The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
Genotypic differences observed among individuals in a population.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The relationships of groups of organisms as reflected by their genetic makeup.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A phenomenon that is observed when a small subgroup of a larger POPULATION establishes itself as a separate and isolated entity. The subgroup's GENE POOL carries only a fraction of the genetic diversity of the parental population resulting in an increased frequency of certain diseases in the subgroup, especially those diseases known to be autosomal recessive.
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
A group of the D-related HLA antigens found to differ from the DR antigens in genetic locus and therefore inheritance. These antigens are polymorphic glycoproteins comprising alpha and beta chains and are found on lymphoid and other cells, often associated with certain diseases.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
Any method used for determining the location of and relative distances between genes on a chromosome.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Transmembrane proteins that form the beta subunits of the HLA-DQ antigens.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A subtype of HLA-DRB beta chains that includes over one hundred allele variants. The HLA-DRB1 subtype is associated with several of the HLA-DR SEROLOGICAL SUBTYPES.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
Individuals whose ancestral origins are in the continent of Europe.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A subclass of HLA-D antigens that consist of alpha and beta chains. The inheritance of HLA-DR antigens differs from that of the HLA-DQ ANTIGENS and HLA-DP ANTIGENS.
Antigens determined by leukocyte loci found on chromosome 6, the major histocompatibility loci in humans. They are polypeptides or glycoproteins found on most nucleated cells and platelets, determine tissue types for transplantation, and are associated with certain diseases.
Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.
The genetic region which contains the loci of genes which determine the structure of the serologically defined (SD) and lymphocyte-defined (LD) TRANSPLANTATION ANTIGENS, genes which control the structure of the IMMUNE RESPONSE-ASSOCIATED ANTIGENS, HUMAN; the IMMUNE RESPONSE GENES which control the ability of an animal to respond immunologically to antigenic stimuli, and genes which determine the structure and/or level of the first four components of complement.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.
Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.
A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)
The male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.
An individual in which both alleles at a given locus are identical.
An HLA-DR antigen which is associated with HLA-DRB1 CHAINS encoded by DRB1*03 alleles.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Genetic loci in the vertebrate major histocompatibility complex that encode polymorphic products which control the immune response to specific antigens. The genes are found in the HLA-D region in humans and in the I region in mice.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Class I human histocompatibility (HLA) surface antigens encoded by more than 30 detectable alleles on locus B of the HLA complex, the most polymorphic of all the HLA specificities. Several of these antigens (e.g., HLA-B27, -B7, -B8) are strongly associated with predisposition to rheumatoid and other autoimmune disorders. Like other class I HLA determinants, they are involved in the cellular immune reactivity of cytolytic T lymphocytes.
An individual having different alleles at one or more loci regarding a specific character.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.
The human male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans.
An independent state, an archipelago in the western Persian Gulf, northwest of Qatar. It comprises low-lying islands of Bahrain (the largest), Muharraq, Sitra, and several islets. It has extensive oil fields. The name comes from the Arabic al-bahrayn, "the two seas", with reference to its lying in the middle of a bay with its "two seas" east and west of it. (From Webster's New Geographical Dictionary, 1988, p107 & Room, Brewer's Dictionary of Names, 1992, p45)
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A country spanning from central Asia to the Pacific Ocean.
Individuals whose ancestral origins are in the continent of Africa.
A specific HLA-B surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-B*08 allele family.
Polymorphic class I human histocompatibility (HLA) surface antigens present on almost all nucleated cells. At least 20 antigens have been identified which are encoded by the A locus of multiple alleles on chromosome 6. They serve as targets for T-cell cytolytic responses and are involved with acceptance or rejection of tissue/organ grafts.
The total genetic information possessed by the reproductive members of a POPULATION of sexually reproducing organisms.
The collective name for the islands of the central Pacific Ocean, including the Austral Islands, Cook Islands, Easter Island, HAWAII; NEW ZEALAND; Phoenix Islands, PITCAIRN ISLAND; SAMOA; TONGA; Tuamotu Archipelago, Wake Island, and Wallis and Futuna Islands. Polynesians are of the Caucasoid race, but many are of mixed origin. Polynesia is from the Greek poly, many + nesos, island, with reference to the many islands in the group. (From Webster's New Geographical Dictionary, 1988, p966 & Room, Brewer's Dictionary of Names, 1992, p426)
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
Genetic loci in the vertebrate major histocompatibility complex which encode polymorphic characteristics not related to immune responsiveness or complement activity, e.g., B loci (chicken), DLA (dog), GPLA (guinea pig), H-2 (mouse), RT-1 (rat), HLA-A, -B, and -C class I genes of man.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.
A specific HLA-A surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-A*01 allele family.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.
Individual members of South American ethnic groups with historic ancestral origins in Asia.
Biochemical identification of mutational changes in a nucleotide sequence.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Genetic loci associated with a QUANTITATIVE TRAIT.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Any of several large carnivorous mammals of the family CANIDAE that usually hunt in packs.
The largest of the continents. It was known to the Romans more specifically as what we know today as Asia Minor. The name comes from at least two possible sources: from the Assyrian asu (to rise) or from the Sanskrit usa (dawn), both with reference to its being the land of the rising sun, i.e., eastern as opposed to Europe, to the west. (From Webster's New Geographical Dictionary, 1988, p82 & Room, Brewer's Dictionary of Names, 1992, p34)
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
A subtype of DIABETES MELLITUS that is characterized by INSULIN deficiency. It is manifested by the sudden onset of severe HYPERGLYCEMIA, rapid progression to DIABETIC KETOACIDOSIS, and DEATH unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence.
Class I human histocompatibility (HLA) antigens encoded by a small cluster of structural genes at the C locus on chromosome 6. They have significantly lower immunogenicity than the HLA-A and -B determinants and are therefore of minor importance in donor/recipient crossmatching. Their primary role is their high-risk association with certain disease manifestations (e.g., spondylarthritis, psoriasis, multiple myeloma).
The major group of transplantation antigens in the mouse.
Deoxyribonucleic acid that makes up the genetic material of plants.
A family of receptors found on NK CELLS that have specificity for a variety of HLA ANTIGENS. KIR receptors contain up to three different extracellular immunoglobulin-like domains referred to as D0, D1, and D2 and play an important role in blocking NK cell activation against cells expressing the appropriate HLA antigens thus preventing cell lysis. Although they are often referred to as being inhibitory receptors, a subset of KIR receptors may also play an activating role in NK cells.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
A group of autosomal recessive disorders marked by a deficiency of the hepatic enzyme PHENYLALANINE HYDROXYLASE or less frequently by reduced activity of DIHYDROPTERIDINE REDUCTASE (i.e., atypical phenylketonuria). Classical phenylketonuria is caused by a severe deficiency of phenylalanine hydroxylase and presents in infancy with developmental delay; SEIZURES; skin HYPOPIGMENTATION; ECZEMA; and demyelination in the central nervous system. (From Adams et al., Principles of Neurology, 6th ed, p952).
A region, north-central Asia, largely in Russia. It extends from the Ural Mountains to the Pacific Ocean and from the Arctic Ocean to central Kazakhstan and the borders of China and Mongolia.
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
A family composed of spouses and their children.
An adrenal microsomal cytochrome P450 enzyme that catalyzes the 21-hydroxylation of steroids in the presence of molecular oxygen and NADPH-FERRIHEMOPROTEIN REDUCTASE. This enzyme, encoded by CYP21 gene, converts progesterones to precursors of adrenal steroid hormones (CORTICOSTERONE; HYDROCORTISONE). Defects in CYP21 cause congenital adrenal hyperplasia (ADRENAL HYPERPLASIA, CONGENITAL).
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
Identification of the major histocompatibility antigens of transplant DONORS and potential recipients, usually by serological tests. Donor and recipient pairs should be of identical ABO blood group, and in addition should be matched as closely as possible for HISTOCOMPATIBILITY ANTIGENS in order to minimize the likelihood of allograft rejection. (King, Dictionary of Genetics, 4th ed)
A constitution or condition of the body which makes the tissues react in special ways to certain extrinsic stimuli and thus tends to make the individual more than usually susceptible to certain diseases.

Association of polymorphism at the type I collagen (COL1A1) locus with reduced bone mineral density, increased fracture risk, and increased collagen turnover. (1/12035)

OBJECTIVE: To examine the relationship between a common polymorphism within intron 1 of the COL1A1 gene and osteoporosis in a nested case-control study. METHODS: We studied 185 healthy women (mean +/- SD age 54.3+/-4.6 years). Bone mineral density (BMD) was measured using dual x-ray absorptiometry, and fractures were determined radiographically. The COL1A1 genotype was assessed using the polymerase chain reaction and Bal I endonuclease digestion. RESULTS: Genotype frequencies were similar to those previously observed and in Hardy-Weinberg equilibrium: SS 61.1%, Ss 36.2%, and ss 2.7%. Carriage of at least one copy of the "s" allele was associated with a significant reduction in lumbar spine BMD (P = 0.02) and an increased risk of total fracture (P = 0.04). Urinary pyridinoline levels were significantly elevated in those with the risk allele (P < 0.05). CONCLUSION: These data support the findings that the COL1A1 gene polymorphism is associated with low BMD and fracture risk, and suggest a possible physiologic effect on total body turnover of type I collagen.  (+info)

A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays. (2/12035)

Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization.  (+info)

The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission. (3/12035)

Genetic variability of citrus tristeza virus (CTV) was studied using the haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of genes p18 and p20 in six virus populations of two origins. The Spanish group included a CTV isolate and subisolates obtained by graft-transmission to different host species. The other included two subisolates aphid-transmitted from a single Japanese isolate. The homozygosity observed for gene p20 was always significantly higher than that expected under neutral evolution, whereas only three populations showed high homozygosity for p18, suggesting stronger host constraints for p20 than for p18. Sequential transmissions of a Spanish isolate to new host species increased the difference between its population and that of the successive subisolates for gene p18, as estimated by the F statistic. Analysis of molecular variance indicated that variation between both groups of populations was not statistically significant, whereas variations between populations of the same group or within populations were significant for both genes studied. Our data indicate that selection affects the haplotype distribution and that adaptation to a new host can be as important or more as the geographical origin. Variation of the CTV populations after host change or aphid transmission may explain in part the wide biological variability observed among CTV isolates.  (+info)

DYT1 mutation in French families with idiopathic torsion dystonia. (4/12035)

A GAG deletion at position 946 in DYT1, one of the genes responsible for autosomal dominant idiopathic torsion dystonia (ITD), has recently been identified. We tested 24 families and six isolated cases with ITD and found 14 individuals from six French families who carried this mutation, indicating that 20% of the affected families carried the DYT1 mutation. Age at onset was always before 20 years (mean, 9+/-4 years). Interestingly, the site of onset was the upper limb in all but one patient. Dystonia was generalized in seven patients and remained focal or segmental in three patients. The absence of common haplotypes among DYT1 families suggests that at least six independent founder mutations have occurred. In addition, one Ashkenazi Jewish family carried the common haplotype described previously in Ashkenazi Jewish patients, but it was absent in the other family. Moreover, the dystonia remained focal in the latter family when compared with the usual generalized phenotype in patients with the common Ashkenazi Jewish haplotype. This indicates that there are at least two founder mutations in this population.  (+info)

A common MSH2 mutation in English and North American HNPCC families: origin, phenotypic expression, and sex specific differences in colorectal cancer. (5/12035)

The frequency, origin, and phenotypic expression of a germline MSH2 gene mutation previously identified in seven kindreds with hereditary non-polyposis cancer syndrome (HNPCC) was investigated. The mutation (A-->T at nt943+3) disrupts the 3' splice site of exon 5 leading to the deletion of this exon from MSH2 mRNA and represents the only frequent MSH2 mutation so far reported. Although this mutation was initially detected in four of 33 colorectal cancer families analysed from eastern England, more extensive analysis has reduced the frequency to four of 52 (8%) English HNPCC kindreds analysed. In contrast, the MSH2 mutation was identified in 10 of 20 (50%) separately identified colorectal families from Newfoundland. To investigate the origin of this mutation in colorectal cancer families from England (n=4), Newfoundland (n=10), and the United States (n=3), haplotype analysis using microsatellite markers linked to MSH2 was performed. Within the English and US families there was little evidence for a recent common origin of the MSH2 splice site mutation in most families. In contrast, a common haplotype was identified at the two flanking markers (CA5 and D2S288) in eight of the Newfoundland families. These findings suggested a founder effect within Newfoundland similar to that reported by others for two MLH1 mutations in Finnish HNPCC families. We calculated age related risks of all, colorectal, endometrial, and ovarian cancers in nt943+3 A-->T MSH2 mutation carriers (n=76) for all patients and for men and women separately. For both sexes combined, the penetrances at age 60 years for all cancers and for colorectal cancer were 0.86 and 0.57, respectively. The risk of colorectal cancer was significantly higher (p<0.01) in males than females (0.63 v 0.30 and 0.84 v 0.44 at ages 50 and 60 years, respectively). For females there was a high risk of endometrial cancer (0.5 at age 60 years) and premenopausal ovarian cancer (0.2 at 50 years). These intersex differences in colorectal cancer risks have implications for screening programmes and for attempts to identify colorectal cancer susceptibility modifiers.  (+info)

Analysis of spinocerebellar ataxia type 2 gene and haplotype analysis: (CCG)1-2 polymorphism and contribution to founder effect. (6/12035)

Spinocerebellar ataxia type 2 is a familial spinocerebellar ataxia with autosomal dominant inheritance. The gene responsible was recently cloned and this disorder was found to be the result of a CAG expansion in its open reading frame. We analysed 13 SCA2 patients in seven unrelated families in Gunma Prefecture, Japan. In four of the seven families, we detected CCG or CCGCCG interruptions in only the expanded alleles. Cosegregation of these polymorphisms with SCA2 patients was established within each family. Together with the results of haplotype analyses, we considered that at least two founders were present in our area and that these (CCG)1-2 polymorphisms may make analysis of founder effects easier. By sequencing analysis we found that although the number of the long CAG repeat varied in each subclone of expanded alleles, these polymorphisms did not change their configuration. This finding suggests that CCG or CCGCCG sequences are stable when surrounded by the long CAG repeat and a single CAG. Moreover, the presence of these polymorphisms may lead to miscounting the repeat size by conventional estimation using a size marker such as an M13 sequencing ladder. Therefore we should consider these polymorphisms and accurately determine the repeat size by sequencing.  (+info)

Der(22) syndrome and velo-cardio-facial syndrome/DiGeorge syndrome share a 1.5-Mb region of overlap on chromosome 22q11. (7/12035)

Derivative 22 (der[22]) syndrome is a rare disorder associated with multiple congenital anomalies, including profound mental retardation, preauricular skin tags or pits, and conotruncal heart defects. It can occur in offspring of carriers of the constitutional t(11;22)(q23;q11) translocation, owing to a 3:1 meiotic malsegregation event resulting in partial trisomy of chromosomes 11 and 22. The trisomic region on chromosome 22 overlaps the region hemizygously deleted in another congenital anomaly disorder, velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS). Most patients with VCFS/DGS have a similar 3-Mb deletion, whereas some have a nested distal deletion endpoint resulting in a 1.5-Mb deletion, and a few rare patients have unique deletions. To define the interval on 22q11 containing the t(11;22) breakpoint, haplotype analysis and FISH mapping were performed for five patients with der(22) syndrome. Analysis of all the patients was consistent with 3:1 meiotic malsegregation in the t(11;22) carrier parent. FISH-mapping studies showed that the t(11;22) breakpoint occurred in the same interval as the 1.5-Mb distal deletion breakpoint for VCFS. The deletion breakpoint of one VCFS patient with an unbalanced t(18;22) translocation also occurred in the same region. Hamster-human somatic hybrid cell lines from a patient with der(22) syndrome and a patient with VCFS showed that the breakpoints occurred in an interval containing low-copy repeats, distal to RANBP1 and proximal to ZNF74. The presence of low-copy repetitive sequences may confer susceptibility to chromosome rearrangements. A 1.5-Mb region of overlap on 22q11 in both syndromes suggests the presence of dosage-dependent genes in this interval.  (+info)

Location score and haplotype analyses of the locus for autosomal recessive spastic ataxia of Charlevoix-Saguenay, in chromosome region 13q11. (8/12035)

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a clinically homogeneous form of early-onset familial spastic ataxia with prominent myelinated retinal nerve fibers. More than 300 patients have been identified, and most of their families originated in the Charlevoix-Saguenay region of northeastern Quebec, where the carrier prevalence has been estimated to be 1/22. Consistent with the hypothesis of a founder effect, we observed excess shared homozygosity at 13q11, among patients in a genomewide scan of 12 families. Analysis of 19 pedigrees demonstrated very tight linkage between the ARSACS locus and an intragenic polymorphism of the gamma-sarcoglycan (SGCG) gene, but genomic DNA sequence analysis of all eight exons of SGCG revealed no disease-causing mutation. On the basis of haplotypes composed of seven marker loci that spanned 11.1 cM, the most likely position of the ARSACS locus was 0.42 cM distal to the SGCG polymorphism. Two groups of ARSACS-associated haplotypes were identified: a large group that carries a common SGCG allele and a small group that carries a rare SGCG allele. The haplotype groups do not appear to be closely related. Therefore, although chromosomes within each haplotype group may harbor a single ARSACS mutation identical by descent, the two mutations could have independent origins.  (+info)

The region spanning the tumor necrosis factor (TNF) cluster in the human major histocompatibility complex (MHC) has been implicated in susceptibility to numerous immunopathological and inflammatory diseases. However, strong linkage disequilibrium in the region creates conserved TNF block haplotypes; hampering identification of specific polymorphisms responsible for disease phenotypes. Here we review studies investigating TNF block haplotypes and their links with cytokine production and inflammatory disease risk.Recent work has done much to characterize TNF block haplotypes in different ethnicities and their associations with the larger overall structure of MHC ancestral haplotypes. There have also been studies examining the effects of TNF block haplotypes on levels of inflammatory cytokine production, with others investigating haplotype association with diseases risk. Carriage of specific TNF block haplotypes have been associated with increased risk of Type II Diabetes, Chronic Venous Leg ...
We describe a novel method for assessing the strength of disease association with single nucleotide polymorphisms (SNPs) in a candidate gene or small candidate region, and for estimating the corresponding haplotype relative risks of disease, using unphased genotype data directly. We begin by estimating the relative frequencies of haplotypes consistent with observed SNP genotypes. Under the Bayesian partition model, we specify cluster centres from this set of consistent SNP haplotypes. The remaining haplotypes are then assigned to the cluster with the nearest centre, where distance is defined in terms of SNP allele matches. Within a logistic regression modelling framework, each haplotype within a cluster is assigned the same disease risk, reducing the number of parameters required. Uncertainty in phase assignment is addressed by considering all possible haplotype configurations consistent with each unphased genotype, weighted in the logistic regression likelihood by their probabilities, calculated
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 transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
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 transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
OBJECTIVES Associations of interleukin-10 (IL-10) promoter single nucleotide polymorphisms (SNPs) and their haplotypes with systemic lupus erythematosus (SLE) are unclear. We extended the analysis of established proximal IL-10 promoter haplotypes to a more distal SNP with functional capacity. METHODS Two hundred and ten German caucasian SLE patients fulfilling the ACR criteria and 160 ethnically, age and sex matched controls were genotyped for IL-10 -2849 G | A, -1082 A | G, -819 T | C and -592 C | A. Haplotypes were reconstructed via a mathematical model, then allele and haplotype distributions were compared between patients and controls and patients with different disease manifestations. RESULTS We detected at -2849, -1082, -819 and -592 the four predominant haplotypes GGCC (22% in patients vs. 29% in controls), AGCC (24% vs. 21%), GACC (30% vs. 25%) and GATA (24% vs. 24%). GGCC was underrepresented in SLE patients, suggesting a protective effect (odds ratio (OR) 0.67, 95% confidence interval (CI)
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of |44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122
BACKGROUND AND AIMS: Recent molecular data suggest that genetic factors may underlie the disease heterogeneity observed in both ulcerative colitis (UC) and Crohns disease (CD). A locus on chromosome 5q has been implicated in susceptibility to CD, and recently refined by linkage disequilibrium mapping to a conserved 250 kb haplotype (5q31). No data regarding the contribution of this locus to clinical phenotype exist. In this case control study, we investigated the contribution of this haplotype to both susceptibility and phenotype of CD and UC. PATIENTS AND METHODS: We studied 330 Caucasian CD and 457 UC patients recruited from a single UK centre. Association with disease susceptibility and phenotype was analysed with haplotypes reconstructed from three single nucleotide polymorphisms chosen to span thissusceptibility region. Evidence for possible genetic epistasis between IBD5 and NOD2/CARD15 was sought. RESULTS: Linkage disequilibrium across this region was confirmed, with two haplotypes ...
Identifying the genetic components of common diseases has long been an important area of research. Recently, genotyping technology has reached the level where it is cost effective to genotype single nucleotide polymorphism (SNP) markers covering the entire genome, in thousands of individuals, and analyse such data for markers associated with a diseases. The statistical power to detect association, however, is limited when markers are analysed one at a time. This can be alleviated by considering multiple markers simultaneously. The Haplotype Pattern Mining (HPM) method is a machine learning approach to do exactly this. We present a new, faster algorithm for the HPM method. The new approach use patterns of haplotype diversity in the genome: locally in the genome, the number of observed haplotypes is much smaller than the total number of possible haplotypes. We show that the new approach speeds up the HPM method with a factor of 2 on a genome-wide dataset with 5009 individuals typed in 491208 markers using
Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem. We define three novel statistical models and give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence. This approach - not assuming statistical dependence for remotely located markers - has two useful properties: it is well-suited for sparse marker maps, such as those used in gene mapping, and it can actually take advantage of long maps. Our experimental results with simulated and real data show that HaploRec is a powerful method for the large
This study investigated polymorphisms of genes in two regions of the T-cell antigen receptor beta-subunit (TCRB) locus, including BV9S2P, and BV6S7 in a 5 linkage group, and BV8S3, BV24S1, BV25S1, BV18S1, BV2S1, BV15S1 and BV3S1 in a 3 linkage group. These loci have been genotyped in individuals from five regions in Africa, including The Gambia, Nigeria, Cameroon, Tanzania, and Zambia, and in individuals from northern Britain, northern India, and Papua New Guinea (PNG). In the 3 linkage group, 11 unique haplotypes were identified in the combined African populations; two equally frequent haplotypes represent the majority of African chromosomes. One haplotype was found in all four regions studied. This is the most frequent haplotype in the northern British, northern Indian and PNG populations. Although present, it is infrequent in the African populations. A North-South gradient in the frequency of a common African haplotype was observed. The distribution did not represent that of a known disease.
TY - JOUR. T1 - Making a haplotype catalog with estimated frequencies based on SNP homozygotes. AU - Yamaguchi-Kabata, Yumi. AU - Tsunoda, Tatsuhiko. AU - Takahashi, Atsushi. AU - Hosono, Naoya. AU - Kubo, Michiaki. AU - Nakamura, Yusuke. AU - Kamatani, Naoyuki. PY - 2010/8. Y1 - 2010/8. N2 - Understanding the structure and frequencies of haplotypes is important for associating genetic polymorphisms with a given trait and for inferring the genetic genealogy of alleles in a population. Single nucleotide polymorphism (SNP) haplotypes can be determined without ambiguity when an individual does not have more than one heterozygous site in a given genomic region. Using genome-wide SNP genotypes for 3397 individuals from the Japanese population, we detected SNP homozygotes in the genomic regions of 1955 genes, determined haplotypes, and examined the efficiency of haplotype frequency estimation based on the proportion of SNP homozygotes in the sample. The estimated haplotype frequencies were very ...
Tables 4 and 5 show the results of eight SNP haplotype analyses (rs941798, rs3787345, rs754118, rs2282147, rs718049, rs718050, rs3787348, and 1484insG) with Si (Table 4) and fasting glucose (Table 5), respectively. The SNPs were chosen to tag all common haplotypes (≥10% frequency) and ,85% of the variation in the LD block and, in addition, includes 1484insG. The Tables show the common (,1%) haplotypes, their frequency, P values for association under different models of inheritance, the mean trait values for the different haplotype combinations, and the effect of the specific haplotype on the trait. The haplotype ACTTCAG0 is significantly associated with lower Si (e.g., greater insulin resistance) and higher fasting glucose in the dominant model, and the haplotype GTCCTGT0 is significantly associated with higher Si (e.g., greater insulin sensitivity) and lower fasting glucose in the additive and recessive models. The remaining haplotype, ATCCTGG0, shows evidence of association with Si under the ...
In the original publications, the haplotypes identified as being of highest risk consisted of the combination of two SNPs together, rs1048661(G) and rs3825942(C), oriented with respect to the dbSNP entry. In the two populations studied combined (from Iceland and Sweden), the (G;C) haplotype has an odds ratio of 27.05, and the (T;C) haplotype has an OR of 8.90, relative to the (G;T) haplotype. The (T;T) haplotype is presumed to be at even lower risk than the (G;T) haplotype, but due at least in part to the high frequency of the rs1048661(G) allele, no individuals in this study carried it. In the populations studied, ~25% of all individuals in the population carry two copies of the (G;C), highest risk haplotype. If the risk of carrying two such haplotypes is multiplicative (which isnt known actually), the authors estimate that individuals carrying two copies of the (G;C) high risk haplotype would have 700 times the risk of developing this type of glaucoma compared to individuals carrying two ...
TY - JOUR. T1 - Complex SNP-based haplotypes in three human helicases. T2 - Implications for cancer association studies. AU - Trikka, Dimitra. AU - Fang, Zhe. AU - Renwick, Alex. AU - Jones, Sally H.. AU - Chakraborty, Ranajit. AU - Kimmel, Marek. AU - Nelson, David L.. PY - 2002/4/25. Y1 - 2002/4/25. N2 - We have initiated a candidate gene approach to study variation and predisposition to cancer in the four major ethnic groups that constitute the U.S. population (African Americans, Caucasians, Hispanics, and Asians). We resequenced portions of three helicase genes (BLM, WRN, and RECQL) identifying a total of 37 noncoding single nucleotide polymorphisms (SNPs). Haplotype inference predicted 50 haplotypes in BLM, 56 in WRN, and 47 in RECQL in a sample of 600 chromosomes. Approximately 10% of the predicted haplotypes were shared among all ethnic groups. Linkage disequilibrium and recombination effects showed that each locus has taken a diverse evolutionary path. Primate DNA analysis of the same ...
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 MHC haplotypes. Taken together, the ...
A haplogroup is a group of similar and ancestrally related haplotypes that all have the same single nucleotide polymorphism (SNP) mutation. It is a genetic marker for a group of organisms with a common ancestor. In human genetics, the haplogroups usually studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups. Both can be used to define genetic populations. Y-DNA is passed only from father to son, while mtDNA is passed only from mother to children. Neither recombines, and thus Y-DNA and mtDNA change only by chance mutations with no intermixture between parents genetic material. Haplogroups are used in some forms of genetic ancestry research such as research determining the most common haplotype(s) in different populations and argued genetic ancestry relationships between the populations based on this. However, haplogroups are not races or some kind of racial essences that define races. Y-DNA and mtDNA haplogroups represent only a very small part of the human ...
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with |99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material; a substantial sample of individuals of the target species or other taxon is used; however, many current studies are based on single individuals. Haplotypes of individuals of closely related, yet different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: these are referred to as an outgroup. The base sequences for the haplotypes are then compared. In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between organisms is usually re-expressed as a percentage divergence, by dividing the number ...
This track shows alignments of alternate locus (also known as alternate haplotype) reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as alternate haplotype) reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as alternate haplotype) reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. ...
This track shows alignments of alternate locus (also known as alternate haplotype) reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct 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 computationally prohibitive, our approach uses a greedy algorithm ...
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 cladogram topology. In a ...
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 speciation and incomplete lineage sorting. G. maculatus was poorly supported as the sister taxon to G. gibbifer and G. brasili despite morphological
In 2009, Tregouet et al. identified the SLC22A3-LPAL2-LPA gene cluster as a risk cluster and haplotypes CTTG and CCTC formed by rs2048327, rs3127599, rs7767084 and rs10755578 as risk haplotypes for CAD in six White populations [1]. From then on, several GWHS have focused on this hot spot. In a study consisted of 3657 patients with MI and 1211 control individuals, Koch et al. observed significant association between haplotypes formed by the same four SNPs in the SLC22A3-LPAL2-LPA region and MI (P = 0.0005), and found 3 risk haplotypes (CTTG, CCTC, and TTTC) [10]. Later, Sawabe M etal analyzed rs2048327 (C/T) and rs10755578 (C/G) in 1,150 Japanese autopsy cases, and ascertained that haplotypes TC and TG worked as risk factors for both coronary sclerosis and CAD [12]. In addition, Shaw et al. found that genetic variants at the SLC22A3-LPAL2-LPA locus were associated with decreased early-outgrowth colony-forming units, thereby increased the risk of MI [13], which may support the findings in ...
Here you can Read online or download a free book: Algorithms for Haplotype Inference and Block Partitioning: Perfect Phylogeny Based Approaches for the Haplotype Inference Problem.pdf Language: English by Ravi Vijaya Satya (Author) A convenient format for reading on any device
DETECTING genetic differentiation of subpopulations is an important problem in several areas of population biology, including areas of evolutionary genetics, ecology, and conservation biology. When data are obtained from two or more localities in the form of allele frequencies at one or more unlinked loci, standard chi-square tests (or likelihood-ratio tests) of homogeneity are appropriate (Workman and Niswander 1970) and can be quite powerful for detecting differentiation. Even when the expected counts in some cells are small, permutation methods can be utilized to give good results (Lewontin and Felsenstein 1965; Roff and Bentzen 1989). If the data consist of DNA sequences, or haplotyping at two or more linked sites, the same methods can be employed, if distinct sequences or haplotypes are treated as alleles. However, if the haplotype diversity is very high and the sample sizes are small, most haplotypes may appear in the sample only once and the methods based on haplotype frequencies will ...
The patterns of linkage disequilibrium (LD) between dense polymorphic markers are shaped by the ancestral population history. It is therefore possible to use multilocus predictors of LD to infer past population history and to infer sharing of identical alleles in quantitative trait locus (QTL) studies. We develop a multilocus predictor of LD for pairs of haplotypes, which we term haplotype homozygosity (HHn) : the probability that any two haplotypes share a given number of n adjacent identical markers or runs of homozygosity. Our method, based on simplified coalescence theory, accounts for recombination and mutation. We compare our HHn predictions, with HHn in simulated populations and with two published predictors of HHn. Our method performs consistently better across a range of population parameters, including populations with a severe bottleneck followed by expansion, compared to two published methods. We demonstrate that we can predict the pattern of HHn observed in dense single nucleotide ...
Khwaja, HA and Green, FR (2004) Analysis of the functional role of interleukin-6 promoter haplotype in a macrophage cell model In: 5th Annual Conference on Arteriosclerosis, Thrombosis, and Vascular Biology, 2004-05-06 - 2004-05-08, San Francisco, CA. Full text not available from this repository ...
Sequencing of the LARS2 cDNA, including 159 bp of the promoter region in 25 type 2 diabetic subjects, revealed eight different SNPs (Fig. 1). We did not find aberrant splicing in any of the samples investigated. Haplotype analysis using four SNPs with allele frequencies ≥2.5% suggests at least six different haplotypes (frequency ≥4%). Two variants (−109 g/a and H324Q) potentially affecting gene function were subsequently investigated in more detail. Double heterozygous subjects were not found, and haplotype and linkage disequilibrium analyses suggest that the two SNPs are present on different haplotypes and haploblocks (D′ = −1, r2 = 0.013; Fig. 1).. Genotype distributions for both SNPs in the different cohorts were all in Hardy-Weinberg equilibrium. The −109 g/a variant was tested for association in the two Dutch cohorts. Allele frequencies were 31.3 and 32.6% for control (n = 329) and type 2 diabetic (n = 215) subjects in the Hoorn study (P , 0.5) and 26.0 and 30.3% for control (n ...
The MDM2 protein is an ubiquitin ligase that plays a critical role in regulating the levels and activity of the p53 protein, which is a central tumor suppressor. A SNP in the human MDM2 gene (SNP309 T/G) occurs at frequencies dependent on demographic history and has been shown to have important differential effects on the activity of the MDM2 and p53 proteins and to associate with altered risk for the development of several cancers. In this report, the haplotype structure of the MDM2 gene is determined by using 14 different SNPs across the gene from three different population samples: Caucasians, African Americans, and the Ashkenazi Jewish ethnic group. The results presented in this report indicate that there is a substantially reduced variability of the deleterious SNP309 G allele haplotype in all three populations studied, whereas multiple common T allele haplotypes were found in all three populations. This observation, coupled with the relatively high frequency of the G allele haplotype in ...
Results In a Han population, the distribution of SNP3 (rs3890011) genotypes showed a significant difference between CAD and control subjects (p=0.030), the distribution of the recessive model of SNP3 (GG vs CC+GC) was significantly higher in CAD patients than control subjects (p=0.011), the significant difference was retained after adjustment for covariates (95%CI: 1.137-2.423, p=0.009). Three SNPs (SNP1, SNP3, SNP4) were located in one haplotype block, and the overall distribution of haplotypes constructed with these SNPs was significant (p=0.023). The G-G-T haplotype in CAD was significantly higher than that in control group (p=0.037). In a Uygur population, neither the distribution of genotypes and alleles for the 4 SNPs showed significant difference nor the distribution of haplotypes constructed with the same three SNPs between CAD and control subjects.. ...
The systematic analysis of polymorphisms across large parts of the human genome has begun to provide the first information on haplotypes and the problem of linkage disequilibrium across large genomic regions. These data suggest that significant regions of the genome show highly conserved haplotypes, potentially enhancing the ability to detect disease associations.
Increased mammographic density is one of the strongest independent risk factors for breast cancer. It is believed that one third of breast cancers are derived from breasts with more than 50% density. Mammographic density is affected by age, BMI, parity, and genetic predisposition. It is also greatly influenced by hormonal and growth factor changes in a womans life cycle, spanning from puberty through adult to menopause. Genetic variations in genes coding for hormones and growth factors involved in development of the breast are therefore of great interest. The associations between genetic polymorphisms in genes from the IGF pathway on mammographic density and circulating levels of IGF1, its binding protein IGFBP3, and their ratio in postmenopausal women are reported here. Samples from 964 postmenopausal Norwegian women aged 55-71 years were collected as a part of the Tromsø Mammography and Breast Cancer Study. All samples were genotyped for 25 SNPs in IGF1, IGF2, IGF1R, IGF2R, IGFALS and IGFBP3 using
TY - JOUR. T1 - Four common HLA haplotypes and their association with diseases in the Japanese population. AU - Sasazuki, T.. AU - Kaneoka, H.. AU - Ohta, N.. AU - Hayase, R.. AU - Iwamoto, I.. PY - 1979/12/1. Y1 - 1979/12/1. UR - http://www.scopus.com/inward/record.url?scp=0018567739&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0018567739&partnerID=8YFLogxK. M3 - Article. C2 - 43610. AN - SCOPUS:0018567739. VL - 11. SP - 1871. EP - 1873. JO - Transplantation Proceedings. JF - Transplantation Proceedings. SN - 0041-1345. IS - 4. ER - ...
David R. Cox, of Perlegen Sciences in Santa Clara, California, and colleagues scanned 20 copies of chromosome 21 using high-density microarrays. In all, they found nearly 36,000 SNPs in the samples. Using the scan data, they identified groups of related SNPs, or haplotypes. Most of these structures turned up on all the chromosomes. Only eight percent of the haplotypes were specific to a particular ethnic group. It is remarkable that such a large fraction of globally diverse chromosomes are represented by such limited haplotype diversity, the researchers write in Science. Three common haplotypes accounted for 80 percent of the genetic diversity among the samples. This means that, for any region of the chromosome, the most common haplotype was found in 50 percent of individuals, the second most common in 25 percent of individuals, and the third most common in 12.5 percent of individuals. The discovery that chromosome 21 is less structurally diverse than expected is potentially good news. It may ...
In admixed populations originating from different base breeds, such as Nordic Red dairy cattle, haplotypes of chromosomal segments instead of single SNP are expected to improve prediction accuracy in genomic evaluations, because linkage disequilibrium with QTL is likely to be more consistent for haplotypes than for SNP. The suggested evaluation approach consists of (i) pre-selecting a limited number of chromosomal segments based on a genome-wide QTL-scan with BayesB, (ii) estimating relative variances of haplotype markers with BayesA, and (iii) obtaining solutions for haplotype effects from mixed model equations including pedigree-based animal effects. For three production traits (milk, protein, fat) and fertility, the highest validation test reliabilities R2 were 0.48, 0.41, 0.42 and 0.33, respectively. For milk, protein and fertility, we observed an improvement over G-BLUP of 3, 1 and 3 %-units, respectively, whereas for fat, a decline of 1 %-unit.. ...
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 of large genomic DNA fragments allows for linkage analysis of other HLA alleles
DESCRIPTION. Haploscope is a software package that facilitates flexible rendering of images to aid interpretation of model-based summaries of population haplotypes. Haploscope is designed to accept haplotype frequency input directly from output files of fastPHASE (Scheet & Stephens, 2006), though output from other cluster-based models for population haplotypes could be adapted for input to Haploscope.. ::DEVELOPER. paul scheet lab. :: SCREENSHOTS. N/A. :: REQUIREMENTS. ...
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 ...
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 ...
A new type of insertion flanked by long stretches of TA repeats, hence named TAFTs for TA-flanked transposons, was discovered during the course of this investigation. TAFTs have the following properties. (i) They are flanked by TA microsatellites with as many as 50 copies of the TA repeat on either side of the insertion. (ii) The corresponding vacant site in haplotypes that lack TAFTs consists generally of a few (three or four) copies of the TA repeat, but there are exceptions. (iii) The elements identified so far possess imperfect TIRs of ≈40 bp and are relatively large (,2 kb). (iv) Related copies are found at other locations in the maize genome, where they are also flanked by TA repeats.. The TAFT1 element in CML258 and Coroico is 2.2-kb long and is flanked on either side by multiple copies of TA. The vacant site in the other haplotypes has three copies of the TA dinucleotide. TAFT1 is 85% identical to oligo-TA flanked sequences of similar length that occur in B73 locus 9009 (GenBank ...
The goal of this study was to determine whether variants associated with age at onset of CFRD affected the expression of SLC26A9. We discovered that the alleles of the CFRD-risk variants are coinherited as 2 common haplotypes, one that is associated with later onset of CFRD (LR), and another that is associated with earlier onset of CFRD (HR). A third less common haplotype similar to HR was also associated with earlier onset of diabetes, and it is possible that other, less common, haplotypes bearing the majority of the CFRD-risk variants also correlate with CFRD, but are not sufficiently frequent to allow detection of association in the 762 individuals studied here. There was no evidence that a coding or rare variant accounted for the CFRD association. Mapping of the major TSS indicated that the noncoding first exon of SLC26A9 was placed in the middle of the cluster of CFRD-risk variants in the 5′ region of SLC26A9. These results suggested that the HR and LR CFRD haplotypes affect ...
Read Mapping-free variant calling using haplotype reconstruction from k-mer frequencies, Bioinformatics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
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 remaining 6 (25%) CML-patients were ...
Recent advances in RNA sequencing technology can generate deep coverage data containing millions of reads. RNA-Seq data are used to identify genetic variants and alternatively spliced isoforms, a common mechanism for diversity in a gene, that may play a role in heritable traits and diseases. Using this type of data, connections can be drawn between genetic expression and one of the two parental haplotypes identified in a diploid organisms transcript. In other words, we can potentially identify the parent from which an individual inherited a group of genes.. These multi-kilobase reads are longer than most transcripts and enable sequencing of complete haplotype isoforms. New computational methods are required for efficient analysis of this highly complex data. In a recent paper, we present HapIso (Haplotype-specific Isoform Reconstruction), a comprehensive method that can accurately reconstruct the haplotype-specific isoforms of a diploid cell. Our software package is the first method capable of ...
Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the ...
Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the ...
Mitochondrial DNA haplotypes from the displacement-loop (D-loop) region (436 bp) were genotyped and sequenced in Japanese Black beef cattle raised in the same herd. Correlation coefficients between mitochondrial DNA haplotypes, maternal lineage, birth weight, preweaning average daily gain, weaning weight, post weaning average daily gain and yearling weight were computed. The objective was to study the relationship between maternal and postnatal growth traits and to investigate if postnatal growth of calves to yearling age could be accurately predicted from mitochondrial DNA haplotypes. Results of the phylogenetic analysis revealed 17 maternal lineages and four mitochondrial DNA haplotypes. There were strong, positive and highly significant (p,0.001) correlations among maternal traits ranging from 0.52 to 0.98. Similarly, among postnatal growth traits, most of the correlations were also strong, positive and highly significant (p,0.001); the highest correlation of 0.94 was between preweaning ...
In this large prospective study of a general population of Northern European descent, no evidence was found for consistent and robust associations between mitochondrial haplogroups and risk of ischemic cardiovascular disease, morbidity from other causes, or mortality. In contrast, several smaller case-control studies have shown associations between mitochondrial haplogroups and myocardial infarction, cerebral infarction, cancer, diabetes mellitus, and neurodegenerative diseases.18-36. The Asian N9b haplogroup (defined by polymorphisms at positions mt5147 and mt16519) has been reported to protect against myocardial infarction in Japanese men (odds ratio [95% CI], 0.2 [0.1 to 0.5]; 920 cases/522 controls) but not in Japanese women (695 cases/434 controls).19 It has been speculated that this reduction in risk of myocardial infarction could be due to a reduction in the production of superoxide and other reactive oxygen species associated with this particular haplogroup19 that thus might confer ...
From previous studies, it is known that the low OA risk haplogroup J is associated with lower serum levels of markers of collagen type-II degradation and of matrix metalloproteinases, but all of these studies failed to address the key question arising from this large body of evidence: What is the functional role of these mtDNA haplogroups?. To answer this question, Fernandez-Moreno et al7 used cytoplasmic hybrid (cybrid) cell lines. Cybrids incorporate mitochondria from human subjects and perpetuate the mtDNA-encoded components while maintaining the nuclear background of different cybrid lines as constant.16 Thus, this technique allows investigators to assess the influence of mtDNA variation on cell function. To investigate the role of mtDNA haplogroups, they also created cybrids using osteosarcoma cell lines with the same nuclear background, one of them harbouring the haplogroup J (which protects against OA) and another harbouring the haplogroup H (linked to higher risk of OA).. The cybrids ...
Haplogroup L1 is believed to have appeared approximately 110,000 to 170,000 years ago.[citation needed] Haplogroup L1 is a daughter of L1-6 and genetic marker changes are 3666, 7055, 7389, 13789, 14178 and 14560. Although it is typically used to denote a group of lineages found within Africa, L1 is sometimes referred to as haplogroup L1-6. The latter is the macrohaplogroup that includes the majority of Africa-based clades and all haplogroups centered outside of the continent. Haplogroup L1-6 is the macrohaplogroup that includes subclades L1, L2, L4, L5, L6, and also L3, which gave rise to the two non-African haplogroups M and N. Haplogroup L1-6 and its only sibling haplogroup L0 are united by the matrilineal most recent common ancestor, (MRCA) of all living humans, Mitochondrial Eve. The existence of these two lineages, implies that Mitochondrial Eve had at least two daughters, one of whom is the maternal common ancestor of haplogroup L1-6 lineages.[citation needed] ...
Effective identification of disease-causing gene locations can have significant impact on patient management decisions that will ultimately increase survival rates and improve the overall quality of health care. Linkage disequilibrium mapping is the process of finding disease gene locations through comparisons of haplotype frequencies between disease chromosomes and normal chromosomes. This work presents a new method for linkage disequilibrium mapping. The main advantage of the proposed algorithm, called LinkageTracker, is its consistency in producing good predictive accuracy under different conditions, including extreme conditions where the occurrence of disease samples with the mutation of interest is very low and there is presence of error or noise. We compared our method with some leading methods in linkage disequilibrium mapping such as HapMiner, Blade, GeneRecon, and Haplotype Pattern Mining (HPM). Experimental results show that for a substantial class of problems, our method has good predictive
TY - JOUR. T1 - Positive association of the human GABA-A-receptor beta 2 subunit gene haplotype with schizophrenia in the Chinese Han population. AU - Liu, Jixia. AU - Shi, Yongyong. AU - Tang, Wei. AU - Guo, Tingwei. AU - Li, Dawei. AU - Yang, Yifeng. AU - Zhao, Xinzhi. AU - Wang, Hongsheng. AU - Li, Xingwang. AU - Feng, Guoyin. AU - Gu, Niufan. AU - Zhu, Shaomin. AU - Liu, Huijun. AU - Guo, Yangling. AU - Shi, Jianguo. AU - Sang, Hong. AU - Yan, Lijuan. AU - He, Lin. N1 - Funding Information: We are grateful to all the participants as well as the psychiatrists and mental health workers working on this project. This work was supported by grants from the Ministry of Education, PRC, the national 973 and 863 Programs of China, the National Natural Science Foundation of China, and the Shanghai Municipal Commission for Science and Technology. PY - 2005/9/2. Y1 - 2005/9/2. N2 - A converging body of evidence implicates the γ-amino butyric acid neurotransmitter system in the pathogenesis of ...
We had previously found that 6-month survival in sepsis patients was significantly associated with platelet COX quantity [4]. However, 1-month survival is a more frequently used parameter in critically ill patients; and we have found that this parameter is also significantly associated with platelet COX quantity. We had previously observed that COX levels can be determined by mtDNA genetic background [6], and other investigators showed that mtDNA haplogroups modified 6-month survival [9]. Here we show that the mtDNA haplogroup determines the platelet COX quantity in sepsis patients and that those patients from the JT mtDNA haplogroup had higher survival rate than those from other mtDNA haplogroups.. The JT mtDNA haplogroup is defined by polymorphisms in nucleotide positions m.4216T , C/MT-ND1, m.11251A , G/MT-ND4, m.15452C , A/MT-CYB and m.16126T , C/MT-DLOOP. The last polymorphism is located in the control region, out of any important sequence for the regulation of mtDNA replication and ...
BACKGROUND:Cholesterol 7-alpha-hydroxylase (CYP7A1) is the rate limiting enzyme for converting cholesterol into bile acids. Genetic variations in the CYP7A1 gene have been associated with metabolic disorders of cholesterol and bile acids, including hypercholesterolemia, hypertriglyceridemia, arteriosclerosis, and gallstone disease. Current genetic studies are focused mainly on analysis of a single nucleotide polymorphism (SNP) at A-278C in the promoter region of the CYP7A1 gene. Here we report a genetic approach for an extensive analysis on linkage disequilibrium (LD) blocks and haplotype structures of the entire CYP7A1 gene and its surrounding sequences in Africans, Caucasians, Asians, Mexican-Americans, and African-Americans.RESULT:The LD patterns and haplotype blocks of CYP7A1 gene were defined in Africans, Caucasians, and Asians using genotyping data downloaded from the HapMap database to select a set of haplotype-tagging SNPs (htSNP). A low cost, microarray-based platform on thin-film ...
To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean - Adriatic - marmoratus haplotypes, which were further delimited into three subdivisions of Mediterranean, marmoratus, and a previously non-described formation of four Adriatic haplotypes (Balkan cluster). Haplotypes of the Balkan cluster and the other Adriatic haplotypes, do not represent a contiguous
This study is to survey 10 Y-STR loci in 241 males from Turkey. In this study, the 241 healthy and unrelated males living in different parts of Turkey for at least three generations were included. Genomic DNAs were isolated from peripheral blood samples by standard phenol-chloroform extraction method. 10 Y-STR loci including DYS19, DYS385a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAIIa/b were analyzed by using PCR and denaturing PAGE. Allele frequencies, gene diversities and haplotype frequencies were analyzed. Gene diversity per locus varied from 0.5788 (DYS388) to 0.8903 (DYS385a/b). The numbers of haplotypes in minHt recommended by YCC and Ht10 have been 208 and 186, respectively. When our minHt haplotypes frequencies compared with the other seven populations, we have found statistically significant differences between our results and other populations (P 0.05). We suggest that an alternative haplotype designated as aHt maybe alternative to minHt in respect of its Y-STR
Human 12/15-lipoxygenase (ALOX15) catalyzes the oxidation of polyunsaturated fatty acids and has been implicated in the pathogenesis of atherosclerosis. We previously reported that a common haplotype of the ALOX15 gene is associated with higher prevalence of coronary artery calcification in a cohort of middle-aged African-Americans. This haplotype was uniquely tagged by a promoter variant (rs2255888). We carried out an in vitro characterization of this promoter variant to further investigate regulatory mechanisms of the ALOX15 gene. We evaluated the activity of ALOX15 variant A-carrying and wild type G-carrying promoter haplotypes using a luciferase assay. We demonstrated a 65% higher activity of the A-carrying promoter haplotype as compared to the G-carrying promoter haplotype. Using mass-spectrometry and electrophoretic mobility shift assay we showed that vimentin, a structural protein, specifically binds to both A-carrying and G-carrying promoter haplotypes in vitro. However, the A ...
Eight Y-chromosome STRs were investigated in a male population sample from Córdoba region (Argentina). Complete Y-chromosomal STRs haplotypes were obtained in 100 individuals, among which 91 different haplotypes were observed. The most common haplotype was shared by 4% of the sample, while 86 haplotypes were unique. The gene diversity was 0.9875 and the discrimination capacity was 0.8600. The combined polymorphism provides a powerful discrimination tool for routine forensic applications.
Holyoake, A. J., McHugh, Patrick C, Wu, M., OCarroll, S., Benny, P., Sin, I. L. and Sin, F. Y. T. (2002) Research of single mitochondrial nucleotide substitutions in male infertility should consider human mitochondrial haplogroups - Reply. International Journal of Andrology, 25 (6). p. 374. ISSN 0105-6263 Metadata only available from this repository ...
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10-4, permutation p = 1.0×10-3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 ...
Little is known about the extent of allelic diversity of genes in the complex polyploid, sugarcane. Using sucrose phosphate synthase (SPS) Gene (SPS) Family III as an example, we have amplified and sequenced a 400 nt region from this gene from two sugarcane lines that are parents of a mapping population. Ten single nucleotide polymorphisms (SNPs) were identified within the 400 nt region of which seven were present in both lines. In the elite commercial cultivar Q165A, 10 sequence haplotypes were identified, with four haplotypes recovered at 9% or greater frequency. Based on SNP presence, two clusters of haplotypes were observed. In IJ76-514, a Saccharum officinarum accession, 8 haplotypes were identified with 4 haplotypes recovered at 13% or greater frequency. Again, two clusters of haplotypes were observed. The results suggest that there may be two SPS Gene Family III genes per genome in sugarcane, each with different numbers of different alleles. This suggestion is supported by sequencing results in
t haplotypes are naturally occurring, variant forms of the t complex on mouse chromosome 17, characterized by the presence of four inversions with respect to wild-type. They harbour mutations causing male sterility, male transmission ratio distortion (TRD) and embryonic lethality. Mice carrying t haplotypes have been found throughout the world, and genetic studies of the lethal mutations have identified at least 16 complementation groups. The embryonic lethal phenotypes of many t haplotypes have been characterized in detail, and are thought to be the consequence of homozygosity for single gene mutations. However, the existence of additional mutations in genes that function at later stages of development would be obscured. Here we investigated the possibility of multiple mutations in t haplotypes by screening the t(w73) haplotype for the presence of novel mutations. Since genetic analysis of t haplotype mutations is hindered by recombination suppression due to the inversions, deletion
The importance of haplotype association and gene-environment interactions (GxE) in the context of rare variants has been underlined in voluminous literature. Recently, a software based on logistic Bayesian LASSO (LBL) was proposed for detecting GxE, where G is a rare (or common) haplotype variant (rHTV)-it is called LBL-GxE. However, it required relatively long computation time and could handle only one environmental covariate with two levels. Here we propose an improved version of LBL-GxE, which is not only computationally faster but can also handle multiple covariates, each with multiple levels. We also discuss details of the software, including input, output, and some options. We apply LBL-GxE to a lung cancer dataset and find a rare haplotype with protective effect for current smokers. Our results indicate that LBL-GxE, especially with the improvements proposed here, is a useful and computationally viable tool for investigating rare haplotype interactions ...
Genetic results also include 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 allows them to be used to distinguish recent genealogy. But it also means that, rather than the population of descendants 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 center, the modal haplotype (presumably similar to the haplotype of the original founding event), and also a haplotype diversity - the degree to which it has become spread out. The further in the past the defining event occurred, and the more that subsequent population growth occurred early, the greater the haplotype diversity will be for a particular number of descendants. However, if the haplotype diversity is smaller for a particular number of descendants, this may indicate a more recent common ancestor, or a ...
We questioned the significance of haplotype structure in gene regulation by testing whether individual single nucleotide polymorphisms (SNPs) within a gene promoter region [interleukin-1-beta (IL1B)] might affect promoter function and, if so, whether function was dependent on haplotype context. We sequenced genomic DNA from 25 individuals of diverse ethnicity, focusing on exons and upstream flanking regions of genes of the cluster. We identified four IL1B promoter region SNPs that were active in transient transfection reporter gene assays. To substantiate allelic differences found in reporter gene assays, we also examined nuclear protein binding to promoter sequence oligonucleotides containing different alleles of the SNPs. The effect of individual SNPs on reporter gene transcription varied according to which alleles of the three other SNPs were present in the promoter construct. The SNP patterns that influenced function reflected common haplotypes that occur in the population, suggesting ...
As resistance to insecticides increases in disease vectors, it has become exceedingly important to monitor populations for susceptibility. Most studies of field populations of Aedes aegypti have largely characterized resistance patterns at the spatial scale of the city or country, which may not be completely informative given that insecticide application occurs at the scale of the house or city block. Phenotypic resistance to pyrethroids dominates in Ae. aegypti, and it has been partially explained by mutations in the voltage-gated sodium channel gene. Here, we assess community-level patterns of four knockdown resistance (kdr) haplotypes (C1534/I1016, F1534/I1016, C1534/V1016 and F1534/V1016) in Ae. aegypti in 24 randomly chosen city blocks from a city in Yucatán State, Mexico, during both the dry and wet season and over two years. Three of the four haplotypes, C1534/I1016, C1534/V1016 and F1534/V1016 were heterogeneous between city blocks at all four sampling time points, and the double mutant
Genotype imputation is the process of predicting unobserved genotypes in a sample of individuals using a reference panel of haplotypes. In the last 10 years reference panels have increased in size by more than 100 fold. Increasing reference panel size improves accuracy of markers with low minor allele frequencies but poses ever increasing computational challenges for imputation methods. Here we present IMPUTE5, a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as
A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167-0.9952, low nucleotide diversity ranging from 0.0288-0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are
Because 4 of the 13 genes identified in the single SNP serous analysis contained multiple candidate SNPs, we carried out haplotype analyses to better understand the patterns of risk in these genes. CDK6 haplotypes of the 4 SNPs (rs2282990, rs3731348, rs17690388, and rs2282983) were suggestive of association with risk of serous invasive ovarian cancer (global haplotype association P = 0.0034; Supplementary Table S5a). The first CDK6 risk haplotype was perfectly tagged by the minor allele (A) of rs17690388 and was associated with a decrease in risk of serous ovarian cancer (OR = 0.63, 95% CI: 0.40-0.99; P = 0.044). The second CDK6 risk haplotype captured the minor alleles of rs2282990 (T) and rs2282983 (C) and the major allele at rs3731348 (G) and was associated with an increase in serous ovarian cancer risk (OR = 2.42, 95% CI: 1.30-4.50; P = 0.0054). SIK3 and TEX14 each contained haplotypes associated with risk of serous ovarian cancer that were captured by variation at single SNPs (Supplementary ...
Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Abstract Genetic studies of the distribution of mitochondrial DNA (mtDNA) haplogroups in human populations residing within the Carpathian Mountain range have been scarce. We present an analysis of mtDNA haplogroup composition of the Boykos, Hutsuls, and Lemkos, three population groups of the Carpathian highlands. In our study Hutsuls had the highest frequency of subhaplogroup H1 in central and eastern Europe. Lemkos shared the highest frequency of haplogroup I ever reported and the highest frequency of haplogroup M* in the region. MtDNA haplogroup frequencies in Boykos were different from most modern European populations. We interpreted these unique mtDNA frequencies to be evidence of diverse and dynamic population histories in the Carpathian highland region. ...
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens and tissue injury. Defective apoptosis of activated immune cells leads to the development of autoantibodies in SLE. FasL initiated apoptosis is central for peripheral tolerance. Fas deficiencies in humans and mice predispose toward systemic autoimmunity. SLE is conferred by many genes. The genetic effects may be concentrated by familial clustering or by stratifying of subphenotypes. We have tested polymorphisms and haplotypes in FAS and FASL for association to SLE or subphenotypes in 126 multiplex American SLE pedigrees and found association of the FAS codon214 AC(C/T) as well as the FAS-670G,A-codon214 AC(C/T) haplotype to thrombocytopenia in SLE. Furthermore we have functionally characterized the FAS/FASL promoter polymorphisms associated with SLE in other populations and demonstrate that the activity depends on the allelic variants as well as on the ...
The Y chromosome has recently been suggested to have an association with prostate cancer risk in human populations. Since this chromosome is haploid and lacks recombination over most of its length, haplotypes constructed from binary markers throughout the chromosome can be used for association studies. To assess the possible Y-chromosomal contribution to prostate cancer risk, we have therefore analyzed 14 Y-chromosomal binary markers in 106 prostate cancer cases and 110 controls from the Korean population. In contrast to previous findings in the Japanese population, no statistically significant difference in the distribution of Y-chromosomal haplogroup frequencies was observed between the case and control groups of Koreans. Thus, our data imply that the previously reported associations between Y-chromosomal lineages and a predisposition to, or protection against, prostate cancer might be explained by statistical fluctuations, or by genetic effects that are seen only in some environments.
Interleukin-8 (IL-8) has been implicated in the pathogenesis of RSV-induced bronchiolitis. Previously, we have described an association between bronchiolitis disease severity and a specific IL-8 haplotype comprising six single-nucleotide polymorphisms (SNPs) (-251A/+396G/+781T/+1238delA/+1633T/+2767T, haplotype 2). Here we investigated the functional basis for this association by measuring haplotype-specific transcription in vivo in human primary cells. We found a significant increase in transcript level derived from the IL-8 haplotype 2 relative to the mirror haplotype 1 (-251T/+396T/+781C/+1238insA/+1633C/+2767A) in respiratory epithelial cells but not in lymphocytes. A promoter polymorphism, -251A, present on the high producer haplotype, had no significant affect on the allele-specific level of transcription when analyzed in reporter gene experiments in human respiratory epithelial A549 cells. We proceeded to systematically screen for allele-specific protein-DNA binding in this functional haplotype,
Single Nucleotide Polymorphism (SNP) information has enabled the use of linkage disequilibrium to detect and localize loci affecting phenotypes. The first methods developed searched for disequilibrium between one or a few marker loci and loci responsible for disease susceptibility. Case-control designs were used [1]. Typically, data were analyzed to compare the frequency of marker alleles between healthy and diseased individuals, for instance using the relative risk criterion [2]. A similar approach for quantitative traits (including production traits in animals or plants) was to model the expectation of their distribution as a linear combination of marker genotype, allele or haplotype effects. Grapes et al. [3] and Zhao et al. [4] demonstrated that the single marker regression model is as powerful and precise as other more sophisticated techniques, such as multiple regression, regression on haplotypes, or the IBD method proposed by Meuwissen and Goddard [5].. Detection of spurious associations ...
Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of
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Results: In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure ...
We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.
Background: The haplotypes of the X chromosome are accessible to direct count in males, whereas the diplotypes of the females may be inferred knowing the haplotype of their sons or fathers. Here, we investigated: 1) the possible large-scale haplotypic structure of the X chromosome in a Caucasian population sample, given the single-nucleotide polymorphism ( SNP) maps and genotypes provided by Illumina and Affimetrix for Genetic Analysis Workshop 14, and, 2) the performances of widely used programs in reconstructing haplotypes from population genotypic data, given their known distribution in a sample of unrelated individuals. Results: All possible unrelated mother-son pairs of Caucasian ancestry ( N = 104) were selected from the 143 families of the Collaborative Study on the Genetics of Alcoholism pedigree files, and the diplotypes of the mothers were inferred from the X chromosomes of their sons. The marker set included 313 SNPs at an average density of 0.47 Mb. Linkage disequilibrium between ...
Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G , T (rs3745274), 785 A , G (rs2279343) and 983 T , C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying ...
Single nucleotide polymorphisms (SNPs) are important markers which can be used in association studies searching for susceptible genes of complex diseases. High-throughput methods are needed for SNP genotyping in a large number of samples. In this study, we applied polyacrylamide gel-based microarray combined with dual-color hybridization for association study of four BDNF polymorphisms with autism. All the SNPs in both patients and controls could be analyzed quickly and correctly. Among four SNPs, only C270T polymorphism showed significant differences in the frequency of the allele (χ2 = 7.809, p = 0.005) and genotype (χ2 = 7.800, p = 0.020). In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (χ2 = 28.19,p = 3.44e-005). We suggest that BDNF has a possible role in the pathogenesis of autism. The study also show that the polyacrylamide gel-based microarray combined with dual-color hybridization is a rapid, simple and high
The t-haplotype is a chromosomal region in Mus musculus characterized by meiotic drive such that heterozygous males transmit t-bearing chromosomes to roughly 90% of their offspring. Most naturally occurring t-haplotypes express a recessive embryonic lethality, preventing fixation of the t-haplotype. Surprisingly, the t-haplotype occurs in nature as a persistent, low-frequency polymorphism. Early modeling studies led LEWONTIN to hypothesize that this low level polymorphism results from a balance between genetic drift in small demes and interdemic migration. Here, we show that while combination of deme size and migration rate that predict natural t-haplotype frequencies exist, the range of such values is too narrow to be biologically plausible, suggesting that small deme size and interdemic migration alone do not explain the observed t-haplotype frequencies. In response, we tested other factors that might explain the observed t-polymorphism. Two led to biologically plausible models: substantially reduced
In 2006, Laoise T. Moore and the folks at Trinity College in Dublin published a paper famous for identifying the modal haplotype of Irish High King Niall of the Nine Hostages. In their work, they used seventeen Y-DNA STR markers. While time to most recent common ancestor (TMRCA) calculations have accuracy issues, having only 17 markers gives a common ancestor over 2,000 years ago. What the Trinity folks really accomplished was the identification of Nialls paternal ancestor from over 400 years earlier. The media in 2006 had a field day in their interpretation that most of Ireland is descended from Niall. Niall may be the most prolific male in Irish history. Also at 17 markers, there is a very high probability of convergence. Through normal mutations, haplotypes can change over time to appear similar or identical to other haplotypes. The lower the number of markers, the higher the chance of convergence. At that time only high level SNPs were tested to determine haplogroup. Without terminal SNPs ...
In 2006, Laoise T. Moore and the folks at Trinity College in Dublin published a paper famous for identifying the modal haplotype of Irish High King Niall of the Nine Hostages. In their work, they used seventeen Y-DNA STR markers. While time to most recent common ancestor (TMRCA) calculations have accuracy issues, having only 17 markers gives a common ancestor over 2,000 years ago. What the Trinity folks really accomplished was the identification of Nialls paternal ancestor from over 400 years earlier. The media in 2006 had a field day in their interpretation that most of Ireland is descended from Niall. Niall may be the most prolific male in Irish history. Also at 17 markers, there is a very high probability of convergence. Through normal mutations, haplotypes can change over time to appear similar or identical to other haplotypes. The lower the number of markers, the higher the chance of convergence. At that time only high level SNPs were tested to determine haplogroup. Without terminal SNPs ...
Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.Median joining networks of Y chromosome STR haplotypes with balanced s
2: 42%, VKORC1*3: 38%, and VKORC1*4: 20%), which were in complete linkage disequilibrium. These haplotypes were further subdivided by additional polymorphisms. Haplotype VKORC1*2 includes a SNP in the promoter region (c.-1639G>A, dbSNP:rs17878363 that was identified as a marker for low dose warfarin requirement.. In a cohort of 50 consecutive patients without mutations in the VKORC1 coding region who presented with phenotypes of either increased coumarin sensitivity or partial coumarin resistance we found a strong association of VKORC1 haplotypes and the observed phenotype. 93% of patients with increased coumarin sensitivity but none of patients with partial coumarin resistance were found to be homozygous for VKORC1*2. Vice versa, non VKORC1*2 haplotypes were found homozygous in 86% of patients with partial coumarin resistance but in none of patients with increased coumarin sensitivity.. The VKORC1*2 haplotype also explains inter-ethnic differences in coumarin requirement. Haplotype analysis ...
Haplotypes[edit]. An HLA haplotype is a series of HLA "genes" (loci-alleles) by chromosome, one passed from the mother and one ... Haplotypes can be obtained by typing family members in areas of the world where SSP-PCR is unable to recognize alleles and ... These haplotypes can be used to trace migrations in the human population because they are often much like a fingerprint of an ... The Super-B8 haplotype is enriched in the Western Irish, declines along gradients away from that region, and is found only in ...
Haplotypes[edit]. Modal[edit]. *R1b1b2a1a2c Modal Haplotype. Ysearch 77ADS. DYS. 393. 390. 19. 391. 385A. 385B. 426. 388. 439. ... This is my paternal haplotype. I don't know how it ended up on this Wikipedia article. All I know is that my earliest known ... If all Your 25 markers are identical with the above, it means that You have a modal haplotype of Your haplogroup. However, many ... people have the modal haplotype. YOMAL SIDOROFF-BIARMSKII (talk) 19:17, 13 August 2013 (UTC). New Research Articles[edit]. ...
Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Gibbens, Pam (April 2006). "Talk of The Town - At ... Michael Hammer (PhD), one of a team of scientists that first published on the Cohen Modal Haplotype in 1997 in the journal ... FamilyTreeDNA became widely known for its Y-chromosome STR testing for the Cohen Modal Haplotype. Soon, they were offering not ...
... with Y-STR values clustered unusually closely around a haplotype known as the Cohen Modal Haplotype (CMH). This could be ... Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Lomax, John Nova (14 April 2005). "Who's Your Daddy ... "Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood". Human Genetics. 126 (5): 707- ...
Ammar R, Paton TA, Torti D, Shlien A, Bader GD (2015). "CYP2D6 variants and haplotypes". F1000Research. 4: 17. doi:10.12688/ ... haplotyping and other applications. Nanopore sequencing took 25 years to fully materialise. It involved close collaboration ...
Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Lomax, John Nova (April 14, 2005). "Who's Your Daddy ... "The impact of additional Y-STR loci on resolving common haplotypes and closely related individuals". Forensic Science ... Electropherogram Family name Forensic genealogy Genealogical DNA test Genealogy Genetic recombination Haplogroup Haplotype ...
2001, see Modal Haplotypes of "J1" (as Eu10) Sanchez, Juan J; Hallenberg, Charlotte; Børsting, Claus; Hernandez, Alexis; Gorlin ... Moreover, the network analysis of J-P58 haplotypes shows that some of the populations with low diversity, such as Bedouins from ... Jobling, Mark A.; Tyler-Smith, Chris (2000). "New uses for new haplotypes". Trends in Genetics. 16 (8): 356-62. doi:10.1016/ ... yJdb: the Y-haplogroup J database haplotypes of haplogroup J. [1] Haplogroup J subclades at International Society of Genetic ...
"Haplotyping Takabuti". KNH Centre for Biomedical Egyptology. Retrieved 2021-01-13. Drosou, Konstantina; Collin, Thomas C.; ... Freeman, Peter J.; Loynes, Robert; Freemont, Tony (2020-10-12). "The first reported case of the rare mitochondrial haplotype ...
"What are variants, alleles and haplotypes? , Human genetic variation". Retrieved 16 November 2020. Seltsam A, Hallensleben M, ...
"The S haplotype-specific F-box protein gene, SFB, is defective in self-compatible haplotypes of Prunus avium and P. mume". ... The units are called S-haplotypes. The translation products of the two regions of the S-locus are two proteins which, by ... However, when a female determinant interacts with a male determinant of a different haplotype, no SI is created, and ... There are possibly up to 100 polymorphs of the S-haplotype in Brassica, and within these there is a dominance hierarchy. The ...
Bowling, AT; Scott, AM; Flint, J; Clegg, JB (1988). "Novel alpha haemoglobin haplotypes in horses". Animal Genetics. 19 (2): 87 ...
2001) as M4 and M2 ... The Andamanese M2 contains two haplotypes ... developed in situ, after an early colonization ... ... The Andaman M4 haplotype ... is still present among populations in India, suggesting it was subject to the late Pleistocene ... Alternatively, it is possible that the haplotypes have become extinct in India or are present at a low frequency and have not ...
There are many haplotypes of DQ6. DQB1*0601 is generally linked to DQA1*0103 as 6.1 haplotype. This haplotype is more common in ... This haplotype is considered to be the longest multigene haplotype known within the human genome as it covers over 4.7 million ... The DR15-DQ6.2 haplotype is the most common DR-DQ haplotype in Europe, and approximately 30% of Americans carry at least DQ6.2 ... This haplotype is found at its highest Eurasian frequencies in Japan. DQB1*0609 is found in Africa and proximal regions of ...
"Global Report Investigating Novel Coronavirus Haplotypes". cov-lineages.org. Pango team. "Living Evidence - SARS-CoV-2 variants ...
This measure is suitable only for haplotype blocks with limited haplotype diversity and it is not clear how to use it for large ... When a disease is found to be associated with a haplotype, some SNPs in that haplotype will have synthetic association with the ... Therefore, tag SNPs are representative of all SNPs within a haplotype. The selection of tag SNPs is dependent on the haplotypes ... By mapping the entire genome to haplotypes, tag SNPs can be identified to represent the haplotype blocks examined by genetic ...
Lately,[when?] two novel susceptibility haplotypes i.e. P2-S2-X1 and P1-S2-X1 have been discovered in ApoAI-CIII-AIV gene ...
2013) studied mitochondrial haplotypes of Semisulcospira libertina from Korea and from Japan. Mixed haplotypes in Korea suggest ... mitochondrial haplotypes have Japanese sister lineages". Journal of Molluscan Studies. 79 (1): 86-89. doi:10.1093/mollus/eys036 ...
Rapone C, Geraci A, Capelli C, De Meo A, D'Errico G, Barni F, Berti A, Lago G (2007). "Y chromosome haplotypes in Central-South ... Melo MM, Carvalho M, Lopes V, Anjos MJ, Serra A, Vieira DN, Sequeiros J, Corte-Real F (2011). "Y-STR haplotypes in three ethnic ... 2012). "Haplotype diversity of 17 Y-str loci in an admixed population from the Brazilian Amazon". Genetics and Molecular ... Sánchez C, Barrot C, Xifró A, Ortega M, de Aranda IG, Huguet E, Corbella J, Gené M (2007). "Haplotype frequencies of 16 Y- ...
Haplotypes including the SNPs g.-786T>C and Glu298Asp and the VNTR in intron 4 affected the susceptibility to hypertension, ... Souza-Costa DC, Belo VA, Silva PS, Sertorio JT, Metzger IF, Lanna CM, Machado MA, Tanus-Santos JE (Mar 2011). "eNOS haplotype ... Sandrim VC, de Syllos RW, Lisboa HR, Tres GS, Tanus-Santos JE (Nov 2006). "Endothelial nitric oxide synthase haplotypes affect ... In addition to analysis of genetic polymorphisms individually, haplotypes including the SNPs g.-786T>C and Glu298Asp and the ...
Diversity of 17-locus Y-STR haplotypes in Upper (Southern) Egyptians Ghada A. Omran, Guy N. Rutty, Mark A. Jobling, 2007, ... Lucotte, G.; Mercier, G. (2003). "Brief communication: Y-chromosome haplotypes in Egypt". American Journal of Physical ... "A Back Migration from Asia to Sub-Saharan Africa is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes". ...
Haplotype V is common in Berbers and has a low frequency outside North Africa. Haplotypes V, XI, and IV are all predominantly ... Lucotte G, Mercier G (May 2003). "Brief communication: Y-chromosome haplotypes in Egypt". American Journal of Physical ... Underhill (2002), Bellwood and Renfrew, ed., Inference of Neolithic Population Histories using Y-chromosome Haplotypes, ... characterized by a high M1 haplotype frequency and a comparatively low L1 and L2 macrohaplogroup frequency of 20.6%. Another ...
"Musical aptitude is associated with AVPR1A-haplotypes". PLOS ONE. 4 (5): e5534. doi:10.1371/journal.pone.0005534. PMC 2678260. ...
The HLA-A antigens can mediate apoptosis in autoimmune disease and HLA A*0201 in with the HLA-DQ8 haplotypes has been ... Understanding DQ Haplotypes and DQ isoforms on the right). HLA-DQ2 primarily presents gliadins with the HLA-DQ isoform DQ2.5 ( ... Understanding DQ haplotypes and DQ isoforms). HLA-DQ8 is generally not as involved in the most severe complications, and it ... see Understanding DQ haplotypes and DQ isoforms on the right) However, numbers of different proteins from the grass tribe ...
HLA-DQ haplotypes in 15 different populations. In: The Major Histocompatibility Complex: Evolution, Structure and Function. M ... "Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern ...
There were no shared haplotypes between species. A. akindynos (Barrier Reef anemonefish) A. clarkii (Clark's anemonefish) A. ...
There were no shared haplotypes between species. A. mccullochi (Whitesnout anemonefish) A. melanopus (Red & Black anemonefish) ...
Six haplotypes were identified in horses Gansu. Cluster E is only present in the Hequ, which probably has the same origin as ...
... "the dingo founder haplotype" A29 (8%). Also present were haplotypes A120 and A145. All 4 haplotypes fall within the a2 mDNA sub ... This short haplotype was named Arc2 and corresponds to mDNA haplotypes A75 and A120, and it could be found in 70% of samples ... The study of mtDNA show they carried two haplotypes: Arc1 and Arc2. In 2011, the mDNA of dogs from the Malay Peninsula found ... All of these dogs carry haplotypes that fall under the mDNA a2 sub-haplogroup and are therefore descendants of a dog/Chinese ...
"mtDNA Haplogroup K: K1a1b1a Subclade Haplotypes" (JPG). mtDNA Haplogroup K Project. Websites PhyloTree.Org [1] The Genographic ... of all Ashkenazi mtDNA haplotypes. Approximately 19% of Ashkenazi Jews with ancestry from Poland are in mtDNA haplogroup ...
and the estimated frequency of haplotype xy is e. [. h. f. x. y. ]. =. D. N. ⋅. B. N. .. {\displaystyle e[hf_{xy}]={\sqrt {{\ ... of the haplotypes in the offspring have not recombined, and are thus copies of a random haplotype in their parents. A fraction ... estimated frequency of haplotype i. j. =. g. f. i. g. f. j. =. 0.0215.. {\displaystyle hf_{ij}={\text{estimated frequency of ... the frequency of the haplotype A. 1. B. 1. {\displaystyle A_{1}B_{1}}. , becomes ...
... The MHC Haplotype Project was conducted between 2000 and 2006 at the Sanger ... MHC Haplotype Project Data. The data from the MHC Haplotype Project are available in .txt file format file for viewing in the ... Haplotype HLA-A HLA-B HLA-C HLA-DRB1 HLA-DQB1 HLA-DPB1 Links:. Vega UCSC. GRC ... The data are colour-coded by haplotype and will initially be displayed showing 1Mb in the centre of the MHC. You are then free ...
... haplotype estimation and haplotype tagging (Homepage). HelixTree - Haplotype analysis software - Haplotype Trend Regression ( ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ... haplotype frequency of each haplotype in the sample and N {\displaystyle N} is the sample size. Haplotype diversity is given ...
... that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). In 2001, ... and which contain only a small number of distinct haplotypes. According to the haplotype-block model, such blocks should show ... In genetics, a haplotype block is a region of an organisms genome in which there is little evidence of a history of genetic ... The boundaries of haplotype blocks cannot be directly observed; they must instead be inferred indirectly through the use of ...
By comparing haplotypes of a mother and father with those of a fetus, scientists can study how new genetic changes arise. See ... Haplotype definition, a combination of closely linked DNA sequences on one chromosome that are often inherited together: ... a combination of closely linked DNA sequences on one chromosome that are often inherited together: By comparing haplotypes of a ...
In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit ... The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. The xor- ... The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. The xor- ... In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit ...
Reference Assembly Alternate Haplotype Sequence Alignments (. All Mapping and Sequencing tracks). Display mode: hide. dense. ... Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete ... Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. ... This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome ...
Haplotype GGCC conferred increased risk in the African American and Nigerian populations. Conversely, haplotype AGGG exhibited ... COX-2 gene promoter haplotypes and prostate cancer risk.. Panguluri RC1, Long LO, Chen W, Wang S, Coulibaly A, Ukoli F, Jackson ... Haplotype analyses revealed modest effects on susceptibility to prostate cancer across populations. ...
is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ... HelixTree - Haplotype analysis software - Haplotype Trend Regression (HTR), haplotypic association tests, and haplotype ...
is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ... BiologyPages/H/Haplotypes.html Kimballs Biology Pages (Creative Commons Attribution 3.0) *^ "haplotype / haplotypes , Learn ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ...
The two full haplotypes of the six SNPs comprising fragment 1 are T-G-T-C-T-T and G-C-C-G-G-C for SNPs 5,6,7,8,9,10. Haplotypes ... Six SNPs in fragment 1 were haplotyped in two groups. Two predominant haplotypes were found for the first (SNPs 5,7,9,10) and ... Direct determination of haplotypes from single DNA molecules.. Xiao M1, Wan E, Chu C, Hsueh WC, Cao Y, Kwok PY. ... Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of ...
A haplotype map of the human genome.. International HapMap Consortium.. Abstract. Inherited genetic variation has a critical ... Genealogical relationships among haplotypes and r2 values in a region without obligate recombination events ... Recombination rates in cM Mb−1 (blue). Non-redundant haplotypes with frequency of at least 5% in the combined sample (bars) and ... The left part of the plot shows the seven different haplotypes observed over this region (alleles are indicated only at SNPs), ...
Number of haplotypes per locus for model HAP_IBD, and average total number of haplotypes for all four models, averaged across ... The number of haplotype effects that needs to be estimated can be reduced by including more markers per haplotype and perhaps ... The estimated haplotype variance at each locus was calculated as the heterozygosity of the haplotypes at that locus multiplied ... In the SNP1 model, a haplotype was defined as a marker allele on a single locus, yielding two random haplotype effects per ...
The present invention includes a method for rapid haplotyping a DNA or RNA segment. Two or more target sites on a segment of ... presence or absence of each luminescent hybridization probe on each DNA or RNA segment is detected to determine the haplotype ... a) Targets of haplotyping are all sorts of DNA and RNA variations that are necessary to define a haplotype. They include any ... The haplotype deduced from a genotype is typically done in bulk as follows (inferred haplotypes). The region of interest is PCR ...
Conditional Probability Methods for Haplotyping in Pedigrees Message Subject (Your Name) has forwarded a page to you from ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ...
... HaploRec [1,2] is a statistical haplotype ... A Markov Chain Approach to Reconstruction of Long Haplotypes. Proceedings of the 9th Pacific Symposium on Biocomputing (PSB04 ... HaploRec: Efficient and accurate large-scale reconstruction of haplotypes. BMC Bioinformatics 7:542, 2006. ... 2.0 (June 2005) This version introduced an EM-based algorithm and a segmentation-based haplotype probability model, and ...
We prove that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is the ... We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree ... Efficient inference of haplotypes from genotypes on a pedigree J Bioinform Comput Biol. 2003 Apr;1(1):41-69. doi: 10.1142/ ... We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree ...
... then a few markers will be sufficient to identify common haplotypes. The approach is identical to the exploitation of haplotype ... Haplotype structure of 1,450 diallelic variants with SDP frequency ,1% between eight inbred strains across a 4.8-Mb region of ... We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple ... Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. B. Yalcin, J. Fullerton, S. Miller ...
In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs)... ... The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. ... The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype ... Gabriel, S.B., et al.: The structure of haplotype blocks in the human genome. Science 296(5576), 2225-2229 (2002)CrossRefGoogle ...
... has been used to determine absolute extended haplotypes in diploid genomes. We describe statistical analyses for comparing ... there has been increased interest in evaluating extended haplotypes in p53 as risk factors for cancer. An allele-specific ... The method can also be applied to any polymorphic system, whether multiple alleles at a single locus or multiple haplotypes ... Recently, there has been increased interest in evaluating extended haplotypes in p53 as risk factors for cancer. An allele- ...
Haplotype: A specific combination of SNPs all occuring together on the same chromosome (i.e. all occuring on the chromosome ... Haplotypes are important for example because many of the SNPs found by genome-wide association studies arent the true cause ... Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct ... Next Gen Sequencing can thus provide not only perfectly phased genome, but also a haplotype map which can be used to impute ...
... T. Graves1, W. Warren1, B. Fulton1, K. Meltz Steinberg1, R. Agarwala2, V. ... In order to discriminate between repeat copy and allelic copies, the sequence from a single haplotype across these regions is ...
... Nature. 2005 Oct 27;437(7063):1299-320. doi: 10.1038/nature04226. ... a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with ...
... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity ... A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) ... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. Haplotype ... Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of ...
In African Americans, the DRB1*07:01 - DQA1*03:01 -DQB1*02:01g haplotype is ass... more ... These high-risk haplotypes are found primarily in people of European descent; other ethnic groups are less well studied. ... These high-risk haplotypes are found primarily in people of European descent; other ethnic groups are less well studied. In ... HLA DR-DQ haplotypes and genotypes and type 1 diabetes risk: analysis of the type 1 diabetes genetics consortium families. ...
... Hana Saoud,1 Oumaima Inoubli,1 Sihem Ben Fredj,2 Mohsen ... Haplotype distribution profile suggests that the observed protection status may be driven more strongly by the MCP-1 -2518G ... Table 3: Haplotype analysis of MCP-1 polymorphisms in patients with schizophrenia and control subjects. ... J. C. Barrett, B. Fry, J. Maller, and M. J. Daly, "Haploview: analysis and visualization of LD and haplotype maps," ...
Transmission of DQ haplotypes to patients with type 1 diabetes.. E Kawasaki, J Noble, H Erlich, C L Mulgrew, P R Fain, G S ... Transmission of DQ haplotypes to patients with type 1 diabetes.. E Kawasaki, J Noble, H Erlich, C L Mulgrew, P R Fain, G S ... Transmission of DQ haplotypes to patients with type 1 diabetes. Message Subject (Your Name) has forwarded a page to you from ...
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. Title. A Note on Efficient Computation of Haplotypes via ... A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. ... For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem ... The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is ...
A First-Generation Haplotype Map of Maize. By Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie ... A First-Generation Haplotype Map of Maize. By Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie ... S6) (22). However, we also found evidence of longer haplotypes extending for thousands and millions of bases. Association ... among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed ...
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  • A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
  • The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. (wikipedia.org)
  • An organism's genotype may not define its haplotype uniquely. (wikipedia.org)
  • The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. (psu.edu)
  • 2002). Given a meiotic model for the combination of a pair of haplotypes into a genotype during mating, and given a set of observed genotypes in a sample from a human population, it is of great interest to identify the underlying haplotypes (Stephens et al. (psu.edu)
  • These data also indicate that the risk associated with specific HLA haplotypes can be influenced by the genotype context and that the trans- complementing heterodimer encoded by DQA1*0501 and DQB1*0302 confers very high risk. (diabetesjournals.org)
  • In this study, we investigated whether haplotype (genotype + phase) information would strengthen the genotype-phenotype relationship for PON1. (aacrjournals.org)
  • Collectively, the genetic (genotype or haplotype) contribution to PON1 enzymatic activity (measured as phenylacetate hydrolysis) was greater in neonates compared with mothers. (aacrjournals.org)
  • Hence genotype (blended) SNP data will be collected, and the desired haplotype (partitioned) data must then be (partially) inferred. (biomedsearch.com)
  • Modern genotyping technologies do not measure haplotypes directly, but the combined sum (or genotype) of alleles at each site. (plos.org)
  • These haplotypes can be used to guide genotype imputation and haplotype estimation. (ashg.org)
  • 5%. I will describe our evaluation of strategies for merging haplotypes and variant lists across studies and advances in methods for genotype likelihood-based haplotype estimation that can be applied to 10,000s of samples. (ashg.org)
  • The majority of haplotypes will also be deposited in the European Genotype Archive. (ashg.org)
  • The method makes use of available offspring genotype information to apportion ambiguous haplotypes for the subjects. (umich.edu)
  • For subjects without offspring genotype information, haplotypes are apportioned as in the standard EM algorithm for case-control data. (umich.edu)
  • These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. (g3journal.org)
  • There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). (wikipedia.org)
  • proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. (wikipedia.org)
  • Six SNPs in fragment 1 were haplotyped in two groups. (nih.gov)
  • The two full haplotypes of the six SNPs comprising fragment 1 are T-G-T-C-T-T and G-C-C-G-G-C for SNPs 5,6,7,8,9,10. (nih.gov)
  • These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. (nih.gov)
  • If single-nucleotide polymorphisms (SNPs) are randomly distributed across the genomes of inbred strains, mapping QTL by SDP association with phenotype will require a very dense set of markers, but if the distribution is segmented, then a few markers will be sufficient to identify common haplotypes. (pnas.org)
  • In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. (springer.com)
  • Most genotyping experts won't admit it in public, but there is a friendly feud simmering between proponents of SNPs and proponents of haplotypes. (genomeweb.com)
  • Haplotypes are just ordered arrays of SNPs, and this is just more information and better information. (genomeweb.com)
  • Do you think haplotypes eventually will usurp SNPs as drug-discovery clues? (genomeweb.com)
  • When you find them - we found there are there are 3,000 of them - you take these genes, sequence the genomes of 15 individuals to find all of the SNPs in those genes, and define haplotypes. (genomeweb.com)
  • The data from this effort will contribute to the development of a map, called the HapMap, of the haplotype patterns in the human genome and of a set of SNPs that are informative about these patterns and the associations among the SNPs. (nih.gov)
  • This means that although a region may contain many SNPs, it can be characterized by a few SNPs that uniquely identify, or "tag", each of the haplotypes in the region. (nih.gov)
  • The goal of the International HapMap Project is to produce a resource that describes the haplotypes in the human genome and the SNPs that tag them. (nih.gov)
  • 5%), while the remaining three SNPs were found on multiple haplotypes, suggesting a complex history of recombination. (nature.com)
  • Significant associations to a single disease outcome were found for two SNPs and one haplotype in AA. (nature.com)
  • In addition, given the important role played by SDF-1 and CXCR4 in HIV-1/AIDS, we looked for the influence of genetic variation in these SNPs and haplotypes on disease in over 3000 subjects enrolled in five USA-based natural history HIV-1/AIDS cohorts. (nature.com)
  • I am a little bit confused about the relationship between LD, haplotypes and SNPs. (biology-online.org)
  • Generally, SNPs together with other genetic variants (like disease alleles) can be inherited in/as haplotypes, which means they are in LD. (biology-online.org)
  • The HapMap project identifies common haplotype blocks and the specific SNPs that uniquely identify them (tag SNPs). (biology-online.org)
  • So the idea of the HapMap Project is to identify haplotypes and tag SNPs. (biology-online.org)
  • Using tag SNPs, one can find chromosome regions that have different haplotype distributions in two groups of people (one with disease, one control). (biology-online.org)
  • Single SNPs and haplotypes were analysed for associations with disease risk, age parameters, mini-mental state examination scores and cerebrospinal fluid biomarkers for AD using logistic or linear regression. (lu.se)
  • The strongest association was found for a haplotype consisting of the 8 OPN SNPs rs2728127-rs2853744-rs11730582-rs11439060-rs28357094-rs112661-rs1126772-rs9138 (omnibus p-value = 2.07×10⁻⁸). (uni-muenchen.de)
  • This book constitutes the post-proceedings of the DIMACS/RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference held in Piscataway, NJ, USA, in November 2002. (springer.com)
  • The haplotype was further studied using a fusion gene containing multiple ERCC1 SNPs. (bmj.com)
  • Haplotype analyses revealed modest effects on susceptibility to prostate cancer across populations. (nih.gov)
  • Haplotype GGCC conferred increased risk in the African American and Nigerian populations. (nih.gov)
  • The SNP1 model considers only two haplotypes at a locus and therefore may be suited for applications in, for instance, double-haploid populations with only two segregating genotypes at each locus ( X u 2003 ). (genetics.org)
  • 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. (snpedia.com)
  • This can lead to over-estimation of the risk by including odds ratio of different SNP's along same haplotype, or flip-flop phenomenon where the effect of the SNP is opposite in different populations due to population-dependent variation in the haplotype. (snpedia.com)
  • 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. (umd.edu)
  • While an individual human could exhibit any of 2k different patterns of markers on a single chromosome, in real populations only a small subset of such patterns-haplotypes-are actually observed (Gabriel et al. (psu.edu)
  • The identification of such haplotypes would have significant implications for the understanding of the migration patterns of ancestral populations of humans. (psu.edu)
  • It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. (psu.edu)
  • Rare haplotypes in mtDNA: applications in the analysis of biosocial aspects of past human populations. (blogspot.com)
  • A combination of haplotype H and 73G in HVS-II, rare in extant populations (0.5-3%), has been found at a frequency of 20% in the ancient population of Aldaieta. (blogspot.com)
  • The major genetic determinants of type 1 diabetes are alleles at the HLA-DRB1 and DQB1 loci, with both susceptible and protective DR-DQ haplotypes present in all human populations. (diabetesjournals.org)
  • Most common haplotypes occur in all human populations, although their frequencies may vary among populations. (nih.gov)
  • The Jewish populations were characterized by a diverse set of 13 haplotypes that were also present in non-Jewish populations from Africa, Asia, and Europe. (pnas.org)
  • Recent developments in statistical methods have permitted the reconstruction of haplotypes and the estimation of haplotype frequencies in unrelated populations based on SNP data. (aacrjournals.org)
  • A practical algorithm for optimal inference of haplotypes from diploid populations. (biomedsearch.com)
  • Recently, we and others made the unexpected finding that V617F JAK2 is not acquired randomly but instead arises preferentially on a specific constitutional JAK2 haplotype, at least in white populations. (bloodjournal.org)
  • A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. (usda.gov)
  • All G6PD*A- alleles share the RFLP-microsatellite haplotype - - /195, the same haplotype described in nearly all the *A- alleles from sub-Saharan, Mexican Mestizo, and Portuguese populations, consistent with a single and recent origin of the G202A mutation on this *A haplotype. (bioone.org)
  • Genetic analysis of human populations worldwide showed that haplotypes with −21M HLA-B rarely encoded the KIR ligands Bw4+HLA-B and C2+HLA-C. Thus, there are two fundamental forms of HLA haplotype: one preferentially supplying CD94/NKG2A ligands and the other preferentially supplying KIR ligands. (ovid.com)
  • Among these we found an individual (young adult male) with a mitochondrial DNA haplotype that had previously only been identified in modern Romani populations. (royalsocietypublishing.org)
  • D). An HMM for this purpose formally requires the calculation of two-locus diplotype probabilities, although if the populations are formed with a large number of mating pairs, the two haplotypes within an individual are independent, and so it is sufficient to calculate two-locus haplotype probabilities. (g3journal.org)
  • The table below lists the eight cell lines used in the project along with their HLA haplotypes and alleles. (ucl.ac.uk)
  • It is thought that identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (wikipedia.org)
  • The models estimated the effect of (1) each single-marker allele [single-nucleotide polymorphism (SNP)1], (2) haplotypes constructed from two adjacent marker alleles (SNP2), and (3) haplotypes constructed from 2 or 10 markers, including the covariance between haplotypes by combining linkage disequilibrium and linkage analysis (HAP_IBD2 and HAP_IBD10). (genetics.org)
  • The underlying assumption of genomic selection is that haplotypes at some loci are in linkage disequilibrium (LD) with QTL alleles that affect the traits that are subject to selection. (genetics.org)
  • Different ways of deriving haplotypes of combinations of marker alleles, and the relationship between haplotypes at a locus, have been described. (genetics.org)
  • One method (SNP1) is to consider each different marker allele at a single locus to be a different haplotype, considering no relationships between different haplotypes, and thus breeding values are estimated directly for the marker alleles ( X u 2003 ). (genetics.org)
  • A third method is to construct haplotypes (HAP_IBD) using two or more surrounding marker alleles and derive identical-by-descent (IBD) probabilities between the different haplotypes at the same locus ( M euwissen and G oddard 2001 ). (genetics.org)
  • A disadvantage of the SNP1 model is that no new haplotypes arise as a result of recombination, while such an event actually might change the linkage between the marker and the QTL alleles. (genetics.org)
  • The method can also be applied to any polymorphic system, whether multiple alleles at a single locus or multiple haplotypes over several loci. (cdc.gov)
  • Subsequently, it was shown that ~50% of Cohanim carry a characteristic suite of alleles at six Y-linked STRs, which defined the Cohen Modal Haplotype (CMH). (springer.com)
  • A specific set of such associated SNP alleles is called a haplotype. (nih.gov)
  • These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness. (aacrjournals.org)
  • Every individual carries two copies of each chromosome (haplotypes), one from each of their parents, that consist of a long sequence of alleles. (plos.org)
  • Genes are inherited together as haplotypes because of LD, i.e. the non random association of alleles at different loci (they form a block of DNA that is inherited together). (biology-online.org)
  • Licínio Manco , Laura R. Botigué , M. Letícia Ribeiro , and Augusto Abade "G6PD Deficient Alleles and Haplotype Analysis of Human G6PD Locus in São Tomé e Príncipe (West Africa)," Human Biology 79(6), 679-686, (1 December 2007). (bioone.org)
  • T is in linkage disequilibrium (LD) with causative alleles, and that these haplotypes are more frequent in Caucasians with melanoma than in healthy Caucasians or African Americans. (bmj.com)
  • Equation (1) is derived by noting that an AA haplotype drawn from generation F s +1 is either an intact AA haplotype at generation F s , transmitted without recombination, or it is a recombinant haplotype bringing two independent A alleles together. (g3journal.org)
  • In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes. (wikipedia.org)
  • By comparing haplotypes of a mother and father with those of a fetus, scientists can study how new genetic changes arise. (dictionary.com)
  • 3 . The method of claim 1 , further including the step of sequentially and repeatedly haplotyping pairs of neighboring genetic makers on DNA segments forming a chromosome. (google.com)
  • Haplotypes have also important applications in genetic genealogy and determining identity by descent . (snpedia.com)
  • To be useful in genetic analysis, the haplotype should be shorter than a typical block. (els.net)
  • Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. (umd.edu)
  • The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7]. (psu.edu)
  • And I can find 10 or so publications that will find that the haplotype is always better than the single genetic variant. (genomeweb.com)
  • These include haplotypes , genetic sequences that we inherit from only one parent , which allows us to solve our problems with tracking genetic traits and ancestry backward through time and geography. (visionlearning.com)
  • Thus, haplotype information may help clarify the genetic influence on PON1 activity. (aacrjournals.org)
  • Haplotypes of IL-4 receptor and CD14 genetic polymorphisms are markers of susceptibility for diisocyanate asthma. (cdc.gov)
  • Since surnames are highly geographically localized, local geographical patterning of Y haplotypes is a potential confounding factor: genetic structure within names could arise as a result of geographical structure within Britain, rather than due to descent. (bl.uk)
  • Haplotype estimation is a key first step of many disease and population genetic studies. (plos.org)
  • 31,500 sequenced whole genomes, aggregated over 20 studies of predominantly European ancestry, to create a very large reference panel of human haplotypes where ~50M genetic variants are observed 5 or more times. (ashg.org)
  • This package has a function that collapses the haplotypes (unique DNA sequences) in a DNA alignment, something which is extremely useful in various analyses and in the calculation of genetic diversity. (r-bloggers.com)
  • Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate. (usda.gov)
  • Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. (wikipedia.org)
  • The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. (umd.edu)
  • The aim of this study is to estimate the risk conferred by specific DR-DQ haplotypes and genotypes. (diabetesjournals.org)
  • Statistical methods are needed to infer (or phase) the haplotypes from the observed genotypes. (plos.org)
  • The estimation of haplotypes from SNP genotypes, commonly referred to as 'phasing', is a well studied problem in the literature. (plos.org)
  • But often we will have offspring for at least some of the spouse pairs, and offspring genotypes provide additional information about the haplotypes of the parents. (umich.edu)
  • For case-control data with some subjects forming spouse pairs and offspring genotypes available for some spouse pairs or individuals, we propose a unified, likelihood-based method of haplotype inference. (umich.edu)
  • Six or five haplotypes were present at frequencies greater than 5% in AA or EA, respectively. (nature.com)
  • B 39:1-38) for case-control data can be used to estimate haplotype frequencies. (umich.edu)
  • Allele frequencies, gene diversities and haplotype frequencies were analyzed. (scirp.org)
  • Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. (ucsc.edu)
  • Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. (ucsc.edu)
  • Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no. (umd.edu)
  • For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979). (umd.edu)
  • These GRC haplotype contigs, called 'alternate loci', are constructed so that they begin with additional anchor sequence derived from the reference. (ucl.ac.uk)
  • For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (wikipedia.org)
  • For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you don't know which haplotype you have, e.g. (wikipedia.org)
  • We describe statistical analyses for comparing cases and controls, or comparing different ethnic groups with respect to haplotypes composed of several biallelic loci, especially in the presence of other covariates. (cdc.gov)
  • However, allelic variation at these loci cannot account fully for the pattern of HLA haplotype sharing among affected sibpairs ( 8 ). (diabetesjournals.org)
  • Expression quantitative trait loci (eQTLs) were investigated for variants tagging six SLE-risk or -protective haplotypes: DRB1*03:01 (rs2187668), DRB1*15:01 (rs3135391), DPB1 (rs3117213, rs2071351, rs2071349), and MSH5 (rs409558). (bl.uk)
  • 2001) Haplotype tagging for the identification of common disease genes. (els.net)
  • 2001) Haplotype variation and linkage disequilibrium in 313 human genes. (els.net)
  • However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. (wur.nl)
  • The comparison of closely related DR-DQ haplotype pairs with different type 1 diabetes risks allowed identification of specific amino acid positions critical in determining disease susceptibility. (diabetesjournals.org)
  • Instead, multiple polymorphisms defined a set of four common haplotypes (of which two were associated with disease susceptibility and two seemed to be protective) and multiple rare haplotypes (associated with increased susceptibility in aggregate). (nature.com)
  • Although the functional significance of these findings is uncertain, these haplotypes could be susceptibility markers for DA and may be useful aids in the diagnosis of DA. (cdc.gov)
  • The role of osteopontin (OPN/SPP1) haplotypes in the susceptibility to Crohn's disease. (uni-muenchen.de)
  • However, several OPN haplotypes showed significant associations with CD susceptibility. (uni-muenchen.de)
  • Our study identified OPN haplotypes as modifiers of CD susceptibility, while the combined effects of certain OPN variants may modulate IL-22 secretion. (uni-muenchen.de)
  • Therefore, given a set of possible haplotype resolutions, these methods choose those that use fewer different haplotypes overall. (wikipedia.org)
  • The benefit from the HAP_IBD approach is that the common background of haplotypes, and thus the probability that different haplotypes are associated with the same QTL allele, is modeled more accurately. (genetics.org)
  • Patients with different haplotypes are assumed to be unrelated and thus to carry independent mutations. (lu.se)
  • Daly MJ, Rioux JD, Schaffner SF, Hudson TJ and Lander ES (2001) High‐resolution haplotype structure in the human genome. (els.net)
  • The association analysis was performed by comparing the frequency of DR-DQ haplotypes among the chromosomes transmitted to an affected child with the frequency of chromosomes not transmitted to any affected child. (diabetesjournals.org)
  • There were seven haplotypes with a frequency of 5% or higher in at least one ethnic group of the study population. (aacrjournals.org)
  • OBJECTIVE: To analyze the frequency of the haplotypes of β-globin gene cluster in randomly selected patients with sickle cell disease (SCD), attended in the Children's Hospital of Panama. (biomedsearch.com)
  • The frequency of the IC haplotype (shared between I75V and C159T) was 0.44 in DA + workers vs. 023 among DA- subjects (p=0.04). (cdc.gov)
  • The QC haplotype frequency (Q576R, C159T) of 0.667 in the DA + group was more frequent (0.425) than in the DA- groups (p=0.03). (cdc.gov)
  • Furthermore, the frequency of IQC haplotype (l75V, Q576R, C159T) was 0.44 in DA + workers vs. 0.217 in the DA - group (p=0.04). (cdc.gov)
  • Our method enables efficient haplotype frequency estimation using an EM algorithm and supports probabilistic haplotype reconstruction with the probability calculated based on the whole sample. (umich.edu)
  • haplotype_pattern_id Frequency OBJECT METHODS See Below for more detailed summaries. (ubuntu.com)
  • Generate reliable Y-STR haplotype frequency estimates for Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and kinship casework. (yhrd.org)
  • Let p s denote the frequency of the AA haplotype at generation F s . (g3journal.org)
  • 2) The frequency of recombinant haplotypes at generation F s is 1 − 2 p s . (g3journal.org)
  • 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. (wikipedia.org)
  • Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. (genetics.org)
  • Browning, S.R., Browning, B.L.: Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. (springer.com)
  • The goal of the Haplotype Reference Consortium is to combine haplotype information from ongoing whole genome sequencing studies to create a large imputation resource. (ashg.org)
  • According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events. (wikipedia.org)
  • We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree data. (nih.gov)
  • Verhoeven KJ and Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. (els.net)
  • We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed 10- to 30-fold variation in recombination rates. (sciencemag.org)
  • This recurrence relation is derived in a similar way to that for the autosome, noting that the male haplotype was drawn from his mother, with a chance for recombination, and a random female haplotype is equally likely to have been drawn from her father, without recombination, or from her mother, with the potential for recombination. (g3journal.org)
  • This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. (ucsc.edu)
  • Despite these findings, SP remains a explored emerging lineages of dhps mutant haplotypes in Malawi,theDemocraticRepublicoftheCongo,andTanza- major tool for malaria control when administered as a partner niabyusinganalysesofgeneticmicrosatellitesflankingthe drug with artemisinins and as intermittent preventive therapy dhps locus. (cdc.gov)
  • G6PD locus haplotype diversity was also investigated using six intragenic RFLPs ( Fok I, Pvu II, Bsp HI, Pst I, Bcl I, Nla III) and a (CTT) n microsatellite 18.61 kb within the G6PD locus. (bioone.org)
  • Using mitochondrial DNA isolated from their cheek cells or hair, students perform PCR and a restriction enzyme digest to determine their haplotypes with respect to a locus in the mitochondrial genome. (carolina.com)
  • The aHt haplotype has found a higher discriminatory potential than minHt haplotype with a better Pd combined value (0.9999936 vs 0.9999836) and has higher average gene diversity per locus (0.7834 vs 0.7518) in Turkish population. (scirp.org)
  • In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. (g3journal.org)
  • Darvasi and Soller (1995) derived the two-locus haplotype probabilities for the autosome in AIL. (g3journal.org)
  • In this article, I derive the two-locus haplotype probabilities for the autosome and X-chromosome in AIL, HS, and the DO. (g3journal.org)
  • Let us first revisit the two-locus autosomal haplotype probabilities in AIL, as they serve as a simple example of the technique used in these calculations (see also Bulmer 1980 , Ch. 3). (g3journal.org)
  • https://learn.genetics.utah.edu/content/basics/haplotype. (utah.edu)
  • The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics. (plos.org)
  • The advantage of the SNP1 approach is that determining the linkage phase of the haplotypes is not required and the markers do not need to be mapped. (genetics.org)
  • The approach is identical to the exploitation of haplotype blocks (regions of complete or almost complete linkage disequilibrium) in the human genome for association mapping ( 9 ) but requires a different analysis to take advantage of the small number of founder animals from which laboratory strains are descended. (pnas.org)
  • A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. (els.net)
  • Currently, the most accurate methods use hidden Markov models (HMMs) to model local haplotype sharing between individuals [1] , [2] , and take advantage of linkage disequilibrium (LD). (plos.org)
  • An allele-specific polymerase chain reaction (PCR) method, confirmed by restriction analysis, has been used to determine absolute extended haplotypes in diploid genomes. (cdc.gov)
  • 7 - 9 This haplotype, which we refer to as 46/1 7 but others have called GGCC, 8 is found in approximately 50% of normal persons and thus is a common, very low penetrance predisposition allele of the type that is typically detected by genome-wide association studies. (bloodjournal.org)
  • A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. (frontiersin.org)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple block-like structure. (pnas.org)
  • A Haplotype Reference Panel of over 31,000 individuals and Next Generation Imputation Methods. (ashg.org)
  • Existing methods may either ignore the offspring information, or reconstruct haplotypes for the subjects using offspring information and discard data from those whose haplotypes cannot be reconstructed with high confidence. (umich.edu)
  • All relevant current issues in computational methods for SNP and haplotype analysis and their applications to disease associations are addressed. (springer.com)
  • Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. (els.net)
  • Morton, Newton E(Dec 2007) Blocks of Limited Haplotype Diversity. (els.net)
  • Correlations between surname rank and degree of diversity exist: the more common the surname, the greater the diversity of Y-chromosomal haplotypes associated with the name. (bl.uk)
  • M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. (apsnet.org)
  • A team from the Plant Pathology department at the US University has developed the extensive wheat diversity map - a haplotype map - of 62 varieties from across the world. (bakeryandsnacks.com)
  • We suggest that an alternative haplotype designated as aHt maybe alternative to minHt in respect of its Y-STR content with the highest gene diversity value. (scirp.org)
  • For single nucleotide polymorphisms 'variation' consists of two letters, firstly, the base in the reference sequence, and secondly, the base in the other haplotype. (ucl.ac.uk)
  • We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases. (nih.gov)
  • In order to determine the minimum number of independent repeats of each mutation we have used PCR to examine the five factor IX polymorphisms forming the most informative combinations and we have characterised thc haplotype of each patient. (lu.se)
  • HaploRec [1,2] is a statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. (helsinki.fi)
  • 2.0 (June 2005) This version introduced an EM-based algorithm and a segmentation-based haplotype probability model, and featured several computational improvements, allowing the use of larger data sets. (helsinki.fi)
  • A polynomial-time exact algorithm for haplotype reconstruction without recombinants is also presented. (nih.gov)
  • Bansal, V., Bafna, V.: HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. (springer.com)
  • 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. (diva-portal.org)
  • 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. (diva-portal.org)
  • Because complete exploration of all possible solutions for constructing haplotypes is computationally prohibitive, our approach uses a greedy algorithm based on windows of fixed sizes. (diva-portal.org)
  • The maximum likelihood-based expectation maximization algorithm and the Bayesian-based algorithm have been the most widely used approaches for haplotype inference. (aacrjournals.org)
  • However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data, though another study suggests that their results are generally consistent. (wikipedia.org)
  • It provides the genomic sequences and gene annotation of 8 different HLA-homozygous typing haplotypes (listed below), their resulting variations (see Data below) and ancestral relationships. (ucl.ac.uk)
  • For the other seven haplotype sequences links are given to GRC entries (numbers with GL prefixes). (ucl.ac.uk)
  • The attribute function above tells you which sequences in x make up which haplotypes in h but it's a bit tedious, particularly when dealing with large data sets. (r-bloggers.com)
  • Only one haplotype can be included in a reference assembly chromosome sequence. (ucsc.edu)
  • In order to discriminate between repeat copy and allelic copies, the sequence from a single haplotype across these regions is necessary. (ashg.org)
  • No difference in sequence, splicing, or expression of JAK2 was found on 46/1 compared with other haplotypes, suggesting that any functional difference of JAK2 on 46/1, if it exists, must be relatively subtle. (bloodjournal.org)
  • and it has not been found in any other human population sampled so far (out of a total of more than 10 000 mtDNA haplotypes for this sequence held in the GenBank sequence repository), except the Castle Mall individual reported on here. (royalsocietypublishing.org)
  • Templeton, A.R., Crandall, K.A. and Sing, C.F. (1992) A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. (scirp.org)
  • Although polyoma virus middle T-driven tumors showed altered primary and metastatic profiles in previous studies, depending upon nuclear and mtDNA haplotype, the magnitude and direction of changes were not the same in the HER2-driven mammary carcinomas. (aacrjournals.org)
  • In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. (frontiersin.org)
  • 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. (wikipedia.org)
  • Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and population studies, and the study of mutations. (inria.fr)
  • Analysis of further MPL -positive, V617F-negative cases confirmed an excess of 46/1 (n = 176, P = .002), but no association between MPL mutations and MPL haplotype was seen. (bloodjournal.org)
  • All but one of thc 13 mutations occur in at least 2 haplotypes thus. (lu.se)
  • All but one of thc 13 mutations occur in at least 2 haplotypes thus pinpointing 12 mutational hotspots and mutations that can be clearly considered detrimental. (lu.se)
  • And those haplotypes will be used as markers to test large cardiovascular cohorts. (genomeweb.com)
  • Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of the Jewish Diaspora. (pnas.org)
  • Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. (frontiersin.org)
  • We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. (plos.org)
  • We infer that VDR haplotypes might influence the risk of HIV-1 acquisition. (ebscohost.com)
  • Our full resource is available to the community through imputation servers that enable scientists to impute missing variants in any study and respect the privacy of subjects contributing to the studies that constitute the Haplotype Reference Consortium. (ashg.org)
  • Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds.We propose that the Asian variants are still present because they affect phenotypes thatwere important for ancient traditional, as well as recent, commercial pig breeding. (wur.nl)
  • Haplotype estimation in such cohorts is a central step in many downstream analyses. (plos.org)
  • Haplotype analyses did not add significantly to the associations found in the single SNP analyses. (lu.se)
  • Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. (frontiersin.org)
  • The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome. (wikipedia.org)
  • Background: Haplotype phasing is an important problem in the analysis of genomics information. (inria.fr)
  • Three haplotypes of F. japonica (including the widespread haplotype) and one F. sachalinensis matched previously identified Japanese haplotypes, supporting the hypothesis of multiple introductions in the US. (springer.com)
  • However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
  • Tests based simply on cross-tabulating all possible haplotypes by disease state cannot be extended to account for other variables measured on the individual. (cdc.gov)
  • In a case-control study, the model can be constructed so that each coefficient gives the log odds ratio for disease for an individual with a single copy of the suspect haplotype and another copy of the most common haplotype, relative to an individual with two copies of the most common haplotype. (cdc.gov)
  • He is working with researchers in Great Britain to uncover haplotypes implicated in cardiovascular disease, and has also begun looking into ways in which gene-expression data and proteomics tools may nurture his project. (genomeweb.com)
  • We describe likelihood ratio and permutation tests to test for disease-haplotype association, and describe three test statistics that are potentially useful for detecting such an association. (umich.edu)
  • This project investigates the effect of (i) SLE-associated MHC haplotypes, and (ii) IFN-α stimulation on gene regulation in ex vivo B cells, in order to further our understanding of how these factors contribute to disease risk. (bl.uk)
  • These results suggest a regulatory role for disease-associated MHC haplotypes, and implicate BTN3A2 as a novel candidate gene on the DRB1*03:01 haplotype. (bl.uk)
  • STRASBURG, PA- A natural history study has provided the first comprehensive clinical description of spinal muscular atrophy (SMA) within the Amish and Mennonite communities and correlates ancestral chromosome 5 haplotypes and SMN2 copy number with disease severity. (clinicforspecialchildren.org)
  • 13 These data not only reflect the severity of the disease but also the effect of haplotypes in modulating the SCA phenotype. (scielo.br)
  • The Bantu haplotype has been associated with higher disease severity and high incidence of organ, damage while the Benin haplotype is associated with an intermediate clinical course. (scielo.br)
  • Then, to ask if a signal of haplotype sharing exists within surnames, 150 pairs of men were recruited, each sharing a British surname, and Y-haplotype sharing assessed within each pair. (bl.uk)
  • methodologies for easy analysis of long stretches of DNA (10000s of base pairs) are now needed for haplotype identification. (soton.ac.uk)
  • In African Americans, the DRB1*07:01 - DQA1*03:01 -DQB1*02:01g haplotype is associated with increased risk (OR 3.96), whereas the DRB1*07:01-DQA1*02:01 - DQB1*02:01g haplotype appears to be protective (OR 0.34). (medscape.com)
  • The most susceptible haplotypes are the DRB1*0301-DQA1*0501-DQB1*0201 (odds ratio [OR] 3.64) and the DRB1*0405-DQA1*0301-DQB1*0302, DRB1*0401-DQA1*0301-DQB*0302, and DRB1*0402-DQA1*0301-DQB1*0302 haplotypes (ORs 11.37, 8.39, and 3.63), followed by the DRB1*0404-DQA1*0301-DQB1*0302 (OR 1.59) and the DRB1*0801-DQB1*0401-DQB1*0402 (OR 1.25) haplotypes. (diabetesjournals.org)
  • A novel trans-eQTL was identified for DRB1*03:01 haplotypes in the exon array data set, in both resting and IFN-α-stimulated cells, involving down-regulation of BTN3A2 (P (bl.uk)
  • Determining the long-range haplotypes in a diploid individual is a major technical challenge. (nih.gov)
  • Haplotype blocks may be as short as 2 kb or more than 150 kb, depending both on block definition and the spacing of LD cold spots, which tend to be shorter than blocks. (els.net)
  • At the next RECOMB, I hope someone has a data compression method [for SNP data] that blows haplotype blocks out of the water," said population geneticist Andrew Clark during his keynote address. (genomeweb.com)
  • The IC, QC and IQC haplotypes are significantly associated with the DA phenotype. (cdc.gov)
  • 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. (jimmunol.org)
  • The data from the MHC Haplotype Project are available in .txt file format file for viewing in the UCSC Genome Browser . (ucl.ac.uk)
  • The data are colour-coded by haplotype and will initially be displayed showing 1Mb in the centre of the MHC. (ucl.ac.uk)
  • The results show that the program performs very well on both types of data and will be useful for large scale haplotype inference projects. (nih.gov)
  • Logistic regression model for analyzing extended haplotype data. (cdc.gov)
  • Citation Query A new statistical method for haplotype reconstruction from population data. (psu.edu)
  • A new statistical method for haplotype reconstruction from population data. (psu.edu)
  • The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. (frontiersin.org)
  • These haplotype data are the first of its kind for PHS genotyping in South Africa. (frontiersin.org)
  • In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. (psu.edu)
  • 7 , 8 , 11 First, 46/1 may be inherently more genetically unstable, acquiring V617F at a faster rate than other haplotypes (hypermutability hypothesis). (bloodjournal.org)
  • Second, V617F may arise on all haplotypes at equal rates, but 46/1 may carry an additional factor that either gives a selective advantage to the V617F-positive clone or interacts in some way to increase the likelihood of abnormal blood counts (fertile ground hypothesis). (bloodjournal.org)
  • Using a novel mouse model, a mitochondrial-nuclear exchange model termed MNX, we tested the hypothesis that inherited mitochondrial haplotypes alter primary tumor latency and metastatic efficiency. (aacrjournals.org)
  • Most chromosome regions have only a few common haplotypes. (nih.gov)
  • Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)
  • A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. (wikipedia.org)
  • SNP1 and SNP2 do not make a distinction between haplotypes that are alike-in-state (AIS) due to a common ancestor ( i.e . (genetics.org)
  • The most common SELE haplotype in this analysis ([C;G;T;C;G;T], 31.2%) showed a negative association with myocardial infarction (MI) (CAD/MI(+) vs. non-CAD) under the additive (p = 0.001), dominant (p = 0.006) and recessive (p = 0.012) model. (termedia.pl)
  • Conclusions: Our results show that constructing haplotypes with HaploPOP can substantially reduce assignment error. (diva-portal.org)
  • Haplotype composition varied substantially with respect to ethnicity. (aacrjournals.org)
  • Furthermore, the authors noted that the Bantu haplotype substantially influences the levels of this cytokine, elevating its plasma concentration. (scielo.br)
  • Haplotypes are important for example because many of the SNP's found by genome-wide association studies aren't the true cause but simply occur on same haplotype and are thus inherited together. (snpedia.com)
  • so, unlike autosomal haplotypes, there is effectively not any randomisation of the Y-chromosome haplotype between generations. (wikipedia.org)
  • The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. (psu.edu)
  • 1 , 2 SCA is characterized by a variable clinical course and differences in response to medication, reflecting its complex pathophysiology and suggesting that it can be affected by modulator factors such as the haplotypes of the beta globin chain or fetal hemoglobin (Hb F) levels. (scielo.br)
  • The haplotype is converted to number , considering the first variation as zero and the alternate value as 1 (see expanded description below). (ubuntu.com)
  • Clear favorable haplotypes, contributing 40-60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. (frontiersin.org)
  • The working directory of the 1000 Genomes ftp site contains phased haplotypes for 2,123 individuals from the 1000 Genomes Project ( US / Europe ). (blogspot.com)
  • The 46/1 haplotype was also overrepresented in cases without V617F (n = 347, P = .009), with an excess seen for both MPL exon 10 mutated and V617F, MPL exon 10 nonmutated cases. (bloodjournal.org)
  • Identification of NURR1 (Exon 4) and FOXA1 (Exon 3) Haplotypes Associated with mRNA Expression Levels in Peripheral Blood Lymphocytes of Parkinson's Patients in Small Indian Population. (thefreelibrary.com)