Genotyping is the process of determining the DNA sequence—the genotype—at specific positions within a gene of an individual. Sequence variations can be used as markers in linkage and association studies to determine genes relevant to specific traits or disease. pipette tips used in genotyping analysis IDENTIFYING SEQUENCE VARIATION Genotyping is used to identify variation at specific positions in the DNA sequence of any biological species, from microorganisms to humans. This variation, the genotype, occurs naturally and can be considered a genetic fingerprint of an individual. It is identified as distinct when compared to a reference sequence derived from the general population or a defined subgroup, and can differ from the reference sequence in numerous ways. Types of variation include single base changes (commonly referred to as single nucleotide variants and polymorphisms, or SNVs and SNPs), insertions and deletions (indels), and even the number of gene copies (copy number variation, or CNV).

SNPs are the most common type of sequence variant; they are typically defined as SNVs that occur at >1% in the population. Based on the number of SNPs cataloged in Build 149 of the SNP database, dbSNP, maintained by the National Center for Biotechnology Information (NCBI) [1] and a genome size of 3.4 x 109 bp [2], the human genome should contain a SNP approximately once every 22 bases! Other common model systems show a similarly high frequency of SNPs