title: Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma.
abstract: BACKGROUND
  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.
  
  
  METHODS
  We used RNA-Seq data from tumor and matched normal samples to investigate somatic mutation spectrum in OSCC.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. quzhang@post.harvard.edu.
authors.forename: Qu
authors.initials: Q
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Zhang
authors.forename: Hong
authors.initials: H
authors.lastname: Jin
authors.forename: Sitong
authors.initials: S
authors.lastname: Sheng
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D004252:DNA Mutational Analysis; D063990:Gene Ontology; D052138:Genes, Neoplasm / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009062:Mouth Neoplasms / Q000235:genetics*; D009154:Mutation; D017423:Sequence Analysis, RNA; D059467:Transcriptome