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Identification of tissue-specific tumor biomarker using different optimization algorithms

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Abstract

Background

Identification of differentially expressed genes, i.e., genes whose transcript abundance level differs across different biological or physiological conditions, was indeed a challenging task. However, the inception of transcriptome sequencing (RNA-seq) technology revolutionized the simultaneous measurement of the transcript abundance levels for thousands of genes.

Objective

In this paper, such next-generation sequencing (NGS) data is used to identify biomarker signatures for several of the most common cancer types (bladder, colon, kidney, brain, liver, lung, prostate, skin, and thyroid)

Methods

Here, the problem is mapped into the comparison of optimization algorithms for selecting a set of genes that lead to the highest classification accuracy of a two-class classification task between healthy and tumor samples. As the optimization algorithms Artificial Bee Colony (ABC), Ant Colony Optimization, Differential Evolution, and Particle Swarm Optimization are chosen for this experiment. A standard statistical method called DESeq2 is used to select differentially expressed genes before being feed to the optimization algorithms. Classification of healthy and tumor samples is done by support vector machine

Results

Cancer-specific validation yields remarkably good results in terms of accuracy. Highest classification accuracy is achieved by the ABC algorithm for Brain lower grade glioma data is 99.10%. This validation is well supported by a statistical test, gene ontology enrichment analysis, and KEGG pathway enrichment analysis for each cancer biomarker signature

Conclusion

The current study identified robust genes as biomarker signatures and these identified biomarkers might be helpful to accurately identify tumors of unknown origin

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Notes

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Authors and Affiliations

  1. Department of Electronics and Communication Engineering, Heritage Institute of Technology, Kolkata, 700107, India

    Shib Sankar Bhowmick

  2. Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India

    Debotosh Bhattacharjee

  3. Department of Informatics, University of Evora, 7004-516, Evora, Portugal

    Luis Rato

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  1. Shib Sankar Bhowmick
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  2. Debotosh Bhattacharjee
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  3. Luis Rato
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Correspondence to Shib Sankar Bhowmick.

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Shib Sankar Bhowmick, Debotosh Bhattacharjee and Luis Rato declare that they have no conflict of interest

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards

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Informed consent was obtained from all individual participants included in the study

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Bhowmick, S.S., Bhattacharjee, D. & Rato, L. Identification of tissue-specific tumor biomarker using different optimization algorithms. Genes Genom 41, 431–443 (2019). https://doi.org/10.1007/s13258-018-0773-2

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  • DOI: https://doi.org/10.1007/s13258-018-0773-2

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