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Barnett GC, Kerns SL, Dorling L, Fachal L, Aguado-Barrera ME, Martínez-Calvo L, Jandu HK, Welsh C, Tyrer J, Coles CE, Haviland JS, Parker C, Gómez-Caamaño A, Calvo-Crespo P, Sosa-Fajardo P, Burnet NG, Summersgill H, Webb A, De Ruysscher D, Seibold P, Chang-Claude J, Talbot CJ, Rattay T, Parliament M, De Ruyck K, Rosenstein BS, Pharoah PDP, Dunning AM, Vega A, West CML. No Association Between Polygenic Risk Scores for Cancer and Development of Radiation Therapy Toxicity. Int J Radiat Oncol Biol Phys 2022; 114:494-501. [PMID: 35840111 DOI: 10.1016/j.ijrobp.2022.06.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE Our aim was to test whether updated polygenic risk scores (PRS) for susceptibility to cancer affect risk of radiation therapy toxicity. METHODS AND MATERIALS Analyses included 9,717 patients with breast (n=3,078), prostate (n=5,748) or lung (n=891) cancer from Radiogenomics and REQUITE Consortia cohorts. Patients underwent potentially curative radiation therapy and were assessed prospectively for toxicity. Germline genotyping involved genome-wide single nucleotide polymorphism (SNP) arrays with nontyped SNPs imputed. PRS for each cancer were generated by summing literature-identified cancer susceptibility risk alleles: 352 breast, 136 prostate, and 24 lung. Weighted PRS were generated using log odds ratio (ORs) for cancer susceptibility. Standardized total average toxicity (STAT) scores at 2 and 5 years (breast, prostate) or 6 to 12 months (lung) quantified toxicity. Primary analysis tested late STAT, secondary analyses investigated acute STAT, and individual endpoints and SNPs using multivariable regression. RESULTS Increasing PRS did not increase risk of late toxicity in patients with breast (OR, 1.000; 95% confidence interval [CI], 0.997-1.002), prostate (OR, 0.99; 95% CI, 0.98-1.00; weighted PRS OR, 0.93; 95% CI, 0.83-1.03), or lung (OR, 0.93; 95% CI, 0.87-1.00; weighted PRS OR, 0.68; 95% CI, 0.45-1.03) cancer. Similar results were seen for acute toxicity. Secondary analyses identified rs138944387 associated with breast pain (OR, 3.05; 95% CI, 1.86-5.01; P = 1.09 × 10-5) and rs17513613 with breast edema (OR, 0.94; 95% CI, 0.92-0.97; P = 1.08 × 10-5). CONCLUSIONS Patients with increased polygenic predisposition to breast, prostate, or lung cancer can safely undergo radiation therapy with no anticipated excess toxicity risk. Some individual SNPs increase the likelihood of a specific toxicity endpoint, warranting validation in independent cohorts and functional studies to elucidate biologic mechanisms.
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Affiliation(s)
- Gillian C Barnett
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom.
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Miguel E Aguado-Barrera
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Laura Martínez-Calvo
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Harkeran K Jandu
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ceilidh Welsh
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Charlotte E Coles
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom
| | - Joanne S Haviland
- Clinical Trials and Statistics Unit, Institute of Cancer Research, London, United Kingdom
| | - Christopher Parker
- Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Patricia Calvo-Crespo
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Paloma Sosa-Fajardo
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Neil G Burnet
- Proton Beam Therapy Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Holly Summersgill
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Adam Webb
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Dirk De Ruysscher
- Department of Radiation Oncology (Maastro Clinic), Maastricht University Medical Center, GROW School for Oncology and Developmental Biology, Maastricht, The Netherlands; Radiation Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | - Christopher J Talbot
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Tim Rattay
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Matthew Parliament
- Division of Radiation Oncology, Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Kim De Ruyck
- Departments of Basic Medical Sciences and Radiotherapy, Ghent University Hospital, Ghent, Belgium
| | - Barry S Rosenstein
- Departments of Radiation Oncology and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Ana Vega
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Biomedical Network on Rare Diseases (CIBERER), Spain
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
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Wu M, Yang Y, Wang H, Ding J, Zhu H, Xu Y. IMPMD: An Integrated Method for Predicting Potential Associations Between miRNAs and Diseases. Curr Genomics 2020; 20:581-591. [PMID: 32581646 PMCID: PMC7290057 DOI: 10.2174/1389202920666191023090215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/07/2019] [Accepted: 10/16/2019] [Indexed: 01/06/2023] Open
Abstract
Background With the rapid development of biological research, microRNAs (miRNAs) have increasingly attracted worldwide attention. The increasing biological studies and scientific experiments have proven that miRNAs are related to the occurrence and development of a large number of key biological processes which cause complex human diseases. Thus, identifying the association between miRNAs and disease is helpful to diagnose the diseases. Although some studies have found considerable associations between miRNAs and diseases, there are still a lot of associations that need to be identified. Experimental methods to uncover miRNA-disease associations are time-consuming and expensive. Therefore, effective computational methods are urgently needed to predict new associations. Methodology In this work, we propose an integrated method for predicting potential associations between miRNAs and diseases (IMPMD). The enhanced similarity for miRNAs is obtained by combination of functional similarity, gaussian similarity and Jaccard similarity. To diseases, it is obtained by combination of semantic similarity, gaussian similarity and Jaccard similarity. Then, we use these two enhanced similarities to construct the features and calculate cumulative score to choose robust features. Finally, the general linear regression is applied to assign weights for Support Vector Machine, K-Nearest Neighbor and Logistic Regression algorithms. Results IMPMD obtains AUC of 0.9386 in 10-fold cross-validation, which is better than most of the previous models. To further evaluate our model, we implement IMPMD on two types of case studies for lung cancer and breast cancer. 49 (Lung Cancer) and 50 (Breast Cancer) out of the top 50 related miRNAs are validated by experimental discoveries. Conclusion We built a software named IMPMD which can be freely downloaded from https://github.com/Sunmile/IMPMD.
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Affiliation(s)
- Meiqi Wu
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
| | - Yingxi Yang
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
| | - Hui Wang
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
| | - Jun Ding
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
| | - Huan Zhu
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
| | - Yan Xu
- 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing100083, China; 2Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China; 3Institute of Computing Technology, Chinese Academy of Sciences, Beijing100080, China
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3
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He G, Song T, Zhang Y, Chen X, Xiong W, Chen H, Sun C, Zhao C, Chen Y, Wu H. TERT rs10069690 polymorphism and cancers risk: A meta-analysis. Mol Genet Genomic Med 2019; 7:e00903. [PMID: 31454181 PMCID: PMC6785442 DOI: 10.1002/mgg3.903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Studies have identified that the telomerase reverse transcriptase (TERT) gene polymorphism rs10069690 (C>T) is associated with cancer risk, but the results remain inconclusive. METHODS To provide a more precise estimation of the relationship, we performed a meta-analysis of 45 published studies including 329,035 cases and 730,940 controls. We conducted a search in PubMed, Google Scholar and Web of Science to select studies on the association between rs10069690 and cancer risk. Stratification by ethnicity, cancer type, cancers' classification, source of control, sample size, and genotype method was used to explore the source of heterogeneity. The pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were evaluated using random effects models. Sensitivity, publication bias, false-positive report probability (FPRP) and statistical power were also assessed. RESULTS The result demonstrated that rs10069690 was significantly associated with an increased risk of cancer overall (OR = 1.09, 95% CI: 1.06-1.12, p < .001) under the allele model. Stratification analysis revealed an increased cancer risk in subgroups of breast cancer, ovarian cancer, lung cancer, thyroid cancer, and renal cell carcinoma (RCC). However, a significantly decreased association was observed in pancreatic cancer in the European population (OR = 0.93,95% CI: 0.87-0.99, p = .031). In the subgroup analysis based on cancer type, no significant association was found in prostate cancer, leukemia, colorectal cancer and glioma. CONCLUSIONS This meta-analysis suggested that the TERT rs10069690 polymorphism may be a risk factor for cancer, especially breast cancer, ovarian cancer, lung cancer, thyroid cancer, and RCC. Further functional studies are warranted to reveal the role of the polymorphism in carcinogenesis.
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Affiliation(s)
- Guisheng He
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Tao Song
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Yazhen Zhang
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Xiuxiu Chen
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Wei Xiong
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Huamin Chen
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Chuanwei Sun
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Chaoyang Zhao
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Yunjing Chen
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
| | - Huangfu Wu
- Department of Surgical OncologySecond Affiliated Hospital of Hainan Medical CollegeHaikouHainan ProvinceChina
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Shao L, Zuo X, Yang Y, Zhang Y, Yang N, Shen B, Wang J, Wang X, Li R, Jin G, Yu D, Chen Y, Sun L, Li Z, Fu Q, Hu Z, Han X, Song X, Shen H, Sun Y. The inherited variations of a p53-responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression. Genome Biol 2019; 20:103. [PMID: 31126313 PMCID: PMC6533720 DOI: 10.1186/s13059-019-1696-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 04/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechanisms of cancers. The tag-SNP rs753955 (A>G) in 13q12.12 is highly associated with lung cancer risk in the Chinese population. Here, we systematically investigate the biological significance and the underlying mechanism behind 13q12.12 risk locus in vitro and in vivo. Results We characterize a novel p53-responsive enhancer with lung tissue cell specificity in a 49-kb high linkage disequilibrium block of rs753955. This enhancer harbors 3 highly linked common inherited variations (rs17336602, rs4770489, and rs34354770) and six p53 binding sequences either close to or located between the variations. The enhancer effectively protects normal lung cell lines against pulmonary carcinogen NNK-induced DNA damages and malignant transformation by upregulating TNFRSF19 through chromatin looping. These variations significantly weaken the enhancer activity by affecting its p53 response, especially when cells are exposed to NNK. The effect of the mutant enhancer alleles on TNFRSF19 target gene in vivo is supported by expression quantitative trait loci analysis of 117 Chinese NSCLC samples and GTEx data. Differentiated expression of TNFRSF19 and its statistical significant correlation with tumor TNM staging and patient survival indicate a suppressor role of TNFRSF19 in lung cancer. Conclusion This study provides evidence of how the inherited variations in 13q12.12 contribute to lung cancer risk, highlighting the protective roles of the p53-responsive enhancer-mediated TNFRSF19 activation in lung cells under carcinogen stress. Electronic supplementary material The online version of this article (10.1186/s13059-019-1696-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lipei Shao
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Xianglin Zuo
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yin Yang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yu Zhang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Nan Yang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211126, China
| | - Jianying Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211126, China
| | - Xuchun Wang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Ruilei Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China
| | - Dawei Yu
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yuan Chen
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Luan Sun
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Zhen Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Qiaofen Fu
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China
| | - Xiao Han
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China
| | - Xin Song
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China.
| | - Hongbin Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China.
| | - Yujie Sun
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China. .,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China.
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5
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Abstract
After more than 10 years of accumulated efforts, genome-wide association studies (GWAS) have led to many findings, most of which have been deposited into the GWAS Catalog. Between GWAS's inception and March 2017, the GWAS Catalog has collected 2429 studies, 1818 phenotypes, and 28,462 associated SNPs. We reclassified the psychology-related phenotypes into 217 reclassified phenotypes, which accounted for 514 studies and 7052 SNPs. In total, 1223 of the SNPs reached genome-wide significance. Of these, 147 were replicated for the same psychological trait in different studies. Another 305 SNPs were replicated within one original study. The SNPs rs2075650 and rs4420638 were linked to the most replications within a single reclassified phenotype or very similar reclassified phenotypes; both were associated with Alzheimer's disease (AD). Schizophrenia was associated with 74 within-phenotype SNPs reported in independents studies. Alzheimer's disease and schizophrenia were both linked to some physical phenotypes, including cholesterol and body mass index, through common GWAS signals. Alzheimer's disease also shared risk SNPs with age-related phenotypes such as age-related macular degeneration and longevity. Smoking-related SNPs were linked to lung cancer and respiratory function. Alcohol-related SNPs were associated with cardiovascular and digestive system phenotypes and disorders. Two separate studies also identified a shared risk SNP for bipolar disorder and educational attainment. This review revealed a list of reproducible SNPs worthy of future functional investigation. Additionally, by identifying SNPs associated with multiple phenotypes, we illustrated the importance of studying the relationships among phenotypes to resolve the nature of their causal links. The insights within this review will hopefully pave the way for future evidence-based genetic studies.
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6
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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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7
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Fang X, Yin Z, Li X, Xia L, Quan X, Zhao Y, Zhou B. Multiple functional SNPs in differentially expressed genes modify risk and survival of non-small cell lung cancer in Chinese female non-smokers. Oncotarget 2017; 8:18924-18934. [PMID: 28148898 PMCID: PMC5386658 DOI: 10.18632/oncotarget.14836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
DNA genotype can affect gene expression, and gene expression can influence the onset and progression of diseases. Here we conducted a comprehensive study, we integrated analysis of gene expression profile and single nucleotide polymorphism (SNP) microarray data in order to scan out the critical genetic changes that participate in the onset and development of non-small cell lung cancer (NSCLC). Gene expression profile datasets were downloaded from the GEO database. Firstly, differentially expressed genes (DEGs) between NSCLC samples and adjacent normal samples were identified. Next, by STRING database, protein-protein interaction (PPI) network was constructed. At the same time, hub genes in PPI network were identified. Then, some functional SNPs in hub genes that may affect gene expression have been annotated. Finally, we carried a study to explore the relationship between functional SNPs and NSCLC risk and overall survival in Chinese female non-smokers. A total of 488 DEGs were identified in our study. There are 29 proteins with a higher degree of connectivity in the PPI network, including FOS, IL6 and MMP9. By using database annotation, we got 8 candidate functional SNPs that may affect the expression level of hub proteins. In the case-control study, we found that rs4754-T allele, rs959173-C allele and rs2239144-G allele were the protective allele of NSCLC risk. In dominant model, rs4754-CT+TT genotype were associated with a shorter survival time. In general, our study provides a novel research direction in the field of multi-omic data integration, and helps us find some critical genetic changes in disease.
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Affiliation(s)
- Xue Fang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Lingzi Xia
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xiaowei Quan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Yuxia Zhao
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
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