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Open Access Research article

Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma

Qu Zhang1*, Jun Zhang2, Hong Jin3 and Sitong Sheng3*

Author Affiliations

1 Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA

2 Department of Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital, Shanghai Jiaotong University, School of Medicine, No.197 Ruijin er Road, Shanghai, P.R. China

3 HYK High-throughput Biotechnology Institute, 4th Floor, Building No.11, Software Park, 2nd Central Keji Rd, Hi-Tech Industrial Park, Shenzhen, China

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BMC Medical Genomics 2013, 6:28  doi:10.1186/1755-8794-6-28

Published: 4 September 2013



The accumulation of somatic mutations in genes and molecular pathways is a major factor in the evolution of oral squamous cell carcinoma (OSCC), which sparks studies to identify somatic mutations with clinical potentials. Recently, massively parallel sequencing technique has started to revolutionize biomedical studies, due to the rapid increase in its throughput and drop in cost. Hence sequencing of whole transcriptome (RNA-Seq) becomes a superior approach in cancer studies, which enables the detection of somatic mutations and accurate measurement of gene expression simultaneously.


We used RNA-Seq data from tumor and matched normal samples to investigate somatic mutation spectrum in OSCC.


By applying a sophisticated bioinformatic pipeline, we interrogated two tumor samples and their matched normal tissues and identified 70,472 tumor somatic mutations in protein-coding regions. We further identified 515 significantly mutated genes (SMGs) and 156 tumor-specific disruptive genes (TDGs), with six genes in both sets, including ANKRA2, GTF2H5, STOML1, NUP37, PPP1R26, and TAF1L. Pathway analysis suggested that SMGs were enriched in cell adhesion pathways, which are frequently indicated in tumor development. We also found that SMGs tend to be differentially expressed between tumors and normal tissues, implying a regulatory role of accumulation of genetic aberrations in these genes.


Our finding of known tumor genes proves of the utility of RNA-Seq in mutation screening, and functional analysis of genes detected here would help understand the molecular mechanism of OSCC.

RNA-Seq; Oral squamous cell carcinoma; Somatic mutations; Significantly mutated genes; Differential expression; Disruptive genes