Short protocols in human genetics : a compendium of methods from Current Protocols in Human Genetics (2004)

Chapter 1: Genetic Mapping.1.0 Introduction.1.1 Collection of Clinical and Epidemiological Data for Linkage Studies.1.2 Pedigree Selection and Information Content.1.3 Single-Sperm Typing.1.4 Use of LINKAGE Programs for Linkage Analysis.1.5 Model-Free Tests for Genetic Linkage.1.6 Homozygosity Mapping Using Pooled DNA.1.7 Disease Associations and Family-Based Tests.1.8 Analysis of Gene-Gene Interactions.Chapter 2: Genotyping.2.0 Introduction.2.1 PCR Methods of Genotyping.2.2 Genotyping by Ligation Assays.2.3 Automated Fluorescent Genotyping.2.4 Single-Nucleotide Polymorphism Genotyping Using Microarrays.2.5 High-Throughput Genotyping Using the TaqMan Assay.2.6 High-Throughput Genotyping with Primer Extension Fluorescent Polarization Detection.Chapter 3: Somatic Cell Hybrids.3.0 Introduction.3.1 Construction of Somatic Cell Hybrids.Chapter 4: Cytogenetics.4.0 Introduction.4.1 Chromosome Preparation from Cultured Peripheral Blood Cells.4.2 Mitotic Chromosome Preparations from Mouse Cells for Karyotyping.4.3 Chromosome Banding Techniques.4.4 In Situ Hybridization to Metaphase Chromosomes and Interphase Nuclei.4.5 High-Resolution FISH Analysis.4.6 Multicolor Fluorescence In Situ Hybridization (FISH) Approaches for Simultaneous Analysis of the Entire Human Genome.4.7 Morphology Antibody Chromosome Technique for Determining Phenotype and Genotype of the Same Cell.4.8 Comparative Genomic Hybridization.Chapter 5: Strategies for Large-Insert Cloning and Analysis.5.0 Chapter Introduction.5.1 Pulsed-Field Gel Electrophoresis for Long-Range Restriction Mapping.5.2 Screening Large-Insert Libraries by Hybridization.5.3 Introduction of Large Insert DNA into Mammalian Cells and Embryos.5.4 Construction of Bacterial Artificial Chromosome (BAC/PAC) LibrariesChapter 6: Identifying Candidate Genes in Genomic DNA.6.0 Introduction.6.1 Gene Identification: Methods and Considerations.6.2 Sequence Databases: Integrated Information Retrieval and Data Submission.6.3 Sequence Similarity Searching Using the BLAST Family of Programs.6.4 Accessing the Human Genome.6.5 Searching the NCBI Databases Using Entrez.Chapter 7: Searching Candidate Genes for Mutations.7.0 Introduction.7.1 Amplification of Sequences from Affected Individuals.7.2 Detection of Mutations by Single-Strand Conformation Polymorphism Analysis.7.3 Single-Strand Conformation Polymorphism Analysis Using Capillary Electrophoresis.7.4 Heterozygote Detection Using Automated Fluorescence-Based Sequencing7.5 Mutation Detection by Cycle Sequencing.7.6 Human Mutation Databases.Chapter 8: Clinical Cytogenetics.8.0 Introduction.8.1 Preparation of Metaphase Spreads from Chorionic Villus Samples.8.2 Preparation, Culture, and Analysis of Amniotic Fluid Samples.8.3 Preparation and Culture of Products of Conception and Other Solid Tissues for Chromosome Analysis.8.4 Analysis of Sister Chromatid Exchanges.8.5 Determination of Chromosomal Aneuploidy Using Paraffin-Embedded Tissue.8.6 Preparation of Amniocytes for Interphase Fluorescence In Situ Hybridization (FISH).8.7 Diagnosis of Fanconi Anemia by Diepoxybutane Analysis.Chapter 9: Clinical Molecular Genetics.9.0 Introduction.9.1 Multiplex PCR for Identification of Dystrophin Gene Deletions9.2 Simultaneous Detection of Multiple Point Mutations Using Allele-Specific Oligonucleotides.9.3 Molecular Analysis of Fragile X Syndrome.9.4 Analysis of Trinucleotide Repeats in Myotonic Dystrophy.9.5 Detection of Nonrandom X Chromosome Inactivation.9.6 Molecular Analysis of Paternity.9.7 Amplification-Refractory Mutation System (ARMS) Analysis of Point Mutations.9.8 Molecular Analysis of Oxidative Phosphorylation Diseases for Detection of Mitochondrial DNA Mutations.9.9 Single-Cell DNA and FISH Analysis for Application to Preimplantation Genetic Diagnosis.9.10 Protein Truncation Test.9.11 Genotyping of Apolipoprotein E: Comparative Evaluation of Different Protocols.Chapter 10: Cancer Genetics.10.0 Introduction.10.1 Metaphase Harvest and Cytogenetic Analysis of Malignant Hematological Specimens.10.2 Metaphase Harvest and Cytogenetic Analysis of Solid Tumor Cultures.10.3 Molecular Analysis of DNA Rearrangements in Leukemias and Non-Hodgkin's Lymphomas.10.4 Molecular Analysis of Gene Amplification in Tumors.10.5 Methylation-Specific PCR.Chapter 11: Transcriptional Profiling.11.0 Introduction.11.1 Oligonucleotide Arrays for Expression Monitoring.11.2 Profiling Human Gene Expression with cDNA Microarrays.11.3 Analysis of Expression Data: An Overview.Chapter 12: Vectors for Gene Therapy.12.0 Introduction.12.1 Biosafety in Handling Gene Transfer Vectors.12.2 Adenoviral Vectors.12.3 Production of Recombinant Adeno-Associated Viral Vectors.12.4 Production of Retroviral Vectors.12.5 Production of Pseudotype-Retroviral Vectors.12.6 Production of High-Titer Lentiviral Vectors.12.7 Construction of Replication-Defective Herpes Simplex Virus Vectors.12.8 Gene Delivery Using Helper Virus-Free HSV-1 Amplicon Vectors.12.9 Liposome Vectors for In Vivo Gene Delivery.Chapter 13: Delivery Systems for Gene Therapy.13.0 Introduction.13.1 Gene Transfer to Arteries.13.2 Gene Delivery to Muscle.13.3 Ex Vivo and In Vivo Gene Delivery to the Brain.13.4 Human Hematopoietic Cell Culture, Transduction, and Analyses.13.5 Gene Delivery to the Airway.13.6 Gene Delivery to the Liver.Appendix 1: Reagents and Solutions.Appendix 2: Useful Information and Data.2A Overview of Human Repetitive DNA Sequences.2B ISCN Standard Idiograms.2C Genetic Linkage Reference Maps: Access to Internet-Based Resources2D Radioisotope Data.2E Centrifuges and Rotors.Appendix 3: Commonly Used Techniques.3A Isolation of Genomic DNA from Mammalian Cells.3B Extraction and Precipitation of DNA.3C Preparation of DNA from Fixed, Paraffin-Embedded Tissue.3D Quantitation of DNA and RNA with Absorption and Fluorescence Spectroscopy.3E Enzymatic Labeling of DNA.3F Denaturing Polyacrylamide Gel Electrophoresis.3G Analysis of DNA by Southern Blot Hybridization.3H Analysis of RNA by Northern Blot Hybridization.3I Techniques for Mammalian Cell Tussue Culture.3J Establishment of Permanent Cell Lines by Epstein-Barr Virus Transformation.3K Karyotyping.Appendix 4: Suppliers.References.Index.