Preface xiii
Acknowledgements xvii
1 Introduction to Molecular Pathology 1
1.1 A Historical Perspective 2
1.1.1 The Development of Molecular Genetics 2
1.1.2 The Development of Molecular Pathology 8
1.2 The Scope of Human Disease 15
1.2.1 The Classification of Disease 15
1.2.2 Morbidity and Mortality 17
1.3 Chromosomal Abnormalities and Disease 19
1.3.1 Chromosomes in Health and Disease 19
1.3.2 Errors of Chromosome Numbers 24
1.3.3 Errors of Sections of Chromosomes 26
1.3.4 Micro-changes to the Genome 32
1.4 The Practice of Molecular Pathology 34
1.4.1 Personalised Medicine 35
1.4.2 National Developments in Molecular Pathology 36
1.4.3 A Move Back to the General Hospital 38
1.5 Conclusion and a View Forwards 39
2 Methods in Molecular Pathology 1 45
2.1 Sample Acquisition and Preparation 46
2.1.1 General Considerations 46
2.1.2 Blood and Soft Tissue 47
2.1.3 Tissues from Solid Organs 48
2.2 Cytogenetics and Karyotyping 49
2.2.1 Practical Considerations 49
2.2.2 Historical Perspective 50
2.2.3 Modern Clinical Applications 52
2.2.4 Paediatrics and Cytogenetics 54
2.3 Fluorescence In situ Hybridisation 54
2.3.1 The Evolution of FISH 55
2.3.2 Uses of FISH Variants in Pathology 56
2.3.3 Developments in FISH 61
2.4 Preparation of Nucleic Acids for Analysis 62
2.4.1 Obtaining DNA 62
2.4.2 Obtaining RNA 63
2.4.3 The Library 65
2.4.4 Amplification of DNA: The Polymerase Chain Reaction 66
2.4.5 Developments in PCR 68
2.5 DNA Sequencing 75
2.5.1 Sanger Sequencing 76
2.5.2 Technical Advances 77
2.5.3 The Human Genome Project 78
2.6 Microarrays 78
2.6.1 The Theory 78
2.6.2 The Practice 80
2.6.3 Disease-linked Gene Panels 83
2.7 Summary of First-generation Techniques 84
2.7.1 Moving On 85
3 Methods in Molecular Pathology 2 87
3.1 Next-generation Sequencing 88
3.1.1 Read Length 88
3.1.2 Pyrosequencing 89
3.1.3 Ion Torrent Technology 92
3.1.4 Illumina Sequencing 94
3.1.5 SOLiD Technology 97
3.1.6 Luminex Multi-analyte Profiling (xMAP) technology 99
3.1.7 RNA Sequencing 100
3.1.8 Wider Applications of Next-generation Sequencing 100
3.1.9 Global and Other Perspectives 104
3.2 Third-generation Sequencing 107
3.2.1 Nanopore Sequencing 108
3.2.2 Pacific Biosystems 110
3.2.3 DNA Nanoball Technology 112
3.3 Bioinformatics 114
3.4 Chapter Summary and Conclusions 115
3.4.1 The Technology 115
3.4.2 The Practice of Molecular Pathology 115
4 Solid Tumour Cancer 1: Carcinoma 119
4.1 Introduction to Cancer 120
4.1.1 General Comments 120
4.1.2 Classification of Cancer 121
4.1.3 The Incidence and Mortality of Malignant Cancer 123
4.2 The Cellular Basis of Cancer 125
4.2.1 Carcinogenesis 125
4.2.2 Genes, Proto-oncogenes and Oncogenes 125
4.2.3 Genes and Cancer 127
4.2.4 Developing Initiatives in Cancer Genetics 130
4.2.5 Summary of Section 4.2 132
4.3 Lung Cancer 133
4.3.1 Introduction 133
4.3.2 Molecular Pathology 134
4.3.3 Which Genes to Test? 136
4.3.4 Molecular Pathology Directing Treatment 138
4.4 Colorectal Cancer 140
4.4.1 Introduction 140
4.4.2 Molecular Pathology 141
4.4.3 Which Genes to Test? 143
4.4.4 Molecular Pathology Directing Treatment 143
4.5 Prostate Cancer 144
4.5.1 Introduction 144
4.5.2 Molecular Pathology 145
4.5.3 Which Genes to Test? 146
4.5.4 Molecular Pathology Directing Treatment 146
4.6 Breast Cancer 147
4.6.1 Introduction 147
4.6.2 Molecular Pathology 148
4.6.3 Which Genes to Test? 149
4.6.4 Molecular Pathology Directing Treatment 151
4.7 Pancreatic Cancer 154
4.7.1 Introduction 154
4.7.2 Molecular Pathology 154
4.7.3 Which Genes to Test? 155
4.7.4 Molecular Pathology Directing Treatment 156
4.8 Other Carcinomas 156
4.8.1 Oesophageal Cancer 156
4.8.2 Liver Cancer 156
4.8.3 Bladder Cancer 157
4.8.4 Renal Cancer 157
4.8.5 Ovarian Cancer 158
4.8.6 Rare Carcinomas 159
4.9 Chapter Summary 161
4.9.1 Ntrk 162
4.9.2 Brca 162
4.9.3 Panels of Genes 164
4.9.4 Bridge to Chapter 5 165
5 Solid Organ Cancers Part 2: Sarcoma, Neurological, Paediatric, Dermal and Others 167
5.1 Sarcomas 168
5.1.1 Tumours Based on Bone 168
5.1.2 Tumours Based on Muscle and Soft Tissues 169
5.2 Tumours of the Central Nervous System 174
5.2.1 Gliomas 174
5.2.2 Meningiomas 177
5.2.3 Medulloblastomas 177
5.2.4 Pituitary Tumours 178
5.3 Paediatric Cancers 178
5.3.1 Introduction to Paediatrics 178
5.3.2 Blood Cancer 182
5.3.3 Neurological Tumours 186
5.3.4 Solid Organ Cancers 190
5.4 Dermal Cancers 194
5.4.1 Squamous Cell Carcinoma and Basal Cell Carcinoma 194
5.4.2 Melanoma 194
5.4.3 Dermatofibrosarcoma Protuberans 195
5.5 Other Cancers 196
5.5.1 Multiple Endocrine Neoplasia 196
5.5.2 Inherited Cancers 197
5.6 Summary 198
6 Blood Cancer 201
6.1 Lymphoma 202
6.1.1 Hodgkin Lymphoma 203
6.1.2 Non-Hodgkin Lymphoma 205
6.2 Leukaemia 211
6.2.1 The Aetiology of Leukaemia 212
6.2.2 Myeloid Leukaemia 213
6.2.3 Lymphoid Leukaemia 221
6.2.4 Other Types of Leukaemia 228
6.2.5 Measurable Residual Disease 232
6.3 Myeloma and Related Diseases 233
6.3.1 The Laboratory 233
6.3.2 Monoclonal Gammopathy of Undetermined Significance 234
6.3.3 Smouldering Multiple Myeloma 235
6.3.4 Myeloma 237
6.3.5 Plasma Cell Leukaemia 240
6.3.6 The Genetics of Disease Progression 241
6.3.7 Routine Molecular Pathology 241
6.4 Other Blood Cancer 242
6.4.1 Myelofibrosis 243
6.4.2 Polycythaemia Vera 244
6.4.3 Essential Thrombocythaemia 245
6.4.4 Myelodysplasia 246
6.4.5 Routine Molecular Pathology of MPNs 247
6.4.6 Erythroleukaemia 249
6.4.7 Basophils and Mast Cells 250
6.4.8 Histiocytosis 252
6.5 Summary 253
7 Rare, Inherited, Metabolic and Other Diseases 257
7.1 Cardiology 259
7.1.1 Structural Heart Disease 260
7.1.2 Arrhythmia 262
7.2 Developmental Disorders 264
7.3 Endocrinology 266
7.3.1 Diabetes 266
7.3.2 Thyroid 267
7.3.3 Adrenals 268
7.3.4 Parathyroids 269
7.3.5 Reproduction 270
7.3.6 The Pituitary/Hypothalamus 272
7.4 Ophthalmology and Audiology 273
7.4.1 Cataracts 273
7.4.2 Albinism 274
7.4.3 The Optic Nerve 275
7.4.4 Other Ocular Diseases 275
7.4.5 Audiology 276
7.5 Foetal and Non-invasive Prenatal Detection 277
7.5.1 The Foetus and Neonate 277
7.5.2 The Parent and Adult 278
7.6 Gastrohepatology 281
7.6.1 Porphyria 281
7.6.2 Cholestasis 281
7.6.3 Polycystic Liver Diseases 281
7.6.4 Pancreatitis 282
7.6.5 Hirschsprung Disease 282
7.7 Haematology 282
7.7.1 Haemoglobinopathies 283
7.7.2 Red Cell Enzymopathies 288
7.7.3 Combined Haemoglobinopathies and Enzymopathies 289
7.7.4 The Red Cell Membrane 290
7.7.5 Other Forms of Anaemia 290
7.7.6 Haemorrhagic Diseases 292
7.7.7 Thrombotic Diseases 295
7.7.8 Iron Metabolism 297
7.8 Immunology 298
7.8.1 Severe Combined Immunodeficiency 298
7.8.2 The Haemophagocytic Syndromes 298
7.8.3 Hereditary Angioedema 298
7.8.4 Other Immunological Diseases 299
7.9 Lipid and Metabolic Diseases 299
7.9.1 Lipids 299
7.9.2 Metabolic Diseases 300
7.10 Mitochondrial Diseases 305
7.11 Musculoskeletal Diseases 307
7.11.1 Diseases Linked to the Fibroblast Growth Factor Receptor 307
7.11.2 Muscular Dystrophy 308
7.11.3 Other Genetic Musculoskeletal Diseases 308
7.12 Neurological Diseases 309
7.12.1 Diseases of the Nerves 310
7.12.2 The Central Nervous System 311
7.12.3 Myopathy 313
7.13 Renal Diseases 314
7.13.1 The Leading Causes 314
7.13.2 Diseases Linked to Electrolyte Disturbances 315
7.13.3 Other Causes 316
7.14 Respiratory Diseases 316
7.14.1 Cystic Fibrosis 316
7.14.2 Other Respiratory Diseases 317
7.15 Dermatological Diseases 318
7.15.1 Xeroderma Pigmentosum 318
7.15.2 Other Dermatological Diseases 319
7.16 Summary 320
Genes Index 323
Text Index 345
