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Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

ABSTRACT: Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

PROVIDER: PRJEB14203 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1429990_1.fastq.gz	Fastqsanger.gz
	ERR1429990_2.fastq.gz	Fastqsanger.gz
	ERR1429991_1.fastq.gz	Fastqsanger.gz
	ERR1429991_2.fastq.gz	Fastqsanger.gz
	ERR1429982_1.fastq.gz	Fastqsanger.gz

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Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.

2018-05-31 | E-MTAB-4653 | biostudies-arrayexpress

Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

2018-05-31 | E-MTAB-4654 | biostudies-arrayexpress

Chemotherapy-induced dynamic remodeling of tumor microenvironment and cellular program in tongue squamous cell carcinoma

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Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

Project description:Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

| PRJEB14202 | ENA

Expression analysis of LncRNA in Tongue Squamous Cell Carcinoma (TSCC) and matched nonmalignant tissues (NC)

Project description:Investigation of LncRNA expression level changes in 9 paired of Tongue Squamous Cell Carcinoma specimens LncRNA profiling: TSCC vs NC

2013-10-30 | E-GEOD-51700 | biostudies-arrayexpress

Altered expression of microRNAs in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)

Project description:Investigation of microRNA expression level changes in 4 paired of Tongue Squamous Cell Carcinoma specimens miRNA profiling: TSCC vs NC

2013-10-30 | E-GEOD-51829 | biostudies-arrayexpress

Project description:MicroRNAs play a crucial role in tumorigenesis. However, the value of microRNAs in the diagnosis and treatment of tongue squamous cell carcinoma (TSCC) still await investigations. To identify the microRNAs associated with the metastasis of TSCC, we analyzed the transcriptomic difference between metastatic and the non-metastatic TSCC tissue. We identified a set of metastasis-related microRNAs with potential prognostic value.

2016-12-31 | GSE81821 | GEO

Circular RNA expression in tongue squamous cell carcinoma patients

Project description:circRNA microarrays were performed with 2 pairs of tongue squamous cell carcinoma and their matched adjacent tissues. The statistical significance of the difference was estimated by t-test. circRNAs having fold changes 1.5 and p-values 0.05 are selected as the significantly differentially expressed. The data from microarray indicated that there were 54 upregulated and 70 downregulated circRNAs in TSCC tissues.

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LncRNA expression profiles in areca nut chewing induced Tongue Squamous Cell Carcinoma (TSCC) and matched paracancerous tissues

Project description:Chewing betel nut is an important risk factor for the carcinogenesis of tongue squamous cell carcinoma (TSCC), but the mechanism is still unknown.To screen the lncRNAs associated with betel nut chewing-induced TSCC and identify potential biomarkers for the TSCC, we collected 5 pairs of TSCC and paracancerous tissues and monitored the resultant lncRNA and mRNA expression profiles using an lncRNA microarray. All 5 patients have a history of areca nut chewing.

2020-10-27 | GSE139869 | GEO

Transcript profiling of normal oral keratinocytes and the tongue squamous cell carcinoma line LK0412

Project description:The current study analyzed a unique, serum-free medium derived tongue squamous cell carcinoma (TSCC) line termed LK0412 relative to the normal state to elucidate biomarkers at the protein and transcript level. A bioinformatics approach using Gene Ontology categories, gene networks and signature evaluation was applied to combine the protein and transcript data for identification of various gene signatures. The generated signatures were further assessed in public available data sets from normal and tumor tongue tissues. The analysis identified a novel gene signature that may improve the diagnosis and treatment of TSCC.

2014-01-31 | GSE21866 | GEO

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