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Series GSE47443 Query DataSets for GSE47443
Status Public on Jul 01, 2013
Title Somatic copy number alterations associating with alcohol drinking and smoking in head and neck squamous cell carcinoma
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Background: The most important risk factors for head and neck squamous carcinoma (HNSCC) are tobacco smoking and alcohol consumption, while subgroups are caused by infection with human papillomaviruses (HPV) or Epstein-Barr virus (EBV). Here, we studied alterations of somatic copy-number in whole genome, p16 protein and TP53 mutations by alcohol drinking, smoking and viral infections.

Methods: We conducted a prospective cohort study. DNA obtained from tumors and margin samples as well as peripheral blood was assayed by array comparative genomic hybridization using Agilent Whole Human Genome 180K. Mutations of p53 gene by direct sequencing, detection of HPV by polymerase-chain-reaction (PCR), quantification of EBV by reverse transcription-PCR and p16 immunohistochemical (IHC) staining were also performed.
 
Overall design prospective cohort study: 225 tumor samples were analyzed by Agilent-022060 SurePrint G3 Human CGH miroarray 4x180K. Log2 Ratio (tumor sample DNA/normal DNA) were compared among none alcohol drinkers, moderate alcohol drinkers, heavy alcohol drinkers, none smokers, moderate smokers, heavy smokers and both.

Sample characteristics weres scored as following;

Human Papilloma Virus Infection (gene detected by PCR in tumor sample): positive=1; negative=0

p16 protein immunohistochemistry: positive=1; negative=0

tumor grade: matured=0; moderate=1; immature=2

Radiotherapy with or without chemotherapy after operation: performed =1; not performed =0

Recurrence/relapse: rec =1; not rec =0

suvival status:death=1; survive=0

smoking status (Pack year of smoking): none smoker=0; pack-year <20 = 1 (moderate smoker); pack-year <=20 = 2 (heavy smoker)

alcohol drinking: Alcohol drinkers were divided into non-drinker or less than one drink per day =0: one and more but less than two drinks per day = moderate drinker 1: two and more drinks per day=heavy drinker 2: during the 20 years preceding their treatment for HNSCC. One drink was defined as containing approximately 10g of alcohol, which is considered equal to 30 ml of hard liquor, 100 ml of wine containing 12% alcohol, or 360 ml of beer.
 
Contributor(s) Urashima M, Hama T
Citation(s) 25658832, 25886176, 24278325
Submission date May 28, 2013
Last update date Feb 05, 2020
Contact name Mitsuyoshi Urashima
E-mail(s) urashima@jikei.ac.jp
Organization name Jikei University School of Medicine
Street address Nishishimbashi 3-25-8, Minato-ku
City Tokyo
ZIP/Postal code 1058461
Country Japan
 
Platforms (1)
GPL10150 Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Probe Name version)
Samples (225)
GSM1149550 head and neck squamous cell carcinoma 1
GSM1149551 head and neck squamous cell carcinoma 2
GSM1149552 head and neck squamous cell carcinoma 3
Relations
BioProject PRJNA205622

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47443_RAW.tar 4.1 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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