Molecular Diagnostics in Hematological Oncology: UNI-MED SCIENCE

1. Basic Principles of Molecular Diagnostics (S. Pfister, P. Lichter) 20 1.1. Introduction 20 1.2. Polymerase Chain Reaction-based methods 20 1.2.1. Quantitative Real-time PCR (QRT-PCR) 20 1.2.1.1. QRT-PCR using a hydrolysis probe ("TaqMan probe") 20 1.2.1.2. QRT-PCR using a hybridization probe 20 1.2.1.3. QRT-PCR using SYBR green dye 20 1.2.1.4. QRT-PCR Applications 21 1.2.2. PCR-based methods to detect promoter methylation of single genes 21 1.2.2.1. Bisulfite genomic sequencing (BGS) 21 1.2.2.2. Methylation-specific PCR (MSP) 21 1.2.2.3. Combined bisulfite restriction analysis (COBRA) 22 1.2.3. Multiplex Ligation-dependent probe amplification (MLPA) 22 1.3. Cytogenetics 22 1.3.1. Conventional Cytogenetics 22 1.3.2. Fluorescence In Situ hybridization (FISH) 22 1.3.3. Comparative Genomic Hybridization (CGH) 23 1.4. Microarray-based Methods 23 1.4.1. Array-based CGH 23 1.4.2. SNP Profiling 23 1.4.3. Messenger-RNA Expression Profiling 24 1.4.4. Epigenetic profiling 24 1.4.5. Micro-RNA Profiling 25 1.5. Immunostaining and Flow Cytometry 25 1.5.1. Immunocytochemistry 25 1.5.2. Flow Cytometry 25 1.6. Proteomics 25 1.6.1. 2D-PAGE 25 1.6.2. Mass spectrometry 26 1.7. Sequencing Methods 26 1.7.1. Pyrosequencing 26 1.7.2. Next-generation sequencing (NGS) approaches 26 1.8. Outlook 27 2. Multiple Myeloma (C. Langer, P. Liebisch, R. Fonseca) 30 2.1. Introduction 30 2.2. Cell Sorting 30 2.3. Chromosome Banding 30 2.4. Molecular Diagnostics 30 2.4.1. High Resolution genome-wide Detection Methods 31 2.4.2. FISH 32 2.4.3. Metaphase spectral karyotype Imaging (SKY) 33 2.4.4. Gene Expression Profiling 33 2.5. Pathogenetic Relevance of chromosomal Abnormalities 33 2.5.1. B-cell Development and Myelomagenesis 33 2.5.2. Primary and secondary IgH Translocations 33 2.5.3. Aneuploidy 35 2.5.4. Genetic Model of Myelomagenesis 35 2.5.5. Implication of GEP Data - TC Classification 36 2.6. Clinical and prognostic Implications of chromosomal Abnormalities 36 2.6.1. Aneuploidy 36 2.6.2. Specific genomic Imbalances 36 2.6.2.1. Monosomy 13/13q Deletion (-13/13q-) 36 2.6.2.2. Chromosome 17p Deletion 37 2.6.2.3. Chromosome 1q Abnormalities 37 2.6.2.4. t(11;14)(q13;q32) 37 2.6.2.5. t(4;14)(p16.3;q32) 38 2.6.2.6. t(14;16)(q32;q23) 38 3. Non-Hodgkin-Lymphoma and Hodgkin Lymphoma (J.I Martín-Subero, A. Rosenwald, R. Siebert, R.D. Gascoyne) 42 3.1. Introduction 42 3.2. Chromosomal Changes associated with non-Hodgkin and Hodgkin Lymphomas 42 3.2.1. B-cell non-Hodgkin Lymphomas 43 3.2.1.1. Follicular Lymphoma 43 3.2.1.2. Mantle Cell Lymphoma 43 3.2.1.3. Diffuse large Cell Lymphoma 44 3.2.1.4. Burkitt Lymphoma 44 3.2.2. T-cell non-Hodgkin Lymphomas 45 3.2.3. Hodgkin Lymphoma 45 3.3. Technical Approaches to detect chromosomal Changes in Lymphomas 46 3.3.1. Conventional Cytogenetics 46 3.3.2. Molecular Genetics 46 3.3.3. Molecular Cytogenetics 47 3.3.3.1. Fluorescence In Situ Hybridization 47 3.3.3.2. Combined interphase Cytogenetics and Fluorescence Immunophenotyping (FICTION technique) 47 3.3.3.3. Array-based Techniques to detect chromosomal Changes 48 3.3.4. Technical Comparison of different Methods for the Detection of chromosomal Changes in Lymphomas 48 3.4. Gene Expression Profiling in Lymphomas 49 3.5. Epigenomic Profiling in Lymphomas 51 3.6. Future Directions 52 4. Chronic Lymphocytic Leukemia (S. Stilgenbauer, T. Zenz, D. Oscier) 58 4.1. Introduction 58 4.2. Chromosome banding 58 4.3. Fluorescence In Situ Hybridization (FISH) 58 4.4. Sequence and Mutation Analysis 60 4.5. Array-based Comparative Genomic Hybridization (Array CGH) 61 4.6. SNP arrays 62 4.7. Next Generation Sequencing (NGS) 62 4.8. Gene expression (mRNA) profiling 63 4.9. MicroRNA profiling 63 4.10. IGHV mutation status by sequencing and surrogate markers for the IGHV status by flow cytometry 63 4.11. Conclusion 64 5. Acute Lymphoblastic Leukemia (M. Brüggemann, M. Kneba, T. Raff, T. Szczepañski, J.J.M van Dongen) 68 5.1. Introduction 68 5.2. Immunologic and molecular diagnostics at diagnosis 68 5.2.1. Immunophenotyping 68 5.2.2. Cytogenetics and molecular Genetics 70 5.2.3. Pharmacogenetics 72 5.2.4. Gene Expression Arrays 74 5.3. Molecular Diagnostics during Treatment - Detection of minimal residual Disease 74 5.3.1. MRD Detection by multiparameter Flow Cytometry 74 5.3.2. MRD Quantification using clonal Immunoglobulin and T-Cell-Receptor Gene Rearrangements 75 5.3.3. MRD Quantification using Fusion Genes as RQ-PCR Targets 76 5.3.4. Methodological Aspects of MRD Monitoring in ALL 77 5.3.5. Clinical Significance of MRD in ALL 77 5.4. Conclusion 79 6. Acute Myeloid Leukemia (L. Bullinger, K. Döhner, J.R. Pollack) 84 6.1. Introduction 84 6.2. Immunophenotyping 84 6.3. Chromosome Banding Analysis (conventional Karyotyping) 85 6.4. Fluoresence In Situ Hybridization (FISH) 86 6.5. Polymerase Chain Reaction (PCR) based Techniques 87 6.6. Molecular Genetics for Mutation Detection/Screening 88 6.7. Altered Gene Expression in AML-gene Expression Profiling (GEP) 90 6.8. Genomics Technologies (Microarray based Technologies) 92 6.8.1. Genome-wide analyses of CNAs and UPDs 92 6.8.2. Altered DNA methylation 93 6.8.3. Histone modifications and leukemogenesis 93 6.9. Conclusion 95 7. The diagnosis of BCR-ABL1 negative myeloproliferative neoplasms (MPNs) (U. Bacher, C. Haferlach, T. Haferlach, A. Hochhaus, W. Kern, S. Schnittger) 102 7.1. Introduction 102 7.2. Preanalytic conditions 102 7.3. Cytomorphology 103 7.4. Histopathology 103 7.5. Cytogenetics 104 7.6. Point mutations 104 7.7. Chronic neutrophilic leukemia 106 7.8. Chronic eosinophilic leukemia, not otherwise specified 106 7.9. Chronic myelomonocytic leukemia 106 7.10. Response criteria 107 7.11. Approach to a diagnostic algorithm 107 7.12. Conclusions 109 8. Chronic Myelogenous Leukemia (P. Erben, T. Ernst, A. Hochhaus, M. Müller) 114 8.1. RQ-PCR for BCR-ABL Transcripts 117 8.2. Key Recommendations for Optimization 118 8.3. Quality Assurance of the RQ-PCR Assay 119 8.4. Current Methods for Reporting Results 119 8.5. Proposal for Expressing Results on an International Scale 120 8.6. Detection of Kinase Mutations 121 8.7. Method of Detection 122 8.8. How Should Mutations be Reported? 122 8.9. Indications for Cytogenetics and RQ-PCR 122 8.10. Indications for Mutation Analysis 124 8.11. Conclusions 124 8.12. References 124 9. Myelodysplastic Syndromes (G. Göhring, E. Hellström-Lindbergh, B. Schlegelberger) 130 9.1. Classical chromosome Banding Analysis 130 9.2. Interphase Fluorescence In Situ Hybridization (I-FISH) 133 9.3. Metaphase Fluorescence In Situ Hybridization (MP-FISH) 134 9.4. Multicolor Fluorescence In Situ Hybridization (mFISH) 134 9.5. Array Comparative Genomic Hybridization (Array CGH) 134 9.6. Single Nucleotide Polymorphism Array (SNP Array) 135 9.7. Gene Expression Analysis 135 9.8. Telomere Length Measurement 136 9.9. Perspectives 136 Index 142