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*  HLA A1-B8-DR3-DQ2 - Wikipedia
A multigene haplotype is set of inherited alleles covering several genes, or gene-alleles; common multigene haplotypes are ... one expects 1/2 of adjacent genes to have new gene-alleles, unless the genes are small and very close together. This dynamic ... There are many other gene-alleles within the haplotype, including more than 250 coding loci that produce transcripts. ... Other haplotypes exist in the region of Europe where this haplotype formed and expanded, some of these haplotypes also are ...
  https://en.wikipedia.org/wiki/HLA_A1-B8-DR3-DQ2
*  Gene polymorphisms of novel immunotolerant molecule BTLA: distribution of alleles, genotypes and haplotypes in Polish Caucasian...
gene polymorphism B lymphocyte T lymphocyte interleukin T helper cell allele distribution genotype haplotype Polish Caucasian ... Gene polymorphisms of novel immunotolerant molecule BTLA: distribution of alleles, genotypes and haplotypes in Polish Caucasian ...
  http://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-0638aecc-d17c-4b32-be09-98f8aa1e2418
*  Center Publications - Genome Technology Center - Stanford University School of Medicine
Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes.. Norman, P.J., Abi-Rached, L ... A haplotype framework for cystic fibrosis mutations in Iran.. Elahi, E., Khodadad, A., Kupershmidt, I., Ghasemi, F., Alinasab, ... A dominant truncation allele identifies a gene, STE20, that encodes a putative protein kinase necessary for mating in ... The HAT4 gene of Arabidopsis encodes a developmental regulator.. Schena, M., Lloyd, A. M., Davis, R. W. (1993). Genes Dev. 1993 ...
  http://med.stanford.edu/sgtc/publications.html
*  HLA-DR3 - Wikipedia
DR3 is a component gene-allele of the AH8.1 haplotype in Northern and Western Europeans. Genes between B8 and DR3 on this ... Ratanachaiyavong S, Lloyd L, Darke C, McGregor A (1993). "MHC-extended haplotypes in families of patients with Graves' disease ... Although it cannot identify the alpha ".5" chain of HLA DQ, DQA1*0501 gene is almost always found within the DR3-DQ2 haplotype ... gene with Graves' disease is a result of linkage disequilibrium with the HLA haplotype DRB1*0304-DQB1*02-DQA1*0501". Clinical ...
  https://en.wikipedia.org/wiki/HLA-DR3
*  C H O R I
... haplotypes. The group A haplotype has six inhibitory genes and only one stimulatory gene (KIR2DS4). The group B haplotype has ... KIR haplotypes are classified into two distinct groups based on their gene content and allele combination 11-15 The group A ... The group B haplotypes have greater heterogeneity in gene content, including additional stimulatory KIR genes (KIR2DS1, KIR2DS2 ... Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes. Genome Res 19, 757-769 (2009 ...
  http://www.chori.org/Principal_Investigators/Trachtenberg_Elizabeth_A/tracht_research.html
*  Genetic Basis of Hypertension | Hypertension
Angiotensinogen gene haplotype and hypertension: interaction with ACE gene I allele. Hypertension. 2003; 41: 9-15. ... Six major haplotypes of AGT account for most of the variation in the AGT gene, although the frequency of each differed ... 20A allele.57 Interestingly, whereas the −20C/−6A/235Thr haplotype would normally be considered the high plasma AGT haplotype, ... 64 generated a haplotype map of each gene in the RAS and then performed association studies with individual SNPs and haplotype ...
  http://hyper.ahajournals.org/content/48/1/14.long
*  An investigation of 10 Y-STR loci and the detection of specific haplotype frequencies in Turkish population
Allele frequencies, gene diversities and haplotype frequencies were analyzed. Gene diversity per locus varied from 0.5788 ( ... When our minHt haplotypes frequencies compared with the other seven populations, we have found statistically significant ... The aHt haplotype has found a higher discriminatory potential than minHt haplotype with a better Pd combined value (0.9999936 ... aHt haplotype can be proposed as an alternative to minHt in paternity testing and forensic medicine applications involving ...
  http://www.scirp.org/journal/PaperInformation.aspx?PaperID=6248
*  Extensive DRB region diversity in cynomolgus macaques: recombination as a driving force | SpringerLink
2008). Many of these haplotype pairs that share certain DRB genes/alleles appear to have additionally a DRB6 pseudogene in ... In humans, there is only one functional DRB gene, DRB1, which is present on all haplotypes and therefore can probably not be ... 2008). Since the microsatellite is highly variable in length and present in most DRB genes/alleles analyzed, each haplotype is ... since all Mafa-DRB6 alleles cluster far apart from the rest of the DRB genes/alleles (Fig. 2), and Mamu-DRB6 sequences are ...
  https://link.springer.com/article/10.1007%2Fs00251-010-0422-7
*  β2-Adrenergic Receptor Genetic Variants and Risk of Sudden Cardiac Death | Circulation
Figure 1. Haplotype tree of the B2AR gene. Ten SNPs differ between the 3 common haplotypes. Two evolutionary distant clades are ... TABLE 1. B2AR Gene Polymorphism Allele Frequencies and Haplotype Structure and Frequency in White and Black CHS Participants ... of the haplotypes seen in this population.8 A haplotype tree of these 3 common haplotypes was constructed with the MEGA program ... Among blacks, 3 haplotypes account for ,95% of the variation seen in the coding and promoter regions of the B2AR gene. The ...
  http://circ.ahajournals.org/content/113/15/1842.long
*  A30-Cw5-B18-DR3-DQ2 (HLA Haplotype) - Wikipedia
A multigene haplotype is a set of inherited alleles covering several genes, or gene-alleles. Long haplotypes, like A30::DQ2, ... Excepting A*3002:Cw*0501:B*1801 haplotype, A*3002, the A30 allele found in the A30-Cw5-B18 haplotype, is rare in Europe. ... and combined these haplotypes represent approximately 30 percent of Sardinians haplotypes by gene frequency, indicating the ... Because the haplotype is indifferent to Cw allele the level is high in the Basque of Northern Spain. A30-B18 frequencies at ...
  https://en.wikipedia.org/wiki/A30-Cw5-B18-DR3-DQ2_(HLA_Haplotype)
*  HLA B7-DR15-DQ6 - Wikipedia
A multigene haplotype is set of inherited alleles covering several genes, or gene-alleles, common multigene haplotypes are ... HLA A*0201Cw*0702 : B*0702 : DRB1*1501 : DQA1*0102 : DQB1*0602 The gene-allele representation of the haplotype is: HLA A*0301Cw ... The appendation of the B7::DQ6 haplotype creates the A2-B7::DQ6 haplotype. This haplotype if found often in Northern Spain, ... Schipper R, Schreuder G, D'Amaro J, Oudshoorn M (1996). "HLA gene and haplotype frequencies in Dutch blood donors". Tissue ...
  https://en.wikipedia.org/wiki/HLA_B7-DR15-DQ6
*  Coeliac disease - Wikipedia
This haplotype is composed of two adjacent gene alleles, DQA1*0501 and DQB1*0201, which encode the two subunits, DQ α5 and DQ ... "Extended HLA haplotypes in a Carib Amerindian population: the Yucpa of the Perija Range". Hum Immunol. 62 (9): 992-1000. doi: ... Most people with coeliac bear a two-gene HLA-DQ2 haplotype referred to as DQ2.5 haplotype. ... The reason these genes produce an increase in risk of coeliac disease is that the receptors formed by these genes bind to ...
  https://en.wikipedia.org/wiki/Coeliac_disease
*  QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and...
The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is ... Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as ... Haplotypes in this context represent the different alleles of a gene in a dataset. The haplotype reconstruction is based on a ... major allele haplotype score and minor allele haplotype score. The major allele is the allele occurring in the majority of the ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-438
*  HLA A1-B8 haplotype - Wikipedia
A multigene haplotype is set of inherited alleles covering several genes, or gene-alleles; common multigene haplotypes are ... These gene-alleles are markers for a haplotype, a stretch of chromosome 6 that contains many gene alleles. In its natural ... Two-point haplotype analysis between TNFB(B*01 allele) and HLA show that the allele is in linkage disequilibrium with HLA-A1, ... This disequilibrium made it appear that A1 and other class I gene-alleles were disease factors, when these alleles were only ...
  https://en.wikipedia.org/wiki/HLA_A1-B8_haplotype
*  History and naming of human leukocyte antigens - Wikipedia
Each person has two HLA haplotypes, a cassette of genes passed on from each parent. The haplotype frequencies in Europeans are ... An HLA allele coding non-expressed gene is termed "Null Allele", for example: HLA-B*15:01:01:02N. The expression level can also ... Currently there are 7,678 Class I alleles and 2,268 Class II alleles. HLA Naming can be quite confusing at first. All alleles ... The next portion (HLA-A or HLA-B) identifies which gene the allele is a modification of. The first two numbers (HLA-A*02) ...
  https://en.wikipedia.org/wiki/History_and_naming_of_human_leukocyte_antigens
*  Population History
Gene Trees Versus Allele or Haplotype trees Wed, 07 Jun 2017 , Population History ... Step 1 in neighbor joining is the calculation of the net molecule genetic distance of each haplotype from all other haplotypes ... a distinction can now be made between gene trees and haplotype trees. Gene trees are genealogies of genes. They describe how ... We have already seen that allele frequencies are altered when gene flow occurs between genetically distinct populations. Gene ...
  https://www.fossilhunters.xyz/population-history/
*  Genetic Diversity in Giant Schnauzers
... and breed-wide allele frequency is provided. DLA haplotypes: STR loci linked to the DLA class I and II genes were used to ... DLA Class I and II Haplotype frequencies and genetic diversity. The DLA consists of four gene rich regions (classes I-IV) ... Groups of genes and their alleles inherited as a block, rather than singly, are called haplotypes. The class II region also ... Thirty-three STRs and their alleles were studied in 133 Giant Schnauzers (Table 1). Allele and allele frequencies were used to ...
  https://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInGiantSchnauzers.php
*  Severe Familial HDL Deficiency in French-Canadian Kindreds | Arteriosclerosis, Thrombosis, and Vascular Biology
Haplotypes of the apo AI gene, determined by use of the restriction enzymes Pst I, Xmn I, and Sst I and of the apo AII gene by ... Quantitative Southern blot analysis of the apo AI-CIII-AIV gene cluster reveals no gene rearrangements or allele deletion. ... Haplotype analysis of the lipoprotein lipase gene did not show segregation with the low HDL trait. Plasma lecithin:cholesterol ... For determination of haplotypes of the apo AI and apo AII genes, DNA was isolated from probands and all family members who were ...
  http://atvb.ahajournals.org/content/15/8/1015
*  Patent WO2009132089A2 - A method to identify asian soybean rust resistance quantitative trait loci ... - Google Patents
The analysis may be used to select for genes, QTL, alleles, or genomic regions (haplotypes) that comprise or are linked to a ... A haplotype within that window can be defined by the unique fingerprint of alleles at each marker. As used herein, an allele is ... Specifically, an "allele of a QTL" in the present invention can denote a haplotype within a haplotype window wherein a ... A genotype may constitute an allele for at least one genetic marker locus or a haplotype for at least one haplotype window. In ...
  http://www.google.com.au/patents/WO2009132089A2?cl=en
*  The relative power of SNPs and haplotype as genetic markers for association tests. - Semantic Scholar
Single nucleotide polymorphisms (SNPs) in disease-related genes are often used as candidates in the search for causative ... Association tests based on haplotypes have also been suggested and, at times, have provided greater statistical power than ... Furthermore, we find that regression tests for the simple main effect of each haplotype are generally more powerful than ANOVA ... we find a simple rule for the relative power of SNP and haplotype markers: SNP-based tests have greater power when the number ...
  https://www.semanticscholar.org/paper/The-relative-power-of-SNPs-and-haplotype-as-genetic-Bader/7f59bc818032af904120fb1ac3aebff6f4ff41fc
*  Genetic diversity testing for Standard Poodles
... and breed-wide allele frequency is provided. DLA haplotypes: STR loci linked to the DLA class I and II genes were used to ... This data will be updated as more dogs are tested, so allele and DLA haplotype frequencies may change to a limited extent over ... Groups of genes and their alleles that are inherited as a block, rather than singly, are called haplotypes. The class II region ... and DQB1 genes. One (or more) STR haplotypes is associated with each of the official DRB1/DQA1/DQB1 haplotypes identified in ...
  http://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInStandardPoodles.php
*  Endothelial Nitric Oxide Synthase Gene Is Positively Associated With Essential Hypertension | Hypertension
Δ values show deviation from linkage equilibrium (Δ=h−p1p2; h, haplotype frequency; p1, p2, frequencies of two alleles at two ... To determine whether a particular linkage was present between any of these polymorphisms, we estimated eNOS haplotypes by ... Comparison of Genotype and Allele Frequencies for Glu298Asp Variants of eNOS Gene in Each Gender Population of Kyoto Group ... Comparison of Genotype and Allele Frequencies for Glu298Asp Variants of eNOS Gene in Two Distinct Areas in Japan ...
  http://hyper.ahajournals.org/content/32/1/3
*  Sharp Look at Complement in Genetics of Macular Degeneration | ALZFORUM
... it is genes and their alleles that matter, not individual polymorphisms. This is one of the reasons haplotype analysis can be ... CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration ... One possibility is that the variants affect complement factor H gene expression. Alleles that change a gene's expression level ... A common haplotype in the complement regulatory gene factor H (HF1/CFH) predisposes individuals to age-related macular ...
  http://www.alzforum.org/news/research-news/sharp-look-complement-genetics-macular-degeneration?id=1449
*  exam 1 Flashcards by Estee C | Brainscape
are alleles from a group of closely linked genes that are inherited together ... how many possible haplotypes are possible for the Rh blood group?. a. 5. b. 3. c.8 d.6 ... the gene that codes for the enzyme α-3-N-acetylgalactosaminyltransferase. a. H gene. b. A gene. c. B gene. d. O gene ... the gene that codes for the enzyme α-3-D-galactosyltransferase. a. H gene. b. A gene. c. B gene. d. O gene ...
  https://www.brainscape.com/flashcards/exam-1-4806974/packs/7123883
*  Logistic Bayesian LASSO for Identifying Association with Rare Haplotypes and Application to Age-Related Macular Degeneration -...
Summary Rare variants have been heralded as key to uncovering "missing heritability" in complex diseases. These variants can now be genotyped using next-generation sequencing technologies; nonetheless, rare haplotypes may also result from combination of common single nucleotide polymorphisms available from genome-wide association studies (GWAS). The National Eye Institute's data on age-related macular degeneration (AMD) is such an example. Studies on AMD had identified potential rare variants; however, due to lack of appropriate statistical tools, effects of individual rare haplotypes were never studied. Here we develop a method for identifying association with rare haplotypes for case-control design. A logistic regression based retrospective likelihood is formulated and is regularized using logistic Bayesian LASSO (LBL). In particular, we penalize the regression coefficients using appropriate priors to weed out unassociated ...
  http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2011.01680.x/full?globalMessage=0&systemMessage=Wiley+Online+Library+will+be+unavailable+on+Saturday+7th+Oct+from+03.00+EDT+%2F+08%3A00+BST+%2F+12%3A30+IST+%2F+15.00+SGT+to+08.00+EDT+%2F+13.00+BST+%2F+17%3A30+IST+%2F+20.00+SGT+and+Sunday+8th+Oct+from+03.00+EDT+%2F+08%3A00+BST+%2F+12%3A30+IST+%2F+15.00+SGT+to+06.00+EDT+%2F+11.00+BST+%2F+15%3A30+IST+%2F+18.00+SGT+for+essential+maintenance.+Apologies+for+the+inconvenience+caused+
*  CRAN Task View: Statistical Genetics
Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements ...
  https://cran.ncc.metu.edu.tr/web/views/Genetics.html
*  CRAN Task View: Statistical Genetics
Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements ...
  https://cran.stat.unipd.it/web/views/Genetics.html
*  Renin-Angiotensin System Gene Polymorphisms and Atrial Fibrillation | Circulation
For comparison of the baseline characteristics, between-group data were compared with the Student's unpaired t test for continuous data and the χ2 test for categorical data. With regard to the 6 polymorphisms within the AGT gene, because they were located on the same chromosome with short distances between each other, they probably did not segregate independently and had linkage disequilibrium (LD) between each other.25 Therefore, we first used haplotype analysis for these 6 polymorphisms to determine whether there were any specific haplotypes that were associated with AF. The methods of the expectation-maximization-based haplotype frequency estimation and permutation-based hypothesis-testing procedure were performed on the basis of the work of Fallin et al.27 After we obtained a significant haplotype profile analysis,27 we performed the individual haplotype analyses27 and single-locus analyses with multiple ...
  http://circ.ahajournals.org/content/109/13/1640
*  MHC haplotypes modulate strength of natural killer (NK) cell licensing (91.10) | The Journal of Immunology
NK cells react to cells that lack self-MHC class I. Yet, since many NK cells cannot recognize self-MHC, mechanisms such as NK cell licensing protect against autoreactivity. To become licensed, i.e. functionally competent to be triggered through its activation receptors, an NK cell must engage host MHC class I via at least one of its MHC class I-specific inhibitory receptors, such as the Ly49 family of receptors in the mouse. However, the general determinants of this process remain largely unknown. Herein, we investigated the licensing impact of the b, d, f, k, q, r, and s H2 haplotypes on Ly49A+ NK cells in MHC-congenic mice. Ex vivo PK136 (anti-NK1.1) stimulation assays indicated that licensing may not be a binary phenomenon as some Ly49A-MHC class I haplotype combinations produced an intermediate licensing phenotype. Ly49A surface accessibility, a measure of cis binding with MHC class I, and Ly49A tetramer binding displayed a similar variability among the ...
  http://www.jimmunol.org/content/182/1_Supplement/91.10
*  HaploPOP : a software that improves population assignment by combining markers into haplotypes
Background: In ecology and forensics, some population assignment techniques use molecular markers to assign individuals to known groups. However, assigning individuals to known populations can be difficult if the level of genetic differentiation among populations is small. Most assignment studies handle independent markers, often by pruning markers in Linkage Disequilibrium (LD), ignoring the information contained in the correlation among markers due to LD. Results: To improve the accuracy of population assignment, we present an algorithm, implemented in the HaploPOP software, that combines markers into haplotypes, without requiring independence. The algorithm is based on the Gain of Informativeness for Assignment that provides a measure to decide if a pair of markers should be combined into haplotypes, or not, in order to improve assignment. Because complete exploration of all possible solutions for constructing haplotypes is ...
  http://www.diva-portal.org/smash/record.jsf?pid=diva2:848853
*  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested...
We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated ...
  http://www.genetics.org/content/134/2/659
*  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence...
We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are ...
  http://www.genetics.org/content/132/2/619.long
*  MtDNA diversity and species phylogeny of western Palaearctic members of the Gerris lacustris group (Hemiptera-Heteroptera:...
The genetic diversity and phylogeny of western Palaearctic members of the Gerris lacustris group was investigated on the basis of 822 bp from the 3´end of the mitochondrial gene encoding COI obtained from 34 specimens of G. lacustris, 16 specimens of G. gibbifer, eight specimens of G. maculatus and seven specimens of G. brasili. Nine haplotypes represented G. lacustris, nine haplotypes represented G. gibbifer, six haplotypes represented G. maculatus, four haplotypes represented G. brasili, and a single haplotype was shared between G. gibbifer and G. brasili. Uncorrected p genetic distances within species averaged from 0.5% in G. gibbifer and G. brasili to 0.8 in G. lacustris and as much as 2.2 in G. maculatus. A phylogenetic analysis showed that G. gibbifer and G. brasili are not reciprocally monophyletic in their mtDNA probably due to relatively recent ...
  http://booksandjournals.brillonline.com/content/journals/10.1163/187631208788784156
*  Single-locus haplotype frequencies in community samples | Open-i
Single-locus haplotype frequencies in community samples. TFR, Day 28 treatment failure rate; haplotypes are labelled according to the patterns indicated in Tabl
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC2820042_1475-2875-9-8-1&req=4
*  In Search of Enlightenment: November 2006
Abstract: At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related ...
  http://colinfarrelly.blogspot.ca/2006/11/
*  Brevet US7615350 - Methods for haplotyping genomic DNA - Google Brevets
The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb). Separation of the haplotypes ...
  http://www.google.fr/patents/US7615350
*  How do we interpret a rooted haplotype network?
mtDNA is usually treated as a non-recombining locus, and so it should evolve along a tree. A rooted global tree has therefore been produced for humans, based on parsimony analysis of the mtDNA genome (Torroni et al. 2000; van Oven and Kayser 2009). Groups and subgroups of this tree have been labelled as haplotypes, such as haplotype group M shown in the top figure, and sub-haplogroups, such as M4b, M49 and M61. These are (monophyletic) clades in the mtDNA tree that have been highlighted for convenience. Parsimony analysis has been used to reconstruct the ancestral sequences in the tree (Behar et al. 2012), and these ancestral sequences can be used to assign new sequences to their appropriate place in the rooted tree (Blanco et al. 2011 ...
  http://phylonetworks.blogspot.ca/2013/09/how-do-we-interpret-rooted-haplotype.html
*  How do we interpret a rooted haplotype network?
mtDNA is usually treated as a non-recombining locus, and so it should evolve along a tree. A rooted global tree has therefore been produced for humans, based on parsimony analysis of the mtDNA genome (Torroni et al. 2000; van Oven and Kayser 2009). Groups and subgroups of this tree have been labelled as haplotypes, such as haplotype group M shown in the top figure, and sub-haplogroups, such as M4b, M49 and M61. These are (monophyletic) clades in the mtDNA tree that have been highlighted for convenience. Parsimony analysis has been used to reconstruct the ancestral sequences in the tree (Behar et al. 2012), and these ancestral sequences can be used to assign new sequences to their appropriate place in the rooted tree (Blanco et al. 2011 ...
  http://phylonetworks.blogspot.pt/2013/09/how-do-we-interpret-rooted-haplotype.html
*  Population structure using haplotype data
The Pith: New software which gives you a more fine-grained understanding of relationships between populations and individuals.. According to the reader survey ,50 percent of you don't know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of Population Structure using Dense Haplotype Data, as it extends the results of those earlier methods. But it's an important paper, and at some point I'll starting using their software. The "big picture" is that earlier methods left "some information on the table." That's partly due to the fact that they were developed (or in the case of PCA leveraged, as it's a very general technique) in an era where very dense marker data sets were not available (today we're shifting to full genome sequences in many cases!). The information left on the table would be haplotype structure. ...
  http://blogs.discovermagazine.com/gnxp/2012/01/population-structure-using-haplotype-data/
*  MDR1/ABCB1 gene polymorphisms in patients with chronic myeloid leukemia
Twenty four CML-patients, 22 (91.7%) with chronic phase and 2 (8.3%) under blast crisis, were studied. Thirteen (54.2%) were males, and 11 (45.8%) were females. The Sokal risk was low in 7 (29.2%), intermediate in 7 (29.2%), high in 6 (25%), and not evaluated in 4 (16.6%). Age, gender, phase of disease, TKI treatment and doses, molecular responses (at 6, 12, and 18 months) and haplotypes are listed in Table 1.. A total of seventeen different haplotypes were identified in CML-patients and controls. The frequency distribution indicates that 6 were only detected in CML-patients, 7 only in controls, and 4 in both groups. Heterozygous T-variant genotypes were observed in all 25 controls (100%), and in 18 CML-patients (75%). In this last group, 9 different T-variant haplotypes were identified as follows: full mutated-homozygote (TT-TT-TT) in 3 (12.5%), full mutated-heterozygous (CT-GT/A-CT) in 6 (25%), and other combinations of T-variants in 9 cases (37.5%). The ...
  http://www.bloodresearch.or.kr/journal/view.html?uid=1794&vmd=Full
*  IL-7 Receptor Polymorphisms and Immune Recovery With HAART - Full Text View - ClinicalTrials.gov
AIM: To examine the association between the four haplotypes of IL-7Rα gene and a cohort of HIV infected patients who have commenced HAART with varying CD4+ T lymphocyte responses.. METHODS: IL-7Rα gene SNPs and haplotypes will be measured by constructing DNA pools, and PCR amplification and DNA sequencing. IL-7Rα expression will be examined using constitutive expression of IL-7Rα, IL-7Rα gene expression, and inducible expression of IL7Rα. ...
  https://clinicaltrials.gov/show/NCT00168207?order=516
*  Plus it
Three MDM2 promoters have been identified and numerous genetic polymorphisms in these promoter regions have been reported in the HapMap and dbSNPs databases. Therefore, besides the reported functional SNP309 in the MDM2 promoter (13), we thought that the other genetic variants of the MDM2 gene may also be important and that their roles in human cancer susceptibility should be evaluated. In the present study, we used a haplotype-based approach to identify tagSNPs and evaluated their associations with risk of bladder cancer. Although we did not observe an association between any of the haplotypes and risk of bladder cancer, we observed a statistically significant association between the C1797G polymorphism in the MDM2 promoter and risk of bladder cancer and showed that the C to G substitution of this polymorphism significantly enhanced the binding affinity of the transcriptional activator C/EBPα and increased the transcription ...
  http://clincancerres.aacrjournals.org/content/14/11/3633
*  The association of INOS promoter haplotypes with rheumatoid arthritis - Nuffield Department of Orthopaedics, Rheumatology and...
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  https://www.ndorms.ox.ac.uk/publications/157047
*  Authors' reply
Researchers J. Karajalainen and colleagues present interesting data on the relationship of IL-1β and IL-1 receptor antagonist haplotypes and the rate of decline of lung function in incident asthmatic subjects in a Finnish cohort. Researchers reported that the IL1RN AI/IL1B-5l1T haplotype was associated with a more rapid decline in lung function in smokers in the Lung Health Study; in contrast, they found that this same haplotype was associated with a slower rate of decline in lung function in patients with asthma. Authors suggest that this apparent contradiction may be because the function of these haplotypes is disease specific ...
  http://connection.ebscohost.com/c/articles/12915595/authors-reply
*  PIPELINES - Edico Genome
The GATK Pipeline is an implementation of GATK Haplotype Variant Caller from the Broad Institute on the DRAGEN Platform. The GATK Pipeline is accelerated by using the API's of the DRAGEN Bio-IT Processor. The result is a haplotype variant calling pipeline that is able to analyze a 30x coverage whole human genome in 18 minutes. Customers with a valid GATK license from the Broad Institute are able to run GATK on the DRAGEN Platform.. ...
  http://edicogenome.com/pipelines/
*  PIPELINES - Edico Genome
The GATK Pipeline is an implementation of GATK Haplotype Variant Caller from the Broad Institute on the DRAGEN Platform. The GATK Pipeline is accelerated by using the API's of the DRAGEN Bio-IT Processor. The result is a haplotype variant calling pipeline that is able to analyze a 30x coverage whole human genome in 18 minutes. Customers with a valid GATK license from the Broad Institute are able to run GATK on the DRAGEN Platform.. ...
  http://edicogenome.com/pipelines/?s=
*  Haplotype - SNPedia
Haplotype: A specific combination of SNPs all occuring together on the same chromosome (i.e. all occuring on the chromosome inherited from Dad, or, inherited from Mom). Common DNA microarrays such as 23andMe, FTDNA and AncestryDNA's will at most identify the number of different alleles at each SNP location - 0, 1 or 2 - but can't identify which sides of the pair of chromosomes they came from. If matching SNP's are available for both parents, it's possible to determine which side they came from with high precision based on Mendelian inheritance, called phasing. Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct pseudo-phasing on large number of unrelated people. Sequencing, on the other hand, directly reads the sequence of nucleotides on a single strand of DNA, therefore preserving phasing. Next Gen Sequencing can thus provide not only perfectly phased genome, but also a ...
  https://snpedia.com/index.php/Haplotype
*  Haplotype - SNPedia
Haplotype: A specific combination of SNPs all occuring together on the same chromosome (i.e. all occuring on the chromosome inherited from Dad, or, inherited from Mom). Common DNA microarrays such as 23andMe, FTDNA and AncestryDNA's will at most identify the number of different alleles at each SNP location - 0, 1 or 2 - but can't identify which sides of the pair of chromosomes they came from. If matching SNP's are available for both parents, it's possible to determine which side they came from with high precision based on Mendelian inheritance, called phasing. Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct pseudo-phasing on large number of unrelated people. Sequencing, on the other hand, directly reads the sequence of nucleotides on a single strand of DNA, therefore preserving phasing. Next Gen Sequencing can thus provide not only perfectly phased genome, but also a ...
  https://www.snpedia.com/index.php/Haplotype
*  rs1050152 - SNPedia
rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31â€"3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T).[PMID 15107849] A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%.[PMID 15107849] ...
  https://www.snpedia.com/index.php/rs1050152