An Introduction to Human Molecular Genetics

Dr. Jack J. Pasternak received his Ph.D. from Indiana University and is now Professor Emeritus at the University of Waterloo. He has authored or co-authored several textbooks, including Molecular Biotechnology: Principles and Applications of Recombinant DNA.

Preface xvii

Preface to the First Edition xix

Chapter 1 Understanding Human Disease 1

Human Genetic Disease 2

Human Genetics from 1900 to 1957 5

Eugenics: Genetics Misinterpreted 9

The Molecularization of Genetics 11

Genes and Phenotypes 12

OMIM: An Important Online Source of Information About Human Genetic Disorders 14

Key Terms 17

Summary 17

References 18

Review Questions 18

Chapter 2 The Genetic System: Chromosomes 19

Human Chromosomes 19

Maintaining the Chromosome Number 19

Cell Division Cycle: The Mitotic Process 20

The Meiotic Process 22

Characterizing Human Chromosomes 24

Chromosome Abnormalities 28

Whole Chromosome Changes: Aneuploidy 28

Chromosome Structural Changes 30

Determining the Phases of the Cell Cycle 32

Key Terms 35

Summary 35

References 36

Review Questions 36

Chapter 3 The Genetic System: Mendel’s Laws of Inheritance and Genetic Linkage 37

Dominance, Recessiveness, and Segregation 38

Independent Assortment 41

Genetic Linkage 44

Constructing Genetic Maps 47

Three-Point Cross 48

Chi-Square Distribution: Testing for Significance 52

Multiple Alleles 54

Human Genetics 55

Autosomal Dominant Inheritance 58

Autosomal Recessive Inheritance 59

X-Linked Inheritance 60

Using Pedigrees to Study Human Genetic Disorders 61

Calculating Mendelian Frequencies 65

Detection and Estimation of Genetic Linkage in Humans 66

The Logarithm of the Likelihood Ratio Method of Linkage Analysis: LOD Score 67

Key Terms 71

Summary 72

References 72

Review Questions 73

Chapter 4 The Molecular Biology of the Gene 75

Properties of Genetic Material 75

Structure of DNA 76

DNA Replication 79

Decoding Genetic Information: RNA and Protein 79

Translation 85

Regulation of mRNA Transcription 89

Hemoglobinopathies and Thalassemias: An Abundance of Mutations 92

Nucleotide Sequence Alteration: Mutation 94

Mutations of Structural Genes 95

Nomenclature for Mutations 100

Dominant Mutations and Genetic Disorders 102

Key Terms 104

Summary 104

References 105

Review Questions 106

Chapter 5 Recombinant DNA Technology 107

Restriction Endonucleases 108

Cloning Vectors 115

Plasmid Cloning Vector pUC 19 116

Screening DNA Constructs by DNA Hybridization 119

In Situ Hybridization 122

Chemical Synthesis of DNA 122

Sequencing DNA 124

Polymerase Chain Reaction 130

Human-Rodent Somatic Cell Hybrids 131

Human DNA Libraries 137

Genomic Libraries 137

Chromosome DNA Libraries 139

Multicolor Karyotyping: Coloring Chromosomes 143

Region-Specific Chromosome Libraries 144

Constructing a cDNA Library 145

Key Terms 149

Summary 149

References 151

Review Questions 151

Chapter 6 Genetic and Physical Mapping of the Human Genome 153

Genetic Mapping of Human Chromosomes 153

Genetic Polymorphism 153

Restriction Fragment Length Polymorphism 155

Short Tandem Repeat Polymorphism 158

Mapping of a Genetic Disease Locus to a Chromosome Location 159

Multilocus Mapping of Human Chromosomes 163

Inserting a Disease Gene into a Linkage Map 165

Homozygosity Mapping 168

Linkage Disequilibrium Mapping 169

Radiation Hybrid Mapping 171

Genotyping Single-Nucleotide Polymorphisms 174

Physical Mapping of the Human Genome 181

Assembling Contigs from BAC Libraries 181

Comparative Genetic Maps 182

Integration of Cytogenetic, Genetic, and Physical Maps 184

Key Terms 186

Summary 186

References 186

Review Questions 187

Chapter 7 Discovering Human Disease Genes 189

Cloning Human Disease Genes 190

Functional/Candidate Gene Cloning 190

Positional-Candidate Gene Cloning 191

Detection of Mutations in Human Genes 191

Single-Strand Conformation Polymorphism Analysis 191

Denaturing Gradient Gel Electrophoresis 193

Heteroduplex Analysis 193

Rapid Detection of Unknown Mutations: Capillary Electrophoresis 197

Chemical Mismatch Cleavage 197

Direct DNA Sequencing 199

Protein Truncation Test 199

Key Terms 201

Summary 202

References 202

Review Questions 202

Chapter 8 Bioinformatics: Genomics, Functional Genomics, and Proteomics 203

Similarity Search of a DNA Database 204

Functional Genomics 207

DNA Microarray Technology 208

Serial Analysis of Gene Expression 211

Proteomics 213

Separation and Identification of Proteins 214

Protein Expression Profiling 217

Protein-Protein Interaction Mapping 219

How Many Genes Do We Have? 220

Key Terms 226

Summary 226

References 227

Review Questions 228

Chapter 9 Human Population Genetics 229

Alleles, Genotypes, and Hardy–Weinberg Equilibrium 230

Hardy–Weinberg Equilibrium with X-Linked Genes 236

Hardy–Weinberg Equilibrium with Two Loci 238

Processes That Alter Allele and Genotype Frequencies in Populations 239

Population Size 239

Genetic Structure of Isolated Human Populations 241

Founder Effect 243

Migration 244

Mating Systems 248

Assortative Mating 248

Inbreeding 250

Effect of Inbreeding on Populations 256

Mutation 260

Fitness and Selection 262

Directional Selection 265

Balancing Selection 269

Disruptive Selection 272

Mutation, Selection, and Founder Effect: A Case Study 273

Dysgenics: Fact or Fiction 276

Coalescence 278

Neutral Theory 279

Testing for Selection 280

Wright’s F ST Statistic 284

Using DNA Polymorphisms to Infer Human History 286

Key Terms 288

Summary 289

References 290

Review Questions 292

Chapter 10 Molecular Genetics of Complex Disorders 295

Phenotypic Variation of Monogenic Disorders 300

Oculocutaneous Albinism Type 1 300

Glucose-6-Phosphate Dehydrogenase Deficiency 301

Cystic Fibrosis 303

Oligogenic Disorders 305

Autosomal Recessive Nonsyndromic Deafness 306

Bardet–Biedl Syndrome 306

Polygenic Inheritance 307

Familial Risk Ratio 309

Twin Studies 311

Locating Quantitative Trait Loci 319

Case-Control Association Studies 319

Genetics of Human Intelligence 320

Genome Scans 321

Transmission/Disequilibrium Test 324

Affected Sib Pair Linkage Analysis 325

Key Terms 327

Summary 327

References 328

Review Questions 330

Chapter 11 Genomic Imprinting: An Epigenetic Modification 333

Parent-of-Origin Effect 333

Gene Silencing 335

Genomic Imprinting and Human Disease 339

Prader–Willi Syndrome 340

Angelman Syndrome 343

X-Chromosome Inactivation 344

Beckwith–Wiedemann Syndrome 345

Key Terms 346

Summary 346

References 347

Review Questions 348

Chapter 12 Molecular Genetics of Mitochondrial Disorders 349

Mitochondria and Oxidative Phosphorylation 349

Mitochondrial Genetics 352

Mitochondrial Disorders 354

Myoclonus Epilepsy and Ragged Red Fibers 355

Mitochondrial Encephalomyopathy with Lactic Acidosis and Strokelike Episodes 355

Leber Hereditary Optic Neuropathy 357

Neuropathy, Ataxia, and Retinitis Pigmentosa 358

Kearns–Sayre Syndrome 358

Nuclear-Encoded Mitochondrial Disorders 359

Mitochondrial Protein Importation Defects 360

Substrate Transport Defects 360

Substrate Utilization Defects 360

Iron Transport Defect 361

Electron Transport Chain Defects 361

Revelations From the Grave: Using Mitochondrial DNA Analysis to Resolve Historical Mysteries 362

Mitochondrial DNA Defects 363

Key Terms 365

Summary 365

References 366

Review Questions 367

Chapter 13 Molecular Genetics of Muscle Disorders 369

Structure of Skeletal Muscle 369

Dystrophin and Associated Muscle Proteins 371

Cardiac and Smooth Muscle 373

Studying Inherited Muscle Disorders 373

Skeletal Muscle Disorders 374

Duchenne Muscular Dystrophy 374

Limb-Girdle Muscular Dystrophy 376

Congenital Muscular Dystrophy 378

Facioscapulohumeral Muscular Dystrophy 380

Cardiac Muscle Disorders 382

Dilated Cardiomyopathy 382

Discovering the DMD Gene 385

Hypertrophic Cardiomyopathy 388

Key Terms 390

Summary 390

References 391

Review Questions 392

Chapter 14 Molecular Genetics of Neurological Disorders 393

Neurons 394

Nonneuronal Cells of the Nervous System 395

Resting Membrane Potential 396

Initiation, Propagation, and Synaptic Transmission of a Nerve Impulse 397

Parts of the Brain 400

Neuronal Channelopathies 402

Alzheimer Disease 403

Biochemistry of Senile Plaques and Neurofibrillary Tangles 405

Genetics of Alzheimer Disease 409

Mutations of the Amyloid Precursor Protein Gene 409

Mutations in the Presenilin Genes 410

Genetic Risk Factor for Alzheimer Disease 411

Huntington Disease and Other Trinucleotide Repeat Expansion Diseases 412

Amyotrophic Lateral Sclerosis 420

Charcot–Marie–Tooth Disease 422

Inherited Prion Diseases 425

Genetically Engineered Animal Models for Studying Inherited Human Disorders 426

Schizophrenia 430

Key Terms 433

Summary 433

References 435

Review Questions 437

Chapter 15 Molecular Genetics of the Eye 439

Human Visual System 440

Structure of the Eye 440

Phototransduction: Conversion of Radiant Energy into Nerve Impulses 442

Studying the Molecular Basis of Inherited Disorders of the Human Eye 444

Genetic Disorders of the Human Eye 445

Corneal Dystrophies 445

Glaucoma 447

Aniridia 450

Cataracts 452

Retinitis Pigmentosa 455

Congenital Stationary Night Blindness 459

Choroideremia 460

Color Vision Defects 461

Searching for the Genetic Basis of Myopia 462

Isolation of Human Rhodopsin and Color Opsin Genes 462

Molecular Genetics of Red and Green Color Vision Defects 463

Blue Cone Monochromacy 466

Blue Color Vision Defects 467

Rod Monochromacy 467

Key Terms 468

Summary 468

References 469

Review Questions 470

Chapter 16 Molecular Genetics of Cancer Syndromes 471

Cell Proliferation and Cancer 472

Signal Transduction Pathway for Cell Proliferation 473

Regulation of the Cell Division Cycle 477

Apoptosis: Programmed Cell Death 480

Tumor Metastasis 481

Oncogenes 482

Alteration of Oncogenes in Cancer Cells 485

Tumor Suppressor Genes 487

Neurofibromatoses 488

Neurofibromatosis Type 1 488

Neurofibromatosis Type 2 490

Breast Cancer 490

Retinoblastoma 493

Wilms Tumor 494

Multiple Endocrine Neoplasia Type 1 495

Multiple Endocrine Neoplasia Type 2 496

Li–Fraumeni Syndrome 498

Colorectal Cancer 500

Familial Adenomatous Polyposis 501

Hereditary Nonpolyposis Colorectal Cancer 503

Philadelphia Chromosome, Two-Hit Hypothesis, and Comparative Genomic Hybridization 504

Bloom Syndrome 509

Xeroderma Pigmentosum 511

Key Terms 514

Summary 514

References 515

Review Questions 516

Chapter 17 Counseling, Diagnostic Testing, and Management of Genetic Disorders 517

Genetic Counseling 518

Diagnostic Testing 519

Principles of Genetic Testing 519

Testing for Genetic Disorders 519

Direct Mutation Detection Methods 521

Clinical Applications of Genetic Tests 526

Bayesian Determination of Recurrent Risks for Genetic Disorders Within Families 528

Screening Programs for Genetic Disorders 535

Treating Genetic Disorders 541

Clinical Features, Diagnosis, and Treatment of Some Genetic Disorders 543

Williams Syndrome 543

Norrie Syndrome (Norrie Disease) 545

Achondroplasia 545

Familial Mediterranean Fever 547

Peutz–Jeghers Syndrome 549

Smith–Lemli–Opitz Syndrome 550

Wilson Disease 552

Protecting Genetic Privacy and Preventing Genetic Discrimination 548

Key Terms 554

Summary 554

References 555

Review Questions 556

Glossary 557

Index 597