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  • CLASSIFICATION  (5)
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  • 1
    Keywords: CLASSIFICATION ; BIOLOGY ; MOLECULAR-BIOLOGY ; genetics ; REPRODUCIBILITY ; molecular biology ; TASK
    Type of Publication: Journal article published
    PubMed ID: 16646817
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  • 2
    Keywords: EXPRESSION ; IN-VITRO ; SURVIVAL ; Germany ; MODEL ; VITRO ; CLASSIFICATION ; CDNA ; GENOME ; microarray ; RNA ; SAMPLE ; SAMPLES ; MESSENGER-RNA ; BREAST-CANCER ; NO ; AMPLIFICATION ; microarrays ; REQUIRES ; PARAMETERS ; STATISTICAL-ANALYSIS ; DIFFERENTIAL EXPRESSION ; QUANTITIES ; LACKING ; REQUIREMENT ; bias ; PNEUMOPERITONEUM
    Abstract: Background: The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10-100 mug of RNA. However, due to their small size, most biopsies do not yield this amount. Several different approaches for RNA amplification in vitro have been described and applied for microarray studies. In most of these, systematic analyses of the potential bias introduced by the enzymatic modifications are lacking. Results: We examined the sources of error introduced by the T7 RNA polymerase based RNA amplification method through hybridisation studies on microarrays and performed statistical analysis of the parameters that need to be evaluated prior to routine laboratory use. The results demonstrate that amplification of the RNA has no systematic influence on the outcome of the microarray experiment. Although variations in differential expression between amplified and total RNA hybridisations can be observed, RNA amplification is reproducible, and there is no evidence that it introduces a large systematic bias. Conclusions: Our results underline the utility of the T7 based RNA amplification for use in microarray experiments provided that all samples under study are equally treated
    Type of Publication: Journal article published
    PubMed ID: 15119961
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  • 3
    Keywords: CANCER ; tumor ; carcinoma ; CELL ; Germany ; PATHWAY ; PATHWAYS ; CLASSIFICATION ; FOLLOW-UP ; DISEASE ; TUMORS ; PATIENT ; primary ; renal ; TYPE-1 ; FREQUENCY ; STAGE ; PATTERNS ; DIFFERENCE ; EVOLUTION ; MORPHOLOGY ; CARCINOMAS ; SERIES ; ABNORMALITIES ; TYPE-2 ; CORTICAL TUMORS ; GAINS
    Abstract: We evaluated clinical characteristics, patient outcome (mean follow-up, 47 months), and cytogenetic abnormalities in the largest as yet reported cytogenetic series of 47 primary and 11 secondary papillary renal cell carcinomas for differences between the recently proposed type 1 and type 2 subtypes. Secondary tumors were more often of type 2 morphology (P = 0.02), whereas primary type 2 tumors were associated with higher clinical stage (P = 0.001) and worse patient outcome (P = 0.02). Although both subtypes had at least one of the primary chromosomal gains at 17q, 7, and 16q, type 2 tumors had moderately lower frequencies of primary gains at 17p (61 versus 94%; P = 0.007) and 17q (72 versus 97%; P = 0.02). On the other hand, type 2 tumors overall had more chromosomal alterations than type 1 tumors (P = 0.01), particularly gains of 1q (28 versus 3%; P = 0.02) and losses of 8p (33 versus 0%; P = 0.001), 11 (28 versus 3%; P = 0.02), and 18 (44 versus 9%; P = 0.01). Hierarchical clustering suggested cytogenetic patterns common but not restricted to type 2 morphology, one characterized by multiple additional gains, and another predominantly showing additional losses. These findings provide genetic evidence that type 1 and type 2 tumors arise from common cytogenetic pathways and that type 2 tumors evolve from type 1 tumors. Independently of type, losses of 9p were statistically correlated with advanced disease (P = 0.0008) and may serve as a potential adverse prognostic marker in papillary renal cell carcinomas
    Type of Publication: Journal article published
    PubMed ID: 14559804
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  • 4
    Keywords: CANCER ; CELLS ; EXPRESSION ; SURVIVAL ; tumor ; TUMOR-CELLS ; carcinoma ; Germany ; PATHWAY ; PATHWAYS ; CLASSIFICATION ; DIAGNOSIS ; CDNA ; GENE ; GENE-EXPRESSION ; GENES ; HYBRIDIZATION ; microarray ; TISSUE ; TUMORS ; PATIENT ; kidney ; GROWTH-FACTOR RECEPTOR ; SEQUENCE ; IDENTIFICATION ; PROGRESSION ; MALIGNANCIES ; PATTERNS ; gene expression ; microarrays ; METASTASIS ; ABNORMALITIES ; C-MYC ; MICROARRAY ANALYSIS ; CDNA MICROARRAYS ; CDNA MICROARRAY ; RENAL-CELL CARCINOMA ; molecular ; MALIGNANCY ; RE ; PATIENT SURVIVAL ; SOLID TUMORS ; EXPRESSED SEQUENCE TAGS ; PROTOONCOGENE ; cytogenetic ; CELL-CARCINOMA ; EXPRESSION PATTERNS ; SIGNATURE
    Abstract: Current diagnosis of renal cancer consists of histopathologic examination of tissue sections and classification into tumor stages and grades of malignancy. Until recently, molecular differences between tumor types were largely unknown. To examine such differences, we did gene expression measurements of 112 renal cell carcinoma and normal kidney samples on renal cell carcinoma-specific cDNA microarrays containing 4,207 genes and expressed sequence tags. The gene expression patterns showed deregulation of complete biological pathways in the tumors. Many of the molecular changes corresponded well to the histopathologic tumor types, and a set of 80 genes was sufficient to classify tumors with a very low error rate. Distinct gene expression signatures were associated with chromosomal abnormalities of tumor cells, metastasis. formation, and patient survival. The data highlight the benefit of microarrays to detect novel tumor classes and to identify genes that are associated with patient variables and tumor properties
    Type of Publication: Journal article published
    PubMed ID: 15701852
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  • 5
    Keywords: CANCER ; Germany ; CLASSIFICATION ; microarray ; COMPLEX ; COMPLEXES ; DOMAIN ; BREAST-CANCER ; microarrays ; NUMBER ; REPRODUCIBILITY ; PREDICTION ; SIZE ; TECHNOLOGY ; GENE-EXPRESSION DATA ; microarray profiling studies ; statistical computation
    Abstract: Objectives: Microarrays are a recent biotechnology that offers the hope of improved cancer classification. A number of publications presented clinically promising results by combining this new kind of biological data with specifically designed algorithmic approaches. But, reproducing published results in this domain is harder than it may seem. Methods: This paper presents examples, discusses the problems hidden in the published analyses and demonstrates a strategy to improve the situation which is based on the vignette technology available from the R and Bioconductor projects. Results. The tool of a compendium is discussed to achieve reproducible calculations and to offer an extensible computational framework. A compendium is a document that bundles primary data, processing methods (computational code), derived data, and statistical output with textual documentation and conclusions. It is interactive in the sense that it allows for the modification of the processing options, plugging in new data, or inserting further algorithms and visualizations. Conclusions. Due to the complexity of the algorithms, the size of the data sets, and the limitations of the medium printed paper it is usually not possible to report all the minutiae of the data processing and statistical computations. The technique of a compendium allows a complete critical assessment of a complex analysis
    Type of Publication: Journal article published
    PubMed ID: 16538278
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