Due to growing throughput and shrinking cost, massively parallel sequencing is rapidly becoming an attractive alternative to microarrays for the genome-wide study of gene expression and copy number alterations in primary tumors. The sequencing of transcripts (RNA-Seq) should offer several advantages over microarray-based methods, including the ability to detect somatic mutations and accurately measure allele-specific expression. To investigate these advantages we have applied a novel, strand-specific RNA-Seq method to tumors and matched normal tissue from three patients with oral squamous cell carcinomas. Additionally, to better understand the genomic determinants of the gene expression changes observed, we have sequenced the tumor and normal genomes of one of these patients. We demonstrate here that our RNA-Seq method accurately measures allelic imbalance and that measurement on the genome-wide scale yields novel insights into cancer etiology. As expected, the set of genes differentially expressed in the tumors is enriched for cell adhesion and differentiation functions, but, unexpectedly, the set of allelically imbalanced genes is also enriched for these same cancer-related functions. By comparing the transcriptomic perturbations observed in one patient to his underlying normal and tumor genomes, we find that allelic imbalance in the tumor is associated with copy number mutations and that copy number mutations are, in turn, strongly associated with changes in transcript abundance. These results support a model in which allele-specific deletions and duplications drive allele-specific changes in gene expression in the developing tumor.

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lung cancer. Tumor biopsy specimens and blood plasma served as the material for the study when tissue biopsy was not possible. The study of diagnostic material was performed by PCR analysis for the main mutations ex19del, L858R and rare mutations L861Q, G719X, ex20ins and S768I.Results: A total of 1,135 samples were tested. EGFR mutation was detected in 195 (17.2%) cases. Due to analyzing various mutations in the EGFR gene, ex19del was detected in 97 patients (49.7%), L858R in 83 (42.6%), L861Q in 3 (1.5%), G719X in 4 (2.1%), ex20ins in 1 (0.5%). The S768I mutation was determined in 2 cases (1.03%) and in both cases, together with the L858R mutation. Also, an additional 3 patients showed a combination of ex19del + T790M, L858R + G719X and L858R + L861Q mutations. Among patients who never received treatment, 2 (1.03%) showed a T790M mutation.Conclusions: From the obtained results of the mutational landscape of EGFR mutations in lung adenocarcinoma, it follows that the occurrence of somatic mutations is due to the territorial feature of the population and the peculiarity of the effect of carcinogenic factors. By the results, the frequency of detection of mutations in the EGFR gene for the region under consideration is characterized by territorial features.