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Encyclopedia > Haplotype

A haplotype is the genetic constitution of an individual chromosome. Haplotype may refer to only one locus or to an entire genome. In the case of diploid organisms such as humans, a genome-wide haplotype comprises one member of the pair of alleles for each locus (that is, half of a diploid genome). An organism's haplotype is studied using a genealogical DNA test. The term haplotype is a portmanteau of "haploid genotype". For a non-technical introduction to the topic, please see Introduction to genetics. ... THERE ARE NOW 30 CHROMOSOMES!!!!!! Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... Short and long arms 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. ... For the hard rock band, see Allele (band). ... 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. ... // 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... Look up portmanteau word in Wiktionary, the free dictionary. ... Ploidy is the number of homologous sets of chromosomes in a biological cell. ... The genotype is the specific genetic genome of an individual, in the form of DNA. It is basically ones DNA including the influence of environmental variation, it codes for the phenotype of that individual. ...


In a second meaning, haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. It is thought that these associations, and the identification of a few alleles of a haplotype block, can unambiguously identify all other polymorphic sites in its region. Such information is very valuable for investigating the genetics behind common diseases and is collected by the International HapMap Project. A Single Nucleotide Polymorphism or S.N.P. (pronounced snip) is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). ... A chromatid forms one part of a chromosome after it has coalesced for the process of mitosis or meiosis. ... In statistics, an association (statistics) comes from two variables who are related. ... A disease is any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected 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

Relation to genotypes

An organism's genotype may not uniquely define its haplotype. For 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 organism's genotype is AaBb, there are two possible sets of haplotypes, corresponding to which pairs occur on the same chromosome: Short and long arms Chromosome. ... THERE ARE NOW 30 CHROMOSOMES!!!!!! Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ...

haplotype at
allele 1
haplotype at
allele 2
haplotype set 1 AB ab
haplotype set 2 Ab aB

In this case, more information is required to determine which particular set of haplotypes occur in the organism (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 theory model, or perfect phylogeny. These models are combined with optimization algorithms such as expectation-maximization algorithm (EM) or Markov chain Monte Carlo (MCMC). Look up parsimony in Wiktionary, the free dictionary. ... Hardy–Weinberg principle for two alleles: the horizontal axis shows the two allele frequencies p and q, the vertical axis shows the genotype frequencies and the three possible genotypes are represented by the different glyphs In population genetics, the Hardy–Weinberg principle (HWP) (also Hardy–Weinberg equilibrium (HWE), or Hardy... In genetics, coalescent theory states that all genes or alleles in a given population are ultimately inherited from a single ancestor shared by all members of the population, known as the most recent common ancestor. ... 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. ...


Y-DNA haplotypes from genealogical DNA tests

Main article: Genealogical DNA test

Unlike other chromosomes, Y chromosomes do not come in pairs. Every human male has one copy only of that chromosome. This means that there is no lottery of which copy to inherit; and also (for much of the chromosome) no shuffling between copies by recombination; so unlike autosomal haplotypes, there is therefore effectively no randomisation of the Y-chromosome haplotype between generations, and a human male should largely share the same Y chromosome as his father, 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... Recombination usually refers to the biological process of genetic recombination and meiosis, a genetic event that occurs during the formation of sperm and egg cells. ... An autosome is a non-sex chromosome. ...


In particular the Y-DNA that is the numbered results of a Y-DNA genealogical DNA test should match, barring mutations. Within genealogical and popular discussion this is sometimes referred to as the "DNA signature" of a particular male human, or of his paternal bloodline. // 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...


UEP results (SNP results)

The results which make up the full Y-DNA haplotype from the Y chromosome DNA test can be divided into two parts: the results for unique event polymorphisms (UEPs), sometimes loosely called the SNP results as most UEPs are single nucleotide polymorphisms; and the results for microsatellite short tandem repeat sequences (Y-STRs), often designated by DYS numbers. In genetic genealogy a Unique Event Polymorphism (UEP) is a genetic marker that corresponds to a mutation which is likely to occur so infrequently that it is believed overwhelmingly probable that all the individuals who share the marker, worldwide, will have inherited it from the same common ancestor, and the... 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. ... Microsatellites, or Simple Sequence Repeats (SSRs), are polymorphic loci present in nuclear DNA that consist of repeating units of 1-4 base pairs in length [1]. They are typically neutral, co-dominant and are used as molecular markers which have wide-ranging applications in the field of genetics, including kinship... A short tandem repeat (STR) in DNA is a class of polymorphisms that occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. ... A Y-STR is a short tandem repeat (STR) on the Y chromosome. ... DYS is short for DNA Y-chromosome Segment, and is used to designate a segment of DNA on the Y chromosome where a sequence of nucleotides repeats. ...


The UEP results reflect the inheritance of events it is believed can be assumed to have happened only once in all human history. These can be used to directly identify the individual's Y-DNA haplogroup, his place on the broad family tree of the whole of humanity. Different Y-DNA haplogroups identify genetic populations which are often intricately geographically orientated, reflecting the migrations of current individuals' direct patrilineal ancestors tens of thousands of years ago. In human genetics, Human Y-chromosome DNA haplogroups are haplogroups defined by differences in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). ... Patrilineality is a system in which one belongs to ones fathers lineage; it generally involves the inheritance of property, names or titles through the male line as well. ...


Y-STR haplotypes

The other possible part of the genetic results is the Y-STR haplotype, the set of results from the Y-STR markers tested.


Unlike the UEPs, the Y-STRs mutate much more easily, which gives them much more resolution to distinguish recent genealogy. But it also means that rather than the population of descendents of a genetic event all sharing the same result, the Y-STR haplotypes are likely to have spread apart, to form a cluster of more or less similar results. Typically, this cluster will have a definite most probable centre, the modal haplotype (presumably close to the haplotype of the original founding event); and also a haplotype diversity - the degree to which it has become spread out. The longer ago the defining event occurred, and the more that subsequent population growth occurred early, the more will be the haplotype diversity for a particular number of descendents. On the other hand, if the haplotype diversity is smaller for a particular number of descendents, this may indicate a more recent common ancestor, or that a population expansion has occurred more recently.


Importantly, unlike for UEPs, there is no guarantee that two individuals with a similar Y-STR haplotype will necessarily share a similar ancestry. There is no uniqueness about Y-STR events. Instead, the clusters of Y-STR haplotype results inheriting from different events and different histories all tend to overlap.


Thus, although sometimes a Y-STR haplotype may be directly indicative of a particular Y-DNA haplogoup, it is in most cases a long time since the haplogoups' defining events, so typically the cluster of Y-STR haplotype results associated with descendents of that event has become rather broad, and will tend to significantly overlap the (similarly broad) clusters of Y-STR haplotypes associated with other haplogroups, making it impossible to predict with absolute certainty which Y-DNA haplogroup a Y-STR haplotype would point to. All that can be done from the Y-STRs, if the UEPs are not actually tested, is to predict probabilities for haplogroup ancestry (as this online program does), but not certainties.


Similarly for surnames. A cluster of similar Y-STR haplotypes may indicate a shared common ancestor, with an identifiable modal haplotype; but only if the cluster is sufficently distinct from what may have arisen by chance from different individuals historically having adopted the same name independently. This may require the typing of quite an extensive haplotype to establish, which has fuelled DNA testing companies to offer ever larger sets of markers - 24 then 37 then 63 and perhaps soon even more.


Plausibly establishing relatedness between different surnames data-mined from a database is significantly harder, because now one must establish not that a randomly selected member of the population is unlikely to have such a close match by accident; but rather that the very nearest member of the population in question, chosen purposely from the population for that very reason, would even under those circumstances be unlikely to match by accident. This is for the foreseeable future likely to be impossible except in special cases where there is further information to drastically limit the size of that population of candidates under consideration.


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... In the study of molecular evolution, a haplogroup is a large group of haplotypes, which are series of alleles at specific locations on a chromosome. ...

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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