University of Agricultural Sciences, Bangalore

Includes bibliographical references and index.

Ethical issues in human genetic research: The global experience / K. Arnold and J. van der Walt -- section 1. Study design -- Population choice as a consideration for genetic analysis study design / J.C. Stephens and M. Bamshad -- Power calculations / D.M. Evans and S. Purcell -- Genetic anaylsis: Moving between linkage and association / A.V. Smith -- NCBI dbSNP database: Content and searching / M.L. Feolo and S.T. Sherry -- Using the HapMap web site / A.V. Smith -- section 2. Laboratory protocols -- pt. 1. Preparation of DNA and RNA -- Isolation of Plant DNA for Genotyping Analysis / N.M. Springer -- Preparing RNA from plant tissues / A.-P. Hsia [and others] -- Preparing DNA from mammalian sources / A. Sahota, A.I. Brooks, and J.A. Tischfield -- pt. 2. SNP variation analysis -- Intermediate-throughput laboratory-scale genotyping solutions / S.J. Macdonald -- Intermediate-throughput laboratory-scale genotyping protocols / E. Cuppen [and others] -- Molecular inversion probes and universal tag arrays: Application to highplex targeted SNP genotyping / G. Karlin-Neumann [and others] -- Whole-genome genotyping / S.B. Gabriel and M.P. Weiner -- pt. 3. Copy number and complex variation analysis -- Comparative genomic hybridization to detect variation in the copy number of large DNA segments / I.N. Holcomb and B.J. Trask -- Representational oligonucleotide microarray analysis detection of genetic variation / R. Lucito -- Whole-genome sampling analysis to detect copy number changes in FFPE samples / S. Jacobs -- Molecular inversion probe targeted genotyping: Application to copy number determination / G. Karlin-Neumann [and others] -- Microsatellite markers for linkage and association studies / J. Gulcher -- section 3. Data analysis -- Considerations for SNP selection / C. Carlson -- Selection and evaluation of tag-SNPs using Tagger and HapMap / P. de Bakker -- Haploview: Visualization and analysis of SNP genotype data / J.C. Barrett -- Considerations for copy number analysis of FFPE samples / S. Jacobs -- Assessing significance in genetic association studies / M.J. Daly -- Assessing human variation data for signatures of natural selection / M. Bamshad and J.C. Stephens -- section 4. Variation studies in model organisms -- Arabidopsis / Y. Li and J.O. Borevitz -- Maize / W.B. Barbazuk [and others] -- Rice / H. Leung, K.L. McNally, and D. Mackill -- The mouse / C.M. Wade and M.J. Daly -- The rat / E. Cuppen [and others] -- The cat / M.J. Lipinski, N. Billings, and L.A. Lyons -- The dog / K. Lindblad-Toh and E.A. Ostrander -- The chimpanzee / T.S. Mikkelsen, M.C. Zody, and K. Lindblad-Toh -- section 5. Insights into human variation -- Genealogical markers: mtDNA and the Y chromosome / M. Stoneking and M. Kayser -- Forensic DNA testing / J.M. Butler -- The human genome: What lies ahead / M.P. Weiner and J.C. Stephens.

This compendium of protocols is specifically geared towards genetic variation studies, and includes thorough discussions on 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. 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.