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Encyclopedia > Haplotypes

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. In traditional grammar, a contraction is the formation of a new word from two or more individual words. ... Ploidy indicates the number of copies of the basic number of chromosomes. ... The genotype is the specific genetic makeup (the specific genome) of an individual, usually in the form of DNA. It codes for the phenotype of that individual. ... Genetics (from the Greek genno γεννώ= give birth) is the science of genes, heredity, and the variation of organisms. ... Figure 1: Chromosome. ... Diploid (meaning double in Greek) cells have two copies (homologs) of each chromosome (both sex- and non-sex determining chromosomes), usually one from the mother and one from the father. ... An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Diploid (meaning double in Greek) cells have two copies (homologs) of each chromosome (both sex- and non-sex determining chromosomes), usually one from the mother and one from the father. ...


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, the identification of a few alleles of a haplotype block unambiguously identifies all other polymorphic sites in this region. Such information is most valuable to investigate the genetics behind common diseases and is collected by the International HapMap Project. A Single Nucleotide Polymorphism or SNP (pronounced snip) is a DNA sequence variation, occurring when a single nucleotide: adenine (A), thymine (T), cytosine (C) or guanine (G) - in the genome is altered. ... In statistics, an association (statistics) comes from two variables who are related. ... A chromatid forms one part of a chromosome after it has coalesced for the process of mitosis or meiosis. ... A disease is an abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person afflicted or those in contact with the person. ... The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ...

Contents


In relation to genotypes

A genotype is distinct from a haplotype because an individual's genotype may not uniquely define that individual's haplotype. The genotype is the specific genetic makeup (the specific genome) of an individual, usually in the form of DNA. It codes for the phenotype of that individual. ...


As an example, consider two loci, each 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: The word locus (plural loci) is Latin for place: In biology and evolutionary computation, a locus is the position of a gene (or other significant sequence) on a chromosome. ... Figure 1: Chromosome. ...

haplotype at
chromosome 1
haplotype at
chromosome 2
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 this method vary - some are based on parsimony, while others use likelihood functions in combinations with algorithms such as expectation-maximization algorithm (EM) or Markov chain Monte Carlo (MCMC). Parsimony, in the general sense, means taking extreme care at arriving at a course of action; or unusual or excessive frugality, extreme economy or stinginess. ... In statistical computing, an expectation-maximization (EM) algorithm is an algorithm for finding maximum likelihood estimates of parameters in probabilistic models, where the model depends on unobserved latent variables. ... Markov chain Monte Carlo (MCMC) methods (which include random walk Monte Carlo methods) are a class of algorithms for sampling from probability distributions based on constructing a Markov chain that has the desired distribution as its stationary distribution. ...


In genealogical DNA testing

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. // A genealogical DNA test involves examining the nucleotides at specific locations on a persons DNA. The tests results are meant to have no informative medical value and do not determine specific genetic diseases or disorders (see possible exceptions in Medical information below); they are intended only for use in...


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. The most recent common ancestor (MRCA) of any set of organisms is the most recent individual which is an ancestor of all of them. ...


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. A haplogroup is a large group of haplotypes, which are series of alleles at specific locations on the chromosome. ...


See also

The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ... // A genealogical DNA test involves examining the nucleotides at specific locations on a persons DNA. The tests results are meant to have no informative medical value and do not determine specific genetic diseases or disorders (see possible exceptions in Medical information below); they are intended only for use in...

External links

  • The Wellcome Trust — Haplotype mapping
  • The integrated Haplotype Analysis Pipeline (iHAP)

  Results from FactBites:
 
Evolution - A-Z - Haplotype (180 words)
A haplotype is the set of genes at more than one locus which is inherited by an individual from one of its parents.
While the theory of population genetics for a single locus is concerned with gene frequencies; the analogous variable in two locus population genetics is haplotype frequency.
The frequency of a haplotype in a population can be counted as the number of gametes bearing a particular combination of genes.
genome.gov | Haplotype Map Development Report (4248 words)
Demographic and social factors: Haplotype and allele frequencies are also affected by population history factors such as population size, bottlenecks or expansions of population size, founder effects, isolation of a population or admixture between populations, and patterns of mate choice.
To the extent that populations differ in their haplotype structure, it may be useful to study different populations during different stages of the process of finding disease genes.
Although the haplotype map would not have any individual medical information, another risk to the groups that participate could arise from later studies that use the haplotype map to find genes contributing to diseases; the participating groups could become more intensely studied, leading to the perception that their members are at high risk for diseases.
  More results at FactBites »

 
 

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