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Delobel D, Furutani Y, Nagoshi S, Tsubota A, Miyasaka A, Watashi K, Wakita T, Matsuura T, Usui K. SEB genotyping: SmartAmp-Eprimer binary code genotyping for complex, highly variable targets applied to HBV. BMC Infect Dis 2022; 22:516. [PMID: 35659601 PMCID: PMC9164387 DOI: 10.1186/s12879-022-07458-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background SmartAmp-Eprimer Binary code (SEB) Genotyping is a novel isothermal amplification method for rapid genotyping of any variable target of interest. Methods After in silico alignment of a large number of sequences and computational analysis to determine the smallest number of regions to be targeted by SEB Genotyping, SmartAmp primer sets were designed to obtain a binary code of On/Off fluorescence signals, each code corresponding to a unique genotype. Results Applied to HBV, we selected 4 targets for which fluorescence amplification signals produce a specific binary code unique to each of the 8 main genotypes (A–H) found in patients worldwide. Conclusions We present here the proof of concept of a new genotyping method specifically designed for complex and highly variable targets. Applied here to HBV, SEB Genotyping can be adapted to any other pathogen or disease carrying multiple known mutations. Using simple preparation steps, SEB Genotyping provides accurate results quickly and will enable physicians to choose the best adapted treatment for each of their patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07458-4.
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Shivam V, Boobalan A, Nallusamy S, Ponnusamy K, Veluchamy P, Siva P. Genomic approach to identify association of environmental bisphenol-A (BPA) in daily use plastics as molecular disruptors in breast cancer. Meta Gene 2022. [DOI: 10.1016/j.mgene.2022.101026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Wu Y, Chen Q, Zhang Q, Li M, Li H, Jia L, Huang Y, Zhang J. Analysis of whole-exome data of cfDNA and the tumor tissue of non-small cell lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1453. [PMID: 34734005 PMCID: PMC8506706 DOI: 10.21037/atm-21-4117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022]
Abstract
Background Non-small cell lung cancer (NSCLC) has the highest cancer mortality rate in the world, but currently there is no effective method of dynamic monitoring. Gene mutation is an important factor in tumorigenesis and can be detected using high-throughput sequencing technology. This study aimed to analyze the driving genes in the tumor of NSCLC patients by whole exon sequencing, and to compare and analyze the subclones of the tumor at different time points. Methods We collected 87 cases of NSCLC tumor tissues, para-cancer tissues, and peripheral blood samples for detecting cell-free DNAs (cfDNAs) from January 2016 to December 2018, and whole-exome sequencing was performed. The gene mutation map of NSCLC was drawn in detail by second-generation sequencing data analysis and new driver genes were found. In addition, we performed a subclonal analysis of tumors from different stages of the same patient to further describe the tumor heterogeneity. Results We found that the clonal analysis obtained by cfDNA detection was similar to the clonal analysis of the tissue samples, so real-time monitoring of tumor changes can be carried out through monitoring cfDNA. Conclusions This study provides evidence for studying the gene mutation information of NSCLC and shows the importance of cfDNA in the analysis of tumor subcloning information.
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Affiliation(s)
- Yuanzhou Wu
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qunqing Chen
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | | | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Li
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Longfei Jia
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Huang
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Bulgakova O, Kussainova A, Bersimbaev R. The cell cycle regulatory gene polymorphisms TP53 (rs1042522) and MDM2 (rs2279744) in lung cancer: a meta-analysis. Vavilovskii Zhurnal Genet Selektsii 2020; 24:777-784. [PMID: 33959694 PMCID: PMC8093851 DOI: 10.18699/vj20.673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the most common types of cancer in the world. Although the mechanism of lung
cancer is still unknown, a large number of studies have found a link between gene polymorphisms and the risk of lung
cancer. The tumor suppressor p53 plays a crucial role in maintaining genomic stability and tumor prevention. MDM2
is a critical regulator of the p53 protein. Despite the importance of p53 pathway in cancer, data on the contribution
of SNPs of TP53 (rs1042522) and MDM2 (rs2279744) to the development of lung cancer are very contradictory. A metaanalysis
that collects quantitative data from individual studies and combines their results has the advantage of improving
accuracy, providing reliable estimates, and resolving those issues in which studies on individual associations
are not effective enough. The aim of this study was to determine whether the TP53 (rs1042522) and MDM2 (rs2279744)
polymorphisms confer susceptibility to lung cancer. A meta-analysis was conducted on the associations between the
TP53 (rs1042522) and MDM2 (rs2279744) polymorphisms and lung cancer. A total of 51 comparison studies including
25,366 patients and 25,239 controls were considered in this meta-analysis. The meta-analysis showed no association
between lung cancer and MDM2 (rs2279744) under any model. A noteworthy association of TP53 (rs1042522) with
susceptibility to lung cancer in overall pooled subjects was observed under three different models (allele contrast,
homozygote contrast (additive) and dominant). Stratification by ethnicity indicated an association between the TP53
(rs1042522) and lung cancer in Asians and Caucasians. This meta-analysis demonstrates that the TP53 (rs1042522), but
not MDM2 (rs2279744) polymorphism may confer susceptibility to lung cancer.
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Affiliation(s)
- O Bulgakova
- L.N. Gumilyov Eurasian National University, Institute of Cell Biology and Biotechnology, Nur-Sultan, Kazakhstan
| | - A Kussainova
- L.N. Gumilyov Eurasian National University, Institute of Cell Biology and Biotechnology, Nur-Sultan, Kazakhstan
| | - R Bersimbaev
- L.N. Gumilyov Eurasian National University, Institute of Cell Biology and Biotechnology, Nur-Sultan, Kazakhstan
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Yin J, Hou W, Vogel U, Ma Y, Wang C, Wang H, Sun Z. Interaction between common variants of MDM2 and PPP1R13L and CD3EAP and TP53 SNPs in relation to lung cancer risk among Chinese. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:934. [PMID: 32953734 PMCID: PMC7475392 DOI: 10.21037/atm-19-4784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Lung cancer is a complex disease that diagnosed the most common cancer and led cause of cancer death. MDM2 (MDM2 proto-oncogene) encodes a nuclear-localized E3 ubiquitin ligase. The encoded protein can promote tumor formation by targeting tumor suppressor proteins, such as TP53, for proteasomal degradation. Epidemiology studies have investigated the association of MDM2 single nucleotide polymorphisms (SNP) and interaction between genetic and environmental factors with lung cancer. Methods This Chinese case-control study comprised 627 cases and 633 controls explored the role of MDM2 five htSNPs (rs1690924, rs1846402, rs2291857, rs3730581 and rs3730635, haplotype-tagging SNP) tagging 95% of the common haplotypes across the gene and the interactions of MDM2, PPP1R13L, CD3EAP and TP53 in the same pathological pathway on lung cancer risk, together with smoking-duration. Results None of the htSNPs in MDM2 were associated with lung cancer risk in co-dominant, dominant, recessive, and log-additive models (adjusted for smoking-duration). Haplotype analysis showed that global haplotype association was statistically significant (P=0.0036, adjusted for smoking-duration) and haplotype5 (rs1690924A-rs1846402G-rs2291857C-rs3730581G-rs3730635A) was associated with reduced risk of lung cancer [OR (95%) =0.52 (0.33–0.82), P=0.0053, adjusted for smoking-duration]. MDR interaction analysis showed that two the best significant models and strong synergy between MDM2 and TP53. Conclusions MDM2 five-htSNPs haplotype exhibited association with lung cancer susceptibility, interaction of MDM2 and TP53 htSNPs and smoking-duration contributed to lung cancer risk and strong synergy between MDM2 and TP53 htSNPs influenced lung cancer predisposition. Our results suggest that MDM2, TP53 and smoking-duration interact in relation to lung carcinogenesis.
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Affiliation(s)
- Jiaoyang Yin
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, China
| | - Wei Hou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Yegang Ma
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, China
| | - Chunhong Wang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, China
| | - Huiwen Wang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, China
| | - Zhenxiang Sun
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, China
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Doulabi MSH, Moghaddam RG, Salehzadeh A. Associations between an MDM2 gene polymorphism and ulcerative colitis by ARMS-PCR. Genomics Inform 2020; 18:e9. [PMID: 32224842 PMCID: PMC7120344 DOI: 10.5808/gi.2020.18.1.e9] [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: 02/11/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022] Open
Abstract
Ulcerative colitis is a form of inflammatory bowel disease characterized by chronic inflammation of the colon and rectum. The abnormal lesions in the digestive system caused by ulcerative colitis and intermittent colitis are of major clinical importance. MDM2 is a phospho-protein that functions as a ubiquitin ligase for p53. Recently, a T>G substitution in the promoter of the MDM2 gene (rs309) has been identified. In this case-control study, 174 ulcerative colitis biopsy samples and 82 control samples were collected from colonoscopy centers, hospitals, and clinics in Mazandaran and Gilan Provinces in Iran from October 2014 to May 2015. This MDM2 polymorphism was investigated in DNA samples (extracted from biopsy samples) by amplification-refractory mutation system polymerase chain reaction. The mean age of patients with ulcerative colitis was 46.5 years (range, 28 to 69 years) and that of control individuals was 45.3 years (range, 26 to 71 years). Seventy-eight patients (44.82%) were men and 96 (55.18%) were women. The distribution of the TT, TG, and GG genotypes was 17.93%, 27.59%, and 34.48%, respectively, in the ulcerative colitis patients and 31.70%, 24.40%, and 43.90%, respectively, in the control individuals (odds ratio of GG for ulcerative colitis, 7.142; 95% confidence interval, 2.400 to 9.542; p = 0.001). It was found that a single-nucleotide polymorphism at rs309 in the MDM2 gene was associated with ulcerative colitis. A direct relationship was found between age and ulcerative colitis, while no relationship was found with sex. This finding is of note because the occurrence of intestinal inflammation and subsequent ulcers can precede the development of cancer.
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Affiliation(s)
| | | | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht 41476-54919, Iran
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Stumbryte A, Gudleviciene Z, Kundrotas G, Dabkeviciene D, Kunickaite A, Cicenas S. Individual and combined effect of TP53, MDM2, MDM4, MTHFR, CCR5, and CASP8 gene polymorphisms in lung cancer. Oncotarget 2017; 9:3214-3229. [PMID: 29423041 PMCID: PMC5790458 DOI: 10.18632/oncotarget.22756] [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: 03/22/2017] [Accepted: 11/01/2017] [Indexed: 01/10/2023] Open
Abstract
Lung cancer (LC) is the second common and with the highest mortality oncological disease. Specific biomarkers for its diagnostics, treatment, and prognosis are still under the investigations. Aim of our study was to evaluate the relationship between the polymorphisms of TP53 pathway genes TP53, MDM2, MDM4, the polymorphisms of HPV-associated genes MTHFR, CASP8, CCR5, and HPV infection with survival of LC patients. SNPs were genotyped using PCR-RFLP. qRT-PCR was used to detect, identify, and quantify HPV. No statistically significant differences were detected between individual SNPs and patient survival with stage I-IV LC. Cluster analysis of SNPs in genes MDM4 A/A, CCR5 wt/Δ32, MTHFR C/T, MDM2 T/T showed possible association with the worse survival. Patients who were diagnosed with C/T polymorphic variant of gene MTHFR tend not to survive stage III-IV LC (P = .12). There is a tendency between MDM2 gene T/T variant and worse survival of patients diagnosed with late stage LC (P = .11). HPV infection is very rear among LC patients (3 of 92). Overall, there is a link, although statistically insignificant, between specific SNPs and LC patient survival frequency and time, meanwhile the combination of specific SNPs showed a statistically significant measure. In conclusion, we determined statistically significant (P = .04) link between the poor survival of LC patients after surgery and the combination of polymorphic variants C/T of the MTHFR and T/T of the MDM2 genes, whereas individually these SNPs do not show significant relationship with the survival of patients after surgery.
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Affiliation(s)
- Ausra Stumbryte
- Biobank, National Cancer Institute, LT-08660 Vilnius, Lithuania.,Institute of Biosciences, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania
| | | | | | - Daiva Dabkeviciene
- Institute of Biosciences, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania
| | - Agne Kunickaite
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, LT-08661 Vilnius, Lithuania
| | - Saulius Cicenas
- Department of Thoracic Surgery and Oncology, National Cancer Institute, LT-08660 Vilnius, Lithuania.,Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania
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Enokida Y, Shimizu K, Atsumi J, Kakegawa S, Takase Y, Kaira K, Yashima H, Araki T, Nakazawa S, Ohtaki Y, Nagashima T, Alexander L, Usui K, Ishikawa T, Hayashizaki Y, Takeyoshi I. Prognostic potential of the MDM2 309T>G polymorphism in stage I lung adenocarcinoma. Cancer Med 2016; 5:1791-801. [PMID: 27228500 PMCID: PMC4884639 DOI: 10.1002/cam4.750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 03/27/2016] [Accepted: 04/04/2016] [Indexed: 11/08/2022] Open
Abstract
The MDM2 protein plays an important role in the regulation of cell proliferation and apoptosis via ubiquitination and proteasome‐mediated degradation of p53. The genetic polymorphism rs2279744 (c.309T>G) of the MDM2 gene is reportedly associated with susceptibility and/or prognosis in various cancers. In this study, we investigated the risk factors for worse survival in patients with lung adenocarcinoma (AC). We examined the association between c.309T>G and the prognosis of lung cancer by retrospectively reviewing 453 lung cancer patients. We studied both, clinicopathological and genetic characteristics, including the c.309T>G, p53 Arg72Pro, EGFR,KRAS, and p53 mutations. Associations between these factors and survival outcome were analyzed using Cox proportional hazards models. The frequencies of MDM2 polymorphisms were T/T, 20.8%; T/G, 48.6%, and G/G, 30.7%. The overall survival (OS) of AC patients with pathological stage I disease and the MDM2 T/T genotype was significantly shorter than that of those with the T/G or G/G genotypes (P = 0.02). Multivariate analysis revealed that the MDM2 T/T genotype was an independent, significant prognostic factor (hazard ratio [HR] = 2.23; 95% confidence interval [CI]: 1.07–4.65; P = 0.03). The MDM2 T/T genotype was predictive of poorer survival in a Japanese population. Genotyping for this polymorphism might predict the clinical outcomes of stage I AC patients.
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Affiliation(s)
- Yasuaki Enokida
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Kimihiro Shimizu
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Jun Atsumi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Seiichi Kakegawa
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Yoshiaki Takase
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Kyoichi Kaira
- Department of Oncology Clinical Development, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Hideaki Yashima
- Department of Clinical Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Takuya Araki
- Department of Clinical Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Seshiru Nakazawa
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Yoichi Ohtaki
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Toshiteru Nagashima
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Lezhava Alexander
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshihisa Ishikawa
- NGO Personalized Medicine & Healthcare, Yokohama, Kanagawa, 226-0016, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, 230-0045, Japan
| | - Izumi Takeyoshi
- Department of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
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Xu L, Yang M, Zhao T, Jin H, Xu Z, Li M, Chen H. The polymorphism of CYP2E1 Rsa I/Pst I gene and susceptibility to respiratory system cancer: a systematic review and meta-analysis of 34 studies. Medicine (Baltimore) 2014; 93:e178. [PMID: 25501063 PMCID: PMC4602815 DOI: 10.1097/md.0000000000000178] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The purpose of this articles is to determine whether the cytochrome P450 2E1 (CYP2E1) Rsa I/Pst I gene polymorphism is correlated with respiratory system cancers. Respiratory system cancers included lung cancer, laryngeal cancer, nasopharyngeal cancer, and cancers of other respiratory organs, which are the most common malignant tumors worldwide; the significant relationship between CYP2E1 Rsa I/Pst I gene polymorphism and some respiratory system cancer have been reported, but results of some other studies are controversial. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to assess the association. PubMed, EMBASE, Cochrane Library Databases, China National Knowledge Infrastructure, and Wanfang Database (up to July 20, 2014) were searched for all case-control studies those mainly studied the relationship between CYP2E1 Rsa I/Pst I gene polymorphism and the susceptibility of respiratory system cancer. A total of 332 articles were collected, among which 34 studies that involved 7028 cases and 9822 controls fulfilled the inclusion criteria after being assessed by 2 reviewers. When stratified by cancer site, the C2/C2 polymorphism could increase the risk of nasopharyngeal cancer under the homozygote model (C2C2 vs C1C1: OR = 1.85, 95% CI = 1.20-2.85, P = 0.005) and recessive model (C2C2 vs C1C2/C1C1: OR = 1.89, 95% CI = 1.23-2.89, P = 0.003). Protection effect was found in lung cancer in heterozygote model (C1C2 vs C1C1: OR = 0.82, 95% CI = 0.74-0.91, P < 0.001), dominant model (C1C2/C2C2 vs C1C1: OR = 0.83, 95% CI = 0.76-0.90, P < 0.001), and allele contrast model (C2 vs C1: OR = 0.85, 95% CI = 0.73-1.00, P = 0.045). With regard to ethnicity subgroup analysis, there was significant association in Asian population in heterozygote model (C1C2 vs C1C1: OR = 0.85, 95% CI = 0.78-0.94, P = 0.001), dominant model (C1C2/C2C2 vs C1C1: OR = 0.88, 95% CI = 0.81-0.95, P = 0.001), and recessive model (C2C2 vs C1C2/C1C1: OR = 1.25, 95% CI = 1.01-1.53, P = 0.036). CYP2E1 Rsa I/Pst I gene polymorphism may reduce the risk of respiratory system cancer. Furthermore, significant association was also found in Asian populations.
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Affiliation(s)
- Li Xu
- From the Department of Cardiothoracic Surgery (LX, TZ, HJ, ZX, HC) ; and Department of Orthopaedics (MY, ML), Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
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