An approach to forecast human cancer by profiling microRNA expressions from NGS data

BMC Cancer

Research Article

R. Amjesh¹  S. S. Vinod Chandra²  A. Salim³ 

[1] Department of Computational Biology and BioInformatics, University of Kerala, Karyavattom, Thiruvananthapuram, India;Department of Computational Biology and BioInformatics, University of Kerala, Karyavattom, Thiruvananthapuram, India;Computer Center, University of Kerala, Thiruvananthapuram, India;Department of Computer Science, College of Engineering Trivandrum, Sreekaryam, Thiruvananthapuram, India;

关键词: MicroRNA;    Expression profiling;    Sequence mapping;    SVM classifiers;   

DOI  :  10.1186/s12885-016-3042-2

 received in 2016-07-04, accepted in 2016-12-28,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundmicroRNAs are single-stranded non-coding RNA sequences of 18 - 24 nucleotides in length. They play an important role in post-transcriptional regulation of gene expression. Evidences of microRNA acting as promoter/suppressor of several diseases including cancer are being unveiled. Recent studies have shown that microRNAs are differentially expressed in disease states when compared with that of normal states. Profiling of microRNA is a good measure to estimate the differences in expression levels, which can be further utilized to understand the progression of any associated disease.MethodsMachine learning techniques, when applied to microRNA expression values obtained from NGS data, could be utilized for the development of effective disease prediction system. This paper discusses an approach for microRNA expression profiling, its normalization and a Support Vector based machine learning technique to develop a Cancer Prediction System. Presently, the system has been trained with data samples of hepatocellular carcinoma, carcinomas of the bladder and lung cancer. microRNAs related to specific types of cancer were used to build the classifier.ResultsWhen the system is trained and tested with 10 fold cross validation, the prediction accuracy obtained is 97.56% for lung cancer, 97.82% for hepatocellular carcinoma and 95.0% for carcinomas of the bladder. The system is further validated with separate test sets, which show accuracies higher than 90%. A ranking based on differential expression marks the relative significance of each microRNA in the prediction process.ConclusionsResults from experiments proved that microRNA expression profiling is an effective mechanism for disease identification, provided sufficiently large database is available.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

Fig. 1