Global transcriptome and sequenome analysis of formalin-fixed XXXX specimens.

@entity1 @entity5 @entity984 @entity189 @entity982 @entity8497 @entity817 @entity8498 @entity10160 @entity2383
Diverse microarray and sequencing technologies have been widely used to characterize molecular changes in malignant epithelial cells in salivary neoplasms. Such gene expression studies to identify markers and targets in @entity5 cells are, however, compromised by the cellular heterogeneity of these @entity5 and by the difficulties to accrue matching controls representing normal salivary glands. Seventeen samples of primary @entity189 along with tissue from six normal major salivary glands were microdissected from @entity982 -embedded tissue. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using a whole-transcriptome shotgun sequencing experiment. In parallel, extracted genomic DNA was used for the 50 gene hotspot panel sequenome. @entity984 mutations in three @entity1 (18%), @entity8497 mutations in one @entity1 (6%), but no @entity8498 , MET, @entity10160 , or @entity817 mutations. Using strict and conservative criteria, 220 differentially expressed transcripts were found, with 36% up- and 64% downregulated. The transcripts were annotated using NCBI Entrez Gene, and computationally analyzed with the Ingenuity Pathway Analysis program. From these significantly changed expressions, the analysis identified 26 @entity5 -related transcripts and 16 transcripts related to @entity2383 overlapping with three @entity5 -related genes. These 220 differentially expressed genes including microRNAs provide here a sufficiently large set to specifically @entity189 and to identify novel and potentially important targets for diagnosis, prognosis, and therapy of this @entity5 .
