Genotyping Methods and Errors
Genetic association studies use data on the genetic variations that occur between individuals (genotypes), and these data are generated by genotyping. Most common genetic variants are single nucleotide variants (that is, SNPs) and, by genotyping them, the two nucleotides at that position in the genotype are determined. It is generally assumed that SNPs provide sufficient coverage for variants that are not SNPs, including repeat polymorphisms such as short tandem repeats (STR) and variable number tandem repeats (VNTR). This chapter will provide background to various genotyping methods and then discuss how errors in genotyping are detected and minimized.