Cold Spring Harbor Laboratory Press Genetic Variation: A Laboratory Manual

Genetic Variation: A Laboratory Manual is the first compendium of protocols specifically geared towards genetic variation studies, and includes thorough discussions of their applications for human and model organism studies. Intended for graduate students and professional scientists in clinical and research settings, it covers the complete spectrum of genetic variation from SNPs and microsatellites to more complex DNA alterations, including copy number variation. Written and edited by leading scientists in the field, 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. Partial contents: 1. Special Considerations: S. Gabriel, J.C. Stephens, and M. Weiner; In Vitro Fluorescence: Section 1: Study Design: Introduction: 2. Population to Address/Collect: J.C. Stephens and M. Bamshad; 3. Power Calculations: D. Purcell and S. Evans; 4. Linkage v. Association Studies: A. Smith; 5. Db-SNP/NCBI/Targeted SNP-Discovery: S. Sherry and M. Feolo; 6. Using HapMap: A. Smith; Section 2: Generating Data: Introduction: Part 1: Preparing Dna: 7. Isolation of Plant DNA for Genotyping Analysis: N. Springer; 8. Preparing Mammal DNA from Buccal Cells or Blood: I.B. King; 9. Preparing DNA from Mammalian Sources: A. Sahota, A.I. Brooks, and J.A. Tischfield; 10. Mammalian DNA from Tissue: E. Cuppen; 11. PCR-based Whole Genome Amplification: C. Brueck, C. Brown, S. Michalik, D. Vassar-Nieto, E. Mueller, and G. Davis; 12. Rolling Circle Amplification Using 'f629 DNA Polymerase N. Burtt Part 2: Snp Variation Analysis 13. Intermediate - throughput Laboratory - scale Genotyping Solutions S.J. Macdonald 14. Lab-scale Genotyping Protocols S.J. Macdonald and E. Cuppen 15. Fluorescence Polarization Detection: Template Directed Dye-Incorporation Assay C. Ha and P.-Y. Kwok 16. Large-scale Tag Affy Arrays G. Karlin-Neumann 17. Large-scale Genotyping (current platforms) M. Weiner and S. Gabriel Part 3: Complex Variation Analysis 18. Microsatellite Analysis J. Gulcher 19. Comparative Genomic Hybridization (CGH) to Detect Variation in the Copy Number of Large DNA Segments I.N. Holcomb and B.J. Trask 20. Representational Oligonucleotide Microarray Analysis for Detection of Genetic Variation R. Lucito 21. Whole Genome Sampling Analysis to Detect Copy Number Changes S. Jacobs Section 3: Data Analysis Introduction 22. Quality Control: Incomplete Data and Genotyping Errors D. Cutler 23. tag SNP Selection C. Carlson 24. Selection and Evaluation of tag SNPs Using Tagger and HapMap P.I. Wen de Bakker 25. Haploview: Visualization and Analysis of SNP Genotype Data J.C. Barrett 26. Considerations for Copy Number Analysis S. Jacobs 27. Statistics: Assessing Significance of Results M. Daly 28. Inference of Selection from Candidate Gene Analysis M. Bamshad and J.C. Stephens 29. Inference of Selection from Whole Genome Analysis C. Bustamante Section 4: Variation Studies In Model Organisms Introduction 30. Arabidopsis J. Borevitz and Y. Li 31. Corn W.B. Barbazuk, A.-P. Hsia, H.D. Chen, Y. Fu, K. Ohtsu, and P.S. Schnable 32. Rice H. Leung, K. McNally, and D. Mackill 33. The Mouse C.M. Wade and M.J. Daly 34. The Rat E. Cuppen, N. Huebner, H.J. Jacob, and A.E. Kwitek 35. Feline L. Lyons 36. Canine K. Lindblad-Toh and E.A. Ostrander 37. Porcine A. Archibald 38. The Chimpanzee T.S. Mikkelsen, M.C. Zody, and K. Lindblad-Toh Section 5: Interpretations Of / Insights into Human Variation