Analysis of next-generation sequencing data of miRNA for the prediction of breast cancer

Indrajit Saha , Shib Sankar Bhowmick , Filippo Geraci , Marco Pellegrini , Debotosh Bhattacharjee , Ujjwal Maulik , Dariusz Plewczyński

Abstract

Recently, Next-Generation Sequencing (NGS) has emerged as revolutionary technique in the fields of ‘-omics’ research. The Cancer Research Atlas (TCGA) is a great example of it where massive amount of sequencing data is present for miRNA and mRNA. Analysing these data could bring out some potential biological insight. Moreover, developing a prognostic system based on this newly available sequencing data will give a greater help to cancer diagnosis. Hence, in this article, we have made an attempt to analyse such sequencing data of miRNA for accurate prediction of Breast Cancer. Generally miRNAs are small non-coding RNAs which are shown to participate in several carcinogenic processes either by tumor suppressors or oncogenes. This is the reason clinical treatment of the breast cancer patient has changed nowadays. Thus, it is interesting to understand the role of miRNAs for the prediction of breast cancer. In this regard, we have developed a technique using Gravitation Search Algorithm, which optimizes the underlying classification performance of Support Vector Machine. The proposed technique is able to select the potential features, in this case miRNAs, in order to achieve better prediction accuracy. In this study, we have achieved the classification accuracy upto 95.29% by considering ≃ 1.5% miRNAs of whole dataset automatically. Thereafter, a list of miRNAs is created after providing a rank. It is found from the list of top 15 miRNAs that 6 miRNAs are associated with the breast cancer while in others, 5 miRNAs are associated with different cancer types and 4 are unknown miRNAs. The performance of the proposed technique is compared with seven other state-of-the-art techniques. Finally, the results have been justified by the means of statistical test along with biological significance analysis of selected miRNAs.

Author Indrajit Saha - [Consiglio Nazionale delle Ricerche]
Indrajit Saha,,
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, Shib Sankar Bhowmick - [Jadavpur University]
Shib Sankar Bhowmick,,
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, Filippo Geraci - [Consiglio Nazionale delle Ricerche]
Filippo Geraci,,
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, Marco Pellegrini - [Consiglio Nazionale delle Ricerche]
Marco Pellegrini,,
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, Debotosh Bhattacharjee - [Jadavpur University]
Debotosh Bhattacharjee,,
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, Ujjwal Maulik - [Jadavpur University]
Ujjwal Maulik,,
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, Dariusz Plewczyński (FMIS / DIPS)
Dariusz Plewczyński,,
- Department of Information Processing Systems
Pages116-127
Publication size in sheets0.55
Book Panigrahi Bijaya Ketan, Suganthan Ponnuthurai Nagaratnam, Das Swagatam, Satapathy Suresh Chandra (eds.): Proceedings of the 6th International Conference on Swarm, Evolutionary, and Memetic Computing, SEMCCO 2015, Lecture Notes In Computer Science, vol. 9873, 2016, Springer, ISBN 978-3-319-48958-2, [978-3-319-48959-9], DOI:10.1007/978-3-319-48959-9
DOIDOI:10.1007/978-3-319-48959-9_11
Languageen angielski
Score (nominal)15
Score sourceconferenceIndex
ScoreMinisterial score = 15.0, 04-06-2020, BookChapterSeriesAndMatConfByConferenceseries
Ministerial score (2013-2016) = 15.0, 04-06-2020, BookChapterSeriesAndMatConfByConferenceseries
Publication indicators Scopus Citations = 2; WoS Citations = 0
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