| |
| |
| Abbreviations | |
| |
| |
| Preface to the first edition | |
| |
| |
| Preface to the second edition | |
| |
| |
| Before we start -- genetic data and the Internet | |
| |
| |
| All students of human molecular genetics should be using the Internet | |
| |
| |
| The World Wide Web is the primary way of using the Internet | |
| |
| |
| Useful Internet starting points for human molecular genetics | |
| |
| |
| The World Wide Web gives access to most human genetic data | |
| |
| |
| Comprehensive DNA and protein sequence databases cover all organisms | |
| |
| |
| OMIM is the standard database of human mendelian characters | |
| |
| |
| Medline is the main way to locate published papers on a topic | |
| |
| |
| Searching for a web page | |
| |
| |
| DNA structure and gene expression | |
| |
| |
| Building blocks and chemical bonds in DNA, RNA and polypeptides | |
| |
| |
| DNA structure and replication | |
| |
| |
| Examples of the importance of hydrogen bonding in nucleic acids and proteins | |
| |
| |
| RNA transcription and gene expression | |
| |
| |
| RNA processing | |
| |
| |
| Translation, post-translational processing and protein structure | |
| |
| |
| Chromosomes in cells | |
| |
| |
| Organization and diversity of cells | |
| |
| |
| Anatomy of animal cells | |
| |
| |
| Development | |
| |
| |
| A brief outline of animal development | |
| |
| |
| The diversity of human cells | |
| |
| |
| Structure and function of chromosomes | |
| |
| |
| Mitosis and meiosis are the two types of cell division | |
| |
| |
| Studying human chromosomes | |
| |
| |
| Chromosome banding | |
| |
| |
| Chromosome nomenclature | |
| |
| |
| Chromosome abnormalities | |
| |
| |
| Nomenclature of chromosome abnormalities | |
| |
| |
| Genes in pedigrees | |
| |
| |
| Mendelian pedigree patterns | |
| |
| |
| Mendelian pedigree patterns | |
| |
| |
| The complementation test to discover whether two recessive characters are determined by allelic genes | |
| |
| |
| Complications to the basic pedigree patterns | |
| |
| |
| Factors affecting gene frequencies | |
| |
| |
| Hardy-Weinberg equilibrium genotype frequencies for allele frequencies p (A[subscript 1]) and q (A[subscript 2]) | |
| |
| |
| The Hardy-Weinberg distribution can be used (with caution) to calculate carrier frequencies and simple risks for counseling | |
| |
| |
| Mutation-selection equilibrium | |
| |
| |
| Selection in favor of heterozygotes for cystic fibrosis | |
| |
| |
| Nonmendelian characters | |
| |
| |
| Cell-based DNA cloning | |
| |
| |
| Fundamentals of DNA technology and the importance of DNA cloning | |
| |
| |
| Principles of cell-based DNA cloning | |
| |
| |
| Restriction endonucleases and modification-restriction systems | |
| |
| |
| Oligonucleotide linkers | |
| |
| |
| Nonsense suppressor mutations | |
| |
| |
| Vector systems for cloning different sizes of DNA fragments | |
| |
| |
| Cloning systems for preparing single-stranded DNA and for studying gene expression | |
| |
| |
| Nucleic acid hybridization assays | |
| |
| |
| Preparation of nucleic acid probes | |
| |
| |
| Principles of autoradiography | |
| |
| |
| Principles of nucleic acid hybridization | |
| |
| |
| Fluorescence labeling and detection systems | |
| |
| |
| Competition hybridization and Cot-1 DNA | |
| |
| |
| Nucleic acid hybridization assays using cloned DNA probes to screen uncloned nucleic acid populations | |
| |
| |
| Standard and reverse nucleic acid hybridization assays | |
| |
| |
| Nucleic acid hybridization assays using cloned target DNA, and microarray hybridization technology | |
| |
| |
| Evolution and applications of DNA microarrays ('DNA chips') | |
| |
| |
| PCR, DNA sequencing and in vitro mutagenesis | |
| |
| |
| Basic features of PCR | |
| |
| |
| Proofreading by DNA polymerase-associated 3' =] 5' exonuclease activity | |
| |
| |
| Applications of PCR | |
| |
| |
| DNA sequencing | |
| |
| |
| In vitro site-specific mutagenesis | |
| |
| |
| Organization of the human genome | |
| |
| |
| General organization of the human genome | |
| |
| |
| The limited autonomy of the mitochondrial genome | |
| |
| |
| Organization and distribution of human genes | |
| |
| |
| Human gene organization | |
| |
| |
| Human multigene families and repetitive coding DNA | |
| |
| |
| Pseudogenes and gene fragments | |
| |
| |
| Extragenic repeated DNA sequences and transposable elements | |
| |
| |
| Classes of mammalian sequence which undergo transposition through an RNA intermediate | |
| |
| |
| Human gene expression | |
| |
| |
| An overview of gene expression in human cells | |
| |
| |
| Spatial and temporal restriction of gene expression in mammalian cells | |
| |
| |
| Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA | |
| |
| |
| Classes of cis-acting sequence elements involved in regulating transcription of polypeptide-encoding genes | |
| |
| |
| Alternative transcription and processing of individual genes | |
| |
| |
| The classical view of a gene is no longer valid | |
| |
| |
| Alternative splicing can alter the functional properties of a protein | |
| |
| |
| Asymmetry as a means of establishing differential gene expression and DNA methylation as means of perpetuating differential expression | |
| |
| |
| CpG islands | |
| |
| |
| Long-range control of gene expression and imprinting | |
| |
| |
| Mechanisms resulting in monoallelic expression from biallelic genes in human (mammalian) cells | |
| |
| |
| The nonequivalence of the maternal and paternal genomes | |
| |
| |
| The unique organization and expression of Ig and TCR genes | |
| |
| |
| Instability of the human genome: mutation and DNA repair | |
| |
| |
| An overview of mutation, polymorphism, and DNA repair | |
| |
| |
| Simple mutations | |
| |
| |
| Mechanisms which affect the population frequency of alleles | |
| |
| |
| Classes of single base substitution in polypeptide-encoding DNA | |
| |
| |
| Genetic mechanisms which result in sequence exchanges between repeats | |
| |
| |
| Pathogenic mutations | |
| |
| |
| How are new mitochondrial mutations fixed (i.e. achieve a frequency of 100% in a population)? | |
| |
| |
| The pathogenic potential of repeated sequences | |
| |
| |
| DNA repair | |
| |
| |
| Physical and transcript mapping | |
| |
| |
| Low resolution physical mapping | |
| |
| |
| Selecting for the chromosome contents of hybrids | |
| |
| |
| Chromosome painting | |
| |
| |
| High resolution physical mapping: chromatin and DNA fiber FISH and restriction mapping | |
| |
| |
| Assembly of clone contigs | |
| |
| |
| The importance of sequence tagged sites (STSs) | |
| |
| |
| Constructing transcript maps and identifying genes in cloned DNA | |
| |
| |
| Commonly used methods for identifying genes in cloned DNA | |
| |
| |
| Genetic mapping of mendelian characters | |
| |
| |
| Recombinants and nonrecombinants | |
| |
| |
| Genetic markers | |
| |
| |
| The development of human genetic markers | |
| |
| |
| Informative and uninformative meioses | |
| |
| |
| Two-point mapping | |
| |
| |
| Calculation of lod scores | |
| |
| |
| Bayesian calculation of linkage threshold | |
| |
| |
| Multipoint mapping is more efficient than two-point mapping | |
| |
| |
| Standard lod score analysis is not without problems | |
| |
| |
| Genetic mapping of complex characters | |
| |
| |
| Parametric linkage analysis and complex diseases | |
| |
| |
| Nonparametric linkage analysis does not require a genetic model | |
| |
| |
| Association is in principle quite distinct from linkage, but where the family and the population merge, linkage and association merge | |
| |
| |
| The transmission disequilibrium test (TDT) | |
| |
| |
| Linkage disequilibrium as a mapping tool | |
| |
| |
| Thresholds of significance are an important consideration in analysis of complex diseases | |
| |
| |
| Sample sizes needed to find a disease susceptibility locus by a whole genome scan using either affected sib pairs (ASP) or the transmission disequilibrium test (TDT) | |
| |
| |
| Strategies for complex disease mapping usually involve a combination of linkage and association techniques | |
| |
| |
| Genome projects | |
| |
| |
| The history, organization, goals and value of the Human Genome Project | |
| |
| |
| Genetic and physical mapping of the human genome | |
| |
| |
| Human gene and DNA segment nomenclature | |
| |
| |
| Cooperation, competition and controversy in the genome projects | |
| |
| |
| Model organism and other genome projects | |
| |
| |
| Model organisms for which genome projects are considered particularly relevant to the Human Genome Project | |
| |
| |
| Life in the post-genome (sequencing) era | |
| |
| |
| Our place in the tree of life | |
| |
| |
| Evolution of the mitochondrial genome and the origin of eukaryotic cells | |
| |
| |
| The three kingdoms of life | |
| |
| |
| Evolution of the eukaryotic nuclear genome: genome duplication and large-scale chromosomal alterations | |
| |
| |
| Paralogy, orthology and homology | |
| |
| |
| Evolution of the human sex chromosomes | |
| |
| |
| Evolution of human DNA sequence families and DNA organization | |
| |
| |
| Evolution of gene structure | |
| |
| |
| Intron groups and intron phases | |
| |
| |
| What makes us human? Comparative mammalian genome organization and the evolution of modern humans | |
| |
| |
| Identifying human disease genes | |
| |
| |
| Principles and strategies in identifying disease genes | |
| |
| |
| Position-independent strategies for identifying disease genes | |
| |
| |
| In positional cloning, disease genes are identified using only knowledge of their approximate chromosomal location | |
| |
| |
| Transcript mapping: how to identify expressed sequences within genomic clones from a candidate region | |
| |
| |
| Pointers to the presence of large-scale mutations | |
| |
| |
| Position effects - a pitfall in disease gene identification | |
| |
| |
| Positional candidate strategies identify candidate genes by a combination of their map position and expression, function or homology | |
| |
| |
| Mapping mouse genes | |
| |
| |
| Confirming a candidate gene | |
| |
| |
| Molecular pathology | |
| |
| |
| Introduction | |
| |
| |
| The main classes of mutation | |
| |
| |
| There are rules for the nomenclature of mutations and databases of mutations | |
| |
| |
| A nomenclature for describing the effect of an allele | |
| |
| |
| Nomenclature for describing mutations | |
| |
| |
| A first classification of mutations is into loss of function vs gain of function mutations | |
| |
| |
| Loss of function mutations | |
| |
| |
| Guidelines for deciding whether a DNA sequence change is pathogenic | |
| |
| |
| Hemoglobinopathies | |
| |
| |
| Molecular pathology of Prader-Willi and Angelman syndromes | |
| |
| |
| Gain of function mutations | |
| |
| |
| Unstable expanding repeats - a novel cause of disease | |
| |
| |
| Laboratory diagnosis of fragile X | |
| |
| |
| Molecular pathology: from gene to disease | |
| |
| |
| Molecular pathology: from disease to gene | |
| |
| |
| Molecular pathology of chromosomal disorders | |
| |
| |
| Genetic testing in individuals and populations | |
| |
| |
| Direct testing is like any other path lab investigation: a sample from the patient is tested to see if it is normal or abnormal | |
| |
| |
| Gene tracking | |
| |
| |
| Gene tracking: four stages in the investigation of a late-onset autosomal dominant disease where direct mutation detection is not possible | |
| |
| |
| Use of Bayes' theorem for combining probabilities | |
| |
| |
| Population screening | |
| |
| |
| DNA profiling can be used for identifying individuals and determining relationships | |
| |
| |
| Cancer genetics | |
| |
| |
| Cancer is the natural end-state of multicellular organisms | |
| |
| |
| Mutations in cancer cells typically affect a limited number of pathways | |
| |
| |
| Two ways of making a series of successive mutations more likely | |
| |
| |
| Oncogenes | |
| |
| |
| Activation of proto-oncogenes | |
| |
| |
| Tumor suppressor genes | |
| |
| |
| Two-hit mechanisms may explain patchy mendelian phenotypes | |
| |
| |
| Control of the cell cycle | |
| |
| |
| Control of the integrity of the genome | |
| |
| |
| The multistep evolution of cancer | |
| |
| |
| Complex diseases: theory and results | |
| |
| |
| Deciding whether a nonmendelian character is genetic: the role of family, twin and adoption studies | |
| |
| |
| Genetic differences between identical twins | |
| |
| |
| Polygenic theory of quantitative traits | |
| |
| |
| Two common misconceptions about regression to the mean | |
| |
| |
| Partitioning of variance | |
| |
| |
| Polygenic theory of discontinuous characters | |
| |
| |
| Segregation analysis allows analysis of characters that are anywhere on the spectrum between purely mendelian and purely polygenic | |
| |
| |
| Correcting the segregation ratio | |
| |
| |
| Seven examples illustrate the varying success of genetic dissection of complex diseases | |
| |
| |
| Applications of genetic insights into complex diseases | |
| |
| |
| Studying human gene structure, expression and function using cultured cells and cell extracts | |
| |
| |
| Gene structure and transcript mapping studies | |
| |
| |
| Obtaining gene clones for studying human gene structure, expression and function | |
| |
| |
| Studying gene expression using cultured cells or cell extracts | |
| |
| |
| Obtaining antibodies | |
| |
| |
| Confocal fluorescence microscopy | |
| |
| |
| Identifying regulatory sequences through the use of reporter genes and DNA-protein interactions | |
| |
| |
| Methods for transferring genes into cultured animal cells | |
| |
| |
| Investigating gene function by identifying interactions between a protein and other macromolecules | |
| |
| |
| Genetic manipulation of animals | |
| |
| |
| An overview of genetic manipulation of animals | |
| |
| |
| The creation and applications of transgenic animals | |
| |
| |
| Isolation and manipulation of mammalian embryonic stem cells | |
| |
| |
| Use of mouse embryonic stem cells in gene targeting and gene trapping | |
| |
| |
| Creating animal models of disease using transgenic technology and gene targeting | |
| |
| |
| The potential of animals for modeling human disease | |
| |
| |
| Manipulating animals by somatic cell nuclear transfer | |
| |
| |
| Gene therapy and other molecular genetic-based therapeutic approaches | |
| |
| |
| Principles of molecular genetic-based therapies and treatment with recombinant proteins or genetically engineered vaccines | |
| |
| |
| General gene therapy strategies | |
| |
| |
| Treatment using conventional animal or human products can be hazardous | |
| |
| |
| The technology of classical gene therapy | |
| |
| |
| Cell therapy | |
| |
| |
| Therapeutics based on targeted inhibition of gene expression and mutation correction in vivo | |
| |
| |
| Gene therapy for inherited disorders | |
| |
| |
| Gene therapy for neoplastic disorders and infectious disease | |
| |
| |
| The ethics of human gene therapy | |
| |
| |
| Glossary | |
| |
| |
| Indexes | |