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Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

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World Journal of Gastroenterology 2021年第14期27卷 1465-1482页

作者： Sarah A Malik Chencan Zhu Jinyu li Joseph F LaComb Paula I Denoya Igor Kravets Joshua D Miller Jie Yang Melissa Kramer W Richard McCombie Charles E Robertson Daniel N Frank ellen li Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794United States Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource Stony Brook UniversityStony BrookNY 11794United States Department of Pathology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Surgery Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Family Population and Preventive MedicineStony Brook UniversityStony BrookNY 11794United States Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource Cold Spring HarborNY 11724United States Department of Medicine University of Colorado Anschutz Medical CampusAuroraCO 80045United States

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human ***-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)*** hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk *** To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection *** Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from *** 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on *** sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥*** PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach *** mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level *** confirmed increased Fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics *** coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor *** expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race *** Recent adoption of additional preoperative antibiotics as sta

关键词： Colorectal cancer Antibiotics African Continental Ancestry Group Diabetes mellitus 16S rRNA gene RNA-sequencing

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Impaired granulocyte-macrophage colony-stimulating factor bioactivity accelerates surgical recurrence in ileal crohn's disease

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World Journal of Gastroenterology 2018年第5期24卷 623-630页

作者： Grace Gathungu Yuanhao Zhang Xinyu Tian Erin Bonkowski Leahana Rowehl Julia Krumsiek Billy Nix Claudia Chalk Bruce Trapnell Wei Zhu Rodney Newberry Lee Denson ellen li Department of Pediatrics Division of Pediatric Gastroenterology Stony Brook University Department of Medicine Division of Gastroenterology Stony Brook University Department of Pediatrics Cincinnati Children’s Hospital Medical Center Department of Medicine Washington University St.Louis Applied Mathematics and Statistics Stony Brook University

AIM To examine the relationship between elevated granulocyte-macrophage colony-stimulating factor(GMCSF) auto-antibodies(Ab) level and time to surgical recurrence after initial surgery for Crohn's disease(CD). METHODS We reviewed 412 charts from a clinical database at tertiary academic hospital. Patients included in the study had ileal or ileocolonic CD and surgical resection of small bowel or ileocecal region for management of disease. Serum samples were analyzed for serological assays including GM-CSF cytokine, GM-CSF Ab, ASCA Ig G and Ig A, and genetic markers including SNPs rs2066843, rs2066844, rs2066845, rs2076756 and rs2066847 in NOD2, rs2241880 in ATG16 L1, and rs13361189 in IRGM. Cox proportional-hazards models were used to assess the predictors of surgical *** Ninety six percent of patients underwent initial ileocecal resection(ICR) or ileal resection(IR) and subsequently 40% of patients required a second ICR/IR for CD. GMCSF Ab level was elevated at a median of 3.81 mcg/mL. Factors predicting faster time to a second surgery included elevated GM-CSF Ab [hazard ratio(HR) 3.52, 95%CI: 1.45-8.53, P = 0.005] and elevated GM-CSF cytokine(HR = 2.48, 95%CI: 1.31-4.70, P = 0.005). Factors predicting longer duration between first and second surgery included use of Immunomodulators(HR = 0.49, 95%CI: 0.31-0.77, P = 0.002), the interaction effect of low GM-CSF Ab levels and smoking(HR = 0.60, 95%CI: 0.45-0.81, P = 0.001) and the interaction effect of low GM-CSF cytokine levels and ATG16 L1(HR = 0.65, 95%CI: 0.49-0.88, P = 0.006).CONCLUSION GM-CSF bioavailability plays a critical role in maintaining intestinal homeostasis. Decreased bioavailability coupled with the genetic risk markers and/or smoking results in aggressive CD behavior.

关键词： Inflammatory bowel disease granulocytemacrophage colony-stimulating factor antibody Crohn’s disease surgery

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Impact of type 2 diabetes on adenoma detection in screening colonoscopies performed in disparate populations

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World Journal of Clinical Cases 2021年第11期9卷 2433-2445页

作者： Dimitri F Joseph ellen li Samuel L Stanley III Yi-Cong Zhu Xiao-Ning li Jie Yang Lorenzo F Ottaviano Juan Carlos Bucobo Jonathan M Buscaglia Joshua D Miller Rajesh Veluvolu Michele Follen Evan B Grossman Department of Medicine Renaissance School of Medicine at Stony Brook UniversityStony BrookNY 11794-8173United States Department of Medicine Division of GastroenterologyStony Brook UniversityStony BrookNY 11794-8173United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794-3600United States Department of Biostatistics and Bioinformatics Shared Resource Stony Brook Cancer CenterStony Brook UniversityStony BrookNY 11794-3600United States Department of Family Populationand Preventative MedicineRenaissance School of Medicine at Stony Brook UniversityStony BrookNY 11794-8461United States Department of Medicine NYC Health and Hospitals/Kings CountyBrooklynNY 11203United States Department of Medicine SUNY Downstate Medical CenterBrooklynNY 11203United States Department of Obstetrics and Gynecology NYC Health and Hospitals/Kings CountyBrooklynNY 11203United States

BACKGROUND The Black/African Ancestry(AA)population has a higher prevalence of type 2 diabetes mellitus(T2DM)and a higher incidence and mortality rate for colorectal cancer(CRC)than all other races in the United States.T2DM has been shown to increase adenoma risk in predominantly white/European ancestry(EA)populations,but the effect of T2DM on adenoma risk in Black/AA individuals is less *** hypothesize that T2DM has a significant effect on adenoma risk in a predominantly Black/AA *** To investigate the effect of T2DM and race on the adenoma detection rate(ADR)in screening colonoscopies in two disparate *** A retrospective cohort study was conducted on ADR during index screening colonoscopies(age 45-75)performed at an urban public hospital serving a predominantly Black/AA population(92%)(2017-2018,n=1606).Clinical metadata collected included basic demographics,insurance,body mass index(BMI),family history of CRC,smoking,diabetes diagnosis,and aspirin *** dataset was combined with a recently reported parallel retrospective cohort data set collected at a suburban university hospital serving a predominantly White/EA population(87%)(2012-2015,n=2882).RESULTS The ADR was higher in T2DM patients than in patients without T2DM or prediabetes(35.2%vs 27.9%,P=0.0166,n=981)at the urban public *** analysis of the combined datasets showed that T2DM[odds ratio(OR)=1.29,95%confidence interval(CI):1.08-1.55,P=0.0049],smoking(current vs never OR=1.47,95%CI:1.18-1.82,current vs past OR=1.32,95%CI:1.02-1.70,P=0.0026),older age(OR=1.05 per year,95%CI:1.04-1.06,Pling for other factors.

关键词： Adenoma Diabetes mellitus,type 2 African continental ancestry group European continental ancestry group Colonoscopy Multivariate analysis

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Confounders in Adenoma Detection at Initial Screening Colonoscopy: A Factor in the Assessment of Racial Disparities as a Risk for Colon Cancer

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Journal of Cancer Therapy 2019年第4期10卷 269-289页

作者： Yakira David Lorenzo Ottaviano Jihye Park Sadat Iqbal Michelle likhtshteyn Samir Kumar Helen Lyo Ayanna E. Lewis Brandon E. Lung Jesse T. Frye li Huang ellen li Jie Yang Laura Martello Shivakumar Vignesh Joshua D. Miller Michele Follen Evan B. Grossman Department of Medicine SUNY Downstate Medical Center Brooklyn NY USA Department of Gastroenterology Icahn School of Medicine at Mount Sinai New York City NY USA Department of Medicine Stony Brook University Stony Brook NY USA Department of Applied Mathematics and Statistics Stony Brook University Stony Brook NY USA Department of Family Population and Preventive Medicine Stony Brook University Stony Brook NY USA Department of Obstetrics and Gynecology NYC HNC/Kings County Brooklyn NY USA Department of Medicine Division of Gastroenterology NYC Health and Hospitals/Kings County Brooklyn NY USA

Background and Aims: The incidence and mortality of colorectal cancer is persistently highest in Black/African-Americans in the United States. While access to care, barriers to screening, and poverty might explain these findings, there in increased interest in examining biological factors that impact the colonic environment. Our group is examining biologic factors that contribute to disparities in development of adenomas prospectively. In preparation for this and to characterize a potential patient population, we conducted a retrospective review of initial screening colonoscopies in a cohort of patients. Methods: A retrospective review was performed on initial average risk screening colonoscopies on patients (age 45 - 75 years) during 2012 at three institutions. Descriptive statistics and multivariable logistic regression models were used to examine the relationship between potential risk factors and the detection of adenomas. Results: Of the 2225 initial screening colonoscopies 1495 (67.2%) were performed on Black/African-Americans and 566 (25.4%) on Caucasians. Multivariable logistic regression revealed that older age, male sex, current smoking and teaching gastroenterologists were associated with higher detection of adenomas and these were less prevalent among Black/African-Americas except for age. Neither race, ethnicity, BMI, diabetes mellitus, HIV nor insurance was associated with adenoma detection. Conclusion: In this sample, there was no association between race and adenoma detection. While this may be due to a lower prevalence of risk factors for adenomas in this sample, our findings were confounded by a lower detection rate by consultant gastroenterologists at one institution. The study allowed us to rectify the problem and characterize patients for future trials.

关键词： Colorectal Cancer Screening Adenoma Quality

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Photocatalysis with visible-light-active uranyl complexes

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Science China Chemistry 2013年第12期56卷 1671-1681页

作者： li Yong SU Jing MITCHELL ellen ZHANG GuoQing li Jun School of Material Science Guangdong University of Technology Department of Chemistry Tsinghua University Department of Chemistry Bridgewater College

Atomic energy is an important part of current energy *** of nuclear weapons and applications of nuclear fuels in nuclear power plants have accumulated numerous spent fuels containing238U compounds,which are critical nuclear *** to reduce the nuclear wastes and to make use of the spent uranium are key scientific issues of environmental and nuclear *** have reviewed here the physiochemical properties and photocatalytic mechanisms of homogeneous and heterogeneous uranium-containing *** current research efforts demonstrate that spent fuels can become promising new photocatalytic materials.

关键词：光催化机理可见光活性铀酰复合光催化材料组成部分能源资源科学问题

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丛枝菌根真菌促进外来植物豚草的生长

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Journal of Plant Ecology 2022年第3期15卷 581-595页

作者： lingjie Kong Xue Chen ellen Heininger Yerger Qiao li Fengxin Chen Haiyun Xu Fengjuan Zhang College of life Science Hebei UniversityBaodingHebei 071002China Department of Biology Indiana University of PennsylvaniaIndianaPA 15705USA State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100081China

丛枝菌根真菌(AMF)可以通过其菌丝增加寄主植物对养分的吸收,从而促进植物生长。丛枝菌根真菌一直与大多数外来植物的成功入侵联系在一起。然而,有关丛枝菌根真菌如何影响植物入侵成功的机制仍然有待研究。豚草(Ambrosia artemisiifolia... 详细信息

丛枝菌根真菌(AMF)可以通过其菌丝增加寄主植物对养分的吸收,从而促进植物生长。丛枝菌根真菌一直与大多数外来植物的成功入侵联系在一起。然而,有关丛枝菌根真菌如何影响植物入侵成功的机制仍然有待研究。豚草(Ambrosia artemisiifolia)是一种外来的菌根植物。通过长期田间实验,我们研究了种间竞争对豚草和狗尾草(Setaria viridis)根系丛枝菌根真菌多样性和组成的影响。此外,在温室实验中探究了摩西球囊霉(Funneliformis mosseae)对这两种植物生长的影响。研究结果表明,豚草入侵改变了本地植物狗尾草根系丛枝菌根真菌的多样性。另外,豚草根系中摩西球囊霉的相对多度显著高于狗尾草根系中。在田间和温室实验中均发现外来种豚草的丛枝菌根真菌侵染率高于本地种狗尾草。温室实验结果表明,丛枝菌根真菌通过影响豚草的光合能力以及磷和钾的吸收而促进豚草生长。这些研究结果揭示了丛枝菌根真菌和豚草成功入侵之间的重要关系。

关键词：豚草(Ambrosia artemisiifolia) 丛枝菌根真菌竞争优势摩西球囊霉(Funneliformis mosseae) 养分吸收成功入侵

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Dexamethasone, tetrahydrobiopterin and uncoupling of endothelial nitric oxide synthase

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Journal of Geriatric Cardiology 2015年第5期12卷 528-539页

作者： Silke Tobias Alice Habermeier Daniel Siuda Gisela Reifenberg Ning Xia ellen I Closs Ulrich Forstermann Huige li Department of Pharmacology Johannes Gutenberg University Medical Center Mainz Germany

ObjectiveTo 发现 dexamethasone 是否导致一 endothelial 解开氮的氧化物 synthase (eNOS ).Methods &；解开的 eNOS 的 ResultsA 主要原因是它的余因子 tetrahydrobiopterin 的缺乏(BH 4) 。有 dexamethasone 的人的 *** 926 endothelial 房间的治疗减少了两 BH 4-synthesizing 酶的 mRNA 和蛋白质表示：GTP cyclohydrolase 我和 dihydrofolate reductase。一致地， BH 4, dihydrobiopterin 的集中依赖者和时间依赖者减小(BH 2) 以及 BH 4 ：BH 2 比率在对待 dexamethasone 的房间被观察。令人惊讶地，为解开的 eNOS 的证据都没被发现。我们然后分析了 eNOS 酶的表示和 phosphorylation。Dexamethasone 处理在丝氨酸 1177 点导致了 eNOS 蛋白质和 eNOS phosphorylation 的减小的一条下面规定。eNOS 表示的减小可以导致相对正常的 BH 4 ：eNOS 在对待 dexamethasone 的房间的臼齿的比率。因为 BH 4-eNOS stoichiometry 而非绝对 BH 4 数量是 eNOS 功能的关键决定因素(即，联合或解开) ， eNOS 的下面规定可以为解开的 eNOS 的缺席代表解释。在丝氨酸 1177 点的 eNOS 的 Phosphorylation 为联合 eNOS 的不生产的活动和解开的 eNOS 的生产 superoxide 活动被需要。因此，丝氨酸 1177 phosphorylation 的减小几乎可以不显示潜在地解开的 eNOS 在 endothelial 房间的 *** dexamethasone 还原剂 BH 4 层次，解开的 eNOS 不是明显的。在对待 dexamethasone 的 endothelial 房间的没有生产的减小对减少的 eNOS 主要可归因在丝氨酸 1177 点的表示和减少的 eNOS phosphorylation。

关键词：内皮型一氧化氮合酶四氢生物蝶呤地塞米松二氢叶酸还原酶 eNOS 内皮细胞解耦 mRNA表达

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同型半胱氨酸水平、MTHFR基因突变与原发性高血压的病例对照研究(英文)

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高血压杂志 2000年第1期8卷 21-25页

作者：詹思延高原原尹香君胡永华李立明 Vivian Ng Lee BL Ong CN 北京医科大学流行病学教研室新加坡国立大学社区职业和家庭医学系

探讨升高的同型半胱氨酸水平、ＭＴＨＦＲ基因突变与原发性高血压的关系。方法：从上海一个社区中随机选取１２７例３５～７５岁的原发性高血压病人和１７０例正常血压者。采用聚合酶链反应－限制性片段长度多态性分析ＭＴＨＦＲ基因多... 详细信息

探讨升高的同型半胱氨酸水平、ＭＴＨＦＲ基因突变与原发性高血压的关系。方法：从上海一个社区中随机选取１２７例３５～７５岁的原发性高血压病人和１７０例正常血压者。采用聚合酶链反应－限制性片段长度多态性分析ＭＴＨＦＲ基因多态性。使用高效液相色谱结合电化学方法检测血清中同型半胱氨酸总浓度，使用放射免疫法同时测定血清中叶酸和Ｂ_（１２）浓度。结果：调整年龄和性别后，病例和对照组同型半胱氨酸水平分别为１０．５６ μｍｏｌ／Ｌ和１０．３４ μｍｏｌ／Ｌ，差异无显著性（Ｐ＝０．６３）。在未服降压药的对象中同型半胱氨酸浓度与收缩压和舒张压亦无关联。该人群ＭＴＨＦＲ不耐热性基因突变频率为１３．１％，突变等位基因频率为３８．７％。病例组与对照组基因型分布和突变等位基因频率无显著性差异。然而，病例组叶酸和Ｂ_（１２）浓度高于对照组。结论：本研究未发现升高的同型半胱氨酸水平、ＭＴＨＦＲ基因突变是原发性高血压的独立危险因素。高血压病人较高的叶酸和Ｂ_（１２）水平可能降低了同型半胱氨酸的危险性。

关键词：同型半胱氨酸 MTHFR基因高血压病例对照研究

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Expression,purification and characterization of the soluble Cu_A domain of cytochrome c oxidase of Paracoccus versutus

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Chinese Science Bulletin 2001年第19期46卷 1608-1612页

作者： li lianzhi SONG Aixin XIE Yi HUANG Zhongxian ellen de Waal Urszula Kolczak Gerard W.Canters Chemical Biology Laboratory Department of ChemistryFudan UniversityShanghai 200433China State Key Laboratory of Genetics School of Life ScienceFudan UniversityShanghai 200433China Leiden Institute of Chemistry Leiden UniversityPO Box 95022300 RA LeidenThe Netherlands

The key subunit II of cytochrome c oxidase (CcO) contains a soluble binuclear copper center (CuA) domain. The CUA domain of Paracoccus versutus was cloned, expressed, purified and characterized. The gene encoding the CUA domain in pETlld vector was expressed in E. coli BL21 (DE3). The results showed that the CuA domain was expressed mostly in inclusion bodies and the CUA domain protein synthesized in E. coli cells represents approximately 10 percent of the total cellular proteins. Dissolved in urea, dia-lyzed and recombined with Cu+/Cu2+ and purified by the Q-sepharose fast flow anion-exchange column and Sephadex G-75 gel filtration column, the soluble purple-colored protein, which shows a single band in electrophoresis, was obtained. The UV-visible absorption spectrum of CUA domain showed that there are intense band at 478 nm and a shoulder peak at 530 nm, and two weak bands at 360 and 806 nm respectively, which can be assigned to the charge transfer and the interactions of obitals of Cu-S and Cu-Cu

关键词： cytochrome coxidase CuA domain protein gene expression purification spectra.

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Transcriptome-wide association analysis identified candidate susceptibility genes for nasopharyngeal carcinoma

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Cancer Communications 2022年第9期42卷 887-891页

作者： Yong-Qiao He Wen-Qiong Xue Dan-Hua li Tong-Min Wang Zhi-Ming Mai Da-Wei Yang Chang-Mi Deng Ying liao Wen-li Zhang Ruo-Wen Xiao Luting Luo Hua Diao Xiating Tong Yanxia Wu Jiang-Bo Zhang Ting Zhou Xi-Zhao li Pei-Fen Zhang Xiao-Hui Zheng Shao-Dan Zhang Ye-Zhu Hu Minzhong Tang Yuming Zheng Yonglin Cai ellen T.Chang Zhe Zhang Guangwu Huang Su-Mei Cao Qing liu lin Feng Ying Sun Maria li Lung Hans-Olov Adami Weimin Ye Tai-Hing Lam Wei-Hua Jia State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat-sen University Cancer CenterGuangzhouGuangdong 510060P.R.China School of Public Health Sun Yat-sen UniversityGuangzhouGuangdong 510080P.R.China School of Public Health The University of Hong KongHong Kong S.A.R.999077P.R.China Center for Nasopharyngeal Carcinoma Research Research Grants Council Area of Excellence SchemeThe University of Hong KongHong Kong S.A.R.999077P.R.China Radiation Epidemiology Branch Division of Cancer Epidemiology and GeneticsNational Cancer InstituteNational Institutes of HealthBethesdaMD 20892USA Wuzhou Red Cross Hospital WuzhouGuangxi 543002P.R.China Wuzhou Cancer Center WuzhouGuangxi 543002P.R.China Center for Health Sciences ExponentInc.Menlo ParkCA94025Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCA 94143USA Department of Otolaryngology-Head and Neck Surgery First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi 530021P.R.China Department of Radiation Oncology Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouGuangdong 510060P.R.China Department of Clinical Oncology The University of Hong KongHong Kong S.A.R.999077P.R.China Clinical Effectiveness Group Institute of Health and SocietyUniversity of OsloOslo 0316Norway Department of Medical Epidemiology and Biostatistics Karolinska InstitutetStockholm 17177Sweden Department of Epidemiology and Health Statistics&Key Laboratory of Ministry of Education for Gastrointestinal Cancer Fujian Medical UniversityFuzhouFujian 350122P.R.China

Dear Editor,Nasopharyngeal carcinoma(NPC)is a common malignancy in East and Southeast Asia,especially in South *** etiology of NPC has been linked to genetic susceptibility,Epstein-Barr virus(EBV)infection,and environmental *** evidence including multiple genome-wide association studies(GWASs)has revealed robust genetic predisposition of ***,GWAS-identified genetic variants collectively account for only 8.2%of NPC heritability[1].The underlying inherited predisposition is largely *** strongest genetic signal for NPC consistently hits the human leukocyte antigen(HLA)region on 6p21[2].However,the highly polymorphic nature and complicated long-range linkage disequilibrium(LD)in the HLA region particularly obscure the causal variants driving the *** addition,most genetic variants located in introns or intergenic *** causal genes mediating genetic effects on NPC risk have rarely been ascertained by GWAS alone.

关键词： nasopharyngeal susceptibility collective

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