RNA-Seq enables discovery of potential biomarker – SSRs (simple sequence repeats)

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. 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, researchers from Shahrekord University 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, the researchers 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.

rna-seq

Alisoltani A, Fallahi H, Shiran B, Alisoltani A, Ebrahimie E. (2015) RNA-Seq SSRs and small RNA-Seq SSRs: New approaches in cancer biomarker discovery. Gene [Epub ahead of print]. [abstract]

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