Dataset Information

Molecular Fingerprinting in Cancer Detection

ABSTRACT: Interventions: Group 1: Study participants with cancer of the lung, prostate, bladder, breast, head and neck, liver, pancreas, ovaries, colon or with leucimia are informed in detail about the course, risks, and benefits of the study. If consent is given, 10 mL of blood will be taken. Serum and/or plasma samples will be prepared and stored. The clinical data of the patients (e.g. age, gender, smoking status, alcohol consumption, diagnosis, treatment, concomitant medication, comorbidities and family history), as well as the results of the pathological assessment will be recorded in a central data base in pseudonymized form. Group 2: Study participants without cancer (healthy volunteers) or patients with benign diseases of the same Organs are informed in detail about the course, risks, and benefits of the study. If consent is given, 10-20 mL of blood will be taken. Serum and/or plasma samples will be prepared and stored. The clinical data of the patients (e.g. age, gender, smoking status, alcohol consumption, diagnosis, treatment, concomitant medication, comorbidities and family history), as well as the results of the pathological assessment (if applicable) will be recorded in a central data base in pseudonymized form. Primary outcome(s): The primary objective of this study is the accuracy of IMF diagnosis for nine cancer entities, assessed by comparison with all data available to the investigator. A diagnoses is regarded as correct if IMF and clinical routine assessing all available data coincide with regard to the nine tumor entities of interest. Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: diagnostic

DISEASE(S): Crohn Disease Of Large Intestine,Leukaemia Of Unspecified Cell Type,Bronchus And Lung,Acute Pancreatitis,Pneumonia, Unspecified,Malignant Neoplasm Of Bronchus And Lung,Malignant Neoplasm Of Breast,Benign Neoplasm Of Ovary,Other Diseases Of Intestine,Malignant Neoplasm Of Colon,Other And Unspecified Cirrhosis Of Liver,Hyperplasia Of Prostate,Fibroadenosis Of Breast,Malignant Neoplasm Of Bladder,Malignant Neoplasms Of Lip, Oral Cavity And Pharynx,Malignant Neoplasm Of Pancreas,Chronic Obstructive Pulmonary Disease With Acute Exacerbation, Unspecified,Malignant Neoplasm Of Liver And Intrahepatic Bile Ducts,Malignant Neoplasm Of Prostate

PROVIDER: 2436268 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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Project description:Background: The incidence of alcohol and tobacco co-abuse is as high as 80%. The molecular mechanism underlying this comorbidity is virtually unknown but interactions between these drugs have important implications for the development of, and recovery from drug dependence. Methods: We investigated the effects of chronic tobacco and alcohol abuse and the interaction of the two behaviours on global gene expression in the human nucleus accumbens using cDNA microarrays and 20 alcoholic and control cases, with and without smoking comorbidity. Changes in gene expression were established by two-way ANOVA. Unsupervised hierarchical clustering was utilized to probe the strength of the data sets. Results: Subjecting the data sets derived from microarray gene expression screening to unsupervised hierarchical clustering tied the cases into distinct groups. When considering all alcohol-responsive genes, alcoholics were separated from non alcoholics with the exception of one control case. All smokers were distinguished from non smokers based on similarity in expression of smoking-sensitive genes. In the nucleus accumbens, alcohol-responsive genes were associated with transcription, lipid metabolism and signalling. Smoking-sensitive genes were predominantly assigned to functional groups concerned with RNA processing and the endoplasmic reticulum. Both drugs influenced the expression of genes involved in matrix remodelling, proliferation and cell morphogenesis. Additionally, a gene set encoding proteins involved in the canonical pathway ‘regulation of the actin cytoskeleton’ was induced in response to alcohol and tobacco co-abuse and included. Conclusions: The region-specific modulation of alcohol-sensitive gene expression by smoking may have important consequences for alcohol-induced aberrations within the mesolimbic dopaminergic system. The data set contained individual RNA samples extracted from the nucleus accumbens from 5 non smoking non drinking control case, 5 non smoking alcoholics, 5 non drinking smokers, and 5 smoking alcoholics. An aliquot if each sample was combined to generate a reference pool. Each sample was amplified individually and labelled with Cy3 in the process, the reference samples was amplified and labelled with Cy5. Each sample was hybridised competitively against the reference sample to 1 array.

Project description: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. 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.

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Molecular Fingerprinting in Cancer Detection

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