Genetic Variation: A Laboratory Manual

, by Weiner, Michael P.; Gabriel, Stacey; Stephens, J. Claiborne

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ISBN: 9780879697808 | 0879697806
Cover: Paperback
Copyright: 9/12/2007

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This is the first compendium of protocols specifically geared towards genetic variations studies. It includes detailed step-by-step experimental protocols that cover the complete spectrum of genetic variation in humans and model organisms, along with advice on study design and the use of statistical and bioinfomatic approaches for analyzing data. Illustrations.

Foreword
Preface
Contributors
Ethical Issues in Human Genetic Research: The Global Experience	p. 7
Population Choice as a Consideration for Genetic Analysis Study Design	p. 71
Power Calculations	p. 79
Genetic Analysis: Moving between Linkage and Association	p. 37
NCBI dbSNP Database: Content and Searching	p. 47
Using the HapMap Web Site	p. 63
Isolation of Plant DNA for Genotyping Analysis	p. 81
Isolation of Plant DNA for PCR and Genotyping Using Organic Extraction and CTAB	p. 82
DNA Extraction from Freeze-dried Plant Tissue with CTAB in a 96-Well Format	p. 84
Purification of Arabidopsis DNA in 96-Well Plates Using the PUREGENE DNA Purification Kit	p. 87
Preparing RNA from Plant Tissues	p. 91
Maize Tissue Preparation and Extraction of RNA from Target Cells	p. 93
T7-based RNA Amplification from Maize SAM	p. 97
Preparing DNA from Mammalian Sources	p. 103
Preparing DNA from Cell Pellets	p. 107
Preparing DNA from Fixed Tissue: Extraction and Whole-Genome Amplification	p. 110
DNA Isolation from Rat Tail or Ear	p. 114
Preparing DNA from Buccal Cells	p. 116
Preparing Genomic DNA from Whole Blood: Small-and Mid-Scale Extraction	p. 120
Preparing DNA from Blood: Large-Scale Extraction	p. 124
Preparing DNA from Saliva	p. 129
Whole-Genome Amplification of Genomic DNA Using PCR	p. 131
Single-Cell Whole-Genome Amplification	p. 136
Whole-Genome Amplification using [phi]29 DNA Polymerase	p. 140
DNA Extraction from Forensic Samples Using Chelex	p. 146
Estimation of DNA Concentration in Forensic Samples Prior to Multiplex PCR Amplification	p. 148
Intermediate-Throughput Laboratory-Scale Genotyping Solutions	p. 155
Intermediate-Throughput Laboratory-Scale Genotyping Protocols	p. 171
Genotyping by Allele-specific Amplification	p. 172
Genotyping by Dideoxy Resequencing	p. 174
Oligonucleotide Ligation Assay	p. 176
Template-directed Dye-Incorporation Assay with Fluorescence Polarization Detection	p. 182
Temperature Gradient Capillary Electrophoresis Assay	p. 192
SNP Mining from Maize 454 EST Sequences	p. 195
Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping	p. 199
Targeted SNP Genotyping with MIP and Universal Tag Arrays	p. 203
Whole-Genome Genotyping	p. 213
Comparative Genomic Hybridization to Detect Variation in the Copy Number of Large DNA Segments	p. 221
Representational Oligonucleotide Microarray Analysis Detection of Genetic Variation	p. 233
Whole-Genome Sampling Analysis to Detect Copy Number Changes in FFPE Samples	p. 241
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination	p. 249
Microsatellite Markers for Linkage and Association Studies	p. 253
Considerations for SNP Selection	p. 263
Selection and Evaluation of tag-SI\lPs Using Tagger and HapMap	p. 283
Haploview: Visualization and Analysis of SNP Genotype Data	p. 289
Considerations for Copy Number Analysis of FFPE Samples	p. 295
Assessing Significance in Genetic Association Studies	p. 303
Assessing Human Variation Data for Signatures of Natural Selection	p. 309
Arabidopsis	p. 317
Maize	p. 325
Rice	p. 335
The Mouse	p. 353
The Rat	p. 361
The Cat	p. 381
The Dog	p. 395
The Chimpanzee	p. 409
Genealogical Markers: mtDNA and the Y Chromosome	p. 421
Forensic DNA Testing	p. 437
The Human Genome: What Lies Ahead	p. 453
Cautions	p. 457
Index	p. 461
Table of Contents provided by Blackwell. All Rights Reserved.

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Genetic Variation: A Laboratory Manual

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Table of Contents

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Genetic Variation: A Laboratory Manual

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