Chapter 47 – Genotyping of Single Nucleotide Polymorphisms by Minisequencing Using Tag Arrays

Publisher Summary An alteration of one nucleotide in a DNA sequence gives different phenotypic outcomes depending on its genomic location. Genomic nucleotide substitutions present in more than 1% of a population are denoted single nucleotide polymorphisms (SNPs). The consequences of SNPs located in noncoding regions of the genome still remain largely unknown, but with the increasing interest in the function of noncoding RNA, their impact may soon become unraveled. Significant advantages of performing assays in the microarray format are the reduced genotyping costs due to the simultaneous analysis of many SNPs in each sample and the small reaction volumes employed. Three major reaction principles are currently used for SNP genotyping on microarrays; hybridization with allele-specific oligonucleotide probes, oligonucleotide ligation, and DNA polymerase-assisted primer extension. The primers are extended with differently labeled nucleotide analogs that is complementary to the nucleotides at the SNP sites. SNPs can be identified either experimentally or in databases. Database searches may be aimed at genes of interest, candidate chromosomal regions, or randomly distributed SNPs with known allele frequencies.