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Gene. 2015 Apr 10;560(1):34-43. doi: 10.1016/j.gene.2015.01.027. Epub 2015 Jan 30.

RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.

Author information

1
Biotechnology Group, Shahrekord University, Shahrekord, Iran. Electronic address: a_alisoltani@ut.ac.ir.
2
Department of Biology, School of Sciences, Razi University, Kermanshah, Iran; Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran. Electronic address: h.fallahi@razi.ac.ir.
3
Biotechnology Group, Shahrekord University, Shahrekord, Iran.
4
School of Veterinary Science, Shahrekord University, Shahrekord, Iran.
5
Institute of Biotechnology, Shiraz University, Shiraz, Iran; Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, Australia; School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia. Electronic address: esmaeil.ebrahimie@adelaide.edu.au.

Abstract

The recent exponential increase in the number of next generation sequencing studies provides a new source of data for the discovery of functional genomics based markers. The RNA-seq and small RNA-seq provide a new source for the discovery of differentially expressed SSRs (simple sequence repeats) as biomarkers in various diseases. In the present study, for the first time, we applied RNA-seq SSR to find new biomarkers for pancreatic cancer (PC) diagnosis. Analysis of RNA-seq data revealed a significant alternation in the frequency of SSR motifs during cancer progression. In particular, RNA-seq SSR showed an increase in the frequencies of GCC/GGC and GCG/CGC motifs in PC samples compared to healthy pancreas. These findings were further confirmed using meta-analysis of EST-SSR data in 11 different cancers. Interestingly, the genes containing GCC/GGC and GCG/CGC motifs in their sequences were involved in many cancer-related biological processes, particularly regulation processes. The small RNA-seq data were also mined for the conserved patterns in SSR frequencies (sRNA-seq SSR) during cancer progression. Based on the results, we suggest the potential use of GCC/GGC and GCG/CGC motifs as biomarkers in PC. Based on the findings of this study, it seems that RNA-seq SSR and sRNA-seq SSR could open a new paradigm in the diagnostic and even therapeutic strategies for PC along the other types of cancers.

KEYWORDS:

Biomarker; EST–SSR; Leukemia; Next Generation Data Sequencing; Pancreatic cancer; RNA-seq; Small RNA-seq

PMID:
25639356
DOI:
10.1016/j.gene.2015.01.027
[Indexed for MEDLINE]

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