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ezQTL:A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 541-548页

作者： Tongwu Zhang Alyssa Klein Jian Sang Jiyeon Choi Kevin M.Brown Division of cancer Epidemiology and Genetics National Cancer InstituteBethesdaMD 20892USA

Genome-wide association studies(GWAS)have identified thousands of genomic loci associated with complex diseases and traits,including *** vast majority of common traitassociated variants identified via GWAS fall in non-coding regions of the genome,posing a challenge in elucidating the causal variants,genes,and mechanisms *** quantitative trait locus(eQTL)and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization *** QTL colocalization is becoming a standard analysis in post-GWAS investigation,an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been ***,we present ezQTL,a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS loci and molecular QTLs under different linkage disequilibrium(LD)patterns(1000 Genomes Project,UK Biobank,or user-provided data).This application allows users to perform data quality control for variants matched between different datasets,LD visualization,and two-trait colocalization analyses using two state-of-the-art methodologies(eCAVIAR and HyPrColoc),including batch *** is a free and publicly available cross-platform web tool,which can be accessed online at https://***/ezqtl.

关键词： Genome-wide association study Expression quantitative trait locus Colocalization Linkage disequilibrium Visualization

Somatic copy number alterations are predictive of progression-free survival in patients with lung adenocarcinoma undergoing radiotherapy

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cancer Biology & Medicine 2022年第5期19卷 685-695页

作者： Fan Kou Lei Wu Yan Guo Bailu Zhang Baihui Li Ziqi Huang Xiubao Ren Lili Yang Department of Immunology Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyKey Laboratory of Cancer Immunology and BiotherapyTianjin 300060China Department of Biotherapy Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin 300060China

Objective:Lung cancer is the most common cause of cancer-related deaths *** copy number alterations(SCNAs)have been used to predict responses to therapies in many cancers,including lung ***,little is known about whether they are predictive of radiotherapy *** aimed to understand the prognostic value and biological functions of ***:We analyzed the correlation between SCNAs and clinical outcomes in The cancer Genome Atlas data for 486 patients with non-small cell lung cancer who received *** set enrichment analyses were performed to investigate the potential mechanisms underlying the roles of SCNAs in the radiotherapy *** results were validated in 20 patients with lung adenocarcinoma(LUAD)receiving ***:SCNAs were a better predictor of progression-free survival(PFS)in LUAD(P=0.024)than in lung squamous carcinoma(P=0.18)in patients treated with *** and multivariate regression analyses revealed the superiority of SCNAs in predicting PFS in patients with *** with stage I cancer and low SCNA levels had longer PFS than those with high SCNA levels(P=0.022).Our prognostic nomogram also showed that combining SCNAs and tumor/node/metastasis provided a better model for predicting long-term ***,high SCNA may activate the cell cycle pathway and induce ***:SCNAs may be used to predict PFS in patients with early-stage LUAD with radiotherapy,in combination with TNM,with the aim of predicting long-term ***,SCNAs are a novel predictive biomarker for radiotherapy in patients with LUAD.

关键词： SCNA radiotherapy lung cancer progression-free survival immune infiltration

Age distribution,polyps and rectal cancer in the Egyptian population-based cancer registry

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World Journal of Gastroenterology 2012年第30期18卷 3997-4003页

作者： Darlene Veruttipong Amr S Soliman Samuel F Gilbert Taylor S Blachley Ahmed Hablas Mohamed Ramadan Laura S Rozek Ibrahim A Seifeldin Department of Epidemiology University of Michigan School of Public HealthAnn ArborMI 48109United States Department of Biostatistics University of Michigan School of Public HealthAnn ArborMI 48109United States Tanta cancer Center and the Gharbiah Population-Based cancer registry Tanta 31512Egypt Department of Environmental Health Science University of Michigan School of Public HealthAnn ArborMI 48109United States

AIM:To describe the clinical and epidemiologic profiles of the disease and to compare the findings with those generated from the previous hospital-based ***:The Gharbiah cancer registry is the only population-based cancer registry in Egypt since *** analyzed the data of all colorectal cancer patients included in the registry for the period of *** medical records of the 1364 patients diagnosed in Gharbiah during the study period were retrieved and the following information abstracted:age,residence,diagnosis date,grade,stage,topology,clinical characteristics,and histology *** census data for 1996 and 2006 were used to provide the general population's statistics on age,sex,residence and other related demographic *** addition to age-and sex-specific incidence rate analyses,we analyze the data to explore the incidence distribution by rural-urban differences among the 8 districts of the *** also compared the incidence rates of Gharbiah to the rates of the Surveillance Epidemiology and End Results(SEER) data of the United ***:Over the 9 year-period,1364 colorectal cancer cases were *** disease incidence under age 40 years was relatively high(1.3/10 5) while the incidence in the age groups 40 and over was very low(12.0/10 5,19.4/10 5 and 21.2/10 5 in the age groups 40-59 years,60-69 years and > 70 years,respectively).The vast majority of tumors(97.2%) had no polyps and 37.2% of the patients presented with primary lesions in the *** cancer was more common in patients from urban(55%) than rural(45%) *** differences in colon and rectal cancer incidence in the 8 districts of the study province may reflect different etiologic patterns in this *** registry data of Egypt shows a slightly higher incidence of colorectal cancer than the United States in subjects under age 40 *** results also shows significantly lower incidence of colorectal cancer in subjects over age

关键词： Colorectal cancer Young-onset Polyps Developing countries Egypt

Ultrasound features of extranodal extension in the metastatic cervical lymph nodes of papillary thyroid cancer:a case-control study

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cancer Biology & Medicine 2018年第2期15卷 171-177页

作者： Jiali Mu Xiaofeng Liang Fangxuan Li Juntian Liu Sheng Zhang Jing Tian Department of Ultrasound Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjinTianjin's Clinical Research Center for CancerTianjin 300060China Department of cancer Prevention Center Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjinTianjin's Clinical Research Center for CancerTianjin 300060China Department of Ultrasound The Secondary Hospital of Tianjin Medical UniversityTianjin 300211China

Objective：Extranodal extension in cervical lymph nodes is an important risk factor for the progression and prognosis of papillary thyroid *** purpose of this study was to identify the common and characteristic preoperative ultrasonography features that are associated with the pathologic extranodal extension of metastatic papillary thyroid ***：We retrospectively assessed and compared clinicopathologic and ultrasound features between 60 papillary thyroid cancer patients with extranodal extension and 120 control patients with papillary thyroid cancer without extranodal ***：With respect to the pathological N stage and clinicopathologic features,N1b stage papillary thyroid carcinomas were more frequently found in patients who were extranodal extension-positive,in comparison with those who were extranodal extension-negative（78.3%vs.63.3%,P=0.043）.Extranodal extension was detected most frequently in level VI cervical lymph nodes（48.7%）.In our univariate analysis of patients with papillary thyroid carcinoma,cervical lymph nodes with extranodal extension showed higher incidences of node matting,microcalcification,cystic area,aspect ratio＆lt;2,and larger diameter than those without extranodal extension（all P〈0.05）.Our multivariate analysis demonstrated that node matting and cystic area were independent risk factors for the presence of extranodal extension[odds ratio（OR）：4.751,95%confidence interval（CI）：1.212~18.626,P=0.025;OR：2.707,95%CI：1.127~6.502,P=0.026].Conclusions：common ultrasound features may indicate the presence of extranodal extension in patients with metastatic cervical lymph nodes of papillary thyroid carcinoma.

关键词： Extranodal extension papillary thyroid cancer ultrasound lymph node metastasis

Absent MicroRNAs in Different Tissues of Patients with Acquired Cardiomyopathy

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Genomics, Proteomics & Bioinformatics 2016年第4期14卷 224-234页

作者： Christine S. Siegismund Maria Rohde Uwe Kiihl Felicitas Escher Heinz Peter Schultheiss Dirk Lassner Institute for Cardiac Diagnostics and Therapy(IKDT) 12203 BerlinGermany Department of Cardiology Campus VirchowCharite-University Hospital Berlin13353 BerlinGermany

MicroRNAs （miRNAs） can be found in a wide range of tissues and body fluids, and their specific signatures can be used to determine diseases or predict clinical courses. The miRNA profiles in biological samples （tissue, serum, peripheral blood mononuelear cells or other body fluids） differ significantly even in the same patient and therefore have their own specificity for the presented condition. Complex profiles of deregulated miRNAs are of high interest, whereas the importance of non-expressed miRNAs was ignored. Since miRNAs regulate gene expression rather negatively, absent miRNAs could indicate genes with unaltered expression that therefore are normally expressed in specific compartments or under specific disease situations. For the first time, non-detectable miRNAs in different tissues and body fluids from patients with different diseases （cardiomyopathies, Alzheimer＇s disease, bladder cancer, and ocular cancer） were analyzed and compared in this study, miRNA expression data were generated by microarray or TaqMan PCR-based platforms. Lists of absent miRNAs of primarily cardiac patients （myocardium, blood cells, and serum） were clustered and analyzed for potentially involved pathways using two prediction platforms, i.e., miRNA enrichment analysis and annotation tool （miEAA） and DIANA miRPath. Extensive search in biomedical publication databases for the relevance of non-expressed miRNAs in predicted pathways revealed no evidence for their involvement in heart-related pathways as indicated by software tools, confirming proposed approach.

关键词： Cardiomyopathy Heart muscle biopsy Absent mi RNAs Peripheral blood mononuclear cell Serum

Human papillomavirus and gastrointestinal cancer: A review

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World Journal of Gastroenterology 2016年第33期22卷 7415-7430页

作者： Dania Bucchi Fabrizio Stracci Nicola Buonora Giuseppe Masanotti Department of Experimental Medicine School of Specialization in Hygiene and Preventive Medicine University of Perugia 06126 Perugia Umbria Italy Department of Experimental Medicine Public Health Section University of Perugia 06126 Perugia Umbria Italy Umbria cancer registry 06126 Perugia Umbria Italy

Human papillomavirus(HPV) is one of the most common sexually transmitted infections worldwide. Exposure to HPV is very common,and an estimated 65%-100% of sexually active adults are exposed to HPV in their lifetime. The majority of HPV infections are asymptomatic,but there is a 10% chance that individuals will develop a persistent infection and have an increased risk of developing a carcinoma. The International Agency for Research on cancer has found that the following cancer sites have a strong causal relationship with HPV: cervix uteri,penis,vulva,vagina,anus and oropharynx,including the base of the tongue and the tonsils. However,studies of the aetiological role of HPV in colorectal and esophageal malignancies have conflicting results. The aim of this review was to organize recent evidence and issues about the association between HPV infection and gastrointestinal tumours with a focus on esophageal,colorectal and anal cancers. The ultimate goal was to highlight possible implications for prognosis and prevention.

关键词： Human papillomavirus Esophageal cancer Colorectal cancer Anal cancer Oncogenesis Prognosis Prevention

Research progress on FASN and MGLL in the regulation of abnormal lipid metabolism and the relationship between tumor invasion and metastasis

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Frontiers of Medicine 2021年第5期15卷 649-656页

作者： Jingyue Zhang Yawen Song Qianqian Shi Li Fu Tianjin Medical University cancer Institute and Hospital National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjinTianjin’s Clinical Research Center for CancerKey Laboratory of Breast Cancer Prevention and TherapyTianjin Medical universityMinistry of EducationTianjin 300060China

Tumorigenesis involves metabolic reprogramming and abnormal lipid metabolism,which is manifested by increased endogenous fat mobilization,hypertriglyceridemia,and increased fatty acid *** acid synthase(FASN)is a key enzyme for the de novo synthesis of fatty acids,and monoacylglycerol esterase(MGLL)is an important metabolic enzyme that converts triglycerides into free fatty *** enzymes play an important role in lipid metabolism and are associated with tumor-related signaling pathways,the most common of which is the PI3K–AKT signaling *** can also regulate the immune microenvironment,participate in epithelial–mesenchymal transition,and then regulate tumor invasion and *** literature have shown that these two genes are abnormally expressed in many types of tumors and are highly correlated with tumor migration and *** article introduces the structures and functions of FASN and MGLL,their relationship with abnormal lipid metabolism,and the mechanism of the regulation of tumor invasion and metastasis and reviews the research progress of the relationship of FASN and MGLL with tumor invasion and metastasis.

关键词： FASN MGLL lipid metabolism tumor invasion metastasis

Risk prediction models for biochemical recurrence after radical prostatectomy using prostate-specific antigen and Gleason score

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Asian Journal of Andrology 2014年第6期16卷 897-901页

作者： Xin-Hai Hu Henning Cammann Hellmuth-A Meyer Klaus Jung Hong-Biao Lu Natalia Levas Ahmed Magheli Carsten Stephan Jonas Busch Department of Urology Charite - Universitatsmedizin Berlin Berlin Germany Institute of Medical Informatics Charite - Universitatsmedizin Berlin Berlin Germany berlin Institute for Urologic Research Berlin Germany Department of Urology Changzhou No. 2 People's Hospital Changzhou China Stanford University School of Medicine Stanford CA USA.

Many computer models for predicting the risk of prostate cancer have been developed including for prediction of biochemical recurrence （BCR）. However, models for individual BCR free probability at individual time-points after a BCR free period are rare. Follow-up data from 1656 patients who underwent laparoscopic radical prostatectomy （LRP） were used to develop an artificial neural network （ANN） to predict BCR and to compare it with a logistic regression （LR） model using clinical and pathologic parameters, prostate-specific antigen （PSA）, margin status （RO/1）, pathological stage （pT）, and Gleason Score （GS）. For individual BCR prediction at any given time after operation, additional ANN, and LR models were calculated every 6 months for up to 7.5 years of follow-up. The areas under the receiver operating characteristic （ROC） curve （AUC） for the ANN （0.754） and LR models （0.755） calculated immediately following LRP, were larger than that for GS （AUC： 0.715; P= 0.0015 and 0.001）, pT or PSA （AUC： 0.619; Palways 〈0.0001） alone. The GS predicted the BCR better than PSA （P = 0.0001）, but there was no difference between the ANN and LR models （P = 0.39）. Our ANN and LR models predicted individual BCR risk from radical prostatectomy for up to 10 years postoperative. ANN and LR models equally and significantly improved the prediction of BCR compared with PSA and GS alone. When the GS and ANN output values are combined, a more accurate BCR prediction is possible, especially in high-risk patients with GS ≥7.

关键词： artificial neural network prostate cancer recurrence

Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy in NSCLC

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Frontiers of Medicine 2023年第3期17卷 493-502页

作者： Wei Rao Yutao Liu Yan Li Lei Guo Tian Qiu Lin Dong Jianming Ying Weihua Li Department of Pathology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China

Anaplastic lymphoma kinase(ALK)is the most common fusion gene involved in non-small cell lung cancer(NSCLC),and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors(ALK-TKIs).However,the clinical efficacy is highly ***-existing intratumoral heterogeneity(ITH)has been proven to contribute to the poor treatment response and the resistance to targeted *** this work,we investigated whether the variant allele frequencies(VAFs)of ALK fusions can help assess ITH and predict targeted therapy *** the application of next-generation sequencing(NGS),7.2%(326/4548)of patients were detected to be ALK *** the basis of the adjusted VAF(adjVAF,VAF normalization for tumor purity)of four different threshold values(adjVAF<50%,40%,30%,or 20%),the association of ALK subclonality with crizotinib efficacy was ***,no statistical association was observed between median progression-free survival(PFS)and ALK subclonality assessed by adjVAF,and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line *** suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.

关键词： ALK fusion next-generation sequencing fluorescence in situ hybridization immunohistochemistry variant allele frequency intratumoral heterogeneity targeted therapy