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.