(It is a bit wordy, but I think it may be what you were looking for.) A haplotype is a combination of genotypes on the same chromosome that tend to be inherited as a group. In other words, it is the genotype for a group of genes. Before I go on, let me define genotype. It is the actual genetic sequence of something, let's say for a gene, in this case. You know that the same gene can differ slightly in its genetic sequence between individuals. These different genotypes for the same gene are called alleles. So you may have inherited an allele for the "A" blood type from your mom and a "B" allele for blood type from your dad. Your resulting phenotype (observable trait) is to have a blood type of "AB". With this in mind, let's modify the definition of haplotype to: the observed patterns (various combinations) of alleles for the genes in a particular gene cluster. Certain patterns of alleles in gene clusters tend to be preserved and inherited as a group because, in general, the closer genes are together on a chromosome, the less likely they are to recombine. Recombination is what happens when the two chromosomes containing those particular genes accidentally get spliced, so that some of the alleles from one chromosome actually end up on the other one, and vice versa. So, haplotypes in which you normally see the inheritance of certain common patterns of various gene alleles might be disrupted by recombination to create less common patterns of alleles. However, the less distance there is between the genes, the fewer places there are for random recombination to occur, and therefore the less probability there is that recombination would actually occur between them. Genes that are far apart, on the other hand, have many more possible places where recombination could occur, and so a higher probability of recombination actually occurring. By studying this phenomenon (i.e. following the various allele patterns of a particular gene cluster in a population in order to determine if recombination has occurred), scientists can estimate the relative distance between genes. For example, you might have noticed that many physical maps have distances marked in centimorgans (cM). This is the percentage of recombination between certain genes. So if two genes are 50 cM apart, then there is a 50% chance of recombination occurring between them. In other words, they are relatively distant from each other. If two genes are 4cM apart, there is a 4% chance of recombination occurring between them. In this case, the genes are relatively close together. (ex. 4 people out of 100 had a recombination event between the two genes, such that it split up common haplotypes of alleles in the gene cluster to uncommon ones.) So, if dad has a particular haplotype of alleles on a chromosome for 4 genes: Q W T G, And mom has a haplotype of q w t g, but you have a haplotype of q w T G on a chromosome, recombination has occurred! But what if mom and dad have the exact same haplotype for a particular gene cluster? Then if recombination occurs in their children, you won’t be able to tell. This is called "uninformative." Okay, so let's say you would like to study the inheritance of a disease, say arthritis. First you would try to locate as many families as you could that have similar genetic backgrounds that have the disease (for example, families of German decent with arthritis.) You would also try to get healthy people that don’t have the disease that are of the same ancestral decent to use as controls. (By controlling for ancestral genetic background, you are trying to keep the genetic differences between your samples to a minimum, so that the genetic differences seen between patients and controls are due more to the presence or absence of disease genes and not due to differences in heritage.) Then you would study the haplotypes of various gene clusters in the DNA of both groups. Haplotypes that tend to be found more often in patients but not controls may be associated with the disease. (So if haplotype "RTyU" of a particular gene cluster is present in all of your patients but not your controls, it may be associated with the disease.) Also, by looking for recombinants the haplotypes of both your patients and controls, you might be able to narrow down the location of a disease gene. For example, if a common haplotype associated with a disease is "T C w b" and you have observed some patients that have uncommon haplotypes such as "t C w b" and "T C W B" but some healthy controls have uncommon haplotypes of " T c w b" and "t c W B" then the region where the C allele is located may be associated with the development of the disease. I hope that helped. Please feel free to contact me if you have any additional questions. Sincerely, Elizabeth Bowen Graduate Research Assitant UT Southwestern > Carefull there- geneticists get rather irate when you confuse genotype and > phenoptype. As a reminder, Genotype is the genetic composition of an > organism. Phenotype is the outward expression or result of a genotype. > For Mendel's peas as an example the genotypes WW and Ww would both produce > round peas while ww would result in wrinkled peas. In this case the > dominant W allele masks the presence of a recessive w allele. > > The haplotype is the genotype of the haploid or gamete stage of an > organism's lifecycle. For most common animals this is hidden. Human egg > and sperm do not have thier own lifecycle free of their parents, yet the > gametes certainly have a genotype. In contrast budding yeast have a > haploid lifecycle where the haplotype can be very important. If the > recessive gene w for instance is required for the cell to live, then any > haploid cell with only the w allele would be dead. If a diplod yeast of > unknown genotype at the W locus is sporulated and dissected in such a way > that each of the 4 resulting spores could be tested, then we could directly > test the genotype of the diploid parent by assaying the haplotype of the > progeny as follows: > WW - all 4 spores live (W W W W) > Ww - 2 spores live and 2 spores never grow (W W w w) > ww - well we didn't need to worry its already dead! > > So in effect, when we can directly assay the haplotype we can more directly > and rapidly assess the genotype of a diploid parent. In effect Parthav is > correct, but the reasoning (at least for a geneticist) is much more > resticted then his original post. > > I hope that this helps, and isn't too long of a reply. > > dale > > > Dale Beach > Department of Biology > University of North Carolina > Chapel Hill, NC > > > > --On Sunday, February 10, 2002 9:27 AM -0800 Parthav Jailwala > wrote: > > > hi > > in my view, the term 'haplotype' is just used to suggest a mix of > > phenotype and genotype information used to discover further insights into > > a problem. haplotypic data would suggest data inwhich the information > > content would contain both phenotypic data as well as genotypic data. > > I might be wrong, to wait for other views. > > > > thanks > > Parthav Jailwala > > Research Student > > Marquette University, WI > > ----- Original Message ----- > > From: "Ayyagari.Kiran" > > To: > > Sent: Friday, February 08, 2002 10:05 PM > > Subject: [BiO BB] whats a haplotype > > > > > >> 1)can anyone tell me exactly what is a haplotype? > >> ( is it just another strain of a species with haploid conditon?or > > results > >> from a internal cross between two strains of any species) > >> 2)how haplotypes are used in studying disease polymorphisms > >> 3)how is it used in cytogenetics studies and genome Maps creation > >> > >> thanks > >> > >> A.S.Kiran > >> i-labs _________________________________________________________________ iVillage.com: Solutions for Your Life Check out the most exciting women's community on the Web http://www.ivillage.com