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DNA microarray analysis in Chinese multiple myeloma.

Wong, Ling Yee. / Thesis submitted in: August 2007. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 110-127). / Abstracts in English and Chinese. / Thesis Abstract --- p.i / 論文摘要 --- p.iv / Acknowledgements --- p.vi / Abbreviations --- p.vii / Thesis Content --- p.xii / List of Figures --- p.xv / List of Tables --- p.xvii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.3 / Chapter 2.1. --- Multiple Myeloma (MM) --- p.3 / Chapter 2.1.1 --- Epidemiology --- p.4 / Chapter 2.1.2 --- Cause and Risk Factors --- p.5 / Chapter 2.1.3 --- Pathophysiology --- p.5 / Chapter 2.1.4 --- Diagnosis and Clinical Presentation --- p.6 / Chapter 2.1.5 --- Classification of Plasma Cell Disorders --- p.6 / Chapter 2.1.5.1 --- Monoclonal Gammopathy of Undetermined Significance (MGUS) --- p.6 / Chapter 2.1.5.2 --- Asymptomatic (Smouldering) MM --- p.7 / Chapter 2.1.5.3 --- Indolent MM --- p.7 / Chapter 2.1.5.4 --- Symptomatic MM --- p.8 / Chapter 2.1.6 --- Staging --- p.9 / Chapter 2.1.7 --- Treatment --- p.11 / Chapter 2.1.8 --- Molecular Abnormality --- p.12 / Chapter 2.2 --- DNA Microarray Analysis in MM --- p.13 / Chapter 2.2.1 --- MM Pathogenesis --- p.15 / Chapter 2.2.2 --- Molecular Classification of MM --- p.18 / Chapter 2.2.3 --- Anti-MM Drug Studies --- p.22 / Chapter 2.3 --- Cancer Treatment Response Prediction --- p.24 / Chapter 2.3.1 --- MP Treatment --- p.24 / Chapter 2.3.1.1 --- Melphalan --- p.25 / Chapter 2.3.1.2 --- Prednisone --- p.27 / Chapter 2.3.1.3 --- MP Treatment Response Prediction in MM --- p.29 / Chapter 2.3.2 --- Cancer Prognosis using DNA Microarray --- p.31 / Chapter Chapter 3 --- Materials and Methods --- p.36 / Chapter 3.1. --- Patient Specimens for Gene Expression Profiling and Quantitative Real-time PCR --- p.36 / Chapter 3.2. --- Magnetic Cell Sorting of CD138-positive Plasma Cells --- p.37 / Chapter 3.2.1 --- Density Gradient Centrifugation --- p.37 / Chapter 3.2.2 --- Positive Selection of CD138-positive Cells --- p.37 / Chapter 3.3 --- Generation of Gene Expression Profiles --- p.39 / Chapter 3.3.1 --- RNA Extraction --- p.39 / Chapter 3.3.2 --- RNA Assessment --- p.40 / Chapter 3.3.3 --- Synthesis and Purification of Double-strand cDNA --- p.40 / Chapter 3.3.4 --- In vitro Transcription (IVT) and Recovery of Biotin-labeled cRNA --- p.41 / Chapter 3.3.5 --- cRNA Fragmentation and Hybridization Reaction Mixture Preparation --- p.41 / Chapter 3.3.6 --- Hybridization --- p.42 / Chapter 3.3.7 --- Post-hybridization Wash --- p.42 / Chapter 3.3.8 --- Detection with Streptavidin-dye Conjugate --- p.43 / Chapter 3.3.9 --- Bioarray Scanning and Spot Signal Quantitation --- p.43 / Chapter 3.4 --- Microarray Data Analysis --- p.45 / Chapter 3.4.1 --- Normalization and Filtering --- p.45 / Chapter 3.4.2 --- Unsupervised Clustering Analysis --- p.45 / Chapter 3.4.3 --- Supervised Class Comparison Analysis --- p.46 / Chapter 3.5 --- Microarray Verification and Candidate Gene Validation --- p.47 / Chapter 3.5.1 --- RNA Extraction --- p.47 / Chapter 3.5.2 --- Reverse Transcription PCR --- p.47 / Chapter 3.5.3 --- Quantitative Real-time PCR --- p.48 / Chapter 3.6 --- Predictive Value Calculation --- p.49 / Chapter 3.7 --- Experimental Flow --- p.49 / Chapter Chapter 4 --- Results --- p.53 / Chapter 4.1 --- Gene Expression Profiling of Chinese MM --- p.53 / Chapter 4.1.1 --- Unsupervised Clustering Analysis --- p.53 / Chapter 4.1.1.1 --- Hierarchical Clustering --- p.53 / Chapter 4.1.1.2 --- Principal Component Analysis (PCA) --- p.54 / Chapter 4.1.2 --- Identification of Statistically Differentially Expressed Genes --- p.58 / Chapter 4.1.2.1 --- Two-Sample t-statistics --- p.58 / Chapter 4.1.2.2 --- Significance Analysis of Microarrays (SAM) --- p.58 / Chapter 4.1.2.3 --- Microarray Verification --- p.66 / Chapter 4.2 --- Development of MP Treatment Response Biomarker in MM --- p.70 / Chapter 4.2.1 --- Unsupervised Clustering Analysis --- p.70 / Chapter 4.2.1.1 --- Hierarchical Clustering --- p.70 / Chapter 4.2.1.2 --- PCA --- p.70 / Chapter 4.2.2 --- Identification of Statistically Differentially Expressed Genes --- p.74 / Chapter 4.2.2.1 --- Two sample t-statistics --- p.74 / Chapter 4.2.2.2 --- SAM --- p.74 / Chapter 4.2.3 --- Verification of Candidate Gene CYB5D1 --- p.76 / Chapter Chapter 5 --- Discussion --- p.79 / Chapter 5.1 --- Global Gene Expression Profiling: DNA Microarray --- p.79 / Chapter 5.2 --- Microarray Data Normalization and Gene Filtering --- p.81 / Chapter 5.3 --- Microarray Data Analysis --- p.83 / Chapter 5.3.1 --- Unsupervised Clustering Analysis --- p.83 / Chapter 5.3.1.1 --- Hierarchical Clustering --- p.83 / Chapter 5.3.1.2 --- PCA --- p.85 / Chapter 5.3.2 --- Identification of Statistically Differentially Expressed Genes --- p.86 / Chapter 5.4 --- Verification of Candidate Genes by Quantitative Real-time PCR --- p.89 / Chapter 5.5 --- Gene Expression Profiling of Chinese MM --- p.90 / Chapter 5.5.1 --- Comparison of Gene Expression Patterns of MM and Normal Plasma Cells --- p.90 / Chapter 5.5.2 --- Differentially Expressed Genes between MM and Normal Plasma Cells..… --- p.91 / Chapter 5.5.2.1 --- Common Differentially Expressed Genes with Previous Studies --- p.94 / Chapter 5.5.2.2 --- Potential Tumor Suppressor Genes in Differentially Expressed Genes..… --- p.96 / Chapter 5.5.2.3 --- Verified Differentially Expressed Genes --- p.98 / Chapter 5.5.3 --- Future Studies --- p.101 / Chapter 5.6 --- Development of MP Treatment Response Biomarker in MM --- p.103 / Chapter 5.6.1 --- Comparison of Gene Expression Patterns of MP Good Responders (GR) and Poor Responders (PR) --- p.103 / Chapter 5.6.2 --- Differentially Expressed Gene between MP GR and PR: CYB5D1 --- p.104 / Chapter 5.6.3 --- Possible Role of CYB5D1 in MP Resistance in MM Cells --- p.104 / Chapter 5.6.4 --- Potential Clinical Application of CYB5D1 in MP Treatment Response Prediction in MM --- p.106 / Chapter 5.6.5 --- Future Studies --- p.106 / Chapter Chapter 6 --- Conclusion --- p.108 / Chapter 6.1 --- Gene Expression Profiling of Chinese MM --- p.108 / Chapter 6.2 --- Development of MP Treatment Response Biomarker in MM --- p.108 / References --- p.110 / Appendix --- p.128

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_326206
Date January 2008
ContributorsWong, Ling Yee., Chinese University of Hong Kong Graduate School. Division of Anatomical and Cellular Pathology.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, xvii, 128 leaves : ill. (some col.) ; 30 cm.
RightsUse of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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