with overall CRC risk was found. This SNP is likely to be protective against CRC in Asian population when compared with Caucasian population. Larger prospective-epidemiological studies are warranted to elucidate the roles of TNF-α –308 G>A SNP in the etiology of CRC and to endorse the present findings.
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100
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Mandal RK, Khan MA, Hussain A, Dar SA, Aloufi S, Jawed A, Wahid M, Panda AK, Lohani M, Akhter N, Khan S, Mishra BN, Haque S. Association of MBL2 gene polymorphisms with pulmonary tuberculosis susceptibility: trial sequence meta-analysis as evidence. Infect Drug Resist 2019; 12:185-210. [PMID: 30666135 PMCID: PMC6333159 DOI: 10.2147/idr.s188980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Mannose-binding lectin (MBL) or mannose-binding protein (MBP), encoded by MBL2 gene and secreted by the liver, activates complement system through lectin pathway in innate immunity against the host’s infection. Conflictingly, a number of MBL2 variants, rs1800450 (A>B), rs1800451 (A>C), rs5030737 (A>D), rs7096206 (Y>X), rs11003125 (H>L), and rs7095891 (P>Q) allele, have been found to be associated with compromised serum levels and pulmonary tuberculosis (PTB) susceptibility. The present meta-analysis study was performed to evaluate the potential association of these MBL2 gene variants with PTB susceptibility. Materials and methods A quantitative synthesis was performed on PubMed (Medline), EMBASE, and Google Scholar web database searches. A meta-analysis was performed to calculate the pooled odds ratios and 95% CIs for all the genetic models. Results A total of 14 eligible studies were included to analyze their pooled data for associations between alleles, genotypes, and minor allele carriers. The statistical analysis revealed the significant reduced PTB risk with homozygous variant genotype of rs1800451 polymorphism (CC vs AA: P=0.043; OR =0.828, 95% CI =0.689–0.994). Contrary to this, the variant allele of rs5030737 polymorphism showed association with increased PTB risk (D vs A: P=0.026; OR =1.563, 95% CI =1.054–2.317). However, the other genetic models of rs1800450 (A>B), rs7096206 (Y>X), and rs11003125 (H>L) MBL2 gene polymorphisms did not divulge any association with PTB susceptibility. Conclusion The current meta-analysis concludes that rs1800451 (A>C) and rs5030737 (A>D) polymorphisms of MBL2 gene play a significant role in PTB susceptibility. Further, well-designed epidemiological studies with larger sample size including consideration of environmental factors are warranted for the future.
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Affiliation(s)
- Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia,
| | - Munawwar Ali Khan
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia,
| | - Sultan Aloufi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia,
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia,
| | - Aditya K Panda
- Centre for Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al Baha University, Al Baha, Saudi Arabia
| | - Saif Khan
- Department of Basic Sciences, College of Dentistry, University of Ha'il, Ha'il, Saudi Arabia
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow, Uttar Pradesh, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia,
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