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A haplotype is, in the simplest terms, a specific group of genes or alleles that progeny inherited from one parent.〔()〕 There are, however, several specific definitions of the term being used in the field of genetics. First, it is a portmanteau word for haploid genotype, which is a collection of specific alleles (that is, specific DNA sequences) in a cluster of tightly-linked genes on a chromosome that are likely to be inherited together—that is, they are likely to be conserved as a sequence that survives the descent of many generations of reproduction.〔(BiologyPages/H/Haplotypes.html Kimball's Biology Pages ) (Creative Commons Attribution 3.0)〕〔(Nature SciTable )〕 A second specific meaning of the term haplotype: a set of single-nucleotide polymorphisms (SNPs) on one chromosome that tend to always occur together, i.e., that are associated statistically. It is thought that identifying these statistical associations and few alleles of a specific haplotype sequence can facilitate identifying ''all other such'' polymorphic sites that are nearby on the chromosome. Such information is critical for investigating the genetics of common diseases; which in fact have been investigated in humans by the International HapMap Project. Another specific definition of haplotype: Many human genetic testing companies use the term 'haplotype' to refer to an individual collection of specific mutations within a given genetic segment; (see short tandem repeat mutation). The term 'haplogroup' refers to the SNP/unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (Clade here refers to a set of people sharing a common ancestor.)〔(Facts & Genes. Volume 7, Issue 3 )〕 ==Haplotype resolution== An organism's genotype may not define its haplotype uniquely. For example, consider a diploid organism and two bi-allelic loci (such as SNPs) on the same chromosome. Assume the first locus has alleles ''A'' or ''T'' and the second locus ''G'' or ''C''. Both loci, then, have three possible genotypes: (''AA'', ''AT'', and ''TT'') and (''GG'', ''GC'', and ''CC''), respectively. For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). For individuals who are homozygous at one or both loci, the haplotypes are unambiguous - meaning that there is not any differentiation of haplotype T1T2 vs haplotype T2T1; where T1 and T2 are labeled to show that they are the same locus, but labeled as such to show it doesn't matter which order you consider them in, the end result is two T loci. For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you don't know which haplotype you have, e.g., TA vs AT. The only unequivocal method of resolving phase ambiguity is by sequencing. However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. 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 that use fewer different haplotypes overall. The specifics of these methods vary - some are based on combinatorial approaches (e.g., parsimony), whereas others use likelihood functions based on different models and assumptions such as the Hardy-Weinberg principle, the coalescent theory model, or perfect phylogeny. The parameters in these models are then estimated using algorithms such as the expectation-maximization algorithm (EM), Markov chain Monte Carlo (MCMC), or hidden Markov models (HMM). Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Haplotype」の詳細全文を読む スポンサード リンク
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