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首页> 外文期刊>BMC Medical Genomics >Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma
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Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma

机译：全转录组测序可鉴定人口腔鳞状细胞癌中的肿瘤特异性突变

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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.
机译：背景技术体细胞突变在基因和分子途径中的积累是口腔鳞状细胞癌（OSCC）进化的主要因素，这引发了研究以鉴定具有临床潜力的体细胞突变。最近，由于大规模并行测序技术的通量快速增加和成本下降，已开始彻底改变生物医学研究。因此，在癌症研究中对整个转录组测序（RNA-Seq）成为一种上乘的方法，它可以检测体细胞突变并同时精确测量基因表达。方法我们使用来自肿瘤的RNA-Seq数据并匹配正常样品来研究OSCC中的体细胞突变谱。结果通过应用复杂的生物信息流水线，我们询问了两个肿瘤样本及其匹配的正常组织，并在蛋白质编码区域鉴定了70,472个肿瘤体细胞突变。我们进一步确定了515个显着突变的基因（SMGs）和156个肿瘤特异性破坏性基因（TDGs），两组中都有6个基因，包括ANKRA2，GTF2H5，STOML1，NUP37，PPP1R26和TAF1L。途径分析表明，SMGs富含细胞粘附途径，这在肿瘤发展中经常出现。我们还发现，SMG倾向于在肿瘤和正常组织之间差异表达，这暗示着这些基因中遗传异常累积的调节作用。结论我们对已知肿瘤基因的发现证明了RNA-Seq在突变筛选中的实用性，对此处检测到的基因进行功能分析将有助于了解OSCC的分子机制。

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