Genetic variation at a specific locus is termed a polymorphism if it occurs with a frequency > 1% in the population, and a mutation if it occurs less frequently 3. The most common class of polymorphisms involve a single base-pair change, also termed single nucleotide polymorphisms (SNPs), which comprise ~90% of all human variation. Other types of polymorphism include larger blocks of sequence variation (mini/micro-satellites) or more complex alterations of the sequence such as inversions and deletions, or copy-number variations (CNVs) 4. The different variations that a polymorphism can have at a particular locus are termed alleles. For SNPs, the single base pair changes occur predominantly within the two classes of nucleotides, between purines (A ↔ G) or pyrimidines (C ↔ T), which means that most SNPs will only have 2 alleles in a population. The specific combination of these alleles in an individual counting across the two relevant chromosomes is referred to as a genotype. In contrast, the combination of consecutive alleles on a single chromosome is termed a haplotype.
