Many organisms contain genetic material (DNA) which is inherited from two parents. Normally these organisms have their DNA organized in two sets of pairwise similar chromosomes. The offspring gets one chromosome in each pair from each parent. A set of pairs of chromosomes is called diploid and a set of only one half of each pair is called haploid. The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. It can be all the chromosomes from one of the parents or a minor part of a chromosome, for example a sequence of 9000 base pairs or a small set of alleles.
Specific contiguous parts of the chromosome are likely to be inherited together and not be split by chromosomal crossover, a phenomenon called genetic linkage.[3][4] As a result, identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome (imputation).[5] Such information is critical for investigating the genetics of common diseases; which in fact have been investigated in humans by the International HapMap Project.[6][7]
Other parts of the genome are almost always haploid and do not undergo crossover: for example, human mitochondrial DNA is passed down through the maternal line and the Y chromosome is passed down the paternal line. In these cases, the entire sequence can be grouped into a simple evolutionary tree, with each branch founded by a unique-event polymorphism mutation (often, but not always, a single-nucleotide polymorphism (SNP)). Each clade under a branch, containing haplotypes with a single shared ancestor, is called a haplogroup.[8][9][10]