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Single nucleotide polymorphisms (SNPs) are by far the most prevalent of all DNA sequence variations. Single nucleotide polymorphisms ; methods and protocols consist of 17 chapters which are written by writers who are masters in nucleotide polymorphisms. In Chapter 1 of Single Nucleotide Polymorphisms: Methods and Protocols, SNPs are the markers of choice in complex disease mapping and will be the focus of the next phase of the human genome project. SNPs are also extremely useful in genetic studies of all organisms, from model organisms to commercially important plants and animals. In Single Nucleotide Polymorphisms: Methods and Protocols, the inventors of the most successful mutation/SNP detection methods (including denaturing high-performance liquid chromatography [dHPLC], single-strand conformation polymorphism [SSCP], conformation-sensitive gel electrophoresis [CSGE], chemical cleavage, and direct sequencing) describe the most current protocols for these methods. The second half of Single Nucleotide Polymorphisms: Methods and Protocols contains chapters written by the inventors of the most robust SNP genotyping methods, including the molecular beacons, Taqman assay, single-base extension approaches, pyrosequencing, ligation, Invader assay, and primer extension with mass spectrometry detection. Hoped that Single Nucleotide Polymorphisms: Methods and Protocols will serve as a guidebook to all interested in SNP discovery and genotyping and will inspire innovative minds to develop even more robust methods to make complex disease mapping and molecular diagnosis a reality in the near term.