Genomics

Dataset Information

28

Copy number variation analysis of nasopharyngeal carcinoma cell lines


ABSTRACT: To analyze the global copy number aberrations of two nasopharyngeal carcinoma cell lines, TW01 and HONE1. Global copy number aberrations were analyzed by using high-resolution oligoarray CGH on two NPC cell lines, TW01 and HONE1. The overviews of array CGH profiles reveal high similarity between both NPC cell lines, but the degree of copy-number alterations were more severe in TW01 than in HONE1. There were 1204 and 1513 genes with copy-number gain (CNVs with aberration score > 0.5 and number of contiguous probes ≥ 3) in TW01 and HONE1, respectively. Among them, 850 were commonly amplified in both cell lines (Gain-TH). There were 3525 genes and 926 genes with copy-number loss (CNVs with aberration score < 0.5 and number of contiguous probe ≥ 3) in TW01 and HONE1, respectively. Among them, 582 were commonly deleted in both cell lines (Loss-TH). The most prominent CNVs observed including gain on 3q26.2-q26.31, loss on 3p21.2-q12.1, 9p24.3-p21.3, and nearly the whole Y chromosome. Overall design: Comparison experiment, genome of NPC cells vs. normal male genome (NM). Biological replicates: TW01-1 vs. NM; TW01-2 vs. NM; HONE1-1 vs. NM; HONE1-2 vs. NM.

INSTRUMENT(S): Agilent-014693 Human Genome CGH Microarray 244A (Feature number version)

SUBMITTER: Chia Huei Lee  

PROVIDER: GSE15172 | GEO | 2010-03-09

SECONDARY ACCESSION(S): PRJNA123125

REPOSITORIES: GEO

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Publications

Independent effect of EBV and cigarette smoking on nasopharyngeal carcinoma: a 20-year follow-up study on 9,622 males without family history in Taiwan.

Hsu Wan-Lun WL   Chen Jen-Yang JY   Chien Yin-Chu YC   Liu Mei-Ying MY   You San-Lin SL   Hsu Mow-Ming MM   Yang Czau-Siung CS   Chen Chien-Jen CJ  

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20090331 4


This study aimed to assess independent effects of EBV and cigarette smoking on nasopharyngeal carcinoma, which have never been assessed in long-term follow-up studies. A cohort of 9,622 men was enrolled from 1984 to 1986. Blood samples collected at study entry were tested for antibodies against EBV antigens (anti-EBV) viral capsid antigen immunoglobulin A and DNase. The cigarette smoking habit was inquired through questionnaire interview. Newly developed nasopharyngeal carcinoma cases were ascer  ...[more]

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