Molecular epidemiology : a practical approach /
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| Imprint: | New York : Oxford University Press, 2001. |
|---|---|
| Description: | xix, 243 p. : ill. ; 26 cm. |
| Language: | English |
| Series: | Practical approach series ; 251 |
| Subject: | |
| Format: | Print Book |
| URL for this record: | http://pi.lib.uchicago.edu/1001/cat/bib/4617169 |
Table of Contents:
- List of protocols
- Abbreviations
- Introduction to molecular epidemiology
- References
- 1. Epidemiological methods for studies of genetic factors that influence infectious diseases
- 1. General considerations
- 2. Types of epidemiological studies
- 3. Cohort study
- Cohort studies: cumulative incidence
- Cohort studies: incidence
- Example of cohort study
- Attributable risk
- 4. Case-control studies
- Example of case-control study
- 5. Cross-sectional studies
- 6. Interpretation of epidemiological associations
- 7. Confouning
- 8. Bradford Hill's criteria for causality
- 9. Statistical considerations
- 10. Further statistical considerations
- 11. Interaction
- 12. Identifying candidate genes for epidemiological studies
- 13. The future of genetic epidemiology
- Reference
- 2. Molecular differentiation of bacterial strains
- 1. Introduction
- 2. PCR-based fingerprinting of the bacterial chromosome
- Preparation of genomic DNA from Gram negative and Gram positive eubacterial species
- Reaction conditions
- The 'ribotype' method
- Repetitive PCR fingerprinting
- RAPD-PCR
- Gel electrophoresis of amplicons
- Analysis and interpretation of PCR fingerprint data
- 3. RFLP analysis of the bacterial chromosome
- General considerations
- Preparation of genomic DNA for RFLP analysis
- Enzymes
- Polyacrylamide gel electrophoresis (PAGE)
- Analysis and interpretation of genomic restriction data
- 4. PFGE analysis of the bacterial chromosome
- General considerations
- Genomic DNA quality
- Restriction enzymes employed in PFGE
- Electrophoretic conditions
- Analysis and interpretations
- 5. DNA sequence analysis of the bacterial ompA gene
- Amplification of the bacterial ompA locus
- Cloning and DNA sequencing of ompA PCR products
- Interpretation of ompA nucleotide sequence variation
- 6. Conclusion
- Acknowledgements
- References
- 3. Detection and quantification of heterogeneous viral targets: HIV as a model
- 1. Introduction
- 2. Impact of sequence heterogeneity on PCR
- 3. Primer and probe design for HIV
- Sequence selection
- Reaction conditions and cycling parameters
- 4. Assay sensitivity and specificity
- 5. Preventing false positives from PCR carryover
- 6. Amplification target: DNA vs. RNA
- 7. Qualitative vs. quantitative assays
- 8. Importance of internal controls and quantitation standards
- Construction of the IC/QS
- Quantitation of the QS
- 9. Evaluation of assay performance
- 10. Qualitative HIV DNA assay
- Sample collection for HIV DNA amplification
- DNA extraction from cells
- Preparation of DNA from dried blood spots
- DNA amplification
- Colorimetric microwell plate detection
- Interpretation of results
- 11. Quantitative HIV RNA assay
- Sample collection for plasma HIV RNA amplification
- Extraction of viral RNA with GuSCN
- RNA amplification
- Quantification of amplified products
- Interpretation of results
- Controls
- 12. Quantitative DNA asay
- Quantification of total genomic DNA
- Quantification of HIV DNA
- 13. Real time detection formats
- TaqMan technology
- Dye intercalation
- Acknowledgements
- References
- 4. Mutation detection by single-stranded conformation polymorphism and denaturing high performance liquid chromatography
- 1. Introduction
- 2. Single-stranded conformation polymorphism (SSCP) and heteroduplex analysis (HA)
- Optimization of the PCR reaction
- SSCP sample preparation
- Optimization of SSCP/HA detection
- Multiplexing
- Interpretation of results
- Applications
- Other methods
- 3. Denaturing high performance liquid chromatography (DHPLC)
- Application of DHPLC to mutation detection
- Sensitivity of detection
- Conclusions
- Interpretation of results
- Genotyping
- References
- 5. DNA pooling methods for association mapping of complex disease loci
- 1. Introduction
- 2. Quantification of DNA samples for pooled amplification
- 3. Genetic analysis of microsatellite markers using pooled DNA samples
- 4. Analysis of pooled microsatellite data
- Correction methods for stutter and differential amplification
- Example of a case-control study using pooled DNA amplification
- DNA pooling using nuclear family-based samples
- Analysis of microsatellite allele image patterns from DNA pools
- 5. SNP allele frequency determination using kinetic PCR
- 6. Experimental design considerations
- Selection of markers for full genome association screen
- Study guidelines
- Technical considerations
- 7. DNA pooling in the era of the human genome sequence
- Acknowledgements
- References
- 6. Single-sperm typing: a rapid alternative to family-based linkage analysis
- 1. Introduction
- 2. Isolation of single sperm
- 3. Whole genome amplification of haploid DNA
- 4. PCR amplification using PEP reaction products as a source of DNA
- Amplification of polymorphic short tandem repeats (STRs)
- Amplification of single nucleotide polymorphisms (SNPs)
- 5. Discriminating alleles by gel electrophoresis
- 6. Interpretation of sperm typing data
- Single-sperm haplotype scoring
- General approaches for analysing recombination data
- References
- 7. PCR-based methods of HLA typing
- 1. Introduction
- 2. The HLA loci
- 3. HLA allelic sequence diversity
- 4. Nomenclature
- 5. HLA typing: a brief history
- Serological and cellular methods
- DNA-based techniques
- 6. HLA typing requirements
- 7. The problem of new alleles and of ambiguity
- Acknowledgements
- References
- 8. Evolutionary analysis of molecular sequence data
- 1. Introduction
- 2. Comparing sequences
- Rationale for statistical models
- Comparing amino acid sequences
- Comparing DNA sequences
- Synonymous and non-synonymous substitution
- Mean nucleotide diversity
- 3. Reconstructing phylogenies
- Overview of the problem
- Methods of phylogenetic reconstruction
- Testing phylogenies
- 4. Applications
- Phylogenetic analysis
- Testing for positive selection
- Nucleotide diversity and population structure
- References
- List of suppliers
- Index
