| Z730947 Sigma |
Genetic Variation: A Laboratory ManualHardback |
General description
This manual is the first compendium of protocols specifically geared towards genetic variation studies, and includes thorough discussions on their applications for human and model organism studies. It covers the complete spectrum of genetic variation-from SNPs and microsatellites to more complex DNA alterations, including copy number variation. The early sections of the manual are devoted to study design and generating genotype data, the use of resources such as HapMap and dbSNP, as well as experimental, statistical, and bioinformatic approaches for analyzing the data. The final sections include descriptions of genetic variation in model organisms and discussions of recent insights into human genetic ancestry, forensics, and human variation.
Table of Contents
1. Ethical Issues in Human Genetic Research: The Global Experience
SECTION 1: STUDY DESIGN
Introduction
2. Population Choice as a Consideration for Genetic Analysis Study Design
3. Power Calculations
4. Genetic Anaylsis: Moving between Linkage and Association
5. NCBI dbSNP Database: Content and Searching
6. Using the HapMap Web Site
SECTION 2: LABORATORY PROTOCOLS
Introduction
PART 1: PREPARATION OF DNA AND RNA
7. Isolation of Plant DNA for Genotyping Analysis
8. Preparing RNA from Plant Tissues
9. Preparing DNA from Mammalian Sources
PART 2: SNP VARIATION ANALYSIS
10. Intermediate-Throughput Laboratory-Scale Genotyping Solutions
11. Intermediate-Throughput Laboratory-Scale Genotyping Protocols
12. Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
13. Whole-Genome Genotyping
PART 3: COPY NUMBER AND COMPLEX VARIATION ANALYSIS
14. Comparative Genomic Hybridization to Detect Variation in the Copy Number of Large DNA Segments
15. Representational Oligonucleotide Microarray Analysis Detection of Genetic Variation
16. Whole-Genome Sampling Analysis to Detect Copy Number Changes in FFPE Samples
17. Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
18. Microsatellite Markers for Linkage and Association Studies
SECTION 3: DATA ANALYSIS
Introduction
19. Considerations for SNP Selection
20. Selection and Evaluation of tag-SNPs Using Tagger and HapMap
21. Haploview: Visualization and Analysis of SNP Genotype Data
22. Considerations for Copy Number Analysis of FFPE Samples
23. Assessing Significance in Genetic Association Studies
24. Assessing Human Variation Data for Signatures of Natural Selection
SECTION 4: VARIATION STUDIES IN MODEL ORGANISMS
Introduction
25. Arabidopsis
26. Maize
27. Rice
28. The Mouse
29. The Rat
30. The Cat
31. The Dog
32. The Chimpanzee
SECTION 5: INSIGHTS INTO HUMAN VARIATION
Introduction
33. Genealogical Markers: mtDNA and the Y Chromosome
34. Forensic DNA Testing
35. The Human Genome: What Lies Ahead
APPENDIX: Cautions
SECTION 1: STUDY DESIGN
Introduction
2. Population Choice as a Consideration for Genetic Analysis Study Design
3. Power Calculations
4. Genetic Anaylsis: Moving between Linkage and Association
5. NCBI dbSNP Database: Content and Searching
6. Using the HapMap Web Site
SECTION 2: LABORATORY PROTOCOLS
Introduction
PART 1: PREPARATION OF DNA AND RNA
7. Isolation of Plant DNA for Genotyping Analysis
8. Preparing RNA from Plant Tissues
9. Preparing DNA from Mammalian Sources
PART 2: SNP VARIATION ANALYSIS
10. Intermediate-Throughput Laboratory-Scale Genotyping Solutions
11. Intermediate-Throughput Laboratory-Scale Genotyping Protocols
12. Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
13. Whole-Genome Genotyping
PART 3: COPY NUMBER AND COMPLEX VARIATION ANALYSIS
14. Comparative Genomic Hybridization to Detect Variation in the Copy Number of Large DNA Segments
15. Representational Oligonucleotide Microarray Analysis Detection of Genetic Variation
16. Whole-Genome Sampling Analysis to Detect Copy Number Changes in FFPE Samples
17. Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
18. Microsatellite Markers for Linkage and Association Studies
SECTION 3: DATA ANALYSIS
Introduction
19. Considerations for SNP Selection
20. Selection and Evaluation of tag-SNPs Using Tagger and HapMap
21. Haploview: Visualization and Analysis of SNP Genotype Data
22. Considerations for Copy Number Analysis of FFPE Samples
23. Assessing Significance in Genetic Association Studies
24. Assessing Human Variation Data for Signatures of Natural Selection
SECTION 4: VARIATION STUDIES IN MODEL ORGANISMS
Introduction
25. Arabidopsis
26. Maize
27. Rice
28. The Mouse
29. The Rat
30. The Cat
31. The Dog
32. The Chimpanzee
SECTION 5: INSIGHTS INTO HUMAN VARIATION
Introduction
33. Genealogical Markers: mtDNA and the Y Chromosome
34. Forensic DNA Testing
35. The Human Genome: What Lies Ahead
APPENDIX: Cautions
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