An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer.
An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer.
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DOI：
10.1186/s12894-015-0056-z
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发表时间：
2015-07-01
期刊：
影响因子：
2
通讯作者：
Dancik GM
中科院分区：
文献类型：
--
作者：
Dancik GM
在过去的15年中，从基因表达数据中识别诊断和预后生物标志物增加了我们对癌症生物学的了解，并导致许多癌症的个性化治疗取得了进展。诊断性生物标志物指示肿瘤状态，如肿瘤分期，而预后生物标志物指示疾病结果。然而，尽管取得了这些进展，临床上还没有批准用于治疗膀胱癌的生物标志物。膀胱癌是美国男性中第四大常见癌症，也是治疗成本最高的癌症之一。虽然膀胱癌患者的基因表达谱是公开的，但生物标志物鉴定需要生物信息学专业知识，而许多研究实验室都无法获得这些专业知识。我们收集了来自13个公开的患者队列（N = 1454）的基因表达数据，并开发了BC-BET，一个在线膀胱癌生物标志物评估工具，用于评估膀胱癌候选诊断和预后基因表达生物标志物。用户只需选择一个基因，BC-BET就会评估该基因表达作为诊断和预后生物标志物的效用。具体来说，BC-BET计算每个队列中所有患者的基因表达与肿瘤存在（区分肿瘤与正常样本）、肿瘤分级（区分低级别肿瘤与高级别肿瘤）、肿瘤分期（区分非肌肉侵入性样本与肌肉侵入性样本）和患者预后（例如疾病特异性生存）的相关性。低级别非肌肉侵袭性肿瘤患者和高级别肌肉侵袭性肿瘤患者也分别进行分析，以评估感兴趣的生物标志物是否具有独立于级别和分期的预后价值。虽然膀胱癌基因表达数据集是公开的，但它们的分析是计算密集型的，需要生物信息学专业知识。BC-BET是一种易于使用的工具，用于快速评估多个患者队列的膀胱癌基因表达生物标志物。本文的在线版本（doi:10.1186/s12894-015-0056-z）包含补充材料，可供授权用户使用。
In the past ~15 years, the identification of diagnostic and prognostic biomarkers from gene expression data has increased our understanding of cancer biology and has led to advances in the personalized treatment of many cancers. A diagnostic biomarker is indicative of tumor status such as tumor stage, while a prognostic biomarker is indicative of disease outcome. Despite these advances, however, there are no clinically approved biomarkers for the treatment of bladder cancer, which is the fourth most common cancer in males in the United States and one of the most expensive cancers to treat. Although gene expression profiles of bladder cancer patients are publicly available, biomarker identification requires bioinformatics expertise that is not available to many research laboratories. We collected gene expression data from 13 publicly available patient cohorts (N = 1454) and developed BC-BET, an online Bladder Cancer Biomarker Evaluation Tool for evaluating candidate diagnostic and prognostic gene expression biomarkers in bladder cancer. A user simply selects a gene, and BC-BET evaluates the utility of that gene’s expression as a diagnostic and prognostic biomarker. Specifically, BC-BET calculates how strongly a gene’s expression is associated with tumor presence (distinguishing tumor from normal samples), tumor grade (distinguishing low- from high-grade tumors), tumor stage (distinguishing non-muscle invasive from muscle invasive samples), and patient outcome (e.g., disease-specific survival) across all patients in each cohort. Patients with low-grade, non-muscle invasive tumors and patients with high-grade, muscle invasive tumors are also analyzed separately in order to evaluate whether the biomarker of interest has prognostic value independent of grade and stage. Although bladder cancer gene expression datasets are publicly available, their analysis is computationally intensive and requires bioinformatics expertise. BC-BET is an easy-to-use tool for rapidly evaluating bladder cancer gene expression biomarkers across multiple patient cohorts. The online version of this article (doi:10.1186/s12894-015-0056-z) contains supplementary material, which is available to authorized users.
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原始基因特征的细胞表明人膀胱癌具有不同的细胞祖细胞。
影响因子：
5.2
作者：
Dancik, Garrett M.;Owens, Charles R.;Iczkowski, Kenneth A.;Theodorescu, Dan
通讯作者：
Theodorescu, Dan
影响因子：
14.9
作者：
Rustici G;Kolesnikov N;Brandizi M;Burdett T;Dylag M;Emam I;Farne A;Hastings E;Ison J;Keays M;Kurbatova N;Malone J;Mani R;Mupo A;Pedro Pereira R;Pilicheva E;Rung J;Sharma A;Tang YA;Ternent T;Tikhonov A;Welter D;Williams E;Brazma A;Parkinson H;Sarkans U
通讯作者：
Sarkans U
影响因子：
14.9
作者：
Barrett T;Troup DB;Wilhite SE;Ledoux P;Evangelista C;Kim IF;Tomashevsky M;Marshall KA;Phillippy KH;Sherman PM;Muertter RN;Holko M;Ayanbule O;Yefanov A;Soboleva A
通讯作者：
Soboleva A
影响因子：
37.3
作者：
Kim WJ;Kim EJ;Kim SK;Kim YJ;Ha YS;Jeong P;Kim MJ;Yun SJ;Lee KM;Moon SK;Lee SC;Cha EJ;Bae SC
通讯作者：
Bae SC
影响因子：
51.1
作者：
Smith, Steven Christopher;Baras, Alexander Spyridon;Dancik, Garrett;Ru, Yuanbin;Ding, Kuan-Fu;Moskaluk, Christopher A.;Fradet, Yves;Lehmann, Jan;Stoeckle, Michael;Hartmann, Arndt;Lee, Jae K.;Theodorescu, Dan
通讯作者：
Theodorescu, Dan