MRD Detection in Acute Lymphoblastic Leukemia Patients Using Ig/TCR Gene Rearrangements as Targets for Real-Time Quantitative PCR

Recent advances in molecular and cellular biology techniques have significantly improved our ability to detect, monitor, model and study the underlying molecular basis and pathogenesis of leukemia, yet we are still in an early discovery stage and much more work is needed in order to develop better strategies to diagnose, classify and treat this biologically and clinically diverse disease. In Leukemia: Methods and Protocols , expert researchers bring together a wide range of state-of-the-art laboratory methods and detailed protocols that are useful for both clinical and basic research scientists working on the disease. The volume provides techniques for prenatal backtracking of leukemic clone, molecular diagnosis, detection of genome-wide genetic abnormalities and profiling, identification of unknown fusion genes, monitoring of minimal residual diseases, disease modeling using murine and human primary hematopoietic cells, studying of normal and malignant hematopoiesis, identification of interacting partners with leukemia associated oncoproteins, and global characterization of genome-wide epigenetic changes in leukemic cells. Written in the highly successful Methods in Molecular Biology TM series format, the convenient chapters contain brief introductions, lists of the necessary materials, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Leukemia: Methods and Protocols will help researchers to advance knowledge and have a better understanding of the disease, which will ultimately facilitate development of anti-cancer therapy and improve quality of life for patients. Methods in Molecular Biology Cover 1 Frontmatter 2 Chapter 1 - An Overview: From Discovery of Candidate Mutations to Disease Modeling and Transformation Mechanisms of Acute Leukemia 11 Chapter 2 - Backtracking of Leukemic Clones to Birth 16 Chapter 3 - Fluorescence In Situ Hybridization (FISH) as a Tool for the Detection of Significant Chromosomal Abnormalities in Childhood Leukaemia 37 Chapter 4 - Specialized Fluorescence In Situ Hybridization (FISH) Techniques for Leukaemia Research 64 Chapter 5 - LDI-PCR: Identification of Known and Unknown Gene Fusions of the Human MLL Gene 78 Chapter 6 - Panhandle PCR Approaches to Cloning MLL Genomic Breakpoint Junctions and Fusion Transcript Sequences 91 Chapter 7 - MRD Detection in Acute Lymphoblastic Leukemia Patients Using Ig/TCR Gene Rearrangements as Targets for Real-Time Quantitative PCR 121 Chapter 8 - Array-Based Comparative Genomic Hybridization as a Tool for Analyzing the Leukemia Genome 157 Chapter 9 - Application of SNP Genotype Arrays to Determine Somatic Changes in Cancer 184 Chapter 10 - Retroviral/Lentiviral Transduction and Transformation Assay 212 Chapter 11 - Gene Expression Profiling of Leukemia Stem Cells 235 Chapter 12 - Humanized Model to Study Leukemic Stem Cells 251 Chapter 13 - Model Systems for Examining Effects of Leukemia-Associated Oncogenes in Primary Human CD34+ Cells via Retroviral Transduction 267 Chapter 14 - Ex Vivo Assays to Study Self-Renewal and Long-Term Expansion of Genetically Modified Primary Human Acute Myeloid Leukemia Stem Cells 290 Chapter 15 - Identification and Characterization of Hematopoietic Stem and Progenitor Cell Populations in Mouse Bone Marrow by Flow Cytometry 304 Chapter 16 - In Vitro Differentiation of Mouse Embryonic Stem Cells as a Model of Early Hematopoietic Development 319 Chapter 17 - Analysis of the Mouse Placenta as a Hematopoietic Stem Cell Niche 337 Chapter 18 - Identification of Protein Interaction Partners by the Yeast Two-Hybrid System 349 Chapter 19 - Complete Array of HOX Gene Expression by RQ-PCR 370 Chapter 20 - Genome-Wide Determination of DNA Methylation by Hpa II Tiny Fragment Enrichment by Ligation-Mediated PCR (HELP) for the Study of Acute Leukemias 395 Chapter 21 - Chromatin Immunoprecipitation (ChIP) for Analysis of Histone Modifications and Chromatin-Associated Proteins 408 Index 423 except for brief excerpts in connection with reviews or scholarly analysis. 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Presents techniques for prenatal backtracking of leukemic clone, molecular diagnosis, detection of genome-wide genetic abnormalities and profiling, identification of unknown fusion genes, monitoring of minimal residual diseases, disease modeling using murine and human primary hematopoietic cells, and studying of normal and malignant hematopoiesis. Front Matter....Pages i-xi Back Matter....Pages 1-5 ....Pages 7-27