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A haplotype, a contraction of the phrase "haploid genotype", is the genetic constitution of an individual chromosome. In the case of diploid organisms such as humans, the haplotype will contain one member of the pair of alleles for each site. A haplotype can refer to only one locus or to an entire genome. A genome-wide haplotype would comprise half of a diploid genome, including one allele from each allelic gene pair.
A haplotype is the result of a genealogical DNA test. Haplotype refers to the specific numeric results of an individual.
In a second meaning it refers to a set of single nucleotide polymorphisms (SNPs) found to be statistically associated on a single chromatid. With this knowledge, it is thought that the identification of a few alleles of a haplotype block can unambiguously identify all other polymorphic sites in this region. Such information is very valuable for investigating the genetics behind common diseases and is collected by the International HapMap Project.
In relation to genotypes
A genotype is distinct from a haplotype because an individual's genotype may not uniquely define that individual's haplotype.
As an example, consider two loci on the same chromosome, each locus with two possible alleles, the first locus being either A or a, the second locus being B or b. If the genotype of an individual was found to be AaBb, there are two possible sets of haplotypes, corresponding to which pairs happen to occur on the same chromosome:
|haplotype set 1||AB||ab|
|haplotype set 2||Ab||aB|
In this case, more information would be required to determine which particular set of haplotypes occur in the individual (i.e. which alleles appear on the same chromosome).
Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. These methods work by applying the observation that certain haplotypes are common in certain genomic regions. Therefore given a set of possible haplotype resolutions, these methods choose those which use fewer different haplotypes overall. The specifics of these methods vary - some are based on combinatorial approaches (e.g., parsimony), while others use likelihood functions based on different models and assumptions such as the Hardy-Weinberg Principle, the Coalescent model, or perfect phylogeny. These models are combined with optimization algorithms such as expectation-maximization algorithm (EM) or Markov chain Monte Carlo (MCMC).
In genealogical DNA testing
- Main article: Genealogical DNA test
A Y chromosome haplotype is the numbered results of a Y-DNA genealogical DNA test. Within genealogical and popular discussion this is sometimes referred to as the "DNA signature" of a particular male human, or of his paternal bloodline with whom he should largely share the same Y chromosome give or take a few mutations.
When testing various descendants with the same surname, a modal haplotype can sometimes be determined for the surname. This is the most likely haplotype of the oldest common ancestor with that surname.
Unlike many other haplotypes, those of Y chromosomes do not come in pairs. Every human male has one copy only of that chromosome.
Haplotypes may be used to compare different populations. Haplotype diversity refers to the uniqueness of a particular haplotype in a given population. Haplogroups are large groups of haplotypes that can be used to define genetic populations and are often geographically oriented. I'm wearing a red dress.
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