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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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O'Brien TR, Yang HI, Groover S, Jeng WJ. Genetic Factors That Affect Spontaneous Clearance of Hepatitis C or B Virus, Response to Treatment, and Disease Progression. Gastroenterology 2019; 156:400-417. [PMID: 30287169 DOI: 10.1053/j.gastro.2018.09.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) and hepatitis B virus (HBV) infections can lead to cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Over the past decade, studies of individuals infected with these viruses have established genetic associations with the probability of developing a chronic infection, risk of disease progression, and likelihood of treatment response. We review genetic and genomic methods that have been used to study risk of HBV and HCV infection and patient outcomes. For example, genome-wide association studies have linked a region containing the interferon lambda genes to spontaneous and treatment-induced clearance of HCV. We review the genetic variants associated with HCV and HBV infection, and how these variants affect specific expression or activities of their products. Further studies of these variants could provide insights into risk factors for and mechanisms of chronic infection and disease progression, as well as new strategies for treatment.
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Affiliation(s)
- Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sarah Groover
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma
| | - Wen-Juei Jeng
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Unit, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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103
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Preston SH, Choi D, Elo IT, Stokes A. Effect of Diabetes on Life Expectancy in the United States by Race and Ethnicity. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2018; 64:139-151. [PMID: 31178981 PMCID: PMC6550350 DOI: 10.1080/19485565.2018.1542291] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We investigated the impact of diabetes on US life expectancy by sex and race/ethnicity using a prospective cohort study design. Cohorts were drawn from 1997-2009 waves of the National Health Interview Survey and linked to death records through December 31, 2011. We combined data on the prevalence of diabetes among decedents with estimates of the hazard ratios of individuals diagnosed with diabetes to calculate population attributable fractions (PAFs) by age, sex, and race/ethnicity at ages 30 and above. These estimates were then applied to deaths in the official US life table for 2010 to estimate effects of diabetes on life expectancy. Diabetes was responsible for a reduction of 0.83 years of life expectancy for men at age 30 and 0.89 years for 30-year-old women. The impact was greatest among Black women at 1.05 years. Estimates based on traditional demographic and actuarial methods using the frequency with which a disease appears as an underlying cause of death on death certificates produced a reduction in life expectancy at age 30 of only 0.33 years. We conclude that diabetes is substantially reducing US longevity and that its effect is seriously underestimated when using data on underlying causes of death.
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Affiliation(s)
- Samuel H. Preston
- Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Daesung Choi
- Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Irma T. Elo
- Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Stokes
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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Wen J, Xu Q, Yuan Y. Single nucleotide polymorphisms and sporadic colorectal cancer susceptibility: a field synopsis and meta-analysis. Cancer Cell Int 2018; 18:155. [PMID: 30337837 PMCID: PMC6180373 DOI: 10.1186/s12935-018-0656-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 01/05/2023] Open
Abstract
Background Although mounting non-hereditary colorectal cancer (NHCRC) associated single nucleotide polymorphisms (SNPs) have been observed, no field synopsis and meta-analysis has been conducted through systematically assessing cumulative evidence, during the past 5 years. Methods We retrieved the database via the PubMed, Web of Science and Embase gateways to identify publications concerning the associations between SNPs and risk of NHCRC, up to May 1st, 2017. To assess the finding credibility, cumulative evidence was graded based on the Venice criteria. Meta-analysis was also performed for three subgroups including ethnicity (Asian vs Caucasian), primary cancer site (colon vs rectum) and TNM stage (I II vs III IV). Then, we arranged those high quality SNPs into different regions according to their locations on genes to evaluate their functional roles on CRC development. Results 5114 publications were collected and 1001 of them met our inclusion criteria, which totally included 1788 SNPs in 793 genes or distinct chromosomal loci. Totally, we performed 359 primary and subgroup meta-analyses for 160 SNPs in 96 distinct genes. By utilizing the Venice criteria, we identified 15 high quality SNPs with 25 high credibility significant associations. Furthermore, we artificially divided the high quality SNPs into different groups, based on their SNP loci (exon region, intron region, promoter region, downstream region, non-coding region and intergenic region). Conclusion We have identified 15 high quality SNPs which may act as promising genetic biomarkers for clinical NHCRC susceptibility screening and explored their functional roles on the NHCRC development based on their locations on genes.
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Affiliation(s)
- Jing Wen
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Qian Xu
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
| | - Yuan Yuan
- 1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001 Liaoning China.,2Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001 China.,3Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001 China
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105
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Cumulative evidence for relationships between multiple variants of HNF1B and the risk of prostate and endometrial cancers. BMC MEDICAL GENETICS 2018; 19:128. [PMID: 30053805 PMCID: PMC6062884 DOI: 10.1186/s12881-018-0640-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
Background To provide a synopsis of the current understanding of the association between variants of HNF1B and cancer susceptibility, we conducted a comprehensive research synopsis and meta-analysis to evaluate associations between HNF1B variants and prostate and endometrial cancers. Results Eighteen studies totaling 34,937 patients and 55,969 controls were eligible for this meta-analysis. Four variants showed a significant association with the risk of individual cancer. Strong significant associations were found between rs4430796 A and the risk of both prostate cancer (OR = 1.247, p = 2.21 × 10− 77) and endometrial cancer (OR = 1.217, p = 8.98 × 10− 16); the AA, AG genotypes also showed strong significant associations with the risk of prostate cancer (OR1 = 1.517, p = 4.46 × 10− 22; OR2 = 1.180, p = 0.002). There was a strong significant association between rs7501939 G and the risk of prostate cancer (OR = 1.201, p = 9.31 × 10− 31). Strong significant association was found between rs11649743 G (OR = 1.138, p = 1.08 × 10− 12), rs3760511 C (OR = 1.214, p = 1.57 × 10− 19) and the prostate cancer risk;the GG, AG genotypes of rs11649743 also showed strong significant associations with the risk of prostate cancer (OR1 = 1.496, p = 3.32 × 10− 6; OR2 = 1.276, p = 7.82 × 10− 6). All the cumulative epidemiological evidence of associations was graded as strong. Conclusions Our study summarizes the evidence and helps to reveal that common variants of HNF1B are associated with risk of prostate and endometrial cancer.
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106
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Roush D, Rhen T. Developmental plasticity in reptiles: Critical evaluation of the evidence for genetic and maternal effects on temperature‐dependent sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2018; 329:287-297. [DOI: 10.1002/jez.2194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/21/2018] [Accepted: 05/30/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Danielle Roush
- Department of Biology, University of North Dakota Grand Forks North Dakota
| | - Turk Rhen
- Department of Biology, University of North Dakota Grand Forks North Dakota
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107
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Giannakou K, Evangelou E, Papatheodorou SI. Genetic and non-genetic risk factors for pre-eclampsia: umbrella review of systematic reviews and meta-analyses of observational studies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:720-730. [PMID: 29143991 DOI: 10.1002/uog.18959] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/09/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To summarize evidence from the literature on genetic and non-genetic risk factors associated with pre-eclampsia (PE), assess the presence of statistical bias in the studies and identify risk factors for which there is robust evidence supporting their association with PE. METHODS PubMed and ISI Web of Science were searched from inception to October 2016, to identify systematic reviews and meta-analyses of observational studies examining associations between genetic or non-genetic risk factors and PE. For each meta-analysis, the summary-effect size was estimated using random-effects and fixed-effects models, along with 95% CIs and the 95% prediction interval. Between-study heterogeneity was expressed using the I2 statistic, and evidence of small-study effects (large studies had significantly more conservative results than smaller studies) and evidence of excess significance bias (too many studies with statistically significant results) were estimated. RESULTS Fifty-eight eligible meta-analyses were identified, which included 1466 primary studies and provided data on 130 comparisons of risk factors associated with PE, covering a wide range of comorbid diseases, genetic factors, exposure to environmental agents and biomarkers. Sixty-five (50%) associations had nominally statistically significant findings at P < 0.05, while 16 (12%) were significant at P < 10-6 . Sixty-five (50%) associations had large or very large heterogeneity. Evidence for small-study effects and excess significance bias was found in 10 (8%) and 26 (20%) associations, respectively. The only non-genetic risk factor with convincing evidence for an association with PE was oocyte donation vs spontaneous conception, which had a summary odds ratio of 4.33 (95% CI, 3.11-6.03), was supported by 2712 cases with small heterogeneity (I2 = 26%) and 95% prediction intervals excluding the null value, and without hints of small-study effects (P for Egger's test > 0.10) or excess of significance (P > 0.05). Of the statistically significant (P < 0.05) genetic risk factors for PE, only PAI-1 4G/5G (recessive model) polymorphism was supported by strong evidence for a contribution to the pathogenesis of PE. Eleven factors (serum iron level, pregnancy-associated plasma protein-A, chronic kidney disease, polycystic ovary syndrome, mental stress, bacterial and viral infections, cigarette smoking, oocyte donation vs assisted reproductive technology, obesity vs normal weight, severe obesity vs normal weight and primiparity) presented highly suggestive evidence for an association with PE. CONCLUSIONS A large proportion of meta-analyses of genetic and non-genetic risk factors for PE have caveats that threaten their validity. Oocyte donation vs spontaneous conception and PAI-1 4G/5G polymorphism (recessive model) showed the strongest consistent evidence for an association with risk for PE. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- K Giannakou
- Cyprus International Institute for Environmental & Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - E 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
| | - S I Papatheodorou
- Cyprus International Institute for Environmental & Public Health, Cyprus University of Technology, Limassol, Cyprus
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108
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Predictive value of excision repair cross-complementing group 2 gene Lys751Gln and Asp312Asn polymorphisms in melanoma risk. Melanoma Res 2018; 28:311-318. [PMID: 29768284 DOI: 10.1097/cmr.0000000000000463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epidemiological studies have assessed the association between excision repair cross-complementing group 2 (ERCC2) Lys751Gln and Asp312Asn polymorphisms and melanoma risk with conflicting results. Relevant articles were searched from PubMed, Embase, and Web of Science with a time limit of 3 September 2016. Pooled odds ratio (OR) with 95% confidence interval (CI) was used to assess the strength of the association. We performed this meta-analysis with 12 studies including 6157 cases and 8873 controls for Lys751Gln and nine studies including 5037 cases and 7542 controls for Asp312Asn polymorphism. Overall, no significant associations were found under all the models for Lys751Gln polymorphism, and significant associations were found for Asp312Asn polymorphism for AA versus GG (OR=1.12, 95% CI=1.00-1.26) and for the recessive model (OR=1.11, 95% CI=1.00-1.24). In the stratification analyses by source of control: for Lys751Gln polymorphism, significant associations were found for CC versus AA (OR=1.19, 95% CI=1.04-1.36) and the recessive model (OR=1.15, 95% CI=1.02-1.30); for Asp312Asn polymorphism, significant associations were found for AA versus GG (OR=1.31, 95% CI=1.11-1.53) and the recessive model (OR=1.29, 95% CI=1.11-1.50). This meta-analysis suggested that both the Lys751Gln and Asp312Asn polymorphisms were risk factors for melanoma risk in population-based subgroup.
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Matana A, Popović M, Torlak V, Punda A, Barbalić M, Zemunik T. Effects of genetic variants on serum parathyroid hormone in hyperparathyroidism and end-stage renal disease patients: A systematic review and meta-analysis. Medicine (Baltimore) 2018; 97:e10834. [PMID: 29794776 PMCID: PMC6392899 DOI: 10.1097/md.0000000000010834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Parathyroid hormone (PTH) is one of the principal regulators of calcium homeostasis, crucial for normal functioning of the kidneys, bones, heart, and nervous system. Different pathologic conditions can affect serum PTH level resulting in hyperparathyroidism or hypoparathyroidism. Our study assessed the association of previously reported polymorphisms with the level of PTH (expressed in pg/mL) among individuals with different pathologic conditions affecting PTH level. METHODS We searched Web of Science, MEDLINE, and Scopus to identify relevant articles published up to July 2017. The search yielded 6967 publications of which 44 fulfilled the inclusion criteria. We conducted meta-analyses for calcium-sensing receptor gene (CaSR) rs1801725 polymorphism in patients with primary hyperparathyroidism and vitamin D receptor gene (VDR) rs1544410 polymorphism in patients with end-stage renal disease (ESRD). RESULTS None of the polymorphisms were significantly associated with PTH levels in the overall population. In subgroup analysis by ethnicity for VDR rs1544410 gene polymorphism, we found significant differences under dominant model (SMD: -0.18 [-0.32, -0.05], P < .01) and AA versus GG comparison (SMD: -0.29 [-0.52, -0.06], P < .01) in Asian patients with ESRD, while nominally significant results (P < .05) were observed for AG versus GG and AA versus GG comparisons in European individuals with ESRD. CONCLUSION Scientific evidence of genetic association of serum PTH level among individuals with different pathologic conditions remains deficient and published results provide weak evidence. Further well-conducted studies on larger sample sets designed according to evidence-based principles are warranted to assure clinically applicable findings.
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Affiliation(s)
- Antonela Matana
- Department of Medical Biology, University of Split, School of Medicine
| | - Marijana Popović
- Department of Medical Biology, University of Split, School of Medicine
| | - Vesela Torlak
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - Ante Punda
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - Maja Barbalić
- Department of Medical Biology, University of Split, School of Medicine
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine
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Genetic susceptibility to bone and soft tissue sarcomas: a field synopsis and meta-analysis. Oncotarget 2018; 9:18607-18626. [PMID: 29719630 PMCID: PMC5915097 DOI: 10.18632/oncotarget.24719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Background The genetic architecture of bone and soft tissue sarcomas susceptibility is yet to be elucidated. We aimed to comprehensively collect and meta-analyze the current knowledge on genetic susceptibility in these rare tumors. Methods We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing sarcomas through searching PubMed, The Cochrane Library, Scopus and Web of Science databases. To evaluate result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Integrative analysis of genetic and eQTL (expression quantitative trait locus) data was coupled with network and pathway analysis to explore the hypothesis that specific cell functions are involved in sarcoma predisposition. Results We retrieved 90 eligible studies comprising 47,796 subjects (cases: 14,358, 30%) and investigating 1,126 polymorphisms involving 320 distinct genes. Meta-analysis identified 55 single nucleotide polymorphisms (SNPs) significantly associated with disease risk with a high (N=9), moderate (N=38) and low (N=8) level of evidence, findings being classified as noteworthy basically only when the level of evidence was high. The estimated joint population attributable risk for three independent SNPs (rs11599754 of ZNF365/EGR2, rs231775 of CTLA4, and rs454006 of PRKCG) was 37.2%. We also identified 53 SNPs significantly associated with sarcoma risk based on single studies.Pathway analysis enabled us to propose that sarcoma predisposition might be linked especially to germline variation of genes whose products are involved in the function of the DNA repair machinery. Conclusions We built the first knowledgebase on the evidence linking DNA variation to sarcomas susceptibility, which can be used to generate mechanistic hypotheses and inform future studies in this field of oncology.
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Abstract
PURPOSE OF REVIEW Pharmacogenomics (PGx) of antipsychotic drug response is an active area of research in the past few years. We reviewed recent PGx studies with an emphasis of development of new methodologies and new research directions. RECENT FINDINGS Traditional candidate gene approach continues to generate evidence to support the associations of antipsychotic response with genes coding for drug targets such as DRD2. Genome-wide association studies have found a few novel genes that may be associated with drug efficacy and adverse events. Recent application of polygenic risk score makes it possible to combine many genetic variants to predict clinical response. Finally, epigenetic research including DNA methylation is emerging and promises new findings that potentially can be applied in clinical practice. New methodologies may advance PGx closer to clinical application. Multiple genes and epigenomic markers can be used in prediction of clinical phenotypes.
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Affiliation(s)
- Jian-Ping Zhang
- Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY, USA.
- Division of Psychiatry Research, Zucker Hillside Hospital, Northwell Health, 75-59 263rd Street, Glen Oaks, NY, 11004, USA.
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA.
| | - Anil K Malhotra
- Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY, USA.
- Division of Psychiatry Research, Zucker Hillside Hospital, Northwell Health, 75-59 263rd Street, Glen Oaks, NY, 11004, USA.
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA.
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Chandra V, Lee YM, Gupta U, Mittal B, Kim JJ, Rai R. Quantitative assessment of CD44 genetic variants and cancer susceptibility in Asians: a meta-analysis. Oncotarget 2018; 7:74286-74302. [PMID: 27521214 PMCID: PMC5342053 DOI: 10.18632/oncotarget.10951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/19/2016] [Indexed: 12/12/2022] Open
Abstract
CD44 is a well-established cancer stem cell marker playing a crucial role in tumor metastasis, recurrence and chemo-resistance. Genetic variants of CD44 have been shown to be associated with susceptibility to various cancers; however, the results are confounding. Hence, we performed a meta-analysis to clarify these associations more accurately. Overall, rs13347 (T vs. C: OR=1.30, p=<0.004, pcorr=0.032; CT vs. CC: OR=1.29, p=0.015, pcorr=0.047; TT vs. CC: OR=1.77, p=<0.000, pcorr=0.018; CT+TT vs. CC: OR=1.34, p=<0.009, pcorr=0.041) and rs187115 (GG vs. AA: OR=2.34, p=<0.000, pcorr=0.025; AG vs. AA: OR=1.59, p=<0.000, pcorr=0.038; G vs. A allele OR=1.56, p=0.000, pcorr=0.05; AG+GG vs. AA: OR=1.63, p=<0.000, pcorr=0.013) polymorphisms were found to significantly increase the cancer risk in Asians. On the other hand, rs11821102 was found to confer low risk (A vs. G: OR=0.87, p=<0.027, pcorr=0.04; AG vs. GG: OR=0.85, p=<0.017, pcorr=0.01; AG+AA vs. GG: OR=0.86, p=<0.020, pcorr=0.02). Based on our analysis, we suggest significant role of CD44 variants (rs13347, rs187115 and rs11821102) in modulating individual's cancer susceptibility in Asians. Therefore, these variants may be used as predictive genetic biomarkers for cancer predisposition in Asian populations. However, more comprehensive studies involving other cancers and/or populations, haplotypes, gene-gene and gene-environment interactions are necessary to delineate the role of these variants in conferring cancer risk.
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Affiliation(s)
- Vishal Chandra
- Department of Biosciences, Integral University, Lucknow, UP, India.,Stephenson Cancer Center (SCC), University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK, USA
| | - Yun-Mi Lee
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Usha Gupta
- Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Balraj Mittal
- Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Rajani Rai
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
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Codeine and opioid metabolism: implications and alternatives for pediatric pain management. Curr Opin Anaesthesiol 2018; 30:349-356. [PMID: 28323671 DOI: 10.1097/aco.0000000000000455] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW Use of perioperative opioids for surgical pain management of children presents clinical challenges because of concerns of serious adverse effects including life-threatening respiratory depression. This is especially true for children with history of obstructive sleep apnea. This review will explore current knowledge of clinically relevant factors and genetic polymorphisms that affect opioid metabolism and postoperative outcomes in children. RECENT FINDINGS Within the past several years, an increasing number of case reports have illustrated clinically important respiratory depression, anoxic brain injuries and even death among children receiving appropriate weight-based dosages of codeine and other opioids for analgesia at home setting particularly following tonsillectomy. Several national and international organizations have issued advisories on use of codeine in pediatrics, based on cytochrome P450 family 2 subfamily D type 6 (CYP2D6) pharmacogenetics. We have discussed the pros and cons of alternatives to codeine for pain management. SUMMARY Although routine preoperative genotyping to identify children at risk and personalized opioid use for pediatric perioperative pain management is still a distant reality, current known implications of CYP2D6 pharmacogenetics on codeine use shows that pharmacogenetics has the potential to guide anesthesia providers on perioperative opioid selection and dosing to maximize efficacy and safety.
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Yako YY, Balti EV, Matsha TE, Dzudie A, Kruger D, Sobngwi E, Agyemang C, Kengne AP. Genetic factors contributing to hypertension in African-based populations: A systematic review and meta-analysis. J Clin Hypertens (Greenwich) 2018; 20:485-495. [PMID: 29520984 PMCID: PMC8031059 DOI: 10.1111/jch.13225] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 01/09/2023]
Abstract
In a systematic review, the authors explored genetic association studies of essential hypertension in African populations. Studies reporting on the association of polymorphism(s) with hypertension in African populations were included. Appropriate studies were pooled using random effects model meta-analysis, under six potential inheritance models. In all, 46 polymorphisms in 33 genes were investigated for their association with hypertension or blood pressure levels. Meta-analysis was possible for three single nucleotide polymorphisms: rs4340, rs699, and rs5186. An association was found between rs5186, rs699, and hypertension under allele contrast and homozygous codominant models (odds ratio, 1.63 [95% confidence interval, 1.04-2.54] and 4.01 [95% confidence interval, 1.17-13.80] for rs5186, respectively; and 1.80 [95% confidence interval, 1.13-2.87] for rs699). Findings were mostly robust in sensitivity analyses. According to the systematic review, there is currently insufficient evidence on the specific polymorphisms that pose the risk of hypertension in African populations. Large-scale genetic studies are warranted to better understand susceptibility polymorphisms that may be specific to African populations.
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Affiliation(s)
- Yandiswa Y. Yako
- Department of Human BiologyFaculty of Health SciencesWalter Sisulu UniversityMthathaSouth Africa
| | - Eric V. Balti
- Diabetes Research Center and Diabetes ClinicDepartment of Internal MedicineFree University of BrusselsBrusselsBelgium
| | - Tandi E. Matsha
- Department of Biomedical SciencesFaculty of Health and Wellness ScienceCape Peninsula University of TechnologyCape TownSouth Africa
| | - Anastase Dzudie
- Faculty of Medicine and Biomedical SciencesUniversity of Yaounde 1YaoundeCameroon
| | - Deirdre Kruger
- Department of SurgeryFaculty of Health SciencesUniversity of WitwatersrandJohannesburgSouth Africa
| | - Eugene Sobngwi
- Department of Internal Medicine and SpecialitiesFaculty of Medicine and Biomedical SciencesUniversity of Yaounde 1YaoundeCameroon
| | - Charles Agyemang
- Department of Public HealthAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Andre P. Kengne
- Non‐Communicable Diseases Research UnitSouth African Medical Research CouncilCape TownSouth Africa
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115
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Zhao Y, Yang L, Wu D, He H, Wang M, Ge T, Liu Y, Tian H, Cui J, Jia L, Wan Z, Han F. Gene-environment interaction for polymorphisms in ataxia telangiectasia-mutated gene and radiation exposure in carcinogenesis: results from two literature-based meta-analyses of 27120 participants. Oncotarget 2018; 7:76867-76881. [PMID: 27764772 PMCID: PMC5363555 DOI: 10.18632/oncotarget.12724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 10/12/2016] [Indexed: 01/02/2023] Open
Abstract
Purpose We conducted two meta-analyses of ATM genetic polymorphisms and cancer risk in individuals with or without radiation exposure to determine whether there was a joint effect between the ATM gene and radiation exposure in carcinogenesis. Results rs1801516, which was the only ATM polymorphism investigated by more than 3 studies of radiation exposure, was eligible for the present study. The meta-analysis of 23333 individuals without radiation exposure from 24 studies showed no association between the rs1801516 polymorphism and cancer risk, without heterogeneity across studies. The meta-analysis of 3787 individuals with radiation exposure from 6 studies showed a significant association between the rs1801516 polymorphism and a decreased cancer risk, with heterogeneity across studies. There was a borderline-significant difference between the ORs of the two meta-analyses (P = 0.066), and the difference was significant when only Caucasians were included (P = 0.011). Materials and methods Publications were identified by searching PubMed, EMBASE, Web of Science, and CNKI databases. Odds ratios (ORs) were calculated to estimate the association between ATM genetic polymorphisms and cancer risk. Tests of interaction were used to compare differences between the ORs of the two meta-analyses. Conclusions Our meta-analyses confirmed the presence of a gene-environment interaction between the rs1801516 polymorphism and radiation exposure in carcinogenesis, whereas no association was found between the rs1801516 polymorphism and cancer risk for individuals without radiation exposure. The heterogeneity observed in the meta-analysis of individuals with radiation exposure might be due to gene-ethnicity or gene-gene interactions. Further studies are needed to elucidate sources of the heterogeneity.
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Affiliation(s)
- Yuguang Zhao
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Lei Yang
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Di Wu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Hua He
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Mengmeng Wang
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Tingwen Ge
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Yudi Liu
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Huimin Tian
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Jiuwei Cui
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Lin Jia
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Ziqiang Wan
- Cancer Center, The First Hospital of Jilin University, Changchun, China
| | - Fujun Han
- Cancer Center, The First Hospital of Jilin University, Changchun, China
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116
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Dong D, Zou Y, Zhang P, Wu Z. Systematic analyses and comprehensive field synopsis of genetic association studies in hepatocellular carcinoma. Oncotarget 2018; 7:45757-45763. [PMID: 27304192 PMCID: PMC5216758 DOI: 10.18632/oncotarget.9937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/23/2016] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancy in the world. In order to comprehensively examine the association between genetic variants and risk of HCC, a systematic literature search and meta-analyses of the evidences have been performed. With the data from 301 articles, we conducted meta-analyses for 69 polymorphisms involving 46 distinct genes. The result showed that 31 polymorphisms in 25 genes are significantly associated with HCC risk. Cumulative epidemiological evidence for a significant association with HCC risk was graded strong for one polymorphism (NQO1 rs1800566). Furthermore, we provided a database to integrate and analyze the association of genetic variants and HCC risk. To the best of our knowledge, this is the first comprehensive field synopsis and systematic meta-analysis of genetic association with HCC risk. We have provided a useful resource and platform for investigators to explore the association of sequence polymorphisms and HCC risk.
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Affiliation(s)
- Dong Dong
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P.R. China.,Beijing Key Laboratory for Genetic Research of Bone and Joint Disease, Beijing, 100730, P.R. China
| | - Yang Zou
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P.R. China
| | - Pan Zhang
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P.R. China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Bone and Joint Disease, Beijing, 100730, P.R. China.,Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
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117
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Houck AL, Seddighi S, Driver JA. At the Crossroads Between Neurodegeneration and Cancer: A Review of Overlapping Biology and Its Implications. Curr Aging Sci 2018; 11:77-89. [PMID: 29552989 PMCID: PMC6519136 DOI: 10.2174/1874609811666180223154436] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND A growing body of epidemiologic evidence suggests that neurodegenerative diseases occur less frequently in cancer survivors, and vice versa. While unusual, this inverse comorbidity is biologically plausible and could be explained, in part, by the evolutionary tradeoffs made by neurons and cycling cells to optimize the performance of their very different functions. The two cell types utilize the same proteins and pathways in different, and sometimes opposite, ways. However, cancer and neurodegeneration also share many pathophysiological features. OBJECTIVE In this review, we compare three overlapping aspects of neurodegeneration and cancer. METHOD First, we contrast the priorities and tradeoffs of dividing cells and neurons and how these manifest in disease. Second, we consider the hallmarks of biological aging that underlie both neurodegeneration and cancer. Finally, we utilize information from genetic databases to outline specific genes and pathways common to both diseases. CONCLUSION We argue that a detailed understanding of the biologic and genetic relationships between cancer and neurodegeneration can guide future efforts in designing disease-modifying therapeutic interventions. Lastly, strategies that target aging may prevent or delay both conditions.
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Affiliation(s)
- Alexander L. Houck
- College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sahba Seddighi
- Clinical and Translational Neuroscience Unit, Laboratory of Behavioral Neuroscience, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jane A. Driver
- Geriatric Research Education and Clinical Center, VA Boston Healthcare System and the Division of Aging, Department of Medicine, Brigham and Women ‘s Hospital, Harvard Medical School (J.A.D.), Boston, MA, USA
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118
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Chen H, Zhu J. Vitamin D receptor rs2228570 polymorphism and susceptibility to ovarian cancer: An updated meta-analysis. J Obstet Gynaecol Res 2017; 44:556-565. [PMID: 29239065 DOI: 10.1111/jog.13534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/08/2017] [Indexed: 01/03/2023]
Abstract
AIM The FokI polymorphism (C>T, rs2228570) of the vitamin D receptor gene is a coding nonsynonymous single nucleotide polymorphism in the translational initiation codon reported to have functional significance. Although the role of rs2228570 in the risk of ovarian cancer has been widely researched, the association is still unclear. We performed an updated meta-analysis to clarify this issue. METHODS Eligible studies were retrieved from electronic databases for the period 2007-2016. The association was measured by unadjusted odds ratio combined with 95% confidence intervals (CIs). Random-effect or fixed-effect models were used according to the heterogeneity of the studies. We further appreciated the strength of evidence according to Venice guidance. RESULTS Fourteen studies (4448 cases and 7242 controls) were included in the meta-analysis. Studies were predominantly conducted in Caucasian populations (4152 cases and 6693 controls). A dominant genetic model was determined to be the most appropriate genetic model. Overall meta-analysis showed a fixed-effect odds ratio of 1.14 (95% CI 1.05-1.23) under a dominant model. The fixed-effect odds ratios were 1.12 (95% CI 1.03-1.21) and 1.49 (95% CI 1.06-2.09) in Caucasian and Asian populations, respectively. The strength of the evidence was moderate. CONCLUSION The rs2228570 polymorphism increased the risk of ovarian cancer in Caucasian populations in a dominant genetic model. The role of this polymorphism in the risk of ovarian cancer in Asian populations should be further studied.
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Affiliation(s)
- Hongmei Chen
- Department of Gynaecology and Obstetrics, Jing'an District Centre Hospital of Shanghai, Shanghai, China
| | - Jin Zhu
- Department of Gynaecology and Obstetrics, Gynecology Hospital of Fudan University, Shanghai, China
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119
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Zhang M, Tang M, Fang Y, Cui H, Chen S, Li J, Xiong H, Lu J, Gu D, Zhang B. Cumulative evidence for relationships between multiple variants in the VTI1A and TCF7L2 genes and cancer incidence. Int J Cancer 2017; 142:498-513. [PMID: 28949031 DOI: 10.1002/ijc.31074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/30/2017] [Accepted: 09/14/2017] [Indexed: 12/24/2022]
Abstract
Genetic studies have linked the VTI1A-TCF7L2 region with risk of multiple cancers. However, findings from these studies were generally inconclusive. We aimed to provide a synopsis of current understanding of associations between variants in the VTI1A-TCF7L2 region and cancer susceptibility. We conducted a comprehensive research synopsis and meta-analysis to evaluate associations between 17 variants in this region and risk of seven cancers using data from 32 eligible articles totaling 224,656 cancer cases and 324,845 controls. We graded cumulative evidence of significant associations using Venice criteria and false-positive report probability tests. We also conducted analyses to evaluate potential function of these variants using data from the Encyclopedia of DNA Elements (ENCODE) Project. Eight variants showed a nominally significant association with risk of individual cancer (p < 0.05). Cumulative epidemiological evidence of an association was graded as strong for rs7903146 [odds ratio (OR) = 1.05, p = 4.13 × 10-5 ] and rs7904519 (OR = 1.07, p = 2.02 × 10-14 ) in breast cancer, rs11196172 (OR = 1.11, p = 2.22 × 10-16 ), rs12241008 (OR = 1.13, p = 1.36 × 10-10 ) and rs10506868 (OR = 1.10, p = 3.98 × 10-9 ) in colorectal cancer, rs7086803 in lung cancer (OR = 1.30, p = 3.54 × 10-18 ) and rs11196067 (OR = 1.18, p = 3.59 × 10-13 ) in glioma, moderate for rs12255372 (OR = 1.12, p = 2.52 × 10-4 ) in breast cancer and weak for rs7903146 (OR = 1.11, p = 0.007) in colorectal cancer. Data from ENCODE suggested that seven variants with strong evidence and other correlated variants might fall within putative functional regions. Collectively, our study provides summary evidence that common variants in the VTI1A and TCF7L2 genes are associated with risk of breast, colorectal, lung cancer and glioma and highlights the significant role of the VTI1A-TCF7L2 region in the pathogenesis of human cancers.
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Affiliation(s)
- Min Zhang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Yanfei Fang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China.,Division of Clinical Research and Evaluation, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Siyu Chen
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Junlong Li
- Division of Clinical Research and Evaluation, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Hongyan Xiong
- Division of Clinical Research and Evaluation, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Jiachun Lu
- Department of Epidemiology, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Dongqing Gu
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China.,Division of Clinical Research and Evaluation, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing, China.,Division of Clinical Research and Evaluation, First Affiliated Hospital and Southwest School of Medicine, Third Military 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, Third Military Medical University, Chongqing, China
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Impact of TNF -308 G>A (rs1800629) gene polymorphism in modulation of leprosy risk: a reappraise meta-analysis of 14 case-control studies. Biosci Rep 2017; 37:BSR20170806. [PMID: 28935761 PMCID: PMC5664359 DOI: 10.1042/bsr20170806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 01/11/2023] Open
Abstract
Purpose: Earlier studies have shown that tumor necrosis factor
(TNF) -308 G>A (rs1800629) gene polymorphism is
implicated in the susceptibility to leprosy, but results were inconsistent. Methods: A meta-analysis of 14 studies involving 3327 leprosy cases and 3203
controls was performed to appraise the association of TNF -308
G>A polymorphism with leprosy using MEDLINE (PUBMED), EMBASE, and Google
Scholar web databases. Results: Overall, no significant association was observed in allelic (A vs. G:
P=0.068; OR = 0.836, 95% CI =
0.689–1.013), homozygous (AA vs. GG: P=0.394; OR
= 0.810, 95% CI = 0.499–1.315), heterozygous (GA vs.
GG: P=0.059; OR = 0.780, 95% CI =
0.603–1.010), dominant (AA + GA vs. GG: P=0.067;
OR = 0.797, 95% CI = 0.625–1.016), and recessive (AA
vs. GG + GA: P=0.594; OR = 0.877, 95% CI
= 0.542– 1.420) genetic models. Subgroup analysis showed no
association in Asians. Whereas, reduced risk was found in allelic contrast (A
vs. G: P=0.014; OR = 0.832, 95% CI
= 0.718–0.963) and dominant models (AA + GA vs. GG:
P=0.004; OR = 0.790, 95% CI =
0.673–0.928) of the mixed population. Conclusions: TNF -308 G>A polymorphism is not associated
with leprosy risk in the overall population. However, subgroup analysis
demonstrated protective effect of the said polymorphism in leprosy risk in the
Latin American population, but showed no association in the Asians.
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121
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IL-10 -1082 A>G (rs1800896) polymorphism confers susceptibility to pulmonary tuberculosis in Caucasians but not in Asians and Africans: a meta-analysis. Biosci Rep 2017; 37:BSR20170240. [PMID: 28951522 PMCID: PMC5658633 DOI: 10.1042/bsr20170240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 01/11/2023] Open
Abstract
Background: Earlier studies have shown that interlukin-10 (IL-10) -1082 A>G gene polymorphism is implicated in susceptibility to pulmonary tuberculosis (PTB), but their results are inconsistent and inconclusive. In the present study, a meta-analysis was performed to analyze the potential association between IL-10 -1082 A>G gene polymorphism and PTB susceptibility. Methods: A quantitative synthesis was done using PubMed (Medline), EMBASE, and Google Scholar web databases search and meta-analysis was performed by calculating pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) for all the genetic models. Results: A total of 22 eligible studies comprising 4956 PTB cases and 6428 healthy controls were included in the analysis. We did not observe any increased or decreased risk of PTB in allelic contrast (G vs. A: P=0.985; OR = 1.001, 95% CI = 0.863–1.162), homozygous (GG vs. AA: P=0.889; OR = 1.029, 95% CI = 0.692–1.529), heterozygous (GA vs. AA: P=0.244; OR = 0.906, 95% CI = 0.767–1.070), dominant (GG + AG vs. AA: P=0.357; OR = 1.196, 95% CI = 0.817–1.752), and recessive (GG vs. AA + AG: P=0.364; OR = 0.921, 95% CI = 0.771–1.100) genetic models. Likewise, no association of IL-10 -1082 A>G polymorphism with PTB risk was observed in Asian and African population for all the genetic models. Interestingly, the dominant model (GG + AG vs. AA: P=0.004; OR = 1.694, 95% CI = 1.183–2.425) demonstrated increased risk of PTB in Caucasian population. Conclusions: This meta-analysis concludes that IL-10 -1082 A>G gene polymorphism is not significantly associated with overall, Asian and African population. However, this polymorphism is associated with Caucasian population.
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Park JH, Kim JH, Jo KE, Na SW, Eisenhut M, Kronbichler A, Lee KH, Shin JI. Field Synopsis and Re-analysis of Systematic Meta-analyses of Genetic Association Studies in Multiple Sclerosis: a Bayesian Approach. Mol Neurobiol 2017; 55:5672-5688. [PMID: 29027112 DOI: 10.1007/s12035-017-0773-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/12/2017] [Indexed: 12/31/2022]
Abstract
To provide an up-to-date summary of multiple sclerosis-susceptible gene variants and assess the noteworthiness in hopes of finding true associations, we investigated the results of 44 meta-analyses on gene variants and multiple sclerosis published through December 2016. Out of 70 statistically significant genotype associations, roughly a fifth (21%) of the comparisons showed noteworthy false-positive rate probability (FPRP) at a statistical power to detect an OR of 1.5 and at a prior probability of 10-6 assumed for a random single nucleotide polymorphism. These associations (IRF8/rs17445836, STAT3/rs744166, HLA/rs4959093, HLA/rs2647046, HLA/rs7382297, HLA/rs17421624, HLA/rs2517646, HLA/rs9261491, HLA/rs2857439, HLA/rs16896944, HLA/rs3132671, HLA/rs2857435, HLA/rs9261471, HLA/rs2523393, HLA-DRB1/rs3135388, RGS1/rs2760524, PTGER4/rs9292777) also showed a noteworthy Bayesian false discovery probability (BFDP) and one additional association (CD24 rs8734/rs52812045) was also noteworthy via BFDP computation. Herein, we have identified several noteworthy biomarkers of multiple sclerosis susceptibility. We hope these data are used to study multiple sclerosis genetics and inform future screening programs.
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Affiliation(s)
- Jae Hyon Park
- Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joo Hi Kim
- Yonsei University Wonju College of Medicine, Seoul, Republic of Korea
| | - Kye Eun Jo
- College of Medicine, University of Debrecen, Debrecen, Hungary
| | - Se Whan Na
- Yonsei University Wonju College of Medicine, Seoul, Republic of Korea
| | - Michael Eisenhut
- Department of Pediatrics, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Andreas Kronbichler
- Department of Internal Medicine IV, Medical University Innsbruck, Innsbruck, Austria
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 120-752, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 120-752, Republic of Korea.
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Benna C, Helfrich-Förster C, Rajendran S, Monticelli H, Pilati P, Nitti D, Mocellin S. Genetic variation of clock genes and cancer risk: a field synopsis and meta-analysis. Oncotarget 2017; 8:23978-23995. [PMID: 28177907 PMCID: PMC5410358 DOI: 10.18632/oncotarget.15074] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The number of studies on the association between clock genes’ polymorphisms and cancer susceptibility has increased over the last years but the results are often conflicting and no comprehensive overview and quantitative summary of the evidence in this field is available. RESULTS Literature search identified 27 eligible studies comprising 96756 subjects (cases: 38231) and investigating 687 polymorphisms involving 14 clock genes. Overall, 1025 primary and subgroup meta-analyses on 366 gene variants were performed. Study distribution by tumor was as follows: breast cancer (n=15), prostate cancer (n=3), pancreatic cancer (n=2), non-Hodgkin's lymphoma (n=2), glioma (n=1), chronic lymphocytic leukemia (n=1), colorectal cancer (n=1), non-small cell lung cancer (n=1) and ovarian cancer (n=1). We identified 10 single nucleotide polymorphisms (SNPs) significantly associated with cancer risk: NPAS2 rs10165970 (mixed and breast cancer shiftworkers), rs895520 (mixed), rs17024869 (breast) and rs7581886 (breast); CLOCK rs3749474 (breast) and rs11943456 (breast); RORA rs7164773 (breast and breast cancer postmenopausal), rs10519097 (breast); RORB rs7867494 (breast cancer postmenopausal), PER3 rs1012477 (breast cancer subgroups) and assessed the level of quality evidence to be intermediate. We also identified polymorphisms with lower quality statistically significant associations (n=30). CONCLUSIONS Our work supports the hypothesis that genetic variation of clock genes might affect cancer risk. These findings also highlight the need for more efforts in this research field in order to fully establish the contribution of clock gene variants to the risk of developing cancer. METHODS We conducted a systematic review and meta-analysis of the evidence on the association between clock genes’ germline variants and the risk of developing cancer. To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Subgroup meta-analysis was also performed based on participant features and tumor type. The breast cancer subgroup was further stratified by work conditions, estrogen receptor/progesterone receptor status and menopausal status, conditions associated with the risk of breast cancer in different studies.
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Affiliation(s)
- Clara Benna
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Senthilkumar Rajendran
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | | | | | - Donato Nitti
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy.,Clinica Chirurgica I, Azienda Ospedaliera Padova, Padova, Italy
| | - Simone Mocellin
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy.,Istituto Oncologico Veneto, IOV-IRCSS, Padova, Italy
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124
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Theodoratou E, Timofeeva M, Li X, Meng X, Ioannidis JPA. Nature, Nurture, and Cancer Risks: Genetic and Nutritional Contributions to Cancer. Annu Rev Nutr 2017; 37:293-320. [PMID: 28826375 DOI: 10.1146/annurev-nutr-071715-051004] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is speculated that genetic variants are associated with differential responses to nutrients (known as gene-diet interactions) and that these variations may be linked to different cancer risks. In this review, we critically evaluate the evidence across 314 meta-analyses of observational studies and randomized controlled trials of dietary risk factors and the five most common cancers (breast, lung, prostate, colorectal, and stomach). We also critically evaluate the evidence across 13 meta-analyses of observational studies of gene-diet interactions for the same cancers. Convincing evidence for association was found only for the intake of alcohol and whole grains in relation to colorectal cancer risk. Three nutrient associations had highly suggestive evidence and another 15 associations had suggestive evidence. Among the examined gene-diet interactions, only one had moderately strong evidence.
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Affiliation(s)
- Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH8 9AG, United Kingdom.,Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - Xiangrui Meng
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - John P A Ioannidis
- Stanford Prevention Research Center, Departments of Medicine and Health Research and Policy, Stanford University School of Medicine, Stanford, California 94305-5411; .,Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, California 94305-5411
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125
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Cliff J, Jorgensen AL, Lord R, Azam F, Cossar L, Carr DF, Pirmohamed M. The molecular genetics of chemotherapy-induced peripheral neuropathy: A systematic review and meta-analysis. Crit Rev Oncol Hematol 2017; 120:127-140. [PMID: 29198326 DOI: 10.1016/j.critrevonc.2017.09.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/12/2017] [Accepted: 09/11/2017] [Indexed: 01/13/2023] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) can adversely affect completion of systemic anti-cancer treatment and cause long-term morbidity. Increasingly pharmacogenetic studies have been performed to explore susceptibility to this important adverse effect. A systematic review was conducted to identify pharmacogenetic studies, assess their quality and findings and undertake meta-analysis where possible. 93 studies were included. Notable methodological issues included lack of standardisation and detail in phenotype definition and acknowledgement of potential confounding factors. Insufficient data was presented in many studies meaning only a minority could be included in meta-analysis showing mainly non-significant effects. Nonetheless, SNPs in CYP2C8, CYP3A4, ARHGEF10, EPHA and TUBB2A genes (taxanes), FARS2, ACYP2 and TAC1 (oxaliplatin), and CEP75 and CYP3A5 (vincristine) are of potential interest. These require exploration in large cohort studies with robust methodology and well-defined phenotypes. Seeking standardisation of phenotype, collaboration and subsequently, individual-patient-data meta-analysis may facilitate identifying contributory SNPs which could be combined in a polygenic risk score to predict those most at risk of CIPN.
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Affiliation(s)
- J Cliff
- University of Liverpool, Liverpool, L69 3BX, UK; Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Wirral, CH63 4JY, UK.
| | | | - R Lord
- University of Liverpool, Liverpool, L69 3BX, UK; Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Wirral, CH63 4JY, UK.
| | - F Azam
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Wirral, CH63 4JY, UK.
| | - L Cossar
- University of Liverpool, Liverpool, L69 3BX, UK; Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Wirral, CH63 4JY, UK.
| | - D F Carr
- University of Liverpool, Liverpool, L69 3BX, UK.
| | - M Pirmohamed
- University of Liverpool, Liverpool, L69 3BX, UK.
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126
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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127
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Wang J, Liu Q, Yuan S, Xie W, Liu Y, Xiang Y, Wu N, Wu L, Ma X, Cai T, Zhang Y, Sun Z, Li Y. Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies. Sci Rep 2017; 7:8371. [PMID: 28827732 PMCID: PMC5567126 DOI: 10.1038/s41598-017-07737-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/04/2017] [Indexed: 01/03/2023] Open
Abstract
More than 1000 candidate-gene association studies on genetic susceptibility to lung cancer have been published over the last two decades but with few consensuses for the likely culprits. We conducted a comprehensive review, meta-analysis and evidence strength evaluation of published candidate-gene association studies in lung cancer up to November 1, 2015. The epidemiological credibility of cumulative evidence was assessed using the Venice criteria. A total of 1018 publications with 2910 genetic variants in 754 different genes or chromosomal loci were eligible for inclusion. Main meta-analyses were performed on 246 variants in 138 different genes. Twenty-two variants from 21 genes (APEX1 rs1130409 and rs1760944, ATM rs664677, AXIN2 rs2240308, CHRNA3 rs6495309, CHRNA5 rs16969968, CLPTM1L rs402710, CXCR2 rs1126579, CYP1A1 rs4646903, CYP2E1 rs6413432, ERCC1 rs11615, ERCC2 rs13181, FGFR4 rs351855, HYKK rs931794, MIR146A rs2910164, MIR196A2 rs11614913, OGG1 rs1052133, PON1 rs662, REV3L rs462779, SOD2 rs4880, TERT rs2736098, and TP53 rs1042522) showed significant associations with lung cancer susceptibility with strong cumulative epidemiological evidence. No significant associations with lung cancer risk were found for other 150 variants in 98 genes; however, seven variants demonstrated strong cumulative evidence. Our findings provided the most updated summary of genetic risk effects on lung cancer and would help inform future research direction.
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Affiliation(s)
- Junjun Wang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Qingyun Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Shuai Yuan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Weijia Xie
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yuan Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Na Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Long Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Tongjian Cai
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Zhang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhifu Sun
- Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China. .,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China.
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128
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Richardson M, Kirkham J, Dwan K, Sloan D, Davies G, Jorgensen A. Influence of genetic variants on toxicity to anti-tubercular agents: a systematic review and meta-analysis (protocol). Syst Rev 2017; 6:142. [PMID: 28701180 PMCID: PMC5508765 DOI: 10.1186/s13643-017-0533-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 06/23/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Tuberculosis patients receiving anti-tuberculosis treatment may experience serious adverse drug reactions, such as hepatotoxicity. Genetic risk factors, such as polymorphisms of the NAT2, CYP2E1 and GSTM1 genes, may increase the risk of experiencing such toxicity events. Many pharmacogenetic studies have investigated the association between genetic variants and anti-tuberculosis drug-related toxicity events, and several meta-analyses have synthesised data from these studies, although conclusions from these meta-analyses are conflicting. Many meta-analyses also have serious methodological limitations, such as applying restrictive inclusion criteria, or not assessing the quality of included studies. Most also only consider hepatotoxicity outcomes and specific genetic variants. The purpose of this systematic review and meta-analysis is to give a comprehensive evaluation of the evidence base for associations between any genetic variant and anti-tuberculosis drug-related toxicity. METHODS We will search for studies in MEDLINE, EMBASE, BIOSIS and Web of Science. We will also hand search reference lists from relevant studies and contact experts in the field. We will include cohort studies, case-control studies and randomised controlled trials that recruited patients with tuberculosis who were either already established on anti-tuberculosis treatment or were commencing treatment and who were genotyped to investigate the effect of genetic variants on any anti-tuberculosis drug-related toxicity outcome. One author will screen abstracts to identify potentially relevant studies and will then obtain the full text for each potentially relevant study in order to assess eligibility. At each of these stages, a second author will independently screen/assess 10% of studies. Two authors will independently extract data and assess the quality of studies using a pre-piloted data extraction form. If appropriate, we will pool estimates of effect for each genotype on each outcome using meta-analyses stratified by ethnicity. DISCUSSION Our review and meta-analysis will update and add to the existing research in this field. By not restricting the scope of the review to a specific drug, genetic variant, or toxicity outcome, we hope to synthesise data for associations between genetic variants and anti-tuberculosis drug-related toxicity outcomes that have previously not been summarised in systematic reviews, and consequently, add to the knowledge base of the pharmacogenetics of anti-tuberculosis drugs. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42017068448.
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Affiliation(s)
- Marty Richardson
- Department of Biostatistics, University of Liverpool, Whelan Building, Liverpool, L69 3GB, UK.
| | - Jamie Kirkham
- Department of Biostatistics, University of Liverpool, Whelan Building, Liverpool, L69 3GB, UK
| | - Kerry Dwan
- Cochrane Editorial Unit, London, SW1Y 4QX, UK
| | - Derek Sloan
- School of Medicine, University of St Andrews, St. Andrews, KY16 9TF, UK
| | - Geraint Davies
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69 3GB, UK
| | - Andrea Jorgensen
- Department of Biostatistics, University of Liverpool, Whelan Building, Liverpool, L69 3GB, UK
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129
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Dimou NL, Pantavou KG, Bagos PG. Apolipoprotein E Polymorphism and Left Ventricular Failure in Beta-Thalassemia: A Multivariate Meta-Analysis. Ann Hum Genet 2017; 81:213-223. [DOI: 10.1111/ahg.12203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 06/05/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Niki L. Dimou
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
| | - Katerina G. Pantavou
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
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130
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Qiu C, Zeng P, Li X, Zhang Z, Pan B, Peng ZYF, Li Y, Ma Y, Leng Y, Chen R. What is the impact of PCSK9 rs505151 and rs11591147 polymorphisms on serum lipids level and cardiovascular risk: a meta-analysis. Lipids Health Dis 2017; 16:111. [PMID: 28606094 PMCID: PMC5469167 DOI: 10.1186/s12944-017-0506-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/30/2017] [Indexed: 12/17/2022] Open
Abstract
Background PCSK9 rs505151 and rs11591147 polymorphisms are identified as gain- and loss-of-function mutations, respectively. The effects of these polymorphisms on serum lipid levels and cardiovascular risk remain to be elucidated. Methods In this meta-analysis, we explored the association of PCSK9 rs505151 and rs11591147 polymorphisms with serum lipid levels and cardiovascular risk by calculating the standardized mean difference (SMD) and odds ratios (OR) with 95% confidence intervals (CI). Results Pooled results analyzed under a dominant genetic model indicated that the PCSK9 rs505151 G allele was related to higher levels of triglycerides (SMD: 0.14, 95% CI: 0.02 to 0.26, P = 0.021, I2 = 0) and low-density lipoproteins cholesterol (LDL-C) (SMD: 0.17, 95% CI: 0.00 to 0.35, P = 0.046, I2 = 75.9%) and increased cardiovascular risk (OR: 1.50, 95% CI: 1.19 to 1.89, P = 0.0006, I2 = 48%). The rs11591147 T allele was significantly associated with lower levels of total cholesterol (TC) and LDL-C (TC, SMD: -0.45, 95% CI: -0.57 to −0.32, P = 0.000, I2 = 0; LDL-C, SMD: -0.44, 95% CI: -0.55 to −0.33, P = 0.000, I2 = 0) and decreased cardiovascular risk (OR: 0.77, 95% CI: 0.60 to 0.98, P = 0.031, I2 = 59.9) in Caucasians. Conclusions This study indicates that the variant G allele of PCSK9 rs505151 confers increased triglyceride (TG) and LDL-C levels, as well as increased cardiovascular risk. Conversely, the variant T allele of rs11591147 protects carriers from cardiovascular disease susceptibility and lower TC and LDL-C levels in Caucasians. These findings provide useful information for researchers interested in the fields of PCSK9 genetics and cardiovascular risk prediction not only for designing future studies, but also for clinical and public health applications.
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Affiliation(s)
- Chengfeng Qiu
- Xiangya school of Pharmaceutical Sciences, Central South University, Changsha, China. .,Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China.
| | - Pingyu Zeng
- Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaohui Li
- Xiangya school of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zhen Zhang
- Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Bingjie Pan
- Xiangya school of Pharmaceutical Sciences, Central South University, Changsha, China.,Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhou Y F Peng
- Xiangya school of Pharmaceutical Sciences, Central South University, Changsha, China.,Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yapei Li
- Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China.,Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yeshuo Ma
- Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China.,Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yiping Leng
- Xiangya school of Pharmaceutical Sciences, Central South University, Changsha, China.,Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ruifang Chen
- Center for Vascular Disease and Translational Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
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131
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A reappraised meta-analysis of the genetic association between vitamin D receptor BsmI (rs1544410) polymorphism and pulmonary tuberculosis risk. Biosci Rep 2017; 37:BSR20170247. [PMID: 28533426 PMCID: PMC5463263 DOI: 10.1042/bsr20170247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 01/11/2023] Open
Abstract
BsmI (rs1544410) polymorphism located in intron 8 at the 3′-end of the vitamin D receptor (VDR) gene is known to be involved in the regulation of mRNA stability. Many studies evaluated the possible correlation between VDR BsmI polymorphism and the risk of pulmonary tuberculosis (PTB), and reported conflicting results. In the present study, an updated meta-analysis was performed to evaluate the above-said association. PubMed, Embase, and Google Scholar web-databases were searched for the relevant studies and a meta-analysis was performed by calculating pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) for all the genetic models. A total of 19 studies comprising 3644 controls and 2635 cases were included in the present study. Overall no association of PTB in allelic contrast (b compared with B: P=0.285; OR =0.909, 95% CI =0.762–1.083), homozygous (bb compared with BB: P=0.881; OR =0.975, 95% CI =0.700–1.359), heterozygous (bB compared with BB: P=0.834; OR =1.017, 95% CI =0.872–1.185), dominant (bb compared with BB + Bb: P=0.451; OR =0.954, 95% CI =0.843–1.079) and recessive (bb + Bb compared with BB: P=0.983; OR =1.002, 95% CI =0.868–1.156) genetic models in comparison with wild-type allele and genotype BB were observed. However, variant allele (b compared with B: P=0.001; OR =2.289, 95% CI =1.661–3.154) showed increased risk of PTB in Asians. In conclusion, VDR BsmI polymorphism is not a risk factor for PTB in overall population. However, this polymorphism may be interrelated to an increased risk of PTB amongst Asians.
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132
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Zwingerman N, Medina-Rivera A, Kassam I, Wilson MD, Morange PE, Trégouët DA, Gagnon F. Sex-specific effect of CPB2 Ala147Thr but not Thr325Ile variants on the risk of venous thrombosis: A comprehensive meta-analysis. PLoS One 2017; 12:e0177768. [PMID: 28552956 PMCID: PMC5446132 DOI: 10.1371/journal.pone.0177768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 05/03/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Thrombin activatable fibrinolysis inhibitor (TAFI), encoded by the Carboxypeptidase B2 gene (CPB2), is an inhibitor of fibrinolysis and plays a role in the pathogenesis of venous thrombosis. Experimental findings support a functional role of genetic variants in CPB2, while epidemiological studies have been unable to confirm associations with risk of venous thrombosis. Sex-specific effects could underlie the observed inconsistent associations between CPB2 genetic variants and venous thrombosis. METHODS A comprehensive literature search was conducted for associations between Ala147Thr and Thr325Ile variants with venous thrombosis. Authors were contacted to provide sex-specific genotype counts from their studies. Combined and sex-specific random effects meta-analyses were used to estimate a pooled effect estimate for primary and secondary genetic models. RESULTS A total of 17 studies met the inclusion criteria. A sex-specific meta-analysis applying a dominant model supported a protective effect of Ala147Thr on venous thrombosis in females (OR = 0.81, 95%CI: 0.68,0.97; p = 0.018), but not in males (OR = 1.06, 95%CI:0.96-1.16; p = 0.263). The Thr325Ile did not show a sex-specific effect but showed variation in allele frequencies by geographic region. A subgroup analysis of studies in European countries showed decreased risk, with a recessive model (OR = 0.83, 95%CI:0.71-0.97, p = 0.021) for venous thrombosis. CONCLUSIONS A comprehensive literature review, including unpublished data, provided greater statistical power for the analyses and decreased the likelihood of publication bias influencing the results. Sex-specific analyses explained apparent discrepancies across genetic studies of Ala147Thr and venous thrombosis. While, careful selection of genetic models based on population genetics, evolutionary and biological knowledge can increase power by decreasing the need to adjust for testing multiple models.
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Affiliation(s)
- Nora Zwingerman
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Alejandra Medina-Rivera
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Santiago de Querétaro, Querétaro, Mexico
| | - Irfahan Kassam
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Pierre-Emmanuel Morange
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) en Santé 1062, Nutrition Obesity and Risk of Thrombosis, Marseille, France
- Faculté de Médecine, Aix Marseille Université, Marseille, France
| | - David-Alexandre Trégouët
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Paris, France
- Institute for Cardiometabolism and Nutrition, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
| | - France Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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Tragante V, Gho JMIH, Felix JF, Vasan RS, Smith NL, Voight BF, Palmer C, van der Harst P, Moore JH, Asselbergs FW. Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. BioData Min 2017; 10:18. [PMID: 28559929 PMCID: PMC5446754 DOI: 10.1186/s13040-017-0137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. RESULTS Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions. Here, we present lessons learned from our experience with GSEA of heart failure, a particularly challenging phenotype due to its underlying heterogeneous etiology. CONCLUSIONS This case study shows that proper data handling is essential to avoid false-positive results. Well-defined pipelines for quality control are needed to avoid reporting spurious results using GSEA.
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Affiliation(s)
- Vinicius Tragante
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Johannes M. I. H. Gho
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Janine F. Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ramachandran S. Vasan
- Departments of Medicine and Preventive Medicine, Boston University School of Medicine, Boston, MA USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, WA USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - CHARGE Heart Failure Working Group
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Departments of Medicine and Preventive Medicine, Boston University School of Medicine, Boston, MA USA
- Department of Epidemiology, University of Washington, Seattle, WA USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Population Pharmacogenetics Group, University of Dundee, Dundee, UK
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Durrer Center for Cardiovascular Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
| | - Colin Palmer
- Population Pharmacogenetics Group, University of Dundee, Dundee, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jason H. Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Durrer Center for Cardiovascular Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
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134
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Hicks C, Ramani R, Sartor O, Bhalla R, Miele L, Dlamini Z, Gumede N. An Integrative Genomics Approach for Associating Genome-Wide Association Studies Information With Localized and Metastatic Prostate Cancer Phenotypes. Biomark Insights 2017; 12:1177271917695810. [PMID: 28469398 PMCID: PMC5391982 DOI: 10.1177/1177271917695810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/05/2017] [Indexed: 01/01/2023] Open
Abstract
High-throughput genotyping has enabled discovery of genetic variants associated with an increased risk of developing prostate cancer using genome-wide association studies (GWAS). The goal of this study was to associate GWAS information of patients with primary organ–confined and metastatic prostate cancer using gene expression data and to identify molecular networks and biological pathways enriched for genetic susceptibility variants involved in the 2 disease states. The analysis revealed gene signatures for the 2 disease states and a gene signature distinguishing the 2 patient groups. In addition, the analysis revealed molecular networks and biological pathways enriched for genetic susceptibility variants. The discovered pathways include the androgen, apoptosis, and insulinlike growth factor signaling pathways. This analysis established putative functional bridges between GWAS discoveries and the biological pathways involved in primary organ–confined and metastatic prostate cancer.
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Affiliation(s)
- Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Ritika Ramani
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Oliver Sartor
- Department of Medicine, Tulane University, New Orleans, LA, USA
| | - Ritu Bhalla
- Department of Pathology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Zodwa Dlamini
- Department of Biology, Mangosuthu University of Technology, Durban, South Africa
| | - Njabulo Gumede
- Department of Biology, Mangosuthu University of Technology, Durban, South Africa
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135
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Allan V, Honarbakhsh S, Casas JP, Wallace J, Hunter R, Schilling R, Perel P, Morley K, Banerjee A, Hemingway H. Are cardiovascular risk factors also associated with the incidence of atrial fibrillation? A systematic review and field synopsis of 23 factors in 32 population-based cohorts of 20 million participants. Thromb Haemost 2017; 117:837-850. [PMID: 28229164 PMCID: PMC5442605 DOI: 10.1160/th16-11-0825] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/02/2017] [Indexed: 12/17/2022]
Abstract
Established primary prevention strategies of cardiovascular diseases are based on understanding of risk factors, but whether the same risk factors are associated with atrial fibrillation (AF) remains unclear. We conducted a systematic review and field synopsis of the associations of 23 cardiovascular risk factors and incident AF, which included 84 reports based on 28 consented and four electronic health record cohorts of 20,420,175 participants and 576,602 AF events. We identified 3-19 reports per risk factor and heterogeneity in AF definition, quality of reporting, and adjustment. We extracted relative risks (RR) and 95 % confidence intervals [CI] and visualised the number of reports with inverse (RR [CI]<1.00), or direct (RR [CI]>1.00) associations. For hypertension (13/17 reports) and obesity (19/19 reports), there were direct associations with incident AF, as there are for coronary heart disease (CHD). There were inverse associations for non-White ethnicity (5/5 reports, with RR from 0.35 to 0.84 [0.82-0.85]), total cholesterol (4/13 reports from 0.76 [0.59-0.98] to 0.94 [0.90-0.97]; 8/13 reports with non-significant inverse associations), and diastolic blood pressure (2/11 reports from 0.87 [0.78-0.96] to 0.92 [0.85-0.99]; 5/11 reports with non-significant inverse associations), and direct associations for taller height (7/10 reports from 1.03 [1.02-1.05] to 1.92 [1.38-2.67]), which are in the opposite direction of known associations with CHD. A systematic evaluation of the available evidence suggests similarities as well as important differences in the risk factors for incidence of AF as compared with other cardiovascular diseases, which has implications for the primary prevention strategies for atrial fibrillation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Harry Hemingway
- Prof. Harry Hemingway, Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London NW1 2AD, UK, Tel.: +44 20 35495329, E-mail:
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136
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Bellou V, Belbasis L, Tzoulaki I, Middleton LT, Ioannidis JP, Evangelou E. Systematic evaluation of the associations between environmental risk factors and dementia: An umbrella review of systematic reviews and meta-analyses. Alzheimers Dement 2017; 13:406-418. [DOI: 10.1016/j.jalz.2016.07.152] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/05/2016] [Accepted: 07/22/2016] [Indexed: 11/16/2022]
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137
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Yang B, Fan S, Zhi X, Xia R, Wang Y, Zheng Q, Sun G. Geographical and ethnic distribution of MTHFR gene polymorphisms and their associations with diseases among Chinese population. Clin Genet 2017; 92:243-258. [PMID: 27888505 DOI: 10.1111/cge.12929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 12/17/2022]
Abstract
Numerous studies have investigated the distribution of methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms and their associations with diseases in China. In this study we conducted a systematic review and meta-analysis of these studies (715 eligible studies in total).Results revealed that the frequencies of the MTHFR C677T and A1298C polymorphisms varied markedly in different areas and ethnicities, and even showed geographical gradients. The MTHFR C677T polymorphism was significantly associated with 42 clinical disorders (p < 0.05), mostly relating to the diseases of circulatory system, birth defects and cancers. The association of the A1298C polymorphism with three diseases (coronary heart disease, breast cancer and neural tube defects fathers) was statistically significant (p < 0.05). However, according to the Venice criteria, only the associations of the C677T polymorphism with breast and ovarian cancers were assessed as having strong epidemiological credibility. This is the first study to provide a comprehensive assessment of the current status and gaps in genetic epidemiological study of the two polymorphisms in China, and its findings may be useful for medical and public health practices. Future studies are warranted to focus on the interactions of MTHFR genes with environmental exposure and with other genes, and to improve their methodological quality and reporting of findings.
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Affiliation(s)
- B Yang
- Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Preventive Medicine, School of Public Health, Sun Yat-Sen University, Guangzhou, China.,Environment and Non-Communicable Disease Research Center, School of Public Health, China Medical University, Shenyang, China
| | - S Fan
- Environment and Non-Communicable Disease Research Center, School of Public Health, China Medical University, Shenyang, China
| | - X Zhi
- Environment and Non-Communicable Disease Research Center, School of Public Health, China Medical University, Shenyang, China
| | - R Xia
- Shanghai Institute of Planned Parenthood Research, School of Medicine, Fudan University, Shanghai, China
| | - Y Wang
- Division of Molecular Preventive Medicine, Shanghai Institute of Targeted Therapy and Molecular Medicine, Shanghai, China
| | - Q Zheng
- Environment and Non-Communicable Disease Research Center, School of Public Health, China Medical University, Shenyang, China
| | - G Sun
- Environment and Non-Communicable Disease Research Center, School of Public Health, China Medical University, Shenyang, China
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138
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Gelemanović A, Dobberpuhl K, Krakar G, Patarčić I, Kolčić I, Polašek O. Host genetics and susceptibility to congenital and childhood cytomegalovirus infection: a systematic review. Croat Med J 2017; 57:321-30. [PMID: 27586547 PMCID: PMC5048223 DOI: 10.3325/cmj.2016.57.321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim To summarize available evidence on the role of host genetics in the susceptibility to congenital and childhood cytomegalovirus (CMV) infections by conducting a systematic review of published studies. Methods We searched online databases (PubMed, Web of Science, Scopus and HuGe Navigator) for relevant studies with well-defined inclusion and exclusion criteria and assessed the risk of bias using novel Confounding-Selection-Information bias score (CSI). Results 5105 studies were initially identified, but only 5 met all the inclusion criteria and were analyzed in detail. Polymorphisms of the toll-like receptors (TLRs) and mannose-binding lectin (MBL) genes were shown to have an impact on the CMV infection in infants. Polymorphisms of the TLR2 (rs3804100, rs1898830), TLR4 (rs4986791), and TLR9 (rs352140) were shown to have a role in congenital CMV infection. Low MBL levels were associated with CMV infection in Chinese individuals, a finding that was not replicated in Caucasians. The overall credibility of evidence was weak. Conclusions Based on currently available very limited amount of evidence, it is uncertain whether congenital and childhood CMV infections are under host genetic control. Additional primary studies are needed with more specific research hypotheses that will enable gradual understanding of specific mechanisms of the CMV pathogenesis. More genetic studies in the future will facilitate better understanding of host susceptibility and likely enable novel preventative and curative measures.
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Affiliation(s)
| | | | | | | | | | - Ozren Polašek
- Ozren Polašek, School of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia,
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139
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Effect of Personalized Nutrition Guidance on the Birth Rate of Fetal Macrosomia in Chinese Population: A Meta-analysis of Nine Randomized Controlled Trials. Cell Biochem Biophys 2017; 72:669-74. [PMID: 27352186 DOI: 10.1007/s12013-015-0512-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The aim of the study was to perform a systematic review and meta-analysis of randomized controlled trials (RCTs) evaluating the efficacy of personalized nutrition guidance on birth rate of fetal macrosomia in the pooled studies. A comprehensive search was conducted to identify all eligible studies using the databases of PubMed, MEDLINE, Embase, Wanfang, Chongqing Weipu Database for Chinese Technical Periodicals and China National Knowledge Infrastructure and reference lists of relevant articles. The methodological quality of the included trials was assessed based on the Jadad scale. We used risk ratios (RRs) to assess the strength of the association, and 95 % confidence intervals (CIs) to evaluate the precision of the estimate. Heterogeneity, publication bias, and sensitivity analysis were also explored. A total of nine RCT studies, including 7,458 pregnant women, were included in the present meta-analysis. The overall results showed that personalized nutrition guidance significantly reduced the birth rate of fetal macrosomia (RR 0.289, 95 % CI 0.184-0.453, P < 0.01) in Chinese population. Simultaneously, publication bias was detected in this meta-analysis. The personalized nutrition guidance can significantly reduce the birth rate of fetal macrosomia. However, due to the limited number of RCTs, especially those with large sample size and multicenter that were quantitatively insufficient, further studies of high quality are required.
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140
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Alshammari EM, Mandal RK, Wahid M, Dar SA, Jawed A, Areeshi MY, Khan S, Khan MEA, Panda AK, Haque S. Genetic association study of P2x7 A1513C (rs 3751143) polymorphism and susceptibility to pulmonary tuberculosis: A meta-analysis based on the findings of 11 case–control studies. ASIAN PAC J TROP MED 2016; 9:1150-1157. [DOI: 10.1016/j.apjtm.2016.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/20/2016] [Accepted: 09/19/2016] [Indexed: 11/16/2022] Open
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141
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Areeshi MY, Mandal RK, Akhter N, Dar SA, Jawed A, Wahid M, Mahto H, Panda AK, Lohani M, Haque S. A Meta-analysis of MBL2 Polymorphisms and Tuberculosis Risk. Sci Rep 2016; 6:35728. [PMID: 27876780 PMCID: PMC5120291 DOI: 10.1038/srep35728] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/03/2016] [Indexed: 01/11/2023] Open
Abstract
MBL2 gene encodes mannose-binding lectin, is a member of innate immune system. Earlier studies revealed that MBL2 gene variants, rs1800451, rs1800450, rs5030737, rs7096206, rs11003125 and rs7095891 are associated with impaired serum level and susceptibility to TB, but their results are inconsistent. A meta-analysis was performed by including 22 studies (7095 TB-patients and 7662 controls) and data were analyzed with respect to associations between alleles, genotypes and minor allele carriers to evaluate the potential association between MBL2 polymorphisms and TB risk. Statistically significant results were found only for the homozygous variant genotype (CC vs. AA: p = 0.045; OR = 0.834, 95% CI = 0.699 to 0.996) of rs1800451 and showed reduced risk of TB in overall population. However, other genetic models of rs1800450, rs5030737, rs7096206, rs11003125, rs7095891 and combined rs1800450, rs1800451, rs5030737 polymorphisms of MBL2 gene did not reveal any association with TB risk. Stratified analysis by ethnicity showed decreased risk of TB in African population for rs1800450 and rs1800451. Whereas, no association was observed between other MBL2 polymorphisms and TB risk in all the evaluated ethnic populations. In conclusion, MBL2 rs1800450 and rs1800451 polymorphisms play a protective role in TB infection and reinforce their critical significance as a potential genetic marker for TB resistance.
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Affiliation(s)
- Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing &Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing &Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha-65431, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing &Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia.,The University College of Medical Sciences >B Hospital (University of Delhi), Delhi-110095, India
| | - Arshad Jawed
- 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
| | - Harishankar Mahto
- Centre for Life Sciences, Central University of Jharkhand, Ranchi-835205, Jharkhand, India
| | - Aditya K Panda
- Centre for Life Sciences, Central University of Jharkhand, Ranchi-835205, Jharkhand, India
| | - Mohtashim Lohani
- Research and Scientific Studies Unit, College of Nursing &Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia.,Department of Biosciences, Integral University, Lucknow-226026, Uttar Pradesh, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing &Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia.,Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi-110025, India
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142
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Systematic review and meta-analysis of genetic association studies in idiopathic recurrent spontaneous abortion. Fertil Steril 2016; 107:150-159.e2. [PMID: 27842992 DOI: 10.1016/j.fertnstert.2016.10.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/12/2023]
Abstract
OBJECTIVES 1) To perform the first comprehensive systematic review of genetic association studies (GASs) in idiopathic recurrent spontaneous abortion (IRSA); 2) to analyze studies according to recurrent spontaneous abortion (RSA) definition and selection criteria for patients and control subjects; and 3) to perform meta-analyses for the association of candidate genes with IRSA. DESIGN Systematic review and meta-analysis. SETTING Not applicable. PATIENT(S) Couples with IRSA and their spontaneously aborted embryos. INTERVENTION(S) Summary odds ratios (ORs) were calculated by means of fixed- or random-effects models. MAIN OUTCOME MEASURE(S) Association of genetic variants with IRSA. RESULT(S) The systematic review included 428 case-control studies (1990-2015), which differed substantially regarding RSA definition, clinical evaluation of patients, and selection of control subjects. In women, 472 variants in 187 genes were investigated. Meta-analyses were performed for 36 variants in 16 genes. Association with IRSA defined as three or more spontaneous abortions (SAs) was detected for 21 variants in genes involved in immune response (IFNG, IL10, KIR2DS2, KIR2DS3, KIR2DS4, MBL, TNF), coagulation (F2, F5, PAI-1, PROZ), metabolism (GSTT1, MTHFR), and angiogenesis (NOS3, VEGFA). However, ORs were modest (0.51-2.37), with moderate or weak epidemiologic credibility. Minor differences in summary ORs were detected between IRSA defined as two or more and as three or more SAs. Male partners were included in 12.1% of studies, and one study included spontaneously aborted embryos. CONCLUSION(S) Candidate gene studies show moderate associations with IRSA. Owing to large differences in RSA definition and selection criteria for participants, consensus is needed. Future GASs should include both partners and spontaneously aborted embryos. Genome-wide association studies and large-scale replications of identified associations are recommended.
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143
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Zhang JP, Lencz T, Zhang RX, Nitta M, Maayan L, John M, Robinson DG, Fleischhacker WW, Kahn RS, Ophoff RA, Kane JM, Malhotra AK, Correll CU. Pharmacogenetic Associations of Antipsychotic Drug-Related Weight Gain: A Systematic Review and Meta-analysis. Schizophr Bull 2016; 42:1418-1437. [PMID: 27217270 PMCID: PMC5049532 DOI: 10.1093/schbul/sbw058] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although weight gain is a serious but variable adverse effect of antipsychotics that has genetic underpinnings, a comprehensive meta-analysis of pharmacogenetics of antipsychotic-related weight gain is missing. In this review, random effects meta-analyses were conducted for dominant and recessive models on associations of specific single nucleotide polymorphisms (SNP) with prospectively assessed antipsychotic-related weight or body mass index (BMI) changes (primary outcome), or categorical increases in weight or BMI (≥7%; secondary outcome). Published studies, identified via systematic database search (last search: December 31, 2014), plus 3 additional cohorts, including 222 antipsychotic-naïve youth, and 81 and 141 first-episode schizophrenia adults, each with patient-level data at 3 or 4 months treatment, were meta-analyzed. Altogether, 72 articles reporting on 46 non-duplicated samples (n = 6700, mean follow-up = 25.1wk) with 38 SNPs from 20 genes/genomic regions were meta-analyzed (for each meta-analysis, studies = 2-20, n = 81-2082). Eleven SNPs from 8 genes were significantly associated with weight or BMI change, and 4 SNPs from 2 genes were significantly associated with categorical weight or BMI increase. Combined, 13 SNPs from 9 genes (Adrenoceptor Alpha-2A [ADRA2A], Adrenoceptor Beta 3 [ADRB3], Brain-Derived Neurotrophic Factor [BDNF], Dopamine Receptor D2 [DRD2], Guanine Nucleotide Binding Protein [GNB3], 5-Hydroxytryptamine (Serotonin) Receptor 2C [HTR2C], Insulin-induced gene 2 [INSIG2], Melanocortin-4 Receptor [MC4R], and Synaptosomal-associated protein, 25kDa [SNAP25]) were significantly associated with antipsychotic-related weight gain (P-values < .05-.001). SNPs in ADRA2A, DRD2, HTR2C, and MC4R had the largest effect sizes (Hedges' g's = 0.30-0.80, ORs = 1.47-1.96). Less prior antipsychotic exposure (pediatric or first episode patients) and short follow-up (1-2 mo) were associated with larger effect sizes. Individual antipsychotics did not significantly moderate effect sizes. In conclusion, antipsychotic-related weight gain is polygenic and associated with specific genetic variants, especially in genes coding for antipsychotic pharmacodynamic targets.
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Affiliation(s)
- Jian-Ping Zhang
- *To whom correspondence should be addressed; Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health System, 75-59 263rd Street, Glen Oaks, NY 11020, US; tel: 718-470-8471, fax: 718-470-1905, e-mail:
| | | | - Ryan X. Zhang
- Department of Psychology and Neuroscience, Duke University, Durham, NY
| | - Masahiro Nitta
- Drug Development Division, Sumitomo Dainippon Pharma Co. Ltd, Tokyo, Japan
| | - Lawrence Maayan
- Department of Psychiatry, New York University School of Medicine, New York, NY
| | - Majnu John
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health System, Glen Oaks, NY;,Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, Manhasset, NY;,Department of Mathematics, Hofstra University, Hempstead, NY
| | | | | | - Rene S. Kahn
- Department of Psychiatry, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Roel A. Ophoff
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA
| | - John M. Kane
- Department of Psychiatry, Albert Einstein College of Medicine, Bronx, NY
| | | | - Christoph U. Correll
- Department of Psychiatry, Albert Einstein College of Medicine, Bronx, NY,Both authors contributed equally to the article
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144
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Li X, Song P, Timofeeva M, Meng X, Rudan I, Little J, Satsangi J, Campbell H, Theodoratou E. Systematic meta-analyses and field synopsis of genetic and epigenetic studies in paediatric inflammatory bowel disease. Sci Rep 2016; 6:34076. [PMID: 27670835 PMCID: PMC5037432 DOI: 10.1038/srep34076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023] Open
Abstract
We provide a comprehensive field synopsis of genetic and epigenetic associations for paediatric Inflammatory Bowel Disease (IBD). A systematic review was performed and included 84 genetic association studies reporting data for 183 polymorphisms in 71 genes. Meta-analyses were conducted for 20 SNPs in 10 genes of paediatric Crohn’s disease (CD) and for 8 SNPs in 5 genes of paediatric ulcerative colitis (UC). Five epigenetic studies were also included, but formal meta-analysis was not possible. Venice criteria and Bayesian false discovery probability test were applied to assess the credibility of associations. Nine SNPs in 4 genes were considered to have highly credible associations with paediatric CD, of which four variants (rs2066847, rs12521868, rs26313667, rs1800629) were not previously identified in paediatric GWAS. Differential DNA methylation in NOD2 and TNF-α, dysregulated expression in let-7 and miR-124 were associated with paediatric IBD, but not as yet replicated. Highly credible SNPs associated with paediatric IBD have also been implicated in adult IBD, with similar magnitudes of associations. Early onset and distinct phenotypic features of paediatric IBD might be due to distinct epigenetic changes, but these findings need to be replicated. Further progress identifying genetic and epigenetic susceptibility of paediatric IBD will require international collaboration, population diversity and harmonization of protocols.
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Affiliation(s)
- Xue Li
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peige Song
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Xiangrui Meng
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh and Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
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145
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Zeng Y, Jiang HY, Wei L, Xu WD, Wang YJ, Wang YD, Liu C. Association between the CYP1A2 rs762551 Polymorphism and Bladder Cancer Susceptibility: a Meta-Analysis Based on Case-Control Studies. Asian Pac J Cancer Prev 2016; 16:7249-54. [PMID: 26514519 DOI: 10.7314/apjcp.2015.16.16.7249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies evaluated associations between the CYP1A2 rs762551 polymorphism and bladder cancer risk. However, the results were inconsistent. We therefore performed a meta-analysis of the published case-control studies to assess in detail the association between CYP1A2 rs762551 polymorphism and bladder cancer risk. MATERIALS AND METHODS PubMed, Embase and Web of Science were searched to identify relevant studies and the pooled odds ratio (OR) and 95 % confidence interval (95%CI) were calculated. RESULTS A total of seven articles including 3,013 cases and 2,771 controls were finally included. Overall, a significant association was found between the CYP1A2 rs762551 polymorphism and bladder cancer susceptibility for CC vs AA (OR=0.82, 95% CI=0.69~0.99), but no significant associations were found for the other three models (AC vs AA: OR=0.91, 95% CI=0.81~1.02; the dominant model: OR=0.90, 95% CI=0.80~1.00; the recessive model: OR=0.84, 95% CI =0.72~1.00). In the subgroup analysis by ethnicity, we detected significant associations between the CYP1A2 rs762551 polymorphism and bladder cancer susceptibility for GA vs GG (OR = 0.78, 95% CI =0.64~0.96) and for the recessive model (OR=0.80, 95% CI=0.66~0.96) in Caucasians, but not for Asians. CONCLUSIONS The results from the meta-analysis suggested that the CYP1A2 rs762551 polymorphism is a protective factor for bladder cancer, especially in Caucasians.
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Affiliation(s)
- Yong Zeng
- Department of Cardiothoracic Surgery, Shaoxing People's Hospital , Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang Province, China E-mail :
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146
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TNF-α -308 G > A (rs1800629) Polymorphism is Associated with Celiac Disease: A Meta-analysis of 11 Case-Control Studies. Sci Rep 2016; 6:32677. [PMID: 27597177 PMCID: PMC5011702 DOI: 10.1038/srep32677] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/12/2016] [Indexed: 12/21/2022] Open
Abstract
Celiac disease (CD) remains one of the most significant autoimmune diseases worldwide. The pathogenesis of CD is not clearly understood and is probably attributed to genomic variations and host genetic make-up. Case-control and cohort studies of the association between the TNF-α -308 G > A (rs1800629) polymorphism and CD susceptibility have yielded inconsistent results. In this study, PubMed, EMBASE, and Google Scholar web-databases were searched for pertinent reports showing association of TNF-α -308 G > A gene with CD risk. A total of eleven reports involving 1774 controls and 1147 CD cases were included. Significant associations in four genetic models, viz. variant allele (A vs. G: p = 0.001; OR = 2.051, 95% CI = 1.452-2.895), variant homozygous (AA vs. GG: p = 0.001; OR = 6.626, 95% CI = 3.569-12.300), recessive (AA vs. GG + AG: p = 0.001; OR = 4.766, 95% CI = 3.177-7.152) and dominant (AA + AG vs. GG: p = 0.008; OR = 1.910, 95% CI = 1.181-3.088) were found in comparison with wild type homozygous GG genotype. However, heterozygous genetic model did not show any association. Sensitivity analysis revealed stable and statistically robust results. Our results suggest that TNF-α -308 G > A gene polymorphism significantly contributes to CD susceptibility.
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147
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Chang H, Zhang C, Xiao X, Pu X, Liu Z, Wu L, Li M. Further evidence of VRK2 rs2312147 associated with schizophrenia. World J Biol Psychiatry 2016; 17:457-66. [PMID: 27382989 DOI: 10.1080/15622975.2016.1200746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Previous genome-wide association studies (GWAS) have reported that rs2312147 near the VRK2 gene was significantly associated with schizophrenia in populations of European descent, but negative results have also been observed. METHODS To perform a systematic meta-analysis, we collected statistical data of rs2312147 from both GWAS and individual replication samples in European and Asian populations, which finally included up to 30,867 schizophrenia patients and 59,863 healthy controls. RESULTS The VRK2 rs2312147 was genome-wide significantly associated with schizophrenia in combined populations (P = 1.31 × 10(-15), odds ratio, OR = 1.10) as well as in Europeans only (P = 2.35 × 10(-12), OR =1.09). In Asian samples, the SNP did not reach genome-wide level of statistical significance (P = 1.23 × 10 (-) (5), OR =1.19), which is likely due to the limited power of small sample size in this population (2,974 cases and 4,786 controls). However, the effect size of rs2312147 did not alter significantly between populations, and is also in agreement with the observed effect sizes of other genetic risk loci in large scale studies. CONCLUSIONS Our data provides further evidence for the genetic contributions of VRK2 rs2312147 to schizophrenia susceptibility especially in Europeans, while further replication analyses in Asian populations are still needed, and future studies, e.g., the underlying molecular mechanisms of genetic risk, are necessary.
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Affiliation(s)
- Hong Chang
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province , Kunming Institute of Zoology , Kunming , Yunnan , China
| | - Chen Zhang
- b Division of Mood Disorders , Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Xiao Xiao
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province , Kunming Institute of Zoology , Kunming , Yunnan , China
| | - Xingfu Pu
- c The Second People's Hospital of Yuxi City , Yuxi , Yunnan , China
| | - Zichao Liu
- d Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province, Department of Biological Science and Technology , Kunming University , Kunming , Yunnan , China
| | - Lichuan Wu
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province , Kunming Institute of Zoology , Kunming , Yunnan , China
| | - Ming Li
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province , Kunming Institute of Zoology , Kunming , Yunnan , China
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148
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Huang T, Liu CL, Li LL, Cai MH, Chen WZ, Xu YF, O'Reilly PF, Cai L, He L. A new method for identifying causal genes of schizophrenia and anti-tuberculosis drug-induced hepatotoxicity. Sci Rep 2016; 6:32571. [PMID: 27580934 PMCID: PMC5007646 DOI: 10.1038/srep32571] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/10/2016] [Indexed: 12/21/2022] Open
Abstract
Schizophrenia (SCZ) may cause tuberculosis, the treatments for which can induce anti-tuberculosis drug-induced hepatotoxicity (ATDH) and SCZ-like disorders. To date, the causal genes of both SCZ and ATDH are unknown. To identify them, we proposed a new network-based method by integrating network random walk with restart algorithm, gene set enrichment analysis, and hypergeometric test; using this method, we identified 500 common causal genes. For gene validation, we created a regularly updated online database ATDH-SCZgenes and conducted a systematic meta-analysis of the association of each gene with either disease. Till now, only GSTM1 and GSTT1 have been well studied with respect to both diseases; and a total of 23 high-quality association studies were collected for the current meta-analysis validation. Finally, the GSTM1 present genotype was confirmed to be significantly associated with both ATDH [Odds Ratio (OR): 0.71, 95% confidence interval (CI): 0.56–0.90, P = 0.005] and SCZ (OR: 0.78, 95% CI: 0.66–0.92, P = 0.004) according to the random-effect model. Furthermore, these significant results were supported by “moderate” evidence according to the Venice criteria. Our findings indicate that GSTM1 may be a causal gene of both ATDH and SCZ, although further validation pertaining to other genes, such as CYP2E1 or DRD2, is necessary.
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Affiliation(s)
- Tao Huang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China.,Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Lin Liu
- School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Lin-Lin Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China
| | - Mei-Hong Cai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China
| | - Wen-Zhong Chen
- Shanghai Mental Health Center, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Yi-Feng Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China.,Shanghai Mental Health Center, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Paul F O'Reilly
- MRC SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London WC2R 2LS, United Kingdom
| | - Lei Cai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China.,Shanghai Mental Health Center, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Jiaotong University, Shanghai 200030, China.,Shanghai Mental Health Center, Shanghai Jiaotong University, Shanghai, 200240, China
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149
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Genetic Association of CHAT rs3810950 and rs2177369 Polymorphisms with the Risk of Alzheimer's Disease: A Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9418163. [PMID: 27597977 PMCID: PMC5002460 DOI: 10.1155/2016/9418163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/03/2016] [Accepted: 07/03/2016] [Indexed: 12/28/2022]
Abstract
Choline acetyltransferase (CHAT) rs3810950 and rs2177369 polymorphisms have been implicated in susceptibility to Alzheimer's disease (AD). Due to the inconsistent results from previous studies, a meta-analysis was performed to estimate the association between these polymorphisms and AD risk more precisely. Pooled results of our meta-analysis indicated CHAT rs2177369 polymorphism was correlated with decreasing AD risk in one of five genetic models (dominant: OR = 0.77, 95% CI: 0.62–0.96), while rs3810950 mutant was associated with AD development in three models (allelic: OR = 1.18, 95% CI: 1.01–1.37, homozygous: OR = 1.63, 95% CI: 1.09–2.42, and recessive: OR = 1.65, 95% CI: 1.20–2.26). In subgroup analysis by ethnicity, the association between CHAT rs3810950 polymorphism and AD risk was just found in the recessive model (OR = 1.47, 95% CI: 1.05–2.07) among Caucasians, while four genetic models (allelic: OR = 1.23, 95% CI: 1.01–1.48; homozygous: OR = 2.24, 95% CI: 1.48–3.39; dominant: OR = 1.21, 95% CI: 1.06–1.40; and recessive: OR = 2.18, 95% CI: 1.45–3.29) assumed this association in Asians. In conclusion, our meta-analysis indicated CHAT rs2177369 polymorphism might play a protective role in AD, while rs3810950 variant was a risk factor for AD but its single heterozygous mutations might not influence susceptibility to AD.
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150
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Fan W, Huang Z, Xiao Z, Li S, Ma Q. The cytochrome P4501A1 gene polymorphisms and endometriosis: a meta-analysis. J Assist Reprod Genet 2016; 33:1373-1383. [PMID: 27525656 DOI: 10.1007/s10815-016-0783-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/25/2016] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Cytochrome P450 1A1 (CYP1A1) polymorphisms were implicated in endometriosis risk, but individual published studies showed inconclusive results. Thus, a meta-analysis was performed to clarify the effect of CYP1A1 polymorphisms on endometriosis risk. METHODS PubMed, Embase, and CNKI databases were searched to identify the eligible studies focusing on the associations between CYP1A1 MspI and Ile462Val polymorphisms and susceptibility to endometriosis. Summary odds ratios (ORs) and 95 % confidence intervals (95 % CIs) for CYP1A1 polymorphisms and endometriosis were calculated. RESULTS Pooled analysis of 12 studies involved a total of 1555 cases and 2868 controls showed that in all genetic models, no significant association between CYP1A1 MspI polymorphism and endometriosis risk was observed in the overall, Asians and Caucasians population, respectively. Interestingly, increased endometriosis risk was associated with carrying the C allele of CYP1A1 combined with GSTM1 null genotypes. For CYP1A1 Ile462Val polymorphism, eight studies were available (878 cases and 1991 controls). In the overall analysis, CYP1A1 Ile462Val polymorphism had a statistically significant association with increased endometriosis risk in allele contrast and all genetic models except the model of Val/Ile vs. Ile/Ile. In the subgroup analysis by ethnicity, significant elevated endometriosis risk was associated with CYP1A1 Ile462Val polymorphism in Asians but not in Caucasians under all genetic models. No publication bias was found in the present studies. CONCLUSIONS This meta-analysis suggested that CYP1A1 Ile462Val polymorphism was associated with an increased risk of endometriosis, particularly in Asians. CYP1A1 MspI polymorphism may not be associated with endometriosis risk, but GSTM1 and CYP1A1 MspI polymorphism may have a joint effect on endometriosis risk.
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Affiliation(s)
- Wei Fan
- Center of Reproductive Medicine, The West China Second University Hospital, Sichuan University, Sichuan, People's Republic of China
| | - Zhongying Huang
- Center of Reproductive Medicine, The West China Second University Hospital, Sichuan University, Sichuan, People's Republic of China
| | - Zhun Xiao
- Center of Reproductive Medicine, The West China Second University Hospital, Sichuan University, Sichuan, People's Republic of China
| | - Shangwei Li
- Center of Reproductive Medicine, The West China Second University Hospital, Sichuan University, Sichuan, People's Republic of China
| | - Qianhong Ma
- Center of Reproductive Medicine, The West China Second University Hospital, Sichuan University, Sichuan, People's Republic of China.
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