Transcriptome Profile of Next-Generation Sequencing Data Relate to Proliferation Aberration of Nasopharyngeal Carcinoma Patients in Indonesia
| Autor: | Afiahayati, Sagung Rai Indrasari, Sofia Mubarika Haryana, Dicka Wahyu Setiasari, Indwiani Astuti, Tirta Wardana, Cita Herawati, Didik Setyo Heriyanto, Digdo Sudigyo, Gisti Rahmawati, Risky Hiskia Poluan, Salsabila Lutfi Sesotyosari |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
proliferation Notch signaling pathway Biology DNA sequencing Transcriptome 03 medical and health sciences 0302 clinical medicine transcriptome analysis Gene expression medicine Biomarkers Tumor Humans Gene Cell Proliferation Nasopharyngeal Carcinoma cDNA library High-Throughput Nucleotide Sequencing Nasopharyngeal Neoplasms General Medicine medicine.disease Prognosis Molecular biology Gene Expression Regulation Neoplastic 030104 developmental biology Nasopharyngeal carcinoma Indonesia 030220 oncology & carcinogenesis next-generation sequencing RNA extraction Research Article |
| Zdroj: | Asian Pacific Journal of Cancer Prevention : APJCP |
| ISSN: | 2476-762X 1513-7368 |
| Popis: | Objective: Nasopharyngeal carcinoma (NPC) is the most common cancer arising from epithelial cells of the nasopharynx in Indonesia. This study aims to determine the differential level of gene expression in NPC patients when compared with normal individuals. Transcriptome profiling analysis was performed using RNA-Seq technology to determine the differential gene expression relate to proliferation aberration that occurs in NPC patients compared with normal individuals. So we get the transcriptomic profile of Indonesia NPC patients. Methods: In this study, we used 9 samples, 7 NPC samples and 2 normal samples as control. Fresh tissue of tumor samples was collected from biopsy, and normal samples were collected brushing technique. The total RNA was isolated from fresh tissue samples and brushing samples using the Rneasy® RNA Extraction Mini Kit. The cDNA library was generated using TruSeq® RNA Library Preparation Kit V2, and its concentration was determined using qPCR. The library was sequenced using the Next-Generation Sequencing (NGS) Illumina Next Seq 550 platform. The raw sequence data quality was analyzed using FastQC and interpreted using HISAT2, HTSeq, edgeR, and PANTHER. Results: From the analysis, 25493 gene transcripts were expressed, with 1956 genes were significantly upregulated, 90 genes were significantly downregulated in NPC samples, and 23897 genes didn’t change the expression level significantly (p |
| Databáze: | OpenAIRE |
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