Haplotypes: 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.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Linkage Disequilibrium: 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.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.Genetic Variation: Genotypic differences observed among individuals in a population.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Polymorphism, Genetic: 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.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Genetics, Population: 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.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Founder Effect: 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.Case-Control Studies: 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.HLA-DQ Antigens: 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.Microsatellite Repeats: 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).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Polymorphism, Restriction Fragment Length: 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.HLA-DQ beta-Chains: Transmembrane proteins that form the beta subunits of the HLA-DQ antigens.Molecular Sequence Data: 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.HLA-DRB1 Chains: 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.Models, Genetic: 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.Pedigree: 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.European Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Europe.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.HLA-DR Antigens: 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.HLA 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.Asian Continental Ancestry Group: Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.Major Histocompatibility Complex: 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.Geography: 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)Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genetic Association Studies: 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.HLA-DQ alpha-Chains: Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.Phylogeography: 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)Y Chromosome: 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.Homozygote: An individual in which both alleles at a given locus are identical.HLA-DR3 Antigen: An HLA-DR antigen which is associated with HLA-DRB1 CHAINS encoded by DRB1*03 alleles.Polymerase Chain Reaction: 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.Genes, MHC Class II: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.HLA-B Antigens: 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.Genealogy and HeraldryHeterozygote: An individual having different alleles at one or more loci regarding a specific character.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Recombination, Genetic: 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 b: Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.Chromosomes, Human, Y: The human male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans.Bahrain: 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)Mutation: 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.China: A country spanning from central Asia to the Pacific Ocean.African Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Africa.HLA-B8 Antigen: A specific HLA-B surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-B*08 allele family.AfricaHLA-A Antigens: 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.Gene Pool: The total genetic information possessed by the reproductive members of a POPULATION of sexually reproducing organisms.Polynesia: 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)EuropeLikelihood Functions: 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.Genes, MHC Class I: 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.Promoter Regions, Genetic: 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.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genetic Loci: 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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Gene Flow: 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.HLA-A1 Antigen: A specific HLA-A surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-A*01 allele family.DNA: 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).Ethnic Groups: A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.Indians, South American: Individual members of South American ethnic groups with historic ancestral origins in Asia.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Exons: 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.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Species Specificity: 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.DNA Primers: 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.Risk Factors: 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.Genome, Human: 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.Wolves: Any of several large carnivorous mammals of the family CANIDAE that usually hunt in packs.South AmericaAsia: 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)Introns: 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.Diabetes Mellitus, Type 1: 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.HLA-C Antigens: 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).H-2 Antigens: The major group of transplantation antigens in the mouse.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Receptors, KIR: 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.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Phenylketonurias: 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).Siberia: 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.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.Nuclear Family: A family composed of spouses and their children.Steroid 21-Hydroxylase: 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).Genome-Wide Association Study: 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.Tandem Repeat Sequences: 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).JapanHaploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.Histocompatibility Testing: 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)Disease Susceptibility: 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.
Renin-Angiotensin System Gene Polymorphisms and Atrial Fibrillation | Circulation... except for the GGAACT haplotype [P=0.0002]). All of these significant haplotypes had high haplotype frequencies (,0.01). The ... Haplotypes of the AGT Gene and Their Association With AF. Table 2 displays the results of 6-locus estimated haplotype frequency ... The omnibus haplotype profile test27 was highly significant (χ2=62.5, P=0.0002), which indicated the overall haplotype ... In multilocus haplotype analysis, the angiotensinogen gene haplotype profile was significantly different between cases and ...
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence...We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or ... Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination ... A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence ... A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence ...
PPT - The Population Haplotyping problem PowerPoint Presentation - ID:6333706HAPLOTYPE : string over 0, 1 GENOTYPE : string over 0, 1, * Slideshow 6333706 by luke-boyer ... The Population Haplotyping problem. NOTATION : each SNP only two values in a population ( bio ). Call them 0 and 1 . Also , ... solution of ,= 2n haplotypes, i.e. ,= SQRT(n) * LB It's difficult, but not impossible, to come up with better approximations, ... Progress in Combinatorial Haplotyping -Three post-hgp\' topics. in the past five years my group has addressed three topics in ...
Authors' replyResearchers reported that the IL1RN AI/IL1B-5l1T haplotype was associated with a more rapid decline in lung function in smokers ... Authors suggest that this apparent contradiction may be because the function of these haplotypes is disease specific. ... Karajalainen and colleagues present interesting data on the relationship of IL-1Î² and IL-1 receptor antagonist haplotypes and ... in the Lung Health Study; in contrast, they found that this same haplotype was associated with a slower rate of decline in lung ...
Complete Aims for Clinical Market as it Readies its WG Haplotyping Tech for Launch | GenomeWebComplete Genomics is planning to introduce technology next year that will enable whole genome sequencing and haplotyping with ... Complete Aims for Clinical Market as it Readies its WG Haplotyping Tech for Launch. Jul 18, 2012 ... Complete Genomics is planning to introduce technology next year that will enable whole genome sequencing and haplotyping with ... Home » Complete Aims for Clinical Market as it Readies its WG Haplotyping Tech for Launch ...
CHiP-qtPCR showing binding of NFκB p50 as well as NFκ | Open-iCHiP-qtPCR showing binding of NFκB p50 as well as NFκBp65 within the genomic segment contained in the 1.2 Kb haplotype window ... Binding of NFkBp50 and p65 to an associated 1.2 Kb haplotype segment was confirmed. A second independent genetic effect was ... Binding of NFkBp50 and p65 to an associated 1.2 Kb haplotype segment was confirmed. A second independent genetic effect was ... Nevertheless, the 1.2 Kb haplotype window with the strongest genetic association and within B3 contained SNP rs2248932 that ...
Single-locus haplotype frequencies in community samples | Open-iTFR, Day 28 treatment failure rate; haplotypes are labelled according to the patterns indicated in Tabl ... Fully wild-type pfdhfr/pfdhps haplotypes were infrequent at all three sites (0.01 to 0.15) and the predominant haplotype at ... Fully wild-type pfdhfr/pfdhps haplotypes were infrequent at all three sites (0.01 to 0.15) and the predominant haplotype at ... Figure 1: Single-locus haplotype frequencies in community samples. TFR, Day 28 treatment failure rate; haplotypes are labelled ...
Logistic Bayesian LASSO for Identifying Association with Rare Haplotypes and Application to Age-Related Macular Degeneration -...Ananda S. Datta, Yuan Zhang, Lei Zhang, Swati Biswas, Association of rare haplotypes on ULK4 and MAP4 genes with hypertension, ... We applied LBL to the AMD data and identified common and rare haplotypes in the complement factor H gene, gaining insights into ... Our results show that LBL is much more powerful in identifying rare associated haplotypes when the false positive rates for ... M. Wang, S. Lin, FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads, ...
onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2011.01680.x/full?globalMessage=0&systemMessage=Wiley Online Library will be unavailable on Saturday 7th Oct from 03.00 EDT / 08:00 BST / 12:30 IST / 15.00 SGT to 08.00 EDT / 13.00 BST / 17:30 IST / 20.00 SGT and Sunday 8th Oct from 03.00 EDT / 08:00 BST / 12:30 IST / 15.00 SGT to 06.00 EDT / 11.00 BST / 15:30 IST / 18.00 SGT for essential maintenance. Apologies for the inconvenience caused
Kinase gene haplotypes and gene-gene interactions in the Ras... : International Clinical PsychopharmacologyHome , September 2013 - Volume 28 - Issue 5 , Kinase gene haplotypes and gene-gene interactions in the Ras... ... The percentage of the CCAGA haplotype that RSK(2/3/4)-RSKL(1/2) gene loci SNPs constructed was markedly lower in the remitter ... Kinase gene haplotypes and gene-gene interactions in the Ras-Raf-MAPK signaling pathway: association with antidepressant ... Kinase gene haplotypes and gene-gene interactions in the Ras-Raf-MAPK signaling pathway: association with antidepressant ...
TGFBR1 Haplotypes and Risk of Non-Small-Cell Lung Cancer | Cancer ResearchTGFBR1 Haplotypes and Risk of Non-Small-Cell Lung Cancer. Zhe Lei, Reng-Yun Liu, Jun Zhao, Zeyi Liu, Xiefang Jiang, Weiming You ... TGFBR1 Haplotypes and Risk of Non-Small-Cell Lung Cancer. Zhe Lei, Reng-Yun Liu, Jun Zhao, Zeyi Liu, Xiefang Jiang, Weiming You ... TGFBR1 Haplotypes and Risk of Non-Small-Cell Lung Cancer. Zhe Lei, Reng-Yun Liu, Jun Zhao, Zeyi Liu, Xiefang Jiang, Weiming You ... TGFBR1 Haplotypes and Risk of Non-Small-Cell Lung Cancer Message Subject (Your Name) has forwarded a page to you from Cancer ...
High-resolution HLA alleles and haplotypes in the United States population.Abstract We extract and present high-resolution HLA allele and haplotype frequency data available from the National Marrow ... Abstract We extract and present high-resolution HLA allele and haplotype frequency data available from the National Marrow ...
RootsWeb: GENEALOGY-DNA-L RE: [DNA] Strathclyde British haplotypeRE: [DNA] Strathclyde British haplotype by 'Peter A. Kincaid' ,. ,. *Re: [DNA] Strathclyde British haplotype by *RE: [DNA] ... Strathclyde British haplotype by 'Peter A. Kincaid' ,. ,*Re: [DNA] Strathclyde British haplotype by 'Ken Nordtvedt' ,. ,*Re: [ ... Re: [DNA] Strathclyde British haplotype by ahunt ,. ,*Re: Re: [DNA] Strathclyde British haplotype by 'Ken Nordtvedt' ,. ,*Re: ... RE: [DNA] Strathclyde British haplotype by 'Peter A. Kincaid' ,. ,*Re: [DNA] Strathclyde British haplotype by (Wayne George)*Re ...
A Population Association Study of Angiotensinogen Polymorphisms and Haplotypes With Left Ventricular Phenotypes | Hypertension... haplotype 4 and MVE, haplotype 6 and MVE, haplotype 3 and MWS, and haplotype 2 and RWT, all in the black population). ... Haplotypes having a ,5% total frequency in the population ("major haplotypes") were included individually in models as 2-df ... We also used Phase 2.0.2 to reconstruct haplotypes from genotype data. Using the same cutoff of P,0.005, we found no haplotypes ... All haplotype regressions were adjusted for age, sex, hypertension status, and heart rate, and haplotype regressions were ...
Complement and HLA: Further Definition of High-Risk Haplotypes in Insulin-dependent Diabetes | DiabetesOne previously identified haplotype (B40-BfS-DR4) showed no complement clustering, while the rare high-risk haplotype (B8-BfS- ... In a recent study, we defined five high-risk haplotypes that were determined solely by HLA-B, Bf, and HLA-DR (B8-BfS-DR3, B8- ... Three haplotypes that exhibited significantly increased risks with complement inclusion were B8-BfS-C2C-C4AQ0-C4B1-DR3 (RR = ... Information at the HLA-A locus was deemed important only in the definition of the B8-BfS-DR3 extended high-risk haplotype. ...
Data on haplotype-supported immunoglobulin germline gene inference... Kirik, Ufuk LU ; Greiff, Lennart LU ; Levander, Fredrik LU ... Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity ... Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity ... This was accomplished based on analysis of the inferred germline genes' association to the donors' different haplotypes as ...
Browsing FAS Scholarly Articles by Subject "haplotype-based association studies"... DSpace/Manakin Repository. * DASH Home ...
https://dash.harvard.edu/handle/1/2/browse?value=haplotype-based association studies&type=subject
NSF project: Haplotype polymorphism in polyploid wheats and their diploid ancestorsand assess haplotype polymorphism in wild and cultivated wheats. Integrate these new SNPs into wheat genetic maps.. (2) ... immediate diploid ancestors, DNA sequences, electropherograms, haplotypes, SNPs, and positions of SNP markers on wheat linkage ...
Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase. ...Phyletic relations among haplotypes are largely reticulate, again except for the high-LD groups of macrostate 4, which form ... This pattern of haplotype clades with high LD among multiple varying sites, emerging from chaotically recombining variation, ... Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase. ... We find extensive intragenic recombination among all haplotypes except the two high-LD groups of macrostate 4, which display ...
Effects of IRF5 Lupus Risk Haplotype on Pathways Predicted to Influence B Cell Functions... Joel M. Guthridge,1 Daniel N. Clark,2 ... J. S. Bates, C. J. Lessard, J. M. Leon et al., "Meta-analysis and imputation identifies a 109kb risk haplotype spanning TNFAIP3 ... R. R. Graham, S. V. Kozyrev, E. C. Baechler et al., "A common haplotype of interferon regulatory factor 5 (IRF5) regulates ... S. Sigurdsson, G. Nordmark, S. Garnier et al., "A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, ...
A second generation human haplotype map of over 3.1 million SNPs.... Author(s): International HapMap Consort, Frazer KA, ...
Dienekes' Anthropology Blog: X-linked haplotype of Neandertal origin in non-AfricansFor example (Table 1), haplotype B006 differs from the modal Eurasian haplotype B001 (which is common to Eurasians and Africans ... It is also not clear why the common haplotype in Neandertals and Eurasians cannot be due to modern human admixture in ... An X-linked haplotype of Neandertal origin is present among all non-African populations. Vania Yotova et al. ... is the presence of African-specific haplotypes that seem quite divergent from the most common human haplotypes. ...
Association analysis for feed efficiency traits in beef cattle using preserved haplotypes. - Agriculture and Agri-Food Canada ...Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple ... Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups ... Association analysis for feed efficiency traits in beef cattle using preserved haplotypes.. Lu, D., Sargolzaei, M., Li, C., Abo ... At nominal significance levels (at least P , 0.05), 23 regions with a total number of 31 haplotypes were found significantly ...
WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Disequilibrium (medicine): Disequilibrium}}Genetic variation: right|thumbInfinite alleles model: The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and American geneticist James F.Gene polymorphismPanmixia: Panmixia (or panmixis) means random mating.King C and Stanfield W.Haplogroup L0 (mtDNA)Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Nested case-control study: A nested case control (NCC) study is a variation of a case-control study in which only a subset of controls from the cohort are compared to the incident cases. In a case-cohort study, all incident cases in the cohort are compared to a random subset of participants who do not develop the disease of interest.HLA-DQ: HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an αβ heterodimer of type MHC Class II.Microsatellite: A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5-50 times. Microsatellites occur at thousands of locations in the human genome and they are notable for their high mutation rate and high diversity in the population.Chromosome regionsGenetic linkage: Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked.Amplified fragment length polymorphismColes PhillipsPedigree chart: A pedigree chart is a diagram that shows the occurrence and appearance or phenotypes of a particular gene or organism and its ancestors from one generation to the next,pedigree chart Genealogy Glossary - About.com, a part of The New York Times Company.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.HLA B7-DR15-DQ6Health geography: Health geography is the application of geographical information, perspectives, and methods to the study of health, disease, and health care.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Phylogeography: Phylogeography is the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals. This is accomplished by considering the geographic distribution of individuals in light of the patterns associated with a gene genealogy.PCDHY: PCDH11Y is a gene unique to human males which competes with FOXP2 for the title of the "language gene." PCDH11Y is the gene for making Protocadherin 11Y, a protein that guides the development of nerve cells.Thermal cyclerCIITA: CIITA is a human gene which encodes a protein called the class II, major histocompatibility complex, transactivator. Mutations in this gene are responsible for the bare lymphocyte syndrome in which the immune system is severely compromised and cannot effectively fight infection.Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Atomic heraldry: Atomic heraldry is heraldry characterised by the appearance of charges including the atom or showing the motion of parts of the atom; more loosely, it may describe heraldry in which atoms or the component parts thereof are represented through a combination of other charges. Obviously, this is a late development in heraldry.Recombination (cosmology): In cosmology, recombination refers to the epoch at which charged electrons and protons first became bound to form electrically neutral hydrogen atoms.Note that the term recombination is a misnomer, considering that it represents the first time that electrically neutral hydrogen formed.List of companies of Bahrain: This is a list of notable companies based in Bahrain, grouped by their Industry Classification Benchmark sector.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Layout of the Port of Tianjin: The Port of Tianjin is divided into nine areas: the three core (“Tianjin Xingang”) areas of Beijiang, Nanjiang, and Dongjiang around the Xingang fairway; the Haihe area along the river; the Beitang port area around the Beitangkou estuary; the Dagukou port area in the estuary of the Haihe River; and three areas under construction (Hanggu, Gaoshaling, Nangang).MIM Pan-African Malaria Conference 2009HLA-A: HLA-A is a group of human leukocyte antigens (HLA) that are coded for by the HLA-A locus, which is located at human chromosome 6p21.3.Gene pool: The gene pool is the set of all genes, or genetic information, in any population, usually of a particular species.Manuae (Cook Islands): Manuae is an uninhabited atoll in the southern group of the Cook Islands, 100 kilometres south-east of Aitutaki. It is administratively part of Aitutaki, but does not belong to any district or tapere of Aitutaki.GA²LENDecoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.GC box: In molecular biology, a GC box is a distinct pattern of nucleotides found in the promoter region of some eukaryotic genes upstream of the TATA box and approximately 110 bases upstream from the transcription initiation site. It has a consensus sequence GGGCGG which is position dependent and orientation independent.Selection (relational algebra): In relational algebra, a selection (sometimes called a restriction to avoid confusion with SQL's use of SELECT) is a unary operation written asClonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Lampreado: thumb | 250px | right | LampreadoAlternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.QRISK: QRISK2 (the most recent version of QRISK) is a prediction algorithm for cardiovascular disease (CVD) that uses traditional risk factors (age, systolic blood pressure, smoking status and ratio of total serum cholesterol to high-density lipoprotein cholesterol) together with body mass index, ethnicity, measures of deprivation, family history, chronic kidney disease, rheumatoid arthritis, atrial fibrillation, diabetes mellitus, and antihypertensive treatment.California Wolf Center: California Wolf Center is a 501(c)3 nonprofit located 50 miles east of San Diego, near the town of Julian, California. It is a one-of-a-kind, conservation, education, and research center dedicated to wolf recovery in the wild.Utiaritichthys: Utiaritichthys is a genus of serrasalmid found in the Amazon and Orinoco basins in tropical South America.Miss Asia Pacific 2005Intron: right|thumbnail|270px|Representation of intron and [[exons within a simple gene containing a single intron.]]Network for Pancreatic Organ Donors with Diabetes: The Network for Pancreatic Organ donors with Diabetes (nPOD), is a collaborative type 1 diabetes research project funded by JDRF (formerly known as the Juvenile Diabetes Research Foundation). nPOD supports scientific investigators by providing, without cost, rare and difficult to obtain tissues beneficial to their research.HLA-C: HLA-C belongs to the MHC (human = HLA) class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and β2-microglobulin.Killer-cell immunoglobulin-like receptor: Killer-cell immunoglobulin-like receptors (KIRs), are a family of cell surface proteins found on important cells of the immune system called natural killer (NK) cells. They regulate the killing function of these cells by interacting with MHC class I molecules, which are expressed on all cell types.Hyperphenylalaninemia: (also includes non-classic PKU)Indigenous peoples of SiberiaUniparental inheritance: Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father.Geranylhydroquinone 3''-hydroxylase: Geranylhydroquinone 3-hydroxylase (, GHQ 3-hydroxylase) is an enzyme with system name geranylhydroquinone,NADPH:oxygen oxidoreductase (3-hydroxylating). This enzyme catalyses the following chemical reactionPopulation stratification: Population stratification is the presence of a systematic difference in allele frequencies between subpopulations in a population possibly due to different ancestry, especially in the context of association studies. Population stratification is also referred to as population structure, in this context.Tandem repeat: Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as Armadillo repeats.Niigata University
(1/12035) Association of polymorphism at the type I collagen (COL1A1) locus with reduced bone mineral density, increased fracture risk, and increased collagen turnover.
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)
(2/12035) A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays.
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)
(3/12035) The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission.
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)
(4/12035) DYT1 mutation in French families with idiopathic torsion dystonia.
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)
(5/12035) A common MSH2 mutation in English and North American HNPCC families: origin, phenotypic expression, and sex specific differences in colorectal cancer.
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)
(6/12035) Analysis of spinocerebellar ataxia type 2 gene and haplotype analysis: (CCG)1-2 polymorphism and contribution to founder effect.
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)
(7/12035) Der(22) syndrome and velo-cardio-facial syndrome/DiGeorge syndrome share a 1.5-Mb region of overlap on chromosome 22q11.
Derivative 22 (der) 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)
(8/12035) Location score and haplotype analyses of the locus for autosomal recessive spastic ataxia of Charlevoix-Saguenay, in chromosome region 13q11.
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 aims of this study were to explore the associations between antidepressant remission and single nucleotide polymorphisms (SNPs), haplotypes, and gene-gene interactions in the Ras-Raf-MAPK intracellular signaling pathway. (lww.com)
- Although this study did not find that SNPs at the five kinase genes in the Ras-Raf-MAPK signaling pathway are important markers for antidepressant outcome, certain haplotypes that SNPs at the RSK(2/3/4)-RSKL(1/2) gene constructed may be important markers for antidepressant drug efficacy. (lww.com)
- In collaboration with Gramene, create public databases of conserved and genome-specific PCR primers for amplification of STSs from genomic DNA of wheat and its immediate relatives, conserved and genome-specific sequencing primers for sequencing STSs from wheat and its immediate diploid ancestors, DNA sequences, electropherograms, haplotypes, SNPs, and positions of SNP markers on wheat linkage maps. (usda.gov)
- A second generation human haplotype map of over 3.1 million SNPs. (omicsonline.org)
- This means that although a block may contain many SNPs, it takes only a few SNPs to uniquely identify or "tag" each of the haplotypes in the block. (nih.gov)
- Although the block boundaries seem to be similar in the various populations, the frequencies of the haplotypes and the associations between blocks do differ among populations, so the optimum choice of tag SNPs will need to be based on information from a number of populations. (nih.gov)
- The present initiative will support the development of the haplotype map, abbreviated the HapMap, which will be a description of the set of haplotype blocks and the SNPs that tag them. (nih.gov)
- Therefore, it is likely that in female depressed patients, different haplotypes and gene-gene interaction in the Ras-Raf-MAPK signaling pathway are involved in mediating the pharmacological action of an antidepressant, and eventually influence antidepressant efficacy. (lww.com)
- This was accomplished based on analysis of the inferred germline genes' association to the donors' different haplotypes as defined by their different, expressed IGHJ alleles and/or IGHD genes/alleles. (lu.se)
- High-resolution HLA alleles and haplotypes in the United States population. (omicsonline.org)
- The specific pattern of particular SNP alleles in a block is called a haplotype. (nih.gov)
- We also used Phase 2.0.2 to reconstruct haplotypes from genotype data. (ahajournals.org)
- We find extensive intragenic recombination among all haplotypes except the two high-LD groups of macrostate 4, which display none. (nih.gov)
- This pattern of haplotype clades with high LD among multiple varying sites, emerging from chaotically recombining variation, may be a "signature" of refinement of complex adaptive sequences by recombination and selection. (nih.gov)
- Recent studies show that most haplotype blocks in the human genome have been transmitted through many generations without recombination. (nih.gov)
- 0.005, we found no haplotypes to be significantly associated with the LV phenotypes. (ahajournals.org)
- This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. (gc.ca)
- 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. (gc.ca)
- Complete Genomics is planning to introduce technology next year that will enable whole genome sequencing and haplotyping with an error rate as low as one in 10 million. (genomeweb.com)
- nonetheless, rare haplotypes may also result from combination of common single nucleotide polymorphisms available from genome-wide association studies (GWAS). (wiley.com)
- The haplotype map is expected to be a key resource for finding genes affecting health, disease, and response to drugs and environmental factors, and for beginning to understand the pattern of human genetic variation. (nih.gov)
- By inclusion of information from the complement polymorphism, we have defined in greater detail three of these five high-risk haplotypes. (diabetesjournals.org)
- One previously identified haplotype (B40-BfS-DR4) showed no complement clustering, while the rare high-risk haplotype (B8-BfS-DR4) was seen only once in this smaller sample. (diabetesjournals.org)
- Three haplotypes that exhibited significantly increased risks with complement inclusion were B8-BfS-C2C-C4AQ0-C4B1-DR3 (RR = 2.4), B15-BfS-C2C-C4A3-C4B2.9-DR4 (RR = 10.2), and B18-BfF1-C2C-C4A3-C4BQ0-DR3 (RR = 10.6). (diabetesjournals.org)
- We applied LBL to the AMD data and identified common and rare haplotypes in the complement factor H gene, gaining insights into rare variants' contributions to AMD beyond the current literature. (wiley.com)
- Macrostate 4 shows significant linkage disequilibrium (LD) among its variants, especially for two groups of five haplotypes each. (nih.gov)
- Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus," Proceedings of the National Academy of Sciences of the United States of America , vol. 104, no. 16, pp. 6758-6763, 2007. (hindawi.com)
- Meng Wang , Shili Lin , Detecting associations of rare variants with common diseases: collapsing or haplotyping? (wiley.com)
- The data will be used to develop a map of the haplotype patterns and of the genetic variants that are most informative for detecting these patterns. (nih.gov)
- Phyletic relations among haplotypes are largely reticulate, again except for the high-LD groups of macrostate 4, which form clades with strong bootstrap support. (nih.gov)
- This analysis also demonstrates the richness of GWAS data for mapping rare haplotypes-a potential largely unexplored. (wiley.com)
- I've always considered the B0006 haplotype as the best genetic evidence (apart from the overwhelming linguistic and kinship data) for a non-African origin of all modern humans. (blogspot.com)
- Amplify STSs from the wheat A, B and D genomes in a sample of wild emmer and bread wheat lines, sequence the amplicons and assess haplotype polymorphism in wild and cultivated wheats. (usda.gov)
- Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase. (nih.gov)
- Abstract We extract and present high-resolution HLA allele and haplotype frequency data available from the National Marrow Donor Program databases from four major U.S. census categories of race and ethnicity. (omicsonline.org)
- Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10.1016/j.molimm.2017.03.012) (Kirik et al. (lu.se)
- To pursue this for phosphoglucose isomerase (PGI) of Colias butterflies, whose polymorphism is maintained by strong natural selection, we assembled a large data set of wild haplotypes, highly variable at the amino acid and DNA levels. (nih.gov)
- These data provide strong support for the idea that a human haplotype map built with samples from populations of African, Asian, and European ancestry would apply to most populations in the world, although further testing of this conclusion is needed. (nih.gov)
- To better understand the association between rs943580 and MVE, we examined AGT haplotype associations with MVE. (ahajournals.org)
- Here we develop a method for identifying association with rare haplotypes for case-control design. (wiley.com)
- Association analysis for feed efficiency traits in beef cattle using preserved haplotypes. (gc.ca)
- It is anticipated that this initiative will become part of an international collaboration to produce a human haplotype map. (nih.gov)
- What I find most interesting, however, is the presence of African-specific haplotypes that seem quite divergent from the most common human haplotypes. (blogspot.com)
- For example (Table 1), haplotype B006 differs from the modal Eurasian haplotype B001 (which is common to Eurasians and Africans) at 13 sites, and B007 (which is African-specific) differs from B001 at 11 sites. (blogspot.com)
- It is also not clear why the common haplotype in Neandertals and Eurasians cannot be due to modern human admixture in Neandertals. (blogspot.com)
- Furthermore, each block has only a few common haplotypes. (nih.gov)
- Recent studies show that most common haplotypes occur in all human populations, though the frequencies may vary. (nih.gov)
- In particular, we penalize the regression coefficients using appropriate priors to weed out unassociated haplotypes, making it possible for the rare associated ones to stand out. (wiley.com)
- Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. (gc.ca)
- In a recent study, we defined five high-risk haplotypes that were determined solely by HLA-B, Bf, and HLA-DR (B8-BfS-DR3, B8-BfS-DR4, B15-BfS-DR4, B18-BfF1-DR3, and B40-BfS-DR4). (diabetesjournals.org)
- however, due to lack of appropriate statistical tools, effects of individual rare haplotypes were never studied. (wiley.com)
- Our results show that LBL is much more powerful in identifying rare associated haplotypes when the false positive rates for both approaches are kept the same. (wiley.com)
- Information at the HLA-A locus was deemed important only in the definition of the B8-BfS-DR3 extended high-risk haplotype. (diabetesjournals.org)
- Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. (gc.ca)