High-Throughput SNP Genotyping

  • B. D. Singh
  • A. K. Singh


The development of next-generation sequencing (NGS) methods has helped the emergence of single nucleotide polymorphism (SNP) as the marker of choice. The SNPs are becoming increasingly popular in view of their abundance, ease in discovery, and the extremely high-throughput SNP genotyping at relatively low cost per data point. High-throughput genotyping may be defined as simultaneous genotyping for few to several hundreds or thousands of markers in hundreds to thousands of individuals. A variety of SNP genotyping strategies have been developed, many of which are applicable to already identified SNP loci with known sequences of their flanking regions. A number of these methods have been designed for high to very-high-throughput SNP genotyping. These methods require moderate to considerable sophistication and expensive instrumentation, and most of them have been commercialized. Therefore, most of them are closed technologies available to the user through the genotyping systems offered by the concerned companies. In addition, several strategies have been developed for simultaneous identification and genotyping of SNP loci; these methods are based on new generation DNA sequencing technologies. The chief methods for high throughput genotyping of already known SNPs and those for simultaneous SNP discovery and genotyping are discussed in some detail in this chapter.


Single Nucleotide Polymorphism Single Nucleotide Polymorphism Genotyping Single Nucleotide Polymorphism Array Single Nucleotide Polymorphism Locus Primary Probe 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Author(s) 2015

Authors and Affiliations

  • B. D. Singh
    • 1
  • A. K. Singh
    • 2
  1. 1.School of BiotechnologyBanaras Hindu UniversityVaranasiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia

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