Genetic Variation: A Laboratory ManualMichael P. Weiner, Stacey B. Gabriel, J. Claiborne Stephens Genetic Variation: A Laboratory Manualis the first compendium of protocols 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. 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. |
Contents
| 1 | |
| 11 | |
| 19 | |
| 31 | |
| 41 | |
6 Using the HapMap Web Site | 63 |
7 Isolation of Plant DNA for Genotyping Analysis | 81 |
8 Preparing RNA from Plant Tissues | 91 |
20 Selection and Evaluation of tagSNPs Using Tagger and HapMap | 283 |
Visualization and Analysis of SNP Genotype Data | 289 |
22 Considerations for Copy Number Analysis of FFPE Samples | 295 |
23 Assessing Significance in Genetic Association Studies | 303 |
24 Assessing Human Variation Data for Signatures of Natural Selection | 309 |
25 Arabidopsis | 317 |
26 Maize | 325 |
27 Rice | 335 |
9 Preparing DNA from Mammalian Sources | 103 |
10 IntermediateThroughput LaboratoryScale Solutions | 155 |
11 IntermediateThroughput LaboratoryScale Genotyping Protocols | 171 |
12 Molecular Inversion Probes and Universal Tag Arrays | 199 |
13 WholeGenome Genotyping | 213 |
14 Comparative Genomic Hybridization to Detect Variation in the Copy Number of Large DNA Segments | 221 |
15 Representational Oligonucleotide Microarray Analysis Detection of Genetic Variation | 233 |
16 WholeGenome Sampling Analysis to Detect Copy Number Changes in FFPE Samples | 241 |
17 Molecular Inversion Probe Targeted Genotyping | 249 |
18 Microsatellite Markers for Linkage and Association Studies | 253 |
19 Considerations for SNP Selection | 263 |
28 The Mouse | 353 |
29 The Rat | 361 |
30 The Cat | 381 |
31 The Dog | 395 |
32 The Chimpanzee | 409 |
mtDNA and the Y Chromosome | 421 |
34 Forensic DNA Testing | 437 |
What Lies Ahead | 453 |
Cautions | 457 |
Index | 461 |
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Common terms and phrases
additional allele amplification analysis application approach array assay association breeds buffer cell centrifuge changes chromosome CNVs collection common compared complex containing copy number database described detect developed disease diversity effect et al example extraction FFPE FIGURE fragment frequency functional gene genetic genome genotyping haplotype HapMap human human genome hybridization identified inbred increase individuals International laboratory lines linkage loci mapping markers method microsatellite minutes mouse mtDNA multiple mutations Nature nucleotide observed oligonucleotide performed phenotypes Plant plate polymorphisms population positive possible primer probes protocol reaction recent reference regions relative represent rice samples Science seconds selection sequence shows single SNPs Solution specific step strains structure studies Table tag-SNP tion tissue trait tube University values variation