AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureHumanitiesInformation ScienceNamed GroupsHealth CareGeographicals
Linkage DisequilibriumHaplotypesGenetic LinkagePolymorphism, Single NucleotideAllelesGenetic MarkersGene FrequencyGenetics, PopulationGenotypeChromosome MappingModels, GeneticPolymorphism, GeneticGenetic VariationGenetic Predisposition to DiseaseMicrosatellite RepeatsQuantitative Trait LociGenome-Wide Association StudyPedigreeGenome, HumanRecombination, GeneticSelection, GeneticGenetic LociFounder EffectEuropean Continental Ancestry GroupCase-Control StudiesPolymorphism, Restriction Fragment LengthLod ScoreQuantitative Trait, HeritableComputer SimulationGenetic Diseases, InbornLikelihood FunctionsNuclear FamilyChromosomes, Human, Pair 6PhenotypeAsian Continental Ancestry GroupHeterozygoteSequence Analysis, DNAModels, StatisticalChromosomes, Human, Pair 1Epistasis, GeneticGenetic Association StudiesHapMap ProjectMolecular Sequence DataGenotyping TechniquesSample SizeAfrican Continental Ancestry GroupChromosomes, Human, Pair 12HomozygoteAlgorithmsBase SequenceGenetic HeterogeneityBreedingHLA-DRB1 ChainsSoftwarePhysical Chromosome MappingChromosomes, Human, Pair 19HLA-DQ beta-ChainsExonsPopulationEvolution, MolecularGenomeIntronsChromosomes, Human, Pair 5HLA AntigensChromosome InversionGenome, PlantGenetic TestingChromosomes, HumanPolymerase Chain ReactionChromosomes, Human, Pair 2Genes, DominantChromosomes, Human, Pair 16HLA-DQ AntigensPhylogenyMutationGenes, RecessiveEuropeAfricaFamily HealthJewsChromosomes, Human, XHeterozygote DetectionBayes TheoremPopulation DensityInbreedingChromosomes, Human, Pair 4Amplified Fragment Length Polymorphism AnalysisSiblingsPrincipal Component AnalysisMultigene FamilyCrosses, GeneticEthnic GroupsFinlandGenomicsHLA-DQ alpha-ChainsDNAMonte Carlo MethodGeographyPhosphoglucomutaseMinisatellite Repeats
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.
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.
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, Single Nucleotide
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the 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.
Genetic Markers
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Gene Frequency
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
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.
Genotype
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Chromosome Mapping
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
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.
Genetic Variation
Genotypic differences observed among individuals in a population.
Genetic Predisposition to Disease
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
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).
Quantitative Trait Loci
Genetic loci associated with a QUANTITATIVE TRAIT.
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.
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.
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.
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.
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.
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.
European Continental Ancestry Group
Individuals whose ancestral origins are in the continent of Europe.
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.
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.
Lod Score
The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."
Quantitative Trait, Heritable
A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)
Computer Simulation
Computer-based representation of physical systems and phenomena such as chemical processes.
Genetic Diseases, Inborn
Diseases that are caused by genetic mutations present during embryo or fetal development, although they may be observed later in life. The mutations may be inherited from a parent's genome or they may be acquired in utero.
Likelihood 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.
Nuclear Family
A family composed of spouses and their children.
Chromosomes, Human, Pair 6
A specific pair GROUP C CHROMSOMES of the human chromosome classification.
Phenotype
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Asian Continental Ancestry Group
Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.
Heterozygote
An individual having different alleles at one or more loci regarding a specific character.
Sequence Analysis, DNA
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Models, Statistical
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
Chromosomes, Human, Pair 1
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
Epistasis, Genetic
A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.
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.
HapMap Project
A coordinated international effort to identify and catalog patterns of linked variations (HAPLOTYPES) found in the human genome across the entire human population.
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.
Genotyping Techniques
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
Sample Size
The number of units (persons, animals, patients, specified circumstances, etc.) in a population to be studied. The sample size should be big enough to have a high likelihood of detecting a true difference between two groups. (From Wassertheil-Smoller, Biostatistics and Epidemiology, 1990, p95)
African Continental Ancestry Group
Individuals whose ancestral origins are in the continent of Africa.
Chromosomes, Human, Pair 12
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Homozygote
An individual in which both alleles at a given locus are identical.
Algorithms
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Base Sequence
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Genetic Heterogeneity
The presence of apparently similar characters for which the genetic evidence indicates that different genes or different genetic mechanisms are involved in different pedigrees. In clinical settings genetic heterogeneity refers to the presence of a variety of genetic defects which cause the same disease, often due to mutations at different loci on the same gene, a finding common to many human diseases including ALZHEIMER DISEASE; CYSTIC FIBROSIS; LIPOPROTEIN LIPASE DEFICIENCY, FAMILIAL; and POLYCYSTIC KIDNEY DISEASES. (Rieger, et al., Glossary of Genetics: Classical and Molecular, 5th ed; Segen, Dictionary of Modern Medicine, 1992)
Breeding
The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.
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.
Software
Sequential operating programs and data which instruct the functioning of a digital computer.
Physical Chromosome Mapping
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
Chromosomes, Human, Pair 19
A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.
HLA-DQ beta-Chains
Transmembrane proteins that form the beta subunits of the HLA-DQ antigens.
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.
Population
The total number of individuals inhabiting a particular region or area.
Evolution, Molecular
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Genome
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
Chromosomes, Human, Pair 5
One of the two pairs of human chromosomes in the group B class (CHROMOSOMES, HUMAN, 4-5).
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.
Chromosome Inversion
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
Genome, Plant
The genetic complement of a plant (PLANTS) as represented in its DNA.
Genetic Testing
Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.
Chromosomes, Human
Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.
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.
Chromosomes, Human, Pair 2
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
Genes, Dominant
Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.
Chromosomes, Human, Pair 16
A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.
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.
Phylogeny
The relationships of groups of organisms as reflected by their genetic makeup.
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.
Genes, Recessive
Genes that influence the PHENOTYPE only in the homozygous state.
Europe
Africa
Family Health
The health status of the family as a unit including the impact of the health of one member of the family on the family as a unit and on individual family members; also, the impact of family organization or disorganization on the health status of its members.
Jews
An ethnic group with historical ties to the land of ISRAEL and the religion of JUDAISM.
Chromosomes, Human, X
The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.
Heterozygote Detection
Identification of genetic carriers for a given trait.
Bayes Theorem
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
Population Density
Number of individuals in a population relative to space.
Inbreeding
The mating of plants or non-human animals which are closely related genetically.
Chromosomes, Human, Pair 4
A specific pair of GROUP B CHROMOSOMES of the human chromosome classification.
Amplified Fragment Length Polymorphism Analysis
The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR amplification of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments.
Siblings
Persons or animals having at least one parent in common. (American College Dictionary, 3d ed)
Principal Component Analysis
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Crosses, Genetic
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
Ethnic Groups
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.
Finland
Genomics
The systematic study of the complete DNA sequences (GENOME) of organisms.
HLA-DQ alpha-Chains
Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.
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).
Monte Carlo Method
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
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)
Phosphoglucomutase
An enzyme that catalyzes the conversion of alpha D-glucose 1-phosphate to alpha D-glucose 6-phosphate. EC 5.4.2.2.
Minisatellite Repeats
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
Chromosomes, Human, Pair 20
A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.
Genetic Structures
The biological objects that contain genetic information and that are involved in transmitting genetically encoded traits from one organism to another.
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.
Probability
The study of chance processes or the relative frequency characterizing a chance process.
X Chromosome
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
Chromosomes, Human, Pair 10
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
China
A country spanning from central Asia to the Pacific Ocean.
Age of Onset
The age, developmental stage, or period of life at which a disease or the initial symptoms or manifestations of a disease appear in an individual.
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).
Chromosomes, Human, Pair 7
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Penetrance
The percent frequency with which a dominant or homozygous recessive gene or gene combination manifests itself in the phenotype of the carriers. (From Glossary of Genetics, 5th ed)
Population Groups
Individuals classified according to their sex, racial origin, religion, common place of living, financial or social status, or some other cultural or behavioral attribute. (UMLS, 2003)
Genes, Plant
The functional hereditary units of PLANTS.
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.
HLA-DR3 Antigen
An HLA-DR antigen which is associated with HLA-DRB1 CHAINS encoded by DRB1*03 alleles.
Databases, Genetic
Databases devoted to knowledge about specific genes and gene products.
Genetics, Medical
A subdiscipline of human genetics which entails the reliable prediction of certain human disorders as a function of the lineage and/or genetic makeup of an individual or of any two parents or potential parents.
DNA, Satellite
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Multifactorial Inheritance
A phenotypic outcome (physical characteristic or disease predisposition) that is determined by more than one gene. Polygenic refers to those determined by many genes, while oligogenic refers to those determined by a few genes.
Data Interpretation, Statistical
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
DNA Mutational Analysis
Biochemical identification of mutational changes in a nucleotide sequence.
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.
Japan
Biological Evolution
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Chromosomes
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
HLA-DP beta-Chains
Transmembrane proteins that form the beta subunits of the HLA-DP antigens.
Chromosomes, Human, Pair 22
A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.
Animals, Inbred Strains
Animals produced by the mating of progeny over multiple generations. The resultant strain of animals is virtually identical genotypically. Highly inbred animal lines allow the study of certain traits in a relatively pure form. (Segen, Dictionary of Modern Medicine, 1992)
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.
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.
DNA, Plant
Deoxyribonucleic acid that makes up the genetic material of plants.
Cohort Studies
Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics.
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.
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Markov Chains
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
Chromosomes, Plant
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
INDEL Mutation
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
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.
African Americans
Persons living in the United States having origins in any of the black groups of Africa.
Haploidy
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
Genetic Drift
The fluctuation of the ALLELE FREQUENCY from one generation to the next.
Chromosomes, Human, Pair 11
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Population Dynamics
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
Consanguinity
The magnitude of INBREEDING in humans.
Chromosomes, Human, Pair 21
A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.
Chromosomes, Mammalian
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
Family
A social group consisting of parents or parent substitutes and children.
France
A country in western Europe bordered by the Atlantic Ocean, the English Channel, the Mediterranean Sea, and the countries of Belgium, Germany, Italy, Spain, Switzerland, the principalities of Andorra and Monaco, and by the duchy of Luxembourg. Its capital is Paris.
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).
Chromosomes, Human, Pair 9
A specific pair of GROUP C CHROMSOMES of the human chromosome classification.
Demography
Statistical interpretation and description of a population with reference to distribution, composition, or structure.
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.
Sheep, Domestic
A species of sheep, Ovis aries, descended from Near Eastern wild forms, especially mouflon.
Chromosomes, Human, Pair 15
A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.
Chromosomes, Human, Pair 3
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
Apolipoproteins C
A group of apolipoproteins that can readily exchange among the various classes of lipoproteins (HDL; VLDL; CHYLOMICRONS). After lipolysis of TRIGLYCERIDES on VLDL and chylomicrons, Apo-C proteins are normally transferred to HDL. The subtypes can modulate remnant binding to receptors, LECITHIN CHOLESTEROL ACYLTRANSFERASE, or LIPOPROTEIN LIPASE.
Ecotype
Geographic variety, population, or race, within a species, that is genetically adapted to a particular habitat. An ecotype typically exhibits phenotypic differences but is capable of interbreeding with other ecotypes.
Sorghum
A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.
Friedreich Ataxia
An autosomal recessive disease, usually of childhood onset, characterized pathologically by degeneration of the spinocerebellar tracts, posterior columns, and to a lesser extent the corticospinal tracts. Clinical manifestations include GAIT ATAXIA, pes cavus, speech impairment, lateral curvature of spine, rhythmic head tremor, kyphoscoliosis, congestive heart failure (secondary to a cardiomyopathy), and lower extremity weakness. Most forms of this condition are associated with a mutation in a gene on chromosome 9, at band q13, which codes for the mitochondrial protein frataxin. (From Adams et al., Principles of Neurology, 6th ed, p1081; N Engl J Med 1996 Oct 17;335(16):1169-75) The severity of Friedreich ataxia associated with expansion of GAA repeats in the first intron of the frataxin gene correlates with the number of trinucleotide repeats. (From Durr et al, N Engl J Med 1996 Oct 17;335(16):1169-75)
Continental Population Groups
Groups of individuals whose putative ancestry is from native continental populations based on similarities in physical appearance.
Chromosomes, Human, Pair 17
A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.
Drosophila melanogaster
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Genetic Techniques
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
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.
Pan troglodytes
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
Gene Conversion
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
Matched-Pair Analysis
A type of analysis in which subjects in a study group and a comparison group are made comparable with respect to extraneous factors by individually pairing study subjects with the comparison group subjects (e.g., age-matched controls).
Chromosomes, Artificial, Yeast
Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.
Chromosomes, Human, Pair 13
A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.
Psoriasis
A common genetically determined, chronic, inflammatory skin disease characterized by rounded erythematous, dry, scaling patches. The lesions have a predilection for nails, scalp, genitalia, extensor surfaces, and the lumbosacral region. Accelerated epidermopoiesis is considered to be the fundamental pathologic feature in psoriasis.
HLA-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.
Lipoxygenases
Dioxygenases that catalyze the peroxidation of methylene-interrupted UNSATURATED FATTY ACIDS.
Alcohol Dehydrogenase
A zinc-containing enzyme which oxidizes primary and secondary alcohols or hemiacetals in the presence of NAD. In alcoholic fermentation, it catalyzes the final step of reducing an aldehyde to an alcohol in the presence of NADH and hydrogen.
Gene Components
The parts of the gene sequence that carry out the different functions of the GENES.
Cleft Lip
Congenital defect in the upper lip where the maxillary prominence fails to merge with the merged medial nasal prominences. It is thought to be caused by faulty migration of the mesoderm in the head region.
Genealogy and Heraldry
Italy
Statistical Distributions
The complete summaries of the frequencies of the values or categories of a measurement made on a group of items, a population, or other collection of data. The distribution tells either how many or what proportion of the group was found to have each value (or each range of values) out of all the possible values that the quantitative measure can have.
Inheritance Patterns
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
Apolipoprotein C-III
A 9-kDa protein component of VERY-LOW-DENSITY LIPOPROTEINS and CHYLOMICRON REMNANTS. Apo C-III, synthesized in the liver, is an inhibitor of LIPOPROTEIN LIPASE. Apo C-III modulates the binding of chylomicron remnants and VLDL to receptors (RECEPTORS, LDL) thus decreases the uptake of triglyceride-rich particles by the liver cells and subsequent degradation. The normal Apo C-III is glycosylated. There are several polymorphic forms with varying amounts of SIALIC ACID (Apo C-III-0, Apo C-III-1, and Apo C-III-2).
Esterases
Apolipoprotein C-I
A 6.6-kDa protein component of VERY-LOW-DENSITY LIPOPROTEINS; INTERMEDIATE-DENSITY LIPOPROTEINS; and HIGH-DENSITY LIPOPROTEINS. Apo C-I displaces APO E from lipoproteins, modulate their binding to receptors (RECEPTORS, LDL), and thereby decrease their clearance from plasma. Elevated Apo C-I levels are associated with HYPERLIPOPROTEINEMIA and ATHEROSCLEROSIS.
Cluster Analysis
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
HLA-DP alpha-Chains
Transmembrane proteins that form the alpha subunits of the HLA-DP antigens.
Picea
A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are evergreen, pyramidal trees with whorled branches and thin, scaly bark. Each of the linear, spirally arranged leaves is jointed near the stem on a separate woody base.
Cattle
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
North America
Regression Analysis
Procedures for finding the mathematical function which best describes the relationship between a dependent variable and one or more independent variables. In linear regression (see LINEAR MODELS) the relationship is constrained to be a straight line and LEAST-SQUARES ANALYSIS is used to determine the best fit. In logistic regression (see LOGISTIC MODELS) the dependent variable is qualitative rather than continuously variable and LIKELIHOOD FUNCTIONS are used to find the best relationship. In multiple regression, the dependent variable is considered to depend on more than a single independent variable.
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.
Mathematics
The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Crops, Agricultural
Cultivated plants or agricultural produce such as grain, vegetables, or fruit. (From American Heritage Dictionary, 1982)
Chromosomes, Human, Pair 8
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Hordeum
A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.
Indians, North American
Individual members of North American ethnic groups with ancient historic ancestral origins in Asia.
Africa, Northern
The geographical area of Africa comprising ALGERIA; EGYPT; LIBYA; MOROCCO; and TUNISIA. It includes also the vast deserts and oases of the Sahara. It is often referred to as North Africa, French-speaking Africa, or the Maghreb. (From Webster's New Geographical Dictionary, 1988, p856)
Deoxyribonucleases, Type II Site-Specific
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.
Genetic Speciation
The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
Reproducibility of Results
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Genes
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Zea mays
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
Germany

Inheritance in erythropoietic protoporphyria: a common wild-type ferrochelatase allelic variant with low expression accounts for clinical manifestation. (1/5532)

Erythropoietic protoporphyria (EPP) is a rare autosomal dominant disorder of heme biosynthesis characterized by partial decrease in ferrochelatase (FECH; EC 4.99.1.1) activity with protoporphyrin overproduction and consequent painful skin photosensitivity and rarely liver disease. EPP is normally inherited in an autosomal dominant pattern with low clinical penetrance; the many different mutations that have been identified are restricted to one FECH allele, with the other one being free of any mutations. However, clinical manifestations of dominant EPP cannot be simply a matter of FECH haploinsufficiency, because patients have enzyme levels that are lower than the expected 50%. From RNA analysis in one family with dominant EPP, we recently suggested that clinical expression required coinheritance of a normal FECH allele with low expression and a mutant FECH allele. We now show that (1) coinheritance of a FECH gene defect and a wild-type low-expressed allele is generally involved in the clinical expression of EPP; (2) the low-expressed allelic variant was strongly associated with a partial 5' haplotype [-251G IVS1-23T IVS2microsatA9] that may be ancestral and was present in an estimated 10% of a control group of Caucasian origin; and (3) haplotyping allows the absolute risk of developing the disease to be predicted for those inheriting FECH EPP mutations. EPP may thus be considered as an inherited disorder that does not strictly follow recessive or dominant rules. It may represent a model for phenotype modulation by mild variation in expression of the wild-type allele in autosomal dominant diseases.  (+info)

The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. II. Individual genotyping. (2/5532)

In this paper we consider test statistics based on individual genotyping. For sibships without parents, but with unaffected as well as affected sibs, we introduce a new test statistic (referred to as TDS), which contrasts the allele frequency in affected sibs versus that estimated for the parents from the entire sibship. For sibships without parents, this test is analogous to the TDT and is completely robust to nonrandom mating patterns. The efficiency of the TDS test is comparable to that of the THS test (which compares affected vs. unaffected sibs and was based on DNA pooling), for sibships with one affected child. However, as the number of affected sibs in the sibship grows, the relative efficiency of the TDS test versus the THS test also increases. For example, for sibships with three affected, one-third fewer families are required; for families with four affected, nearly half as many are required. Thus, when sibships contain multiple affected individuals, the TDS test provides both an increase in power and robustness to nonrandom mating.  (+info)

High-resolution physical and genetic mapping of the critical region for Meckel syndrome and Mulibrey Nanism on chromosome 17q22-q23. (3/5532)

Previously, we assigned the genes for two autosomal recessive disorders, Meckel syndrome (MKS; MIM 249000) and Mulibrey Nanism [MUL (muscle-liver-brain-eye Nanism); MIM 253250] that are enriched in the Finnish population, to overlapping genomic regions on chromosome 17q. Now, we report the construction of a bacterial clone contig over the critical region for both disorders. Several novel CA-repeat markers were isolated from these clones, which allowed refined mapping of the MKS and MUL loci using haplotype and linkage disequilibrium analysis. The localization of the MKS locus was narrowed to <1 cM between markers D17S1290 and 132-CA, within an approximately 800-kb region. The MUL locus was refined into an approximately 1400-kb interval between markers D17S1290 and 52-CA. The whole MKS region falls within the MUL region. In the common critical region, the conserved haplotypes were different in MKS and MUL patients. A trancript map was constructed by assigning expressed sequence tags (ESTs) and genes, derived from the human gene map, to the bacterial clone contig. Altogether, four genes and a total of 20 ESTs were precisely localized. These data provide the molecular tools for the final identification of the MKS and the MUL genes.  (+info)

Linkage disequilibrium and haplotype analysis in German Friedreich ataxia families. (4/5532)

The main mutation causing Friedreich ataxia (FRDA) is the expansion of a GAA repeat localized within the intron between exon 1 and exon 2 of the gene X25. This expansion has been observed in 98% of FRDA chromosomes. To analyze frequencies of markers tightly linked to the Friedreich ataxia gene and to investigate wheter a limited number of ancestral chromosomes are shared by German FRDA families, a detailed analysis employing nine polymorphic markers was performed. We found strong linkage disequilibria and association of FRDA expansions with a few haplotypes. FRDA haplotypes differ significantly from control haplotypes. Our results confirm that GAA repeat expansions in intron 1 of the frataxin gene are limited to a few chromosomes and indicate an obvious founder effect in German patients. Based on these analyses, we estimate a minimum age of the mutation of 107 generations.  (+info)

The 2588G-->C mutation in the ABCR gene is a mild frequent founder mutation in the Western European population and allows the classification of ABCR mutations in patients with Stargardt disease. (5/5532)

In 40 western European patients with Stargardt disease (STGD), we found 19 novel mutations in the retina-specific ATP-binding cassette transporter (ABCR) gene, illustrating STGD's high allelic heterogeneity. One mutation, 2588G-->C, identified in 15 (37.5%) patients, shows linkage disequilibrium with a rare polymorphism (2828G-->A) in exon 19, suggesting a founder effect. The guanine at position 2588 is part of the 3' splice site of exon 17. Analysis of the lymphoblastoid cell mRNA of two STGD patients with the 2588G-->C mutation shows that the resulting mutant ABCR proteins either lack Gly863 or contain the missense mutation Gly863Ala. We hypothesize that the 2588G-->C alteration is a mild mutation that causes STGD only in combination with a severe ABCR mutation. This is supported in that the accompanying ABCR mutations in at least five of eight STGD patients are null (severe) and that a combination of two mild mutations has not been observed among 68 STGD patients. The 2588G-->C mutation is present in 1 of every 35 western Europeans, a rate higher than that of the most frequent severe autosomal recessive mutation, the cystic fibrosis conductance regulator gene mutation DeltaPhe508. Given an STGD incidence of 1/10,000, homozygosity for the 2588G-->C mutation or compound heterozygosity for this and other mild ABCR mutations probably does not result in an STGD phenotype.  (+info)

Ancestral origins and worldwide distribution of the PRNP 200K mutation causing familial Creutzfeldt-Jakob disease. (6/5532)

Creutzfeldt-Jakob disease (CJD) belongs to a group of prion diseases that may be infectious, sporadic, or hereditary. The 200K point mutation in the PRNP gene is the most frequent cause of hereditary CJD, accounting for >70% of families with CJD worldwide. Prevalence of the 200K variant of familial CJD is especially high in Slovakia, Chile, and Italy, and among populations of Libyan and Tunisian Jews. To study ancestral origins of the 200K mutation-associated chromosomes, we selected microsatellite markers flanking the PRNP gene on chromosome 20p12-pter and an intragenic single-nucleotide polymorphism at the PRNP codon 129. Haplotypes were constructed for 62 CJD families originating from 11 world populations. The results show that Libyan, Tunisian, Italian, Chilean, and Spanish families share a major haplotype, suggesting that the 200K mutation may have originated from a single mutational event, perhaps in Spain, and spread to all these populations with Sephardic migrants expelled from Spain in the Middle Ages. Slovakian families and a family of Polish origin show another unique haplotype. The haplotypes in families from Germany, Sicily, Austria, and Japan are different from the Mediterranean or eastern European haplotypes. On the basis of this study, we conclude that founder effect and independent mutational events are responsible for the current geographic distribution of hereditary CJD associated with the 200K mutation.  (+info)

Age estimates of two common mutations causing factor XI deficiency: recent genetic drift is not necessary for elevated disease incidence among Ashkenazi Jews. (7/5532)

The type II and type III mutations at the FXI locus, which cause coagulation factor XI deficiency, have high frequencies in Jewish populations. The type III mutation is largely restricted to Ashkenazi Jews, but the type II mutation is observed at high frequency in both Ashkenazi and Iraqi Jews, suggesting the possibility that the mutation appeared before the separation of these communities. Here we report estimates of the ages of the type II and type III mutations, based on the observed distribution of allelic variants at a flanking microsatellite marker (D4S171). The results are consistent with a recent origin for the type III mutation but suggest that the type II mutation appeared >120 generations ago. This finding demonstrates that the high frequency of the type II mutation among Jews is independent of the demographic upheavals among Ashkenazi Jews in the 16th and 17th centuries.  (+info)

Genetic linkage of IgA deficiency to the major histocompatibility complex: evidence for allele segregation distortion, parent-of-origin penetrance differences, and the role of anti-IgA antibodies in disease predisposition. (8/5532)

Immunoglobulin A (IgA) deficiency (IgAD) is characterized by a defect of terminal lymphocyte differentiation, leading to a lack of IgA in serum and mucosal secretions. Familial clustering, variable population prevalence in different ethnic groups, and a predominant inheritance pattern suggest a strong genetic predisposition to IgAD. The genetic susceptibility to IgAD is shared with a less prevalent, but more profound, defect called "common variable immunodeficiency" (CVID). Here we show an increased allele sharing at 6p21 in affected members of 83 multiplex IgAD/CVID pedigrees and demonstrate, using transmission/diseqilibrium tests, family-based associations indicating the presence of a predisposing locus, designated "IGAD1," in the proximal part of the major histocompatibility complex (MHC). The recurrence risk of IgAD was found to depend on the sex of parents transmitting the defect: affected mothers were more likely to produce offspring with IgAD than were affected fathers. Carrier mothers but not carrier fathers transmitted IGAD1 alleles more frequently to the affected offspring than would be expected under random segregation. The differential parent-of-origin penetrance is proposed to reflect a maternal effect mediated by the production of anti-IgA antibodies tentatively linked to IGAD1. This is supported by higher frequency of anti-IgA-positive females transmitting the disorder to children, in comparison with female IgAD nontransmitters, and by linkage data in the former group. Such pathogenic mechanisms may be shared by other MHC-linked complex traits associated with the production of specific autoantibodies, parental effects, and a particular MHC haplotype.  (+info)

Hitchhikers Guide to the Galaxy on Linkage disequilibrium
In population genetics, linkage disequilibrium is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly.[1]. Linkage disequilibrium is influenced by many factors, including selection, the rate of recombination, the rate of mutation, genetic drift, the system of mating, population structure, and genetic linkage. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it.. In spite of its name, linkage disequilibrium may exist between alleles at different loci without any genetic linkage between them and independently of whether or not allele frequencies are in equilibrium (not changing with time).[1] Furthermore, linkage disequilibrium is sometimes referred to as gametic phase ...
http://hitchhikersgui.de/Linkage_disequilibrium
Efficient mining of haplotype patterns for linkage disequilibrium mapp by Lin L., Wong L. et al.Efficient mining of haplotype patterns for linkage disequilibrium mapp by Lin L., Wong L. et al.
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
http://ink.library.smu.edu.sg/sis_research/3016/
Single-nucleotide variations and linkage disequilibrium patterns in three candidate genes for attention deficit hyperactivity...
Abstract: Allelic variations in the genes involving the dopaminergic system, particularly the dopamine transporter (DAT1/SLC6A3), dopamine receptor 4 (DRD4) and Catecol-O-Methyltransferase (COMT) genes have been associated with Attention Deficit Hyperactivity Disorder (AD/HD). However, the results of these studies have been variable and inconclusive in part due to the inconsistencies of experimental and statistical methodologies, phenotypic heterogeneity, low penetrance of the genes implicated, and population stratification. Genetic association studies based on linkage disequilibrium (LD) offer a promising approach to the study of common complex diseases. This study characterized LD patterns in three human populations (CEU, YRI, CHB+JPT) in the three genes mentioned above and identified factors affecting the inconsistencies of genetic association studies in AD/HD. We used the HapMap database and the Haploview program to evaluate linkage disequilibrium patterns of SNPs in these genes. The ...
http://libres.uncg.edu/ir/listing.aspx?id=2368
A first-generation metric linkage disequilibrium map of bovine chromosome 6 - USPA first-generation metric linkage disequilibrium map of bovine chromosome 6 - USP
Descrição: We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming ...
http://www.buscaintegrada.usp.br/primo_library/libweb/action/display.do?ct=display&fn=search&doc=TN_medline16816421&indx=6&recIds=TN_medline16816421&recIdxs=5&elementId=0&renderMode=poppedOut&displayMode=full&vl
Leicester Research Archive: High levels of sequence polymorphism and linkage disequilibrium at the telomere of 12q:...
The human Xp/Yp telomere-junction region exhibits high levels of sequence polymorphism and linkage disequilibrium. To determine whether this is a general feature of human telomeres, we have undertaken sequence analysis at the 12q telomere and have extended the analysis at Xp/Yp. A total of 22 single-nucleotide polymorphisms (SNPs) and one 30-bp duplication were detected in the 1,870 bp adjacent to the 12q telomere. Twenty polymorphic positions were in almost complete linkage disequilibrium, creating three common diverged haplotypes accounting for 80% of 12q telomeres in the white population. A further 6% of 12q telomeres contained a 1,439-bp deletion in the DNA flanking the telomere. The remaining 13% of 12q telomeres did not amplify with the primers used (nulls). The distribution of telomere (TTAGGG) and variant repeats within 12q telomeres was hypervariable, but alleles with similar distribution patterns were associated with the same haplotype in the telomere-adjacent DNA. These data suggest ...
https://lra.le.ac.uk/handle/2381/25319
Linkage disequilibrium mapping of the chromosome 6q21-22.31 bipolar I disorder susceptibility locus. - Oxford Neuroscience
We previously reported genome-wide significant evidence for linkage between chromosome 6q and bipolar I disorder (BPI) by performing a meta-analysis of original genotype data from 11 genome scan linkage studies. We now present follow-up linkage disequilibrium mapping of the linked region utilizing 3,047 single nucleotide polymorphism (SNP) markers in a case-control sample (N = 530 cases, 534 controls) and family-based sample (N = 256 nuclear families, 1,301 individuals). The strongest single SNP result (rs6938431, P = 6.72 x 10(-5)) was observed in the case-control sample, near the solute carrier family 22, member 16 gene (SLC22A16). In a replication study, we genotyped 151 SNPs in an independent sample (N = 622 cases, 1,181 controls) and observed further evidence of association between variants at SLC22A16 and BPI. Although consistent evidence of association with any single variant was not seen across samples, SNP-wise and gene-based test results in the three samples provided convergent evidence for
https://www.neuroscience.ox.ac.uk/publications/168301
Genetic variability and linkage disequilibrium patterns in the bovine DNAJA1 gene. | GenPhySE
Correlation between expression level of the bovine DNAJA1 gene and meat tenderness was recently found in Charolais longissimus thoracis muscle samples, suggesting that this gene could play an important role in meat tenderness. Here, we report the validation of polymorphisms within the bovine DNAJA1 gene, and the haplotype variability and extent of linkage disequilibrium in the three main French beef breeds (Blonde dAquitaine, Charolais, Limousin). Genotyping 18 putative SNPs revealed that 16 SNPs were polymorphic within the breeds tested. Two SNPs were removed from further analyses as one SNP had a low genotyping call rate, while the other SNP was not in Hardy-Weinberg equilibrium. The degree of heterozygosity observed for the remaining 14 SNPs varied between breeds, with Charolais being the breed with the highest genetic variation and Blonde dAquitaine the lowest. Linkage disequilibrium and haplotype structure of DNAJA1 were different between breeds. Eighteen different haplotypes, including ...
https://genphyse.toulouse.inra.fr/content/genetic-variability-and-linkage-disequilibrium-patterns-bovine-dnaja1-gene
Single-nucleotide polymorphisms in the interleukin-10 gene: Differences in frequencies, linkage disequilibrium patterns, and...
TY - JOUR. T1 - Single-nucleotide polymorphisms in the interleukin-10 gene: Differences in frequencies, linkage disequilibrium patterns, and haplotypes in three United States ethnic groups. AU - Lazarus, R. AU - Klimecki, WT. AU - Palmer, Lyle. AU - Kwiatkowski, DJ. AU - Silverman, EK. AU - Brown, A. AU - Martinez, F. AU - Weiss, ST. PY - 2002. Y1 - 2002. N2 - Interleukin-10 (IL-10) is a cytokine that seems to function as a downregulator of the innate (nonadaptive) immune system. Approximately three-quarters of interindividual variability in human IL-10 levels has been attributed to genetic variation, and there is evidence suggesting a potential role for IL-10 in a range of human diseases. To provide a basis for haplotype analysis and future disease association studies, we characterized genetic variation in IL10 by sequencing all exons, and 2.5 kb of the 5- and the 3-flanking region in a panel of DNA samples from 24 African Americans, 23 European Americans, and 24 Hispanic Americans. The ...
https://research-repository.uwa.edu.au/en/publications/single-nucleotide-polymorphisms-in-the-interleukin-10-gene-differ
Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 geneLinkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene
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 ...
http://archie.kumc.edu/handle/2271/609
Linkage disequilibrium between four intragenic polymorphic microsatellites of the NF1 gene and its implications for genetic...Linkage disequilibrium between four intragenic polymorphic microsatellites of the NF1 gene and its implications for genetic...
Four intragenic polymorphic microsatellite markers, AAAT Alu repeat, IVS27AC28.4, ACI27.2, and IVS38GT53.0, located along a 65 kb DNA region of the NF1 gene, were used to genotype 64 Spanish families with neurofibromatosis type 1 (NF1). Linkage disequilirium between each pair of markers was evaluated. Three of these markers, AAAT Alu repeat, ACI27.2, and IVS38GT53.0, exhibit linkage disequilibrium between each other. Analysis of extended haplotypes provides further evidence of the disequilibrium within this region since only 11 haplotypes account for 52% of the total chromosomes. Because of linkage disequilibrium, the informativeness of marker combinations for genotyping of NF1 families is diminished. There was no difference in the overall distribution of alleles between affected and normal chromosomes. An at risk haplotype was not found, as expected for a disease with at least 50% of cases being sporadic.. ...
http://jmg.bmj.com/content/33/7/590
Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster.Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster.
Author(s): Smit-McBride, Z; Moya, A; Ayala, FJ | Abstract: We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to
https://escholarship.org/uc/item/61x2d33w
Experimental Designs for Reliable Detection of Linkage Disequilibrium in Unstructured Random Population Association Studies |...Experimental Designs for Reliable Detection of Linkage Disequilibrium in Unstructured Random Population Association Studies |...
THE advent of dense maps of single-nucleotide polymorphisms (SNPs) covering the genome with 300,000 or more markers offers new opportunities to find and identify genes, by testing for population-level associations between the SNP and disease or other trait of interest. Associations occur because of linkage disequilibrium between the marker and trait. Linkage disequilibrium (LD) mapping aims to detect and locate genes relative to a map of existing genetic markers. Location information is obtained because the distance between the gene and a marker on a chromosome is one factor influencing the closeness of association between the gene and marker. In a population, recombinations affecting the association between a gene and marker may occur over many generations. This potentially gives a much finer resolution than pedigrees used for quantitative trait loci (QTL) mapping. Finer resolution comes at a cost, however. More genotyping is needed per individual and as we shall show, larger sample sizes are ...
http://www.genetics.org/content/170/2/859.full
PLOS ONE: Handling Missing Data in Transmission Disequilibrium Test in Nuclear Families with One Affected OffspringPLOS ONE: Handling Missing Data in Transmission Disequilibrium Test in Nuclear Families with One Affected Offspring
The Transmission Disequilibrium Test (TDT) compares frequencies of transmission of two alleles from heterozygote parents to an affected offspring. This test requires all genotypes to be known from all members of the nuclear families. However, obtaining all genotypes in a study might not be possible for some families, in which case, a data set results in missing genotypes. There are many techniques of handling missing genotypes in parents but only a few in offspring. The robust TDT (rTDT) is one of the methods that handles missing genotypes for all members of nuclear families [with one affected offspring]. Even though all family members can be imputed, the rTDT is a conservative test with low power. We propose a new method, Mendelian Inheritance TDT (MITDT-ONE), that controls type I error and has high power. The MITDT-ONE uses Mendelian Inheritance properties, and takes population frequencies of the disease allele and marker allele into account in the rTDT method. One of the advantages of using the MITDT
http://journals.plos.org/plosone/article/related?id=10.1371/journal.pone.0046100&imageURI=info:doi/10.1371/journal.pone.0046100.t001
A meta-analysis and transmission disequilibrium study of association between the dopamine D3 receptor gene and schizophrenia ...A meta-analysis and transmission disequilibrium study of association between the dopamine D3 receptor gene and schizophrenia ...
We performed a meta-analysis of over 30 case-control studies of association between schizophrenia and a bi-allelic, Bali polymorphism in exon 1 of the dopamine D3 receptor gene. We observed a significant excess of both forms of homozygote in patients (P = 0.0009, odds ratio (OR) = 1.21, 95% Confidence Interval (CI) = 1.07-1.35) in the combined sample of 5351 individuals. No significant heterogeneity was detected between samples and the effects did not appear to be the product of publishing bias. In addition we undertook an independent, family-based association study of this polymorphism in 57 parent/proband trios, taken from unrelated European multiplex families segregating schizophrenia. A transmission disequilibrium test (TDT) showed a significant excess of homozygotes in schizophrenic patients (P = 0.004, odds ratio (OR) = 2.7, 95% CI = 1.35-5.86). Although no significant allelic association was observed, a significant association was detected with the 1-1 genotype alone (P = 0.02, OR = 2.32, ...
https://orca.cf.ac.uk/81730/
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads | BMC Bioinformatics | Full TextLinkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads | BMC Bioinformatics | Full Text
Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping. In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage. A software package implementing our algorithm, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/GeneSeq/ . Integration of LD information leads
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-S1-S53
Transmission disequilibrium test - WikipediaTransmission disequilibrium test - Wikipedia
The transmission disequilibrium test (TDT) was proposed by Spielman, McGinnis and Ewens (1993) as a family-based association test for the presence of genetic linkage between a genetic marker and a trait. It is an application of McNemars test. A specificity of the TDT is that it will detect genetic linkage only in the presence of genetic association. While genetic association can be caused by population structure, genetic linkage will not be affected, which makes the TDT robust to the presence of population structure. We first describe the TDT in the case where families consist of trios (two parents and one affected child). Our description follows the notations used in Spielman, McGinnis & Ewens (1993). The TDT measures the over-transmission of an allele from heterozygous parents to affected offsprings. The n affected offsprings have 2n parents. These can be represented by the transmitted and the non-transmitted alleles M 1 {\displaystyle M_{1}} and M 2 {\displaystyle M_{2}} at some genetic ...
https://en.wikipedia.org/wiki/Transmission_disequilibrium_test
Genotype at the -174G/C polymorphism of the interleukin-6 gene is associated with common carotid artery intimal-medial...Genotype at the -174G/C polymorphism of the interleukin-6 gene is associated with common carotid artery intimal-medial...
BACKGROUND AND PURPOSE: Studies in unrelated individuals have produced conflicting findings concerning the putative association between the interleukin-6 (IL-6) -174G/C polymorphism and carotid intimal-medial thickness (IMT). We have used a family-based genetic association design to assess the heritability of carotid IMT and to investigate the hypothesized association of carotid IMT with the IL-6 to -174G/C polymorphism. METHODS: We studied 854 members of 224 white British families. The heritability of carotid IMT was determined using Multipoint Engine for Rapid Likelihood Inference. Genetic association analyses were carried out using ANOVA and family-based tests of association implemented in Quantitative Transmission Disequilibrium Test. A meta-analysis of previous studies of the association was conducted to place our result in context. RESULTS: The heritability of carotid IMT was 24%. Under a recessive model (GG+GC versus CC), there was significant evidence of association between IL-6 to the -174G/C
https://www.rdm.ox.ac.uk/publications/104221
Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium testUndetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test
The transmission/disequilibrium test (TDT), a family-based test of linkage and association, is a popular and intuitive statistical test for studies of complex inheritance, as it is nonparametric and robust to population stratification. We carried out a literature search and located 79 significant TD …
https://pubmed.ncbi.nlm.nih.gov/12587097/?dopt=Abstract
Transmission disequilibrium test (TDT) when only one parent is available : The 1-TDT. | Base documentaire | BDSP
The transmission disequilibrium test TDT is a useful method to locate mutations linked to disease genes associated with complex diseases. TDT requires genotypes of affected individuals and their parents. Recently, Ewens and Spielman Am J Hum Genet 1998 ; 62 : 450-8 extended the TDT for use in sibships with at least one affected and one...
http://www.bdsp.ehesp.fr/Base/192823/
Structure of linkage disequilibrium and phenotypic associations in the maize genome. - Semantic ScholarStructure of linkage disequilibrium and phenotypic associations in the maize genome. - Semantic Scholar
Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) | 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial
https://www.semanticscholar.org/paper/Structure-of-linkage-disequilibrium-and-phenotypic-Remington-Thornsberry/cfa9750e27cf941e97aa636a123d126b198756b8
Leicester Research Archive: Localized breakdown in linkage disequilibrium does not always predict sperm crossover hot spots in...
To investigate the relationship between meiotic crossover hot spots and block-like linkage disequilibrium (LD), we have extended our high-resolution studies of the human MHC class II region to a 90-kb segment upstream of the HLA-DOA gene. LD blocks in this region are not as well defined as in the neighboring 210-kb DNA segment but do show two regions of LD breakdown in which coalescent analysis indicates substantial historical recombination. Sperm crossover analysis of one region revealed a novel localized hot spot similar in intensity and morphology to most other MHC hot spots. Crossovers at this hot spot are not obviously affected by a large insertion/deletion polymorphism near the hot spot. The second region of LD breakdown, within the DPB1 gene, shows an extremely low level of sperm crossover activity and does not contain a sperm crossover hot spot. These results highlight the complexity of LD patterns and the importance of experimentally verifying crossover hot spots ...
https://lra.le.ac.uk/handle/2381/15426
Genetic variation at the chromosome 16 chemokine gene cluster: development of a strategy for association studies in complex...
The chemokine gene cluster [CCL22, CX3CL1, CCL17] (previously known as [SCYA22, SCYD1, SCYA17]) is a candidate locus for one of the susceptibility genes for inflammatory bowel disease that are located in the peri-centromeric region of chromosome 16. Screening for sequence variation at this locus led to the detection of 14 single nucleotide polymorphisms (SNPs). An efficient experimental and computational approach was developed to estimate allele frequencies and pairwise linkage disequilibrium relationships between SNPs at this locus, and to test them for association with inflammatory bowel disease. The 12 common SNPs were assigned to 5 distinct linkage disequilibrium groups. Genotyping of one SNP from each linkage disequilibrium group in a large cohort of families with inflammatory bowel disease did not provide convincing evidence of association with either Crohns disease or ulcerative colitis. We describe an efficient experimental design from SNP screening to association testing. This ...
http://www.ikmb.uni-kiel.de/publications/genetic-variation-chromosome-16-chemokine-gene-cluster-development-strategy-association
Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate...Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate...
Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436-0.566) were generally much higher than individual SNPs (0.247-0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024861
Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus - Immunology
Four cytokine receptor genes are located on Chr21q22.11, encoding the alpha and beta subunits of the interferon-alpha receptor (IFNAR1 and IFNAR2), the beta subunit of the interleukin 10 receptor (IL10RB) and the second subunit of the interferon-gamma receptor (IFNGR2). We previously reported that two variants in IFNAR1 were associated with susceptibility to malaria in Gambians. We now present an extensive fine-scale mapping of the associated region utilizing 45 additional genetic markers obtained from public databases and by sequencing a 44 kb region in and around the IFNAR1 gene in 24 Gambian children (12 cases/12 controls). Within the IFNAR1 gene, a newly studied C -| G single-nucleotide polymorphism (IFNAR1 272354c-g) at position -576 relative to the transcription start was found to be more strongly associated with susceptibility to severe malaria. Association was observed in three populations: in Gambian (P=0.002), Kenyan (P=0.022) and Vietnamese (P=0.005) case-control studies. When all three
https://www.immunology.ox.ac.uk/publications/27232/
Linkage disequilibrium questionsLinkage disequilibrium questions
Hello! My name is Franco and I have been involved in the field of epidemiology and molecular biology for few months. The purpose of my research group is to perform a case-control study on a multifactorial disease, such as myocardial infarction, on the basis of different genotypes among an Italian population. Differences, or polymorphism, at different genetic loci (such as at all known risk factors for myocardial infarction genetic sites) is one of the topics of my group. Anyway, I have some unsolved questions and I would appreciate very much if someone helped me suggesting appropriate literature (sendind correctly references) or directly answering me by e-mail. Which are the mathematical basis of the linkage disequilibrium? Which are the parameters considered in the analysis? I dont understand, in a correct and simple way, the methods to analyze DNA changes on the basis of polymorphic sites (already linked, previously, to the disease!) more or less in linkage disequilibrium. Why the ...
http://www.bio.net/bionet/mm/gen-link/1995-July/000762.html
Linkage disequilibrium mapping via cladistic analysis of SNP haplotypes. - Wellcome Centre for Human Genetics
We use cookies to ensure that we give you the best experience on our website. If you click Continue well assume that you are happy to receive all cookies and you wont see this message again. Click Find out more for information on how to change your cookie settings ...
https://www.well.ox.ac.uk/publications/50021
Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish SaamiGenome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami
The Saami from Fennoscandia are believed to represent an ancient, genetically isolated population with no evidence of population expansion. Theoretical work has indicated that under this demographic scenario, extensive linkage disequilibrium (LD) is generated by genetic drift. Therefore, it has been suggested that the Saami would be particularly suited for genetic association studies, offering a substantial power advantage and allowing more economic study designs. However, no study has yet assessed this claim. As part of a GWAS for a complex trait, we evaluated the relative power for association studies of common variants in the Finnish Saami. LD patterns in the Saami were very similar to those in the non-African HapMap reference panels. Haplotype diversity was reduced and, on average, levels of LD were higher in the Saami as compared with those in the HapMap panels. However, using a hidden SNP approach we show that this does not translate into a power gain in association studies. Contrary to ...
http://liu.diva-portal.org/smash/record.jsf?pid=diva2:666273
LDlink | An Interactive Web Tool for Exploring Linkage Disequilibrium in Population Groups
LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.
https://ldlink.nci.nih.gov/?tab=ldmatrix
Genome-Wide Association Study of Intracranial Aneurysms Confirms Role of Anril and SOX17 in Disease Risk | StrokeGenome-Wide Association Study of Intracranial Aneurysms Confirms Role of Anril and SOX17 in Disease Risk | Stroke
We found the strongest evidence of association with a SNP in CDKN2BAS, also known as ANRIL. Previous studies reported an association of IA,2-6,18,19 as well as myocardial infarction,18 largevessel ischemic stroke subtype,20 and aortic aneurysm,18,21 with SNP in this region. Others6 examined the association in multiplex families as well as sporadic IA and found consistent evidence of association with rs1333040 (allele T), located in intron 12 of CDKN2BAS and having limited linkage disequilibrium spanning introns 7 through 15 of CDKN2BAS. The association of this SNP with both sporadic and familial IA parallels our findings. In DS1, we found evidence for association with the highrisk T allele (P=0.02; odds ratio, 1.26). We imputed this SNP in the ARIC sample and saw even greater evidence of this association in DS2 (P=1.4 × 10−5; odds ratio, 1.29). When the 2 samples were combined, the association strengthened (P=7.6 × 10−6; odds ratio, 1.29).. The linkage disequilibrium structure of the ...
http://stroke.ahajournals.org/content/43/11/2846.long
Multiple loci on 8q24 associated with prostate cancer susceptibility. - Oxford Clinical Trials Research Unit
Previous studies have identified multiple loci on 8q24 associated with prostate cancer risk. We performed a comprehensive analysis of SNP associations across 8q24 by genotyping tag SNPs in 5,504 prostate cancer cases and 5,834 controls. We confirmed associations at three previously reported loci and identified additional loci in two other linkage disequilibrium blocks (rs1006908: per-allele OR = 0.87, P = 7.9 x 10(-8); rs620861: OR = 0.90, P = 4.8 x 10(-8)). Eight SNPs in five linkage disequilibrium blocks were independently associated with prostate cancer susceptibility.
https://www.octru.ox.ac.uk/publications/107751
Ancestry-informative marker - WikipediaAncestry-informative marker - Wikipedia
In population genetics, an ancestry-informative marker (AIM) is a single-nucleotide polymorphism that exhibits substantially different frequencies between populations from different geographical regions. A set of many AIMs can be used to estimate the proportion of ancestry of an individual derived from each geographical region. As one example, the Duffy Null allele (FY*0) has a frequency of almost 100% of Sub-Saharan Africans, but occurs very infrequently in populations outside of this region. A person having this allele is thus more likely to have Sub-Saharan African ancestors. Examining a suite of these markers more or less evenly spaced across the genome is also a cost-effective way to discover novel genes underlying complex diseases in a technique called admixture mapping or mapping by admixture linkage disequilibrium. There are an estimated 15 million SNP (Single-nucleotide polymorphism) sites (out of roughly 3 billion base pairs, or about 0.4%) from among which AIMs may potentially be ...
https://en.wikipedia.org/wiki/Ancestry-informative_marker
Pesquisa | Portal Regional da BVSPesquisa | Portal Regional da BVS
BACKGROUND: Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of limited statistical power and experimental constraints. Fitness epistasis is inferred from non-independence between unlinked loci. We previously observed ancestral block correlation between chromosomes 4 and 6 in African Americans. The same approach fails when examining ancestral blocks on the same chromosome due to the strong confounding effect observed in a recently admixed population. RESULTS: We developed a novel approach to eliminate the bias caused by admixture linkage disequilibrium when searching for fitness epistasis on the same chromosome. We applied this approach in 16,252 unrelated African Americans and identified significant ancestral correlations in two pairs of ...
https://pesquisa.bvsalud.org/portal/?lang=pt&q=au:%22Wang,%20Heming%22
MULTIVARIATE ANALYSIS OF GAMETIC DISEQUILIBRIUM IN THE YANOMAMA | GeneticsMULTIVARIATE ANALYSIS OF GAMETIC DISEQUILIBRIUM IN THE YANOMAMA | Genetics
The gametic disequilibria between all possible pairs of loci were examined for a set of eight codominant loci in each of fifty Yanomama villages, using a multivariate correlation analysis which reduces the results to a single measure of departure from multiple-locus-gametic equilibrium. Thirty-two of the fifty villages departed significantly from multiple-locus gametic equilibrium. The largest contributions to the departure from multiple-locus equilibrium were due to the disequilibria between MN and Ss and between Rh(Cc) and Rh(Ee), indicating the effects of tight linkage. After removing the effects of these obvious sources of disequilibrium, sixteen of the fifty villages still remained significantly out of equilibrium. The disequilibrium between any particular pair of loci was highly erratic from village to village, and (with the exception of the MN-Ss and Cc-Ee disequilibria) averaged out very close to zero overall, suggesting a lack of systematic forces (epistatic selection). The departure ...
http://www.genetics.org/content/85/4/733
Genie 2.7.2.1 - Analyze Association and Transmission Disequilibrium (TDT) - My Biosoftware - Bioinformatics Softwares BlogGenie 2.7.2.1 - Analyze Association and Transmission Disequilibrium (TDT) - My Biosoftware - Bioinformatics Softwares Blog
DESCRIPTION. GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests ...
https://www.mybiosoftware.com/genie-2-7-2-1-analyze-association-transmission-disequilibrium-tdt.html
MCP-1-MCP-3-Eotaxin Gene Cluster Influences HIV-1 Transmission by William Modi, James J. Goedert et al.MCP-1-MCP-3-Eotaxin Gene Cluster Influences HIV-1 Transmission by William Modi, James J. Goedert et al.
Background: MCP-1 (CCL2), MCP-3 (CCL7), and eotaxin (CCL11) are genes for CC chemokines clustered on the long arm of chromosome 17. Previous studies have implicated these chemokines in monocyte recruitment, viral replication, and anti-HIV cytotoxic T cell responses. An epidemiological analysis identified genetic variants influencing HIV-1 transmission and disease progression. Methods: Genomic DNA from over 3000 participants enrolled in five natural history cohorts in the United States were analyzed. Nine single nucleotide polymorphisms (SNP) covering 33 kb containing these three genes were genotyped using the polymerase chain reaction. Distortions in allele, genotype, and haplotype frequencies were assessed with respect to HIV-1 transmission and rates of disease progression using categorical and survival analyses. Results: Extensive linkage disequilibrium was observed. Three SNP (−2136T located in theMCP-1 promoter region, 767G in intron 1 of MCP-1, and −1385A in the Eotaxin promoter) were nearly
http://nsuworks.nova.edu/cnso_bio_facarticles/626/
Publication : USDA ARSPublication : USDA ARS
Citation: Perez OBrien, A.M., Meszaros, G., Utsunomiya, Y.T., Sonstegard, T.S., Fernando Garcia, J., Van Tassell, C.P., Carvalheiro, R., Da Silva, M.V., Solkner, J. 2014. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. Livestock Science. 166:121-132. Interpretive Summary: Technical Abstract: Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r² measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777000 single nucleotide ...
https://www.ars.usda.gov/research/publications/publication/?seqNo115=302845
Comparison of the QTDT analysis for IgE in the CSGA data set<...
TY - JOUR. T1 - Comparison of the QTDT analysis for IgE in the CSGA data set. AU - Page, G. P.. AU - Wilcox, M. A.. AU - Occhiuto, J.. AU - Adak, S.. AU - Neuberg, D.. AU - Bajorunaite, R.. AU - George, V.. PY - 2001. Y1 - 2001. N2 - Over the past few years at least 13 transmission/disequilibrium test (TDT)-based tests have been developed for quantitative (Q) traits for the assessment of association or linkage in the presence of the other. A total of six of these QTDT methods were used to analyze log10IgE in the Collaborative Study on the Genetics of Asthma data set. Only moderate agreement was found between the tests. The results of the QTDT analyses were only slightly affected by the use of gender and age as covariates. Results from analysis of IgE and log10IgE were inconsistent. Our conclusion is that there is only modest agreement among the QTDT methods examined, covariates should be used even if they have a small effect, and that data should be normalized before analysis.. AB - Over the ...
https://augusta.pure.elsevier.com/en/publications/comparison-of-the-qtdt-analysis-for-ige-in-the-csga-data-set
Contributions of linkage disequilibrium and co-segregation information to the accuracy of genomic prediction | Genetics...Contributions of linkage disequilibrium and co-segregation information to the accuracy of genomic prediction | Genetics...
In the Common QTL scenario with high historical LD, the LD model had higher accuracy than either the CS or LD-CS model (Fig. 3). For all three pedigrees, the LD-CS model had slightly lower accuracy than the LD model, but the CS model had much lower accuracy than the LD model. Accuracies from the LD and LD-CS models only decreased marginally across the eight validation generations, but the accuracy of the CS model decreased rapidly (Fig. 3). These results suggest that when historical LD between QTL and SNPs is high, the LD model has persistently high accuracy across validation generations without retraining by accurately capturing QTL effects. The CS model estimates only the values of founder alleles, and the values of recombinant alleles that are generated across generations cannot be accurately estimated. Accuracies of the LD and LD-CS models were similar for all three pedigrees, because accuracy was mostly contributed by LD that was generated historically, which was not eroded within a limited ...
https://gsejournal.biomedcentral.com/articles/10.1186/s12711-016-0255-4
Investigation of recombination hotspots and blocks of linkage disequilibrium within the human PGM1 gene - UCL DiscoveryInvestigation of recombination hotspots and blocks of linkage disequilibrium within the human PGM1 gene - UCL Discovery
UCL Discovery is UCLs open access repository, showcasing and providing access to UCL research outputs from all UCL disciplines.
http://discovery.ucl.ac.uk/182204/
Variation summary | EMBL-EBI Train onlineVariation summary | EMBL-EBI Train online
When you click on a variation ID (for example, rs1333049) from Ensembl views, the variation tab will open up (Figure 31). Figure 31. Information about rs1333049 is accessible through links in the left-hand menu, and through icons. Click on any link or icon to go to information such as population genetics, linkage disequilibrium, or phenotypes and diseases associated with this SNP. Click on the icons to find information about this SNP. Specifically: Genomic context. View the variant graphically on the genome Genes and regulation. Find out what genes might be affected by this variant Population genetics. See allele frequencies across populations Individual genotypes. Find out which alleles are carried by individuals Linkage disequilibrium. View LD plots and export values Phenotype data. See diseases and phenotypes associated with the variant Phylogenetic context. Compare the nucleotide across species Flanking sequence. View the sequence upstream and downstream of the variant Figure 32. The top panel
https://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/navigating-ensembl/investigating-sequence-variation/varia-1
Oalib searchOalib search
Abstract: In this study, five proposed causal SNPs in SERPINE2 were genotyped in 327 COPD patients and 349 controls, all of which belonged to the Han population sampled from Southwest China. The frequency of each SNP was compared both individually and in combination between patients and controls. The potential relationship between these SNPs and severity of COPD was also investigated.Three SNPs (rs3795877, rs6747096, and rs3795879) showed complete linkage disequilibrium (r2 = 1), and the minor allele frequencies were 13.0% and 12.9% in case and control cohorts, respectively, with no significant difference observed (P = 0.96). We also failed to observe any significant correlation between these SNPs and COPD severity (P = 0.67). The other two SNPs (rs7579646 and rs840088) also presented a similar pattern. Moreover, four major haplotypes were observed in our sample but none showed a significant difference between case and control groups (P > 0.1).Our results failed to obtain the evidence that these ...
http://www.oalib.com/search?kw=Ya-Ping%20Zhang&searchField=authors
mendel-gpu - GPU enabled Haplotying and Genotype Imputation - My Biosoftware - Bioinformatics Softwares Blogmendel-gpu - GPU enabled Haplotying and Genotype Imputation - My Biosoftware - Bioinformatics Softwares Blog
DESCRIPTION. mendel-gpu uses OpenCL kernels to rapidly impute genotypes using linkage disequilibrium patterns in unrelated subjects. It is appropriate for resequencing data. ...
https://mybiosoftware.com/mendel-gpu-gpu-enabled-haplotying-and-genotype-imputation.html
Using Coalescent-Based Modeling for Large-Scale Fine Mapping of Complex Trait Loci using Sequencing Data in Large-Scale Case...Using Coalescent-Based Modeling for Large-Scale Fine Mapping of Complex Trait Loci using Sequencing Data in Large-Scale Case...
Association mapping based on linkage disequilibrium (LD) is widely used to identify genomic regions containing disease variants. However, due to the complicated genetic dependence structure, identifying the underlying risk variants for complex diseases is challenging. By modeling the evolutionary process that produces our sequencing data, coalescent-based approaches may extract more information to improve such mapping. Such methods provide the genealogy at all sites in the region we have sequenced. Therefore, we can model the probability of carrying risk variants at all loci jointly, and obtain Bayesian confidence intervals (CIs) where true risk variants are most likely to occur. Additionally, the genealogy at each position provides more information about the shared ancestry of neighboring sites. Indeed, such careful modeling of the shared ancestry of sequences may also be beneficial in haplotyping and variant calling in regions of interests (ROI) where traditional hidden Markov approaches ...
http://www.ashg.org/2013meeting/abstracts/fulltext/f130121751.htm
Plus itPlus it
Seven exons (exon B and 1-6) and ∼12 kb of the PPARγ2-specific promoter were sequenced in 24 Pima Indians. Nine SNPs were identified (Fig. 1). Two of the SNPs were in the coding region, a C/G in exon B predicting a Pro12Ala substitution (SNP8) and a C/T in exon 6 predicting a silent His477His substitution (SNP9). The other seven SNPs were in the promoter. Based on the genotypes of the 24 Pima Indians, SNP 1 appeared to be in complete linkage disequilibrium with SNP 2. SNP 6 was a common variant (allele frequency 0.58) and was positioned within a putative δEF1 binding site relatively close to the transcriptional start site of the PPARγ2 gene. Therefore, SNP 6 (C-2821T) and SNP 8, the well-documented Pro12Ala variant, were selected for our initial detailed analysis.. The C-2821T and the Pro12Ala variants were further genotyped in DNA from 985 full-blooded Pima Indians for association analyses. Both SNPs were in Hardy-Weinberg equilibrium. In addition, both SNPs were modestly associated with ...
http://diabetes.diabetesjournals.org/content/52/7/1864
GENOMEPOP: A program to simulate genomes in populations | BMC Bioinformatics | Full TextGENOMEPOP: A program to simulate genomes in populations | BMC Bioinformatics | Full Text
There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using backward or forward strategies. Backward simulations, also called coalescent-based simulations, are computationally efficient. The reason is that they are based on the history of lineages with surviving offspring in the current population. On the contrary, forward simulations are less efficient because the entire population is simulated from past to present. However, the coalescent framework imposes some limitations that forward simulation does not. Hence, there is an increasing interest in forward population genetic simulation and efficient new tools have been developed recently. Software tools that allow efficient simulation of large DNA fragments under complex evolutionary models will be very helpful when trying to better understand the trace left on the DNA by the different interacting
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-223
Of association & evolution - Gene ExpressionOf association & evolution - Gene Expression
These nuances of genetic architecture are not irrelevant to the possible evolutionary arc of the traits in question. One model of the adaptation leading to the high frequency of a trait or disease is that a novel mutation rapidly sweeps to fixation, or nearly to fixation. In other words, it shifts from nearly ~0% to nearly ~100% frequency in the population of alleles at that locus, driven by positive selection. This sort of rapid hard sweep would also result in hitchhiking of associated variants in the genomic regions adjacent to the originally favored mutant, producing regions of high linkage disequilibrium in the genome and haplotype blocks of associated alleles across loci. Such a model does seem possible in the case of some of the variants which are responsible for diversity of pigmentation. But this neat dovetailing between the strong association of a few variants with trait variance, and signatures of positive selection being driven by adaptation, is not so easy to come by in many ...
http://blogs.discovermagazine.com/gnxp/2011/01/of-association-amp-evolution/
Mathematical Biology at the University of UtahMathematical Biology at the University of Utah
Pairwise linkage disequilibrium, haplotype blocks and recombination hot spots provide only a partial description of the patterns of dependences and independences between the allelic states at proximal loci. On the gross scale, where recombination and spatial relationships dominate, the associations can be reasonably described in these terms. However, on the fine scale of current high density maps the mutation process is also important and creates associations between loci which are independent of the physical ordering and which can not be summarized with pairwise measures of association. Graphical modeling provides a standard statistical framework for characterizing precisely this sort of complex stochastic data. While graphical models are often used in situations where assumptions lead naturally to specific models, it is less well known that estimation of graphical models is also a developed field. We show how decomposable graphical models can be fitted to dense genetic data. The objective ...
http://www.math.utah.edu/research/mathbio/seminar/mathbio_seminar_abstracts/Thomas_abstract.html
ATRIUM Software PageATRIUM Software Page
ATRIUM is a C++ program that performs case-control association testing between a binary trait and an untyped SNP, based on genotype data from multiple typed SNPs that are in linkage disequilibrium with the untyped SNP, where information on the joint distribution of typed and untyped SNPs is obtained from an external reference panel. A special feature of ATRIUM is that both related and unrelated individuals can be included in the case-control sample. The user specifies a set of untyped SNPs on which external reference panel information is available, and the ATRIUM program computes a test statistic for association with each untyped SNP in the set. This test is suitable for case-control analysis in any outbred sample with related and/or unrelated individuals, including large pedigrees, provided that the relationships are known ...
http://www.stat.uchicago.edu/~mcpeek/software/ATRIUM/index.html
A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp,...A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp,...
Jones, DB, Jerry, DR, Khatkar, MS, Raadsma, HW, Steen, HV, Prochaska, J, Foret, S and Zenger, KR (2017). A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei. Scientific Reports 7(1): 10360 ...
https://www.coralcoe.org.au/publication/a-comparative-integrated-gene-based-linkage-and-locus-ordering-by-linkage-disequilibrium-map-for-the-pacific-white-shrimp-litopenaeus-vannamei
Epistatic control of human obesity as revealed by linkage disequilibrium mapping: A report from the NHLBI-sponsored WISE study<...
TY - JOUR. T1 - Epistatic control of human obesity as revealed by linkage disequilibrium mapping. T2 - A report from the NHLBI-sponsored WISE study. AU - Li, Hongying. AU - Wu, Rongling. AU - Lin, Min. AU - Terra, Steve G.. AU - Pepine, Carl J.. AU - McGorray, Susan P.. AU - Johnson, B. Delia. AU - Johnson, Julie A.. PY - 2006/11/1. Y1 - 2006/11/1. N2 - Obesity is a major risk factor for type II diabetes, hypertension, cardiovascular disease and certain forms of cancers. Obesity is a complex, multifactorial disorder, influenced by a network of genes, as well as diet, age, ethnicity, gender and exercise. Single nucleotide polymorphisms (SNPs) genotyped in six candidate genes for lipolysis and thermogenesis in human adipose tissue were used to identify and estimate epistatic quantitative trait loci (QTL) predisposing to human obesity based on linkage disequilibrium analysis for 105 black women and 538 white women drawn from the Womens Ischemia Syndrome Evaluation (WISE) study. A few pairs of ...
https://pennstate.pure.elsevier.com/en/publications/epistatic-control-of-human-obesity-as-revealed-by-linkage-disequi
Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in...
The objective of this study was to identify single-nucleotide polymorphisms using a bovine chromosome 14 high-density SNP panel after accounting for the effect of DGAT1. Linkage disequilibrium information and sire heterozygosity were used to select m
http://www.biomedsearch.com/nih/Identification-candidate-markers-bovine-chromosome/21749477.html
Enhanced Linkage Maps From Family-Based Genetics Studies - Full Text View - ClinicalTrials.govEnhanced Linkage Maps From Family-Based Genetics Studies - Full Text View - ClinicalTrials.gov
BACKGROUND:. Meiotic linkage maps are the foundation of both linkage and linkage disequilibrium studies for mapping disease genes. Despite the importance of precise maps, existing genome-wide linkage maps were built using only a small collection of pedigrees, and so have wide confidence intervals surrounding estimates of map distance. Incorrect marker order and map distances can have a profound effect on linkage analyses. Using a sex-averaged map instead of a sex-specific map biases the lod scores upward, markedly increasing the false positive rate. Since it is very costly to follow-up many false-positive results, there is a clear need for more precise and accurate sex-specific genetic maps. Accurate estimates of meiotic map distance cannot be obtained by any means other than by linkage analysis using genotype data.. The study is in response to a Request for Applications entitled NHLBI Innovative Research Grant Program released in July, 2001. The purpose of the initiative is to support new ...
https://clinicaltrials.gov/ct2/show/NCT00049868
Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk ScoresModeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to associati …
https://pubmed.ncbi.nlm.nih.gov/26430803/?dopt=Abstract
Dienekes Anthropology Blog: Population structure in the NetherlandsDienekes Anthropology Blog: Population structure in the Netherlands
Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the ...
http://dienekes.blogspot.com/2013/03/population-structure-in-netherlands.html?showComment=1364468068487
A low-cost open-source SNP genotyping platform for association mapping applications | Genome Biology | Full TextA low-cost open-source SNP genotyping platform for association mapping applications | Genome Biology | Full Text
Understanding the genetic architecture of complex polygenic traits is a fundamental goal of modern biological and medical research, and the currently favored experimental paradigm is association mapping (reviewed by Carlson et al. [1]). Association studies genotype a dense set of single nucleotide polymorphisms (SNPs) in a large panel of individuals and test each SNP, or set of local haplotypes constructed from the SNP data, for a phenotype/disease association. A significant association at a query SNP suggests it is the causal polymorphism, or is in strong linkage disequilibrium with the causal site [2-4]. As a class, SNPs represent the most abundant form of genetic variation, with approximately two intermediate frequency SNPs per kilobase in the human genome [5]. Thus, even with some a priori knowledge of a candidate gene region contributing to a disease phenotype, a large number of SNPs need to be genotyped in an association mapping study to ensure one of the genotyped SNPs is causative or is ...
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-12-r105
CRAN Task View: Statistical GeneticsCRAN Task View: Statistical Genetics
Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
https://cran.ncc.metu.edu.tr/web/views/Genetics.html
CRAN Task View: Statistical GeneticsCRAN Task View: Statistical Genetics
Linkage Disequilibrium and haplotype mapping : A number of packages provide haplotype estimation for unrelated individuals with ambiguous haplotypes (due to unknown linkage phase) and allow testing for associations between the estimated haplotypes and phenotypes (including co-variates) under a GLM framework. hapassoc performs likelihood inference of trait associations with haplotypes in GLMs. haplo.stats also contains tests for haplotype associations under a GLM framework, but also provides score tests of association as well as providing novel functionality for building haplotypes in a sequential manner, power and sample-size calculations and the preparation of data matrices for use in other methods. haplo.ccs utilises the haplotype estimation of haplo.stats and performs case-control association tests via weighted logistic regression. tdthap implements transmission/disequilibrium tests for extended marker haplotypes. LDheatmap creates a heat map plot of measures of pairwise LD ...
https://cran.stat.unipd.it/web/views/Genetics.html
Genotype-phenotype analysis of the Crohns disease susceptibility haplotype on chromosome 5q31Genotype-phenotype analysis of the Crohns disease susceptibility haplotype on chromosome 5q31
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 ...
http://repository.kln.ac.lk/handle/123456789/1556
Frontiers | Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance...Frontiers | Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance...
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all
https://www.frontiersin.org/articles/10.3389/fpls.2017.01905/full
Identification of seven novel mutations in LH β-subunit gene by SSCP<...Identification of seven novel mutations in LH β-subunit gene by SSCP<...
TY - JOUR. T1 - Identification of seven novel mutations in LH β-subunit gene by SSCP. AU - Roy, Ashim C.. AU - Liao, Wu Xiang. AU - Chen, Ying. AU - Arulkumaran, Sabaratnam. AU - Ratnam, Shan S.. PY - 1996. Y1 - 1996. N2 - Seven new point mutations have been identified from LH β-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.. AB - Seven new point mutations have been identified from LH β-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.. KW - Luteinizing hormone. KW - Mutation. KW - Polymerase chain reaction. KW - Restriction enzyme ...
https://pure.unic.ac.cy/en/publications/identification-of-seven-novel-mutations-in-lh-%CE%B2-subunit-gene-by-s
Haplotype Variation and Linkage Disequilibrium in 313 Human Genes | ScienceHaplotype Variation and Linkage Disequilibrium in 313 Human Genes | Science
Nucleotide diversity provides a measure of genetic variation that is normalized by the number of chromosomes sampled. We calculated two conventional measures of nucleotide diversity for each gene: π, the average heterozygosity per site (28, 29), and θ, the population mutation parameter (13, 30). The average nucleotide diversity for the 292 autosomal genes (π = 0.058% and θ = 0.096%) and the 21 X-linked genes (π = 0.028% and θ = 0.045%) were within the range of values previously described (2-4). The fact that the average nucleotide diversity for the X-linked genes was reduced compared with the average autosomal nucleotide diversity is consistent with an equal number of males and females in the human population, in which males have only a single copy of the X chromosome.. We also calculated the autosomal nucleotide diversity values separately for each functional gene region and for each population. Exon-intron boundaries showed significantly higher average π values (P , 0.01 by ...
https://science.sciencemag.org/content/293/5529/489?ijkey=b460c6f5fa0ead596c3210fe4d2bcc3905fd6d3a&keytype2=tf_ipsecsha
Plus itPlus it
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 ...
https://diabetes.diabetesjournals.org/content/54/6/1892
Haplotype block structure of the cytochrome P450 CYP2C gene cluster on chromosome 10. - Wellcome Centre for Human Genetics
We use cookies to ensure that we give you the best experience on our website. If you click Continue well assume that you are happy to receive all cookies and you wont see this message again. Click Find out more for information on how to change your cookie settings ...
https://www.well.ox.ac.uk/publications/383356
Q-A Section 11-GWAS, Linkage Analysis | Honglang Wangs BlogQ-A Section 11-GWAS, Linkage Analysis | Honglang Wangs Blog
eQTL tries to regress each gene expression against each SNP, in order to find those regulatory elements. And eQTL uses normal samples, right? (by normal I mean no disease like those in 1000genome project). GWAS compares SNPs between normal(control) and disease(test) samples, trying to find out those higher-frequency variants enriched for diseases.. linkage mapping/recombination mapping/positional cloning - rely on known markers (typically SNPs) that are close to the gene responsible for a disease or trait to segregate with that marker within a family. Works great for high-penetrance, single gene traits and diseases.. QTL mapping/interval mapping - for quantitative traits like height that are polygenic. Same as linkage mapping except the phenotype is continuous and the markers are put into a scoring scheme to measure their contribution - i.e. marker effects or allelic contribution. Big in agriculture.. GWAS/linkage disequilibrium mapping - score thousands of SNPs at once from a population ...
https://honglangwang.wordpress.com/2012/07/15/q-a-section-11-gwas-linkage-analysis/
Causal Relevance of Blood Lipid Fractions in the Development of Carotid AtherosclerosisClinical Perspective | Circulation:...Causal Relevance of Blood Lipid Fractions in the Development of Carotid AtherosclerosisClinical Perspective | Circulation:...
The validity of the MR analysis may be compromised by (1) population stratification, where allele frequencies and disease rates differ between population subgroups; (2) pleiotropy, where genetic instruments affect the outcome through ,1 intermediate risk factor, though this is not an issue for cis-acting SNPs used as instruments for a protein biomarker; (3) linkage disequilibrium, where another polymorphism in close proximity (and in linkage disequilibrium) to the variant of interest, is causing disease through another pathway; and (4) weak instrument bias. Analysis in the WHII was restricted to whites, and principal component analysis revealed no substantial population stratification. In the IMPROVE study, although all individuals were whites, there was population stratification that reflected the geographical location from which the samples were obtained.22 However, the SNPs used to generate the GLGC genetic scores were also discovered in individuals of European descent from the United States, ...
http://circgenetics.ahajournals.org/content/6/1/63
Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence « Research...
by Barbara Stranger, Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Simon V, Lee C. Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus ...
http://www.igsb.org/papers/balancing-selection-on-a-regulatory-region-exhibiting-ancient-variation-tha
Information Processing: Penalized regression from summary statisticsInformation Processing: Penalized regression from summary statistics
Polygenic scores (PGS) summarize the genetic contribution of a persons genotype to a disease or phenotype. They can be used to group participants into different risk categories for diseases, and are also used as covariates in epidemiological analyses. A number of possible ways of calculating polygenic scores have been proposed, and recently there is much interest in methods that incorporate information available in published summary statistics. As there is no inherent information on linkage disequilibrium (LD) in summary statistics, a pertinent question is how we can make use of LD information available elsewhere to supplement such analyses. To answer this question we propose a method for constructing PGS using summary statistics and a reference panel in a penalized regression framework, which we call lassosum. We also propose a general method for choosing the value of the tuning parameter in the absence of validation data. In our simulations, we showed that pseudovalidation often resulted in ...
http://infoproc.blogspot.com/2017/04/penalized-regression-from-summary.html
Recently with the rapid improvements in high-throughout genotyping techniques, researchers are | Thioredoxin Reductase and its...Recently with the rapid improvements in high-throughout genotyping techniques, researchers are | Thioredoxin Reductase and its...
Recently with the rapid improvements in high-throughout genotyping techniques, researchers are facing the very challenging task of analyzing large-scale genetic associations, especially at the whole-genome level, without an optimal solution. genotype data, it does not require any computationally rigorous phasing program to account for uncertain haplotype phase. Background Currently, with Artesunate the availability of large-scale genotyping technologies, the genotyping cost of genome-wide association (GWA) studies has been largely reduced and a boom of large-scale GWA studies is underway. Nevertheless, the success of most association studies is based on the linkage disequilibrium (LD) between the functional mutations and markers in a local region of the genome. Varieties of statistical methods that rely on LD pattern have been developed to map functional variants (Spielman et al. 1993; Olson et al. 1994; Rannala and Reeve 2001; Ardlie et al. 2002). The most straightforward approach of LD-based ...
http://livingseas.org/recently-with-the-rapid-improvements-in-high-throughout-genotyping-techniques-researchers-are/
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19...An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19...
While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility. Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb)) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00904-z
Plus itPlus it
Genetic susceptibility factors are known to be important in NPC pathogenesis. Given the strong link between EBV and NPC, and the role of HLA gene products in the presentation of viral antigens to the adaptive immune response, HLA genes have been extensively studied as risk factors for NPC. In the present report, we have extended previous findings by demonstrating an association between two HLA-Cw alleles and NPC: HLA-Cw*0302 and HLA-Cw*0401. Whereas the association with HLA-Cw*0302 might mirror the previously reported association between HLA-B*5801 and NPC (due to tight linkage disequilibrium between the two alleles), the association between HLA-Cw*0401 and NPC seems to be independent of previously reported associations.. In contrast to the extensive work done to date to evaluate the role of adaptive immune response in the etiology of NPC, surprisingly little is known about the role of innate immunity in the control of EBV infection and its contribution to NPC risk. To address this issue, we ...
https://cebp.aacrjournals.org/content/14/11/2673
Gene Expression: R1a1 and the peopling of Eurasia
Both Dienekes and Polish Genetics and Anthropology suggest that the calibration is wrong on these coalescence times. They argue that one should reduce the time to a common ancestor by a factor of 3. This would of course make a huge difference. In regards to the Reich et al. paper which argued for a plausible two-way admixture between ANI and Ancestral South Indians (ASI), the linkage disequilibrium has decayed too much from the time of admixture to peg a date. This was a method used to calculate the emergence of the Uyghurs as a hybrid population, on the order of 2-3 thousand years ago (admixture between two very different populations generates linkage disequilibrium which decays over time due to recombination). In terms of Fst the ANI have a value in relation to Northern Europeans which is about 3 times larger than the mean between population differences in Europe. This is somewhat greater than the pairwise values between any European populations except for the Baltic peoples (in ...
http://www.gnxp.com/blog/2009/11/r1a1-and-peopling-of-eurasia.php
Molecular Biosciences
Applications of probability and statistics to genetics and molecular biology. Case-control association testing with related individuals, multipoint linkage disequilibrium mapping, identification of polymorphisms that explain a linkage result, relationship inference, analysis of quantitative trait loci in a complex pedigree, analysis of recombination and interference.. ...
http://molbio.uchicago.edu/faculty/mary-sara-mcpeek
genetics - What is the cause of imbalanced linkage disequilibrium? - Biology Stack Exchangegenetics - What is the cause of imbalanced linkage disequilibrium? - Biology Stack Exchange
This can occur if the Ab genotype is lethal, i.e. you wont observe individuals with a Ab genotype.. Allele lethality is a common mechanisms that can explain non-mendelian inheritance of a trait.. For the question of which LD metric to use, this is tricky. Under the assumption that allele lethality is indeed at play, you observed perfect haplotypes, so D=1 wouldnt be incorrect. Yet the correlation coefficient is also correct in the sense that SNP A is not a perfect proxy for SNP B.. ...
https://biology.stackexchange.com/questions/84113/what-is-the-cause-of-imbalanced-linkage-disequilibrium
Linkage Disequilibrium | Colorado PROFILES
Sims R, van der Lee SJ, Naj AC, Bellenguez C, Badarinarayan N, Jakobsdottir J, Kunkle BW, Boland A, Raybould R, Bis JC, Martin ER, Grenier-Boley B, Heilmann-Heimbach S, Chouraki V, Kuzma AB, Sleegers K, Vronskaya M, Ruiz A, Graham RR, Olaso R, Hoffmann P, Grove ML, Vardarajan BN, Hiltunen M, Nöthen MM, White CC, Hamilton-Nelson KL, Epelbaum J, Maier W, Choi SH, Beecham GW, Dulary C, Herms S, Smith AV, Funk CC, Derbois C, Forstner AJ, Ahmad S, Li H, Bacq D, Harold D, Satizabal CL, Valladares O, Squassina A, Thomas R, Brody JA, Qu L, Sánchez-Juan P, Morgan T, Wolters FJ, Zhao Y, Garcia FS, Denning N, Fornage M, Malamon J, Naranjo MCD, Majounie E, Mosley TH, Dombroski B, Wallon D, Lupton MK, Dupuis J, Whitehead P, Fratiglioni L, Medway C, Jian X, Mukherjee S, Keller L, Brown K, Lin H, Cantwell LB, Panza F, McGuinness B, Moreno-Grau S, Burgess JD, Solfrizzi V, Proitsi P, Adams HH, Allen M, Seripa D, Pastor P, Cupples LA, Price ND, Hannequin D, Frank-García A, Levy D, Chakrabarty P, Caffarra P, ...
https://profiles.ucdenver.edu/display/223485
Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local...Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local...
Background: Epistasis (synergistic interaction) among SNPs governing gene expression is likely to arise withintranscriptional networks. However, the power to detect it is limited by the large number of combinations to betested and the modest sample sizes of most datasets. By limiting the interaction search space firstly to cis-trans andthen cis-cis SNP pairs where both SNPs had an independent effect on the expression of the most variabletranscripts in the liver and brain, we greatly reduced the size of the search space.Results: Within the cis-trans search space we discovered three transcripts with significant epistasis. Surprisingly, allinteracting SNP pairs were located nearby each other on the chromosome (within 290 kb-2.16 Mb). Despite theirproximity, the interacting SNPs were outside the range of linkage disequilibrium (LD), which was absent betweenthe pairs (r2 , 0.01). Accordingly, we redefined the search space to detect cis-cis interactions, where a cis-SNP waslocated within 10 Mb of the ...
http://researchrepository.ucd.ie/handle/10197/6519
Novel variants of the il-10 receptor 1 affect inhibition of monocyte tnf-alpha productionNovel variants of the il-10 receptor 1 affect inhibition of monocyte tnf-alpha production
IL-10-deficient mice exhibit spontaneous enterocolitis and other symptoms akin to Crohns disease, indicating that IL-10 might regulate normal physiology in the gut. However, clinical trials with IL-10 in Crohns disease were disappointing, although some patients showed healing of intestinal mucosa. This study searched for genetic polymorphisms within the IL-10 pathway. We decided to screen for mutations of the IL-10R1 cDNA in healthy volunteers and Crohns disease patients and identified two novel variants: a serine 138-to-glycine (S138G) and a glycine 330-to-arginine (G330R) substitution. The allelic frequency in a European cohort was relatively high (16% for the S138G and 33% for the G330R), and S138G was in strong linkage disequilibrium with G330R. A similar allele frequency was found in a group of Crohns patients. In IL-10R1 G330R-expressing monocytes, the inhibitory effect of IL-10 on TNF-alpha production was diminished, indicating that this variant may be a loss-of-function allele. No ...
https://vivo.scripps.edu/display/endnote90103
Targeted association analysis identified japonica rice varieties achieving Na <sup>+</sup>/K <sup>+</sup> homeostasis without...
TY - JOUR. T1 - Targeted association analysis identified japonica rice varieties achieving Na +/K + homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra. AU - Ahmadi, N.. AU - Cabrita Negrao, Sonia. AU - Katsantonis, D.. AU - Frouin, J.. AU - Ploux, J.. AU - Letourmy, P.. AU - Droc, G.. AU - Babo, P.. AU - Trindade, H.. AU - Bruschi, G.. AU - Greco, R.. AU - Oliveira, M. M.. AU - Piffanelli, P.. AU - Courtois, B.. PY - 2011/6/29. Y1 - 2011/6/29. N2 - During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these ...
https://research.kaust.edu.sa/en/publications/targeted-association-analysis-identified-japonica-rice-varieties-
The Population Genetics of PAH | The Online Metabolic and Molecular Bases of Inherited Disease | OMMBID | McGraw-Hill MedicalThe Population Genetics of PAH | The Online Metabolic and Molecular Bases of Inherited Disease | OMMBID | McGraw-Hill Medical
Soon after the PAH cDNA was cloned, it was used as a probe to detect restriction fragment length polymorphisms (RFLPs) by Southern blotting (Lidsky et al, 45; Woo et al, 63). The linkage between PKU and PAH was, of course, very strong. In the effort to discover the mutation(s) leading to the hyperphenylalanemias, searching for a nonrandom association of disease with alleles of normal polymorphisms [linkage disequilibrium (LD)] in the PAH gene was a strategy to consider. The use of this strategy has now reached epidemic proportions in human genetics, especially for complex diseases (Capon et al, 6; Horikawa et al, 32; Kim et al, 41; Myers et al, 47; Sawcer et al, 52; Scapoli et al, 53; Vaessen et al, 60), but often has low power unless there is strong prior support for a specific gene. In the case of PAH and PKU there was no question that the disorder is biochemically a deficiency of the enzyme and genetically inherited at (or very close to) the PAH gene. This is the very circumstance in which LD ...
http://ommbid.mhmedical.com/content.aspx?bookid=971§ionid=62673385
GenomeRef: May 2012GenomeRef: May 2012
The GRC currently favors a model in which haplotypic integrity is retained within blocks of linkage disequilibrium (LD) as best possible, every base is found at an MAF ,5% in some population (i.e. no universally rare alleles) and coding alleles are favored over non-coding alleles, so long as they too are not universally rare. However, additional analyses will be performed before any bases changes are made. Examples of genomic regions where the existing reference base is associated with disease (ASPN, PMID:15640800) or non-coding variants (CYP3A5, PMID:11279519) are presented below in Figures 1 and 2. In the former case, the reference base is the minor allele, while in the latter, it is the major allele. We invite you to consider examples such as these as you form your own views of what should be represented in the reference assembly. If you have questions or concerns about base updates for GRCh38, let us know! ...
http://genomeref.blogspot.no/2012/05/
The maintenance of strain structure in populations of recombining infectious agents. - Immunology
Using mathematical models that combine population genetic and epidemiological processes, we resolve the paradox that many important pathogens appear to persist as discrete strains despite the constant exchange of genetic material. We show that dominant polymorphic determinants (that is, those that elicit the most effective immune responses) will be organized into nonoverlapping combinations as a result of selection by the host immune system, thereby defining a set of discrete independently transmitted strains. By analysing 222 isolates of Neisseria meningitidis, we show that two highly polymorphic epitopes of the outer membrane protein PorA exist in nonoverlapping combinations as predicted by this general framework. The model indicates that dominant polymorphic determinants will be in linkage disequilibrium, despite frequent genetic exchange, even though they may be encoded by several unlinked genes. This suggests that the detection of nonrandom associations between epitope regions can be employed as a
https://www.immunology.ox.ac.uk/publications/894768
Exploring Diallelic genetic markers: The Hardy Weinberg packageExploring Diallelic genetic markers: The Hardy Weinberg package
Testing genetic markers for Hardy-Weinberg equilibrium is an important issue in genetic association studies. The HardyWeinberg package o ers the classical tests for equilibrium, functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Functions for testing equilibrium in the presence of missing data by using multiple imputation are provided. The package also supplies various graphical tools such as ternary plots with acceptance regions, log-ratio plots and Q-Q plots for exploring the equilibrium status of a large set of diallelic markers. Classical tests for equilibrium and graphical representations for diallelic marker data are reviewed. Several data sets illustrate the use of the package ...
http://upcommons.upc.edu/handle/2117/76647
Human Gene CCHCR1 (uc011gwf.2) Description and Page IndexHuman Gene CCHCR1 (uc011gwf.2) Description and Page Index
POLYMORPHISM: HCR*WWCC is associated with susceptibility to psoriasis. Psoriasis is a chronic inflammatory dermatosis that affects approximately 2% of the population. It is a multifactorial disease characterized by red, scaly skin lesions that are usually found on the scalp, elbows, and knees, and may be associated with severe arthritis. The lesions are caused by hyperproliferative keratinocytes and infiltration of inflammatory cells into the dermis and epidermis. The usual age of onset of psoriasis is between 15 and 30 years, although it can present at any age. Association of HCR with psoriasis seem to be due to linkage disequilibrium with Cw*06:02 (PubMed:11348465). HCR is unlikely to be directly involved in psoriasis development ...
http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgGene?hgg_gene=uc011gwf.2&hgg_prot=Q8TD31&hgg_chrom=chr6_mann_hap4&hgg_start=2458573&hgg_end=2474393&hgg_type=knownGene&db=hg19&hgsid=1289098_rEYyzmWZ9Xw4hhMOGbGzlYRwArae
Nephron Power: CLINICAL CASE 48: Answers and SummaryNephron Power: CLINICAL CASE 48: Answers and Summary
This phenomenon might be epigenetic from protection from the Sleeping sickness disease caused by the tsetse fly. Apparently on the same chromosome 22, APOL1(apolipoprotein -1) and MHY9 sit next to each other. The studies are now showing that due to natural selection and linkage disequilibrium, the APOL1 gene might be the strong candidate for a gene that is responsible for increased incidence of renal disease in African Origin Americans. Recent JASN articles in Nov 2011 issue also shed light on newer findings as described above: Having the APOL-1 variant can lead to more arterilopathy and renal vessel changes and that was confirmed on biopsy findings. Interestingly, only certain glomerular diseases are at risk- FSGS types including HIVAN but not IgA nephropathy or diabetic nephropathy. Given the severity of the disease, these patients need dialysis at an earlier age. More copies of this gene- more you are at risk of FSGS and ESRD. ...
http://www.nephronpower.com/2011/12/clinical-case-48-answers-and-summary.html
New paper on dispersal in Atlantic cod - Bradbury Population Genomics LabNew paper on dispersal in Atlantic cod - Bradbury Population Genomics Lab
Just out: Complex post-larval dispersal processes in Atlantic cod revealed by age-based genetics and relatedness analysis John Horn uses relatedness analysis to reveal age-based differences in relatedness and linkage disequilibrium indicative of behavioural influences on connectivity of Atlantic cod in coastal Newfoundland. Looks like post-larval process may matter more than we thought.
https://bradburygeneticslab.com/2016/09/08/new-paper-on-dispersal-in-atlantic-cod/
JoVE Author Search: Lie BA
Risk, Association, Gene, Associations, Arthritis, Alleles, Hla-drb1, Disease, Rheumatoid Arthritis, Genes, Histocompatibility, Histocompatibility Complex, Major Histocompatibility Complex, Snps, Patients, Antigen, Linkage Disequilibrium, Population, Risk Factors, Diseases
http://labindex.jove.com/author/Lie-BA
The Irish population haemorrhage: mapping 160 years of data | Family history across the seasThe Irish population haemorrhage: mapping 160 years of data | Family history across the seas
Alerted by tweets from @IrishWattle @CaroleRiley and @QueenslandFHS, I investigated the link theyd provided for 160 years of Irish population data. The National Centre for Geocomputations (NCG) Online Atlas Portal is an absolute goldmine for family historians with ancestry in Ireland. There are two options: mapping and data relating to 2002 together with a timeline…
https://cassmobfamilyhistory.com/2011/08/05/the-irish-population-haemorrhage-mapping-160-years-of-data/?replytocom=435
Download Chinese Economy In DisequilibriumDownload Chinese Economy In Disequilibrium
Leiden; Boston: Brill, 2010. New York: Cambridge University Press, 1994. books of Education Series, vaccines in the Postmodern Theory of Education, Vol. New York: Peter Lang Publishing, involuntary, 2000.
http://windhover.org/images/library/download-chinese-economy-in-disequilibrium
Smr95c-2os#7ld at Boca BearingsSmr95c-2os#7ld at Boca Bearings
Smr95c-2os#7ld found in: SMR95C-2OS #7 LD, Stainless Steel, Ceramic Hybrid, Orange Sealed bearings are specially designed for any application seeking..
https://www.bocabearings.com/parts/Smr95c--2os%237ld
Linkage disequilibriumLinkage disequilibrium
The level of linkage disequilibrium between A and B can be quantified by the coefficient of linkage disequilibrium D A B {\ ... The coefficient of linkage disequilibrium D {\displaystyle D} is not always a convenient measure of linkage disequilibrium ... In spite of its name, linkage disequilibrium may exist between alleles at different loci without any genetic linkage between ... and genetic linkage. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population ...
https://en.wikipedia.org/wiki/Linkage_disequilibrium
Linkage disequilibrium score regressionLinkage disequilibrium score regression
Here, the "linkage disequilibrium score" for a SNP "is the sum of LD r2 measured with all other SNPs". LDSC can be used to ... In statistical genetics, linkage disequilibrium score regression (LDSR or LDSC) is a technique that aims to quantify the ... The approach involves using regression analysis to examine the relationship between linkage disequilibrium scores and the test ... "Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood". The ...
https://en.wikipedia.org/wiki/Linkage_disequilibrium_score_regression
PLINK (genetic tool-set)PLINK (genetic tool-set)
Linkage disequilibrium (LD) calculation; Identity by descent (IBD) and identity by state (IBS) matrix calculation; population ... a toolset for whole-genome association and population-based linkage analysis". American Journal of Human Genetics. 81 (3): 559- ...
https://en.wikipedia.org/wiki/PLINK_(genetic_tool-set)
Detlef WeigelDetlef Weigel
"Recombination and linkage disequilibrium in Arabidopsis thaliana". Nat. Genet. 39 (9): 1151-1155. doi:10.1038/ng2115. PMID ...
https://en.wikipedia.org/wiki/Detlef_Weigel
Race and geneticsRace and genetics
May 2005). "Linkage disequilibrium patterns vary substantially among populations". European Journal of Human Genetics. 13 (5): ...
https://en.wikipedia.org/wiki/Race_and_genetics
Biological networkBiological network
Another measure of correlation is linkage disequilibrium. Linkage disequilibrium describes the non-random association of ... Linkage Disequilibrium - ISOGG Wiki, International Society of Genetic Genealogy, https://isogg.org/wiki/Linkage_disequilibrium ... Two nodes are connected by an edge if their linkage disequilibrium is greater than the average across all 81 genomic windows. ... It then pulls nodes together using linear interpolation by their linkage as a percentage. The figure illustrates strong ...
https://en.wikipedia.org/wiki/Biological_network
Genetic isolateGenetic isolate
The presence of disequilibrium linkage in disease alleles enhances linkage analysis and aids in determining the precise ... Language isolate Linkage disequilibrium Tóth, Endre Gy; Tremblay, Francine; Housset, Johann M.; Bergeron, Yves; Carcaillet, ... Besides that, the vast majority of cases are caused by the same mutation, and diseased alleles expose linkage of disequilibrium ... and families with numerous sick members become common enough to be employed in locus-identifying linkage analyses. ...
https://en.wikipedia.org/wiki/Genetic_isolate
Hannu Toivonen (professor)Hannu Toivonen (professor)
"Data mining applied to linkage disequilibrium mapping". Google Scholar. Retrieved 8 November 2016. "Hannu Toivonen". Google ...
https://en.wikipedia.org/wiki/Hannu_Toivonen_(professor)
Complete linkageComplete linkage
"Asymmetric linkage disequilibrium: Tools for assessing multiallelic LD". Human Immunology. 77 (3): 288-94. doi:10.1016/j.humimm ... Linkage mapping can also be useful in determining the inheritance patterns of traits such as psychological disease. Linkage ... "Mapping quantitative trait loci using linkage disequilibrium: marker- versus trait-based methods". Behavior Genetics. 35 (2): ... Being able to determine linkage between genes can also have major economic benefits. Learning about linkage of traits in sugar ...
https://en.wikipedia.org/wiki/Complete_linkage
Drosophila subobscuraDrosophila subobscura
Studies on linkage disequilibrium in four natural populations. Genetics. 1979;93:497-523". Genetics. 93 (2): 497-523. doi: ... allowing for the finding of more than 600 different linkages and genetic markers, which encompass a majority of the euchromatic ...
https://en.wikipedia.org/wiki/Drosophila_subobscura
MitochondrionMitochondrion
Awadalla P, Eyre-Walker A, Smith JM (December 1999). "Linkage disequilibrium and recombination in hominid mitochondrial DNA". ...
https://en.wikipedia.org/wiki/Mitochondrion
Martin KreitmanMartin Kreitman
"The extent of linkage disequilibrium in Arabidopsis thaliana". Nature Genetics. 30 (2): 190-193. doi:10.1038/ng813. PMID ...
https://en.wikipedia.org/wiki/Martin_Kreitman
Paternal mtDNA transmissionPaternal mtDNA transmission
Awadalla P, Eyre-Walker A, Smith JM (December 1999). "Linkage disequilibrium and recombination in hominid mitochondrial DNA". ...
https://en.wikipedia.org/wiki/Paternal_mtDNA_transmission
Transmembrane protein 151ATransmembrane protein 151A
TMEM151A is in linkage disequilibrium with gene CACNA1C; CACNA1C mutation is significantly associated with bipolar disorder p ...
https://en.wikipedia.org/wiki/Transmembrane_protein_151A
Haplotype blockHaplotype block
According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one ... Wall, Jeffrey D.; Pritchard, Jonathan K. (1 August 2003). "Haplotype blocks and linkage disequilibrium in the human genome". ... one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one ...
https://en.wikipedia.org/wiki/Haplotype_block
Finnish heritage diseaseFinnish heritage disease
Linkage and linkage disequilibrium in the Finnish disease heritage]". Duodecim; Lääketieteellinen Aikakauskirja (in Finnish). ...
https://en.wikipedia.org/wiki/Finnish_heritage_disease
Locus heterogeneityLocus heterogeneity
Wang D, Huang J (May 2006). "Detecting linkage disequilibrium in the presence of locus heterogeneity". Annals of Human Genetics ... of causal genes for diseases impacted by locus heterogeneity is difficult with genetic analysis methods such as linkage ...
https://en.wikipedia.org/wiki/Locus_heterogeneity
Matthew Stephens (statistician)Matthew Stephens (statistician)
He then went on to develop the influential Li and Stephens model as an efficient model for linkage disequilibrium. Stephens was ... Song, Yun S. (1 July 2016). "Na Li and Matthew Stephens on Modeling Linkage Disequilibrium". Genetics. 203 (3): 1005-1006. doi: ...
https://en.wikipedia.org/wiki/Matthew_Stephens_(statistician)
Non-coding DNANon-coding DNA
The association is referred to as tight linkage disequilibrium.) About 12% of these polymorphisms are found in coding regions; ... The association establishes a linkage that helps map the DNA region responsible for the trait but it doesn't necessarily ... Genome-wide association studies (GWAS) identify linkages between alleles and observable traits such as phenotypes and diseases ...
https://en.wikipedia.org/wiki/Non-coding_DNA
Eukaryote hybrid genomeEukaryote hybrid genome
Methods based on linkage disequilibrium decay or methods inferring ancestry tracts can be used to date recent admixture or ... It is also possible to gain more power by combining information from linkage disequilibrium decay patterns and the allele ... "Inferring admixture histories of human populations using linkage disequilibrium". Genetics. 193 (4): 1233-54. doi:10.1534/ ... and linkage among incompatibilities to each other and to adaptive variants. Extrinsic ecological barriers against parent ...
https://en.wikipedia.org/wiki/Eukaryote_hybrid_genome
Richard LewontinRichard Lewontin
Lewontin later introduced the D' measure of linkage disequilibrium. (He also introduced the term "linkage disequilibrium", ... Slatkin, Montgomery (June 2008). "Linkage disequilibrium - understanding the evolutionary past and mapping the medical future ... Lewontin, R. C. (1964). "The interaction of selection and linkage. I. General considerations; heterotic models". Genetics 49: ...
https://en.wikipedia.org/wiki/Richard_Lewontin
Polygenic scorePolygenic score
SNPs that are physically close to each other are more likely to be in linkage disequilibrium, meaning they are often inherited ... October 2015). "Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores". American Journal of Human ... One of the most popular modern Bayesian methods uses "linkage disequilibrium prediction" (LDpred for short). Many other ... higher degrees of linkage disequilibrium among individuals, and a higher average genetic relatedness among individuals within a ...
https://en.wikipedia.org/wiki/Polygenic_score
Host microbe interactions in Caenorhabditis elegansHost microbe interactions in Caenorhabditis elegans
Barrière A, Félix MA (2007). "Temporal dynamics and linkage disequilibrium in natural Caenorhabditis elegans populations". ...
https://en.wikipedia.org/wiki/Host_microbe_interactions_in_Caenorhabditis_elegans
GABRB3GABRB3
Scapoli L, Martinelli M, Pezzetti F, Carinci F, Bodo M, Tognon M, Carinci P (January 2002). "Linkage disequilibrium between ... "Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers". American Journal of Human Genetics. 62 (5): 1077- ... "Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13". Journal of ...
https://en.wikipedia.org/wiki/GABRB3
Homologous recombinationHomologous recombination
Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase ... This represents linkage between the two genes greater than would be expected from genes that independently assort during ...
https://en.wikipedia.org/wiki/Homologous_recombination
COVID-19 pandemic on Diamond PrincessCOVID-19 pandemic on Diamond Princess
Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase ...
https://en.wikipedia.org/wiki/COVID-19_pandemic_on_Diamond_Princess
History and naming of human leukocyte antigensHistory and naming of human leukocyte antigens
The haplotype frequencies in Europeans are in strong linkage disequilibrium. This means there are much higher frequencies of ... This linkage disequilibrium in Europeans explains why A1, A2, A3, "A7"[B7], and "A8"[B8] were identified, first. It would have ... This linkage is not necessarily a function of either gene, but a consequence of the way AH8.1 evolved. A series of tests on ...
https://en.wikipedia.org/wiki/History_and_naming_of_human_leukocyte_antigens
Transmission disequilibrium testTransmission disequilibrium test
McGinnis RE, Ewens WJ, Spielman RS (1995). "The TDT reveals linkage and linkage disequilibrium in a rare disease". Genet ... Spielman RS, Ewens WJ (Nov 1996). "The TDT and other family-based tests for linkage disequilibrium and association". Am J Hum ... Beagle Spielman RS, McGinnis RE, Ewens WJ (Mar 1993). "Transmission test for linkage disequilibrium: the insulin gene region ... The transmission disequilibrium test (TDT) was proposed by Spielman, McGinnis and Ewens (1993) as a family-based association ...
https://en.wikipedia.org/wiki/Transmission_disequilibrium_test
Dopamine transporterDopamine transporter
"Evidence for linkage disequilibrium between the dopamine transporter and bipolar disorder". American Journal of Medical ...
https://en.wikipedia.org/wiki/Dopamine_transporter
CRMP1CRMP1
Sivakumaran TA, Lesperance MM (2005). "Haplotype and linkage disequilibrium analysis of the CRMP1 and EVC genes". Int. J. Mol. ...
https://en.wikipedia.org/wiki/CRMP1
HLA A1-B8-DR3-DQ2HLA A1-B8-DR3-DQ2
Two-point haplotype analysis between TNFB(B*01 allele) and HLA show that the allele is in linkage disequilibrium with HLA-A1, ... And while the level of A-B linkage in general was nowhere near Cw-B linkage, the linkage between A1-Cw7-B8 was reasonably ... Hiller C, Bischoff M, Schmidt A, Bender K (April 1978). "Analysis of the HLA-ABC linkage disequilibrium: decreasing strength of ... Thus, A1::DQ2 haplotype is both long and shows greater deficiency of recombination (called linkage disequilibrium). The ...
https://en.wikipedia.org/wiki/HLA_A1-B8-DR3-DQ2
Fusarium oxysporum f.sp. cubenseFusarium oxysporum f.sp. cubense
One study of the linkage disequilibrium of gametes showed relatively high disequilibrium and another a high degree of ... Other post-sequencing data analysis performed by the disequilibrium study also failed to reject recombination however this ...
https://en.wikipedia.org/wiki/Fusarium_oxysporum_f.sp._cubense
Snagger (software)Snagger (software)
Snagger is a bioinformatics software program for selecting tag SNPs using pairwise r2 linkage disequilibrium. It is implemented ...
https://en.wikipedia.org/wiki/Snagger_(software)
Genetic linkageGenetic linkage
Genetic epidemiology Genome-wide association study Identity by descent Lander-Green algorithm Linkage disequilibrium Structural ... is due to the existence of linkage (with a given linkage value) or to chance. Non-parametric linkage analysis, in turn, studies ... A linkage map is not a physical map (such as a radiation reduced hybrid map) or gene map. Linkage analysis is a genetic method ... Linkage maps were first developed by Alfred Sturtevant, a student of Thomas Hunt Morgan. A linkage map is a map based on the ...
https://en.wikipedia.org/wiki/Genetic_linkage
Molecular anthropologyMolecular anthropology
These studies roughly plot to the expected fixation distribution of alleles, given linkage disequilibrium between adjacent ... The other linkage group is the mitochondrial DNA (mtDNA). MtDNA is almost always only passed to the next generation by females ... There are two continuous linkage groups in humans that are carried by a single sex. The first is the Y chromosome, which is ...
https://en.wikipedia.org/wiki/Molecular_anthropology
GABRG1GABRG1
2008). "Interpopulation linkage disequilibrium patterns of GABRA2 and GABRG1 genes at the GABA cluster locus on human ... 2008). "Markers in the 5'-region of GABRG1 associate to alcohol dependence and are in linkage disequilibrium with markers in ... "Interpopulation linkage disequilibrium patterns of GABRA2 and GABRG1 genes at the GABA cluster locus on human chromosome 4". ...
https://en.wikipedia.org/wiki/GABRG1
Darwins finchesDarwin's finches
... but two loci with linkage disequilibrium is a possibility. Another interesting dimorphism is for the bills of young finches, ...
https://en.wikipedia.org/wiki/Darwin's_finches
Locus (genetics)Locus (genetics)
... "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage ... disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering ...
https://en.wikipedia.org/wiki/Locus_(genetics)
IDDM11IDDM11
The present researchers use LD (Linkage disequilibrium) analyses and TDT (transmission disequilibrium test) to analyze the ... This loci is identified by linkage to D14S67 marker via a sibling-pair linkage analysis Based on the previous study, the ... Genome-wide linkage analysis could be used for identification in susceptibility genes of insulin-dependent (type I) diabetes ...
https://en.wikipedia.org/wiki/IDDM11
Fair trade coffeeFair trade coffee
... trade and market linkages', Proceedings of the 18th International Farming Symposium, 31 October-3 November, Rome: Food and ... The Dissipation of Producer Benefits in a Disequilibrium Market. Retrieved December 24, 2012, from http://are.berkeley.edu/~ ... The Dissipation of Producer Benefits in a Disequilibrium Market. Retrieved December 24, 2012, from http://are.berkeley.edu/~ ... The Dissipation of Producer Benefits in a Disequilibrium Market. Retrieved December 24, 2012, from http://are.berkeley.edu/~ ...
https://en.wikipedia.org/wiki/Fair_trade_coffee
Mestizos in MexicoMestizos in Mexico
"Evaluation of Ancestry and Linkage Disequilibrium Sharing in Admixed Population in Mexico". ASHG. Archived from the original on ... "Evaluation of Ancestry and Linkage Disequilibrium Sharing in Admixed Population in Mexico". ASHG. Archived from the original on ... "Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population samples". Journal of the ...
https://en.wikipedia.org/wiki/Mestizos_in_Mexico
Sp7 transcription factorSp7 transcription factor
BMD were analyzed showing that several common variant SNPs within the 12q13 region were in an area of linkage disequilibrium. ...
https://en.wikipedia.org/wiki/Sp7_transcription_factor
GRIA4GRIA4
... linkage disequilibrium mapping using SNPs evenly distributed across the gene region". American Journal of Medical Genetics. ...
https://en.wikipedia.org/wiki/GRIA4
COX7A2LCOX7A2L
2001). "A genomewide linkage-disequilibrium scan localizes the Saguenay-Lac-Saint-Jean cytochrome oxidase deficiency to 2p16". ...
https://en.wikipedia.org/wiki/COX7A2L
Evolutionary tradeoffEvolutionary tradeoff
... or when linkage disequilibrium is present (non-random association of alleles at different loci during the gametic phase). The ...
https://en.wikipedia.org/wiki/Evolutionary_tradeoff
Balancer chromosomeBalancer chromosome
... is in strong linkage disequilibrium with it), recombination resulting in a wild-type chromosome is very unlikely, regardless of ...
https://en.wikipedia.org/wiki/Balancer_chromosome
DbSNPDbSNP
2003). "Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans". ...
https://en.wikipedia.org/wiki/DbSNP
River terraces (tectonic-climatic interaction)River terraces (tectonic-climatic interaction)
Clift, P. D., Tada, R., and Zheng, H., Monsoon evolution and tectonics-climate linkages in Asian:an introduction: Geological ... and U-Th disequilibria. Additionally, if there is a succession of preserved fossils, biostratigraphy can be used. Scale of ...
https://en.wikipedia.org/wiki/River_terraces_(tectonic–climatic_interaction)
HPS1HPS1
Fukai K, Oh J, Frenk E, Almodovar C, Spritz RA (Feb 1996). "Linkage disequilibrium mapping of the gene for Hermansky-Pudlak ...
https://en.wikipedia.org/wiki/HPS1
Mark Daly (scientist)Mark Daly (scientist)
In the early days of the Human Genome Project, Daly helped develop the genetic model by which linkage disequilibrium could be ...
https://en.wikipedia.org/wiki/Mark_Daly_(scientist)
Genetic associationGenetic association
... this is known as genetic linkage.[citation needed] Linkage disequilibrium (LD) is a term used in the study of population ... mapping Family based QTL mapping Genetic epidemiology Genetic linkage Genome-wide association study Linkage disequilibrium ... or be in linkage disequilibrium with a polymorphism which does. Haplotypes can also show association with a disease or trait. ... It is not the same as linkage, which is the phenomenon whereby two or more loci on a chromosome have reduced recombination ...
https://en.wikipedia.org/wiki/Genetic_association
MFN2MFN2
November 2001). "Genome-wide linkage disequilibrium mapping of late-onset Alzheimer's disease in Finland". Neurology. 57 (9): ...
https://en.wikipedia.org/wiki/MFN2
DNA encryptionDNA encryption
In another study, the nature of linkage disequilibrium is utilized in selecting the most useful datasets while maximizing ...
https://en.wikipedia.org/wiki/DNA_encryption
HLA-B7HLA-B7
HLA-B*07/B*27 combination with D6S273-134 genomic marker allele and was found not to be the result of linkage disequilibrium. B ... One haplotype A3-B7-DR15-DQ1 can be found over a vast region and is in apparent selective disequilibrium. B7 is a risk factor ... Nonetheless, a linkage has been found between A3-B7 haplotype and haemochromatosis. The region is almost 1.4 million ...
https://en.wikipedia.org/wiki/HLA-B7
HLA B7-DR15-DQ6HLA B7-DR15-DQ6
... linkage disequilibrium with other HLA loci and population genetic affinities". European Journal of Immunogenetics. 21 (3): 143- ... February 2002). "Linkage analysis conditional on HLA status in a large North American pedigree supports the presence of a ...
https://en.wikipedia.org/wiki/HLA_B7-DR15-DQ6
Aquaculture of tilapiaAquaculture of tilapia
Dense markers are considered good enough to capture the gene content because they are in linkage disequilibrium with the genes ... 23 Linkage groups because of the sex chromosomes. About 1 billion base pairs in length, 3,010 contigs made 2,460 scaffolds ...
https://en.wikipedia.org/wiki/Aquaculture_of_tilapia
Phenotypic integrationPhenotypic integration
At the genetic level, integration can be caused by pleiotropy, close linkage, or linkage disequilibrium among unlinked genes. ... Integration can be found at the genetic level due to genetic linkage. Genetic linkage involves multiple genes being inherited ... Selection will favor tight linkage because it is maintained better. Poorly linked genetic correlations will not last. ... "The genetic correlation between characters maintained by selection, linkage and inbreeding." Genetical research 44.03 (1984): ...
https://en.wikipedia.org/wiki/Phenotypic_integration
Browsing by Subject Linkage DisequilibriumBrowsing by Subject "Linkage Disequilibrium"
sustaining voluntary medical male circumcision services and linkages with adolescent sexual and reproductive health: the ...
https://extranet.who.int/iris/restricted/browse?authority=Linkage+Disequilibrium&type=mesh
Holdings: An insight into the linkage disequilibrium map of the Canchim beef cattle breed.Holdings: An insight into the linkage disequilibrium map of the Canchim beef cattle breed.
An insight into the linkage disequilibrium map of the Canchim beef cattle breed. The development of linkage disequilibrium (LD ... Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. by: MOKRY, F. B., et al. Published: ( ... Estimation of linkage disequilibrium, persistence of phase and effective population size of Brazilian Hereford and Braford ... Desequilíbrio de ligação., Gado., Linkage disequilibrium, Cattle, Zebu, Haplotypes,. Online Access:. http://www.alice.cnptia. ...
https://www.sidalc.net/search/Record/dig-alice-doc-946432
Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel | BMC...Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel | BMC...
The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for ... From: Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-187/tables/1
Linkage Disequilibrium Calculator - Homo sapiens - GRCh37 Archive browser 108Linkage Disequilibrium Calculator - Homo sapiens - GRCh37 Archive browser 108
Configure this page. Custom tracks. Export data. Share this page. Bookmark this page ...
http://grch37.ensembl.org/Homo_sapiens/Tools/LD?g=ENSG00000197943
Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density. - Nuffield...
... and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results ... We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments ... and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results ... Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density. ...
https://www.ndph.ox.ac.uk/publications/937860
Bayesian estimates of linkage disequilibrium | BMC Genomic Data | Full TextBayesian estimates of linkage disequilibrium | BMC Genomic Data | Full Text
... a standard measure of linkage disequilibrium - is biased toward disequilibrium, and the bias is particularly evident in small ... A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a ... Our Bayesian estimator of D corrects the bias toward disequilibrium that affects the maximum likelihood estimator. ...
https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-8-36/tables/1
Implications of inter-population linkage disequilibrium patterns on the approach to a disease association study in the human...
There is presently much interest in utilizing patterns of linkage disequilibrium (LD) to further genetic association studies. ... Implications of inter-population linkage disequilibrium patterns on the approach to a disease association study in the human ... Implications of inter-population linkage disequilibrium patterns on the approach to a disease association study in the human ... There is presently much interest in utilizing patterns of linkage disequilibrium (LD) to further genetic association studies. ...
https://www.bdi.ox.ac.uk/publications/133635
Refined Linkage Disequilibrium and Physical Mapping of the Gene Locus for X-Linked Dystonia-Parkinsonism (DYT3) - Nuffield...
Refined Linkage Disequilibrium and Physical Mapping of the Gene Locus for X-Linked Dystonia-Parkinsonism (DYT3) ... Refined Linkage Disequilibrium and Physical Mapping of the Gene Locus for X-Linked Dystonia-Parkinsonism (DYT3) ...
https://www.ndcn.ox.ac.uk/publications/31552
Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant | BMC...Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant | BMC...
The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A ... approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both ... Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. *Fabio ... The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-896
Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans...Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans...
... and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were ... Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven ... we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of ... the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those ...
https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-020-01669-6/tables/6
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global...RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global...
... ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual ... RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global ... ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual ...
https://www.pacb.com/publications/rad-sequencing-and-a-hybrid-antarctic-fur-seal-genome-assembly-reveal-rapidly-decaying-linkage-disequilibrium-global-population-structure-and-evidence-for-inbreeding/
linkagedisequilibrium
As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal ... As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal ... As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal ... Tag: linkagedisequilibrium. Identification of causal genes for complex traits (CAVIAR-gene). Posted on October 26, 2015. by ...
http://zarlab.cs.ucla.edu/tag/linkagedisequilibrium/
Inferring Linkage Disequilibrium blocks from genotypesInferring Linkage Disequilibrium blocks from genotypes
... Shubham Chaturvedi, Pierre Neuvial, Nathalie Vialaneix. 2022-03-31. ... where the similarity between SNPs is defined by linkage disequilibrium (LD).. This function implements the algorithm described ... Performance of a blockwise approach in variable selection using linkage disequilibrium information. BMC Bioinformatics, 16, 148 ...
https://mran.revolutionanalytics.com/snapshot/2022-04-08/web/packages/adjclust/vignettes/snpClust.html
Analysis of linkage disequilibrium within the HLA region in 10 European populations - Oxford Vaccine Group
Analysis of linkage disequilibrium within the HLA region in 10 European populations ... Analysis of linkage disequilibrium within the HLA region in 10 European populations ...
https://www.ovg.ox.ac.uk/publications/175368
Frontiers | Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napusFrontiers | Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus
2.3.3. Assessment of Linkage Disequilibrium. In order to determine the physical map distance in which LD decays in our B. napus ... 2013). High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics ... However, the results of Linkage disequilibrium (LD) analyses suggested that the number of such SSR-markers is at the lower end ... Hill, W. G., and Weir, B. S. (1988). Variances and covariances of squared linkage disequilibria in finite populations. Theor. ...
https://www.frontiersin.org/articles/10.3389/fpls.2016.00386/full
Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. - Radcliffe Department of...Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. - Radcliffe Department of...
Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. ... Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. ... Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. ... Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. ...
https://www.rdm.ox.ac.uk/publications/135340
IMSEAR at SEARO: Linkage disequilibrium and haplotypes of five TP53 polymorphisms in oesophageal cancer patients
The aim of present study was to evaluate the linkage disequilibrium (LD) of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[ ... Linkage disequilibrium and haplotypes of five TP53 polymorphisms in oesophageal cancer patients. Journal of Genetics. 2020 Jul ... Linkage disequilibrium and haplotypes of five TP53 polymorphisms in oesophageal cancer patients. ...
https://imsear.searo.who.int/handle/123456789/215498
ASPPH | UAB Professor Illustrates the Notion of Confounding by Linkage DisequilibriumASPPH | UAB Professor Illustrates the Notion of Confounding by Linkage Disequilibrium
Linkage disequilibrium (the non-random association of genetic variants in a population) and confounding are two widely- ... in the Journal of Human Genetics the high potential for confounding in association studies due to linkage disequilibrium (LD), ...
https://aspphbeta.org/uab-professor-illustrates-the-notion-of-confounding-by-linkage-disequilibrium/
Detecting Disease Associations due to Linkage Disequilibrium Using Haplotype Tags: A Class of Tests and the Determinants of...
Detecting Disease Associations due to Linkage Disequilibrium Using Haplotype Tags: A Class of Tests and the Determinants of ... Detecting Disease Associations due to Linkage Disequilibrium Using Haplotype Tags: A Class of Tests and the Determinants of ...
https://www.well.ox.ac.uk/publications/656299
Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers. | Profiles RNS
Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers. Am J Hum Genet. 1998 May; 62(5):1077-83. ...
https://profiles.uchicago.edu/profiles/display/213324
Table 4 - Bacillus cereus-Attributable Primary Cutaneous Anthrax-Like Infection in Newborn Infants, India - Volume 25, Number 7...
Estimation of linkage disequilibrium of Bacillus cereus, Assam Medical College & Hospital, Dibrugarh, Assam, India, 2018 ...
https://wwwnc.cdc.gov/eid/article/25/7/18-1493-t4
Part II: Methods and Approaches 1: Assessing Disease Associations and Interactions Chapter 10 | HUGE | CDCPart II: Methods and Approaches 1: Assessing Disease Associations and Interactions Chapter 10 | HUGE | CDC
... so far data on linkage disequilibrium for SNPs show that the extent of linkage disequilibrium varies by region of the genome, ... potentially could result from linkage disequilibrium. Linkage disequilibrium depends on population history and on the genetic ... Linkage disequilibrium in the human genome. Nature 2001;411:199-204.. *. Altshuler D, Pollara VJ, Cowles CR et al. An SNP map ... Teng J, Risch N. The relative power of family-based and case-control designs for linkage disequilibrium studies of complex ...
https://www.cdc.gov/genomics/resources/books/huge/chap10.htm
Genetic isolates in Corsica (France): linkage disequilibrium extension analysis on the Xq13 regionGenetic isolates in Corsica (France): linkage disequilibrium extension analysis on the Xq13 region
... LATINI, VERONICA;Sole G; ... In these populations, the disease allele reveals linkage disequilibrium (LD) with markers over significant genetic intervals, ... In these populations, the disease allele reveals linkage disequilibrium (LD) with markers over significant genetic intervals, ...
https://iris.unica.it/handle/11584/108131
Association Analysis on Source Sink-related Traits in Rice Based on Linkage Disequilibrium
Key words: SNP marker, linkage disequilibrium, association analysis 摘要： 为挖掘水稻源库相关性状优异等位基因, 利用分布于12条染色体的6 704个SNP标记与来自31个国家和地区的 ... Structure of linkage disequilibrium in plants[J]. Annual Review of Plant Biology, 2003, 54:357-374. [18] Collins A R. Linkage ... Association Analysis on Source Sink-related Traits in Rice Based on Linkage Disequilibrium ZHAO Hongliang1, CHEN Kai2, ZHANG ... LD analysis showed that there was certain extent
https://www.hnxb.org.cn/EN/10.11869/j.issn.100-8551.2015.04.0674
Browsing by SubjectBrowsing by Subject
Linkage Disequilibrium [‎1]‎. Lip Neoplasms [‎1]‎. Lipid Metabolism [‎1]‎. Lipid Peroxidation [‎2]‎. ...
https://apps.who.int/iris/browse?rpp=20&offset=3463&etal=-1&sort_by=-1&type=mesh&starts_with_previous=P&order=ASC
Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes<...Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes<...
Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Ji Rong Long, Lan Juan Zhao, Peng ... Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. / Long, Ji Rong; Zhao, Lan Juan; Liu ... Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. In: BMC Genetics. 2004 ; Vol. 5. ... Dive into the research topics of Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. ...
https://scholars.houstonmethodist.org/en/publications/patterns-of-linkage-disequilibrium-and-haplotype-distribution-in-
An integrated map of genetic variation from 1,092 human genomes | NatureAn integrated map of genetic variation from 1,092 human genomes | Nature
b, The average number of variants in linkage disequilibrium (r2 , 0.5 among EUR) to focal SNPs identified in GWAS47 as a ... We find that, in Europeans, each previously reported GWAS signal31 is, on average, in linkage disequilibrium (r2 ≥ 0.5) with 56 ... 1b). By integrating linkage disequilibrium information, genotypes from low-coverage data are as accurate as those from high- ... Our current resource increases the number of variants in linkage disequilibrium with each GWAS signal by 25% compared with the ...
https://www.nature.com/articles/nature11632?error=cookies_not_supported
Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci | Parasites & Vectors | Full TextPopulation genetics of Glossina palpalis palpalis from central African sleeping sickness foci | Parasites & Vectors | Full Text
Linkage disequilibrium. Among the 28 possible pairs of loci that could be tested, four displayed significant linkage (14%). ... Linkage disequilibrium was assessed through the G-based randomization procedure per pair of locus overall subsamples, this ... Bartley D, Bagley M, Gall G, Bentley B: Use of linkage disequilibrium data to estimate effective size of hatchery and natural ... Waples RS, Do C: LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour ...
https://parasitesandvectors.biomedcentral.com/articles/10.1186/1756-3305-4-140
Impact of common variation in bone-related genes on type 2 diabetes and related traitsImpact of common variation in bone-related genes on type 2 diabetes and related traits
... variants in linkage disequilibrium (r(2) , 0.5), and BMD candidate genes. SNP rs6867040, at the ITGA1 locus, was associated ...
https://pubmed.ncbi.nlm.nih.gov/22698912/
Issue: The American Journal of Human GeneticsIssue: The American Journal of Human Genetics
By haplotype and linkage-disequilibrium analyses in Finnish carriers of a putative founder mutation, the critical region was ... To characterize linkage disequilibrium (LD) levels in human populations, we have analyzed 10 independent noncoding segments in ... Gene Conversion and Different Population Histories May Explain the Contrast between Polymorphism and Linkage Disequilibrium ... We report here a genomewide linkage study of IA in 104 Japanese affected sib pairs in which positive evidence of linkage on ...
https://www.cell.com/ajhg/issue?pii=S0002-9297
GeneticPolymorphismHaplotypes and linkageSNPsVariantsPatternsPopulationsLociAnalysesAllele frequenciesPolymorphismsGenesGenotypeMarkersHomozygosityEstimationAllelesMappingAnalysisGenePopulationRevealsResultsGlobalApproachState
Genetic10
  • There is presently much interest in utilizing patterns of linkage disequilibrium (LD) to further genetic association studies. (ox.ac.uk)
  • The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. (biomedcentral.com)
  • The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for the determination of the genetic basis of traits [ 12 ]. (biomedcentral.com)
  • Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. (ox.ac.uk)
  • Linkage disequilibrium (the non-random association of genetic variants in a population) and confounding are two widely-discussed concepts in genetics and in epidemiology, yet their relationship has received only intuitive or no considerations. (aspphbeta.org)
  • Dr. Brahim Aissani, research assistant professor in the department of epidemiology at the University of Alabama at Birmingham School of Public Health, recently outlined in the Journal of Human Genetics the high potential for confounding in association studies due to linkage disequilibrium (LD), a simple but novel concept that may help understand some of the unexplained but consistently replicated genetic associations. (aspphbeta.org)
  • In these populations, the disease allele reveals linkage disequilibrium (LD) with markers over significant genetic intervals, therefore facilitating disease locus identification. (unica.it)
  • To investigate the relationship between the LPL gene and lipid profiles, especially TG, in 148 hypertensive families, we have chosen seven flanking microsatellite markers and four internal markers of the LPL gene and conducted linkage analysis by SOLAR and S.A.G.E. (statistical analysis for genetic epidemiology)/SIBPAL 2 programs, and linkage disequilibrium analysis by QTDT (quantitative transmission/ disequilibrium test) and GOLD (graphical overview of linkage disequilibrium). (elsevier.com)
  • Considering the diverse differences of allelic frequency and linkage disequilibrium pattern in different continental populations [ 28 ], performing GWAS in non-European populations will provide new insights into genetic etiology of SCZ. (biomedcentral.com)
  • Population-based candidate-gene studies can be an effective strategy for identifying genes involved in the etiology of disorders where family-based linkage studies are compromised by lack of access to affected members, low penetrance, and/or genetic heterogeneity. (elsevier.com)
Polymorphism2
  • The aim of present study was to evaluate the linkage disequilibrium (LD) of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[a polymorphism of TP53 and their haplotypes association with oesophageal cancer risk in patients from Punjab, northwest India. (who.int)
  • Lack of linkage disequilibrium between transforming growth factor alpha Taq I polymorphism and cleft lip with or without cleft palate in families from Northeastern Italy « Dott. (carinci.org)
Haplotypes and linkage2
  • The results, including the haplotypes and linkage disequilibria, are compared to patterns reported for other populations in the world. (who.int)
  • Extended haplotypes and linkage disequilibrium in the IL1R1-IL1A-IL1B-IL1RN gene cluster: association with knee osteoarthritis. (cdc.gov)
SNPs6
  • performs adjacency-constrained hierarchical clustering of single nucleotide polymorphisms (SNPs), where the similarity between SNPs is defined by linkage disequilibrium (LD). (revolutionanalytics.com)
  • Two SNPs (single nucleotide polymorphisms), HindIII and HinfI, were found in linkage disequilibrium with LDL-cholesterol levels (P = 0.0178 and P = 0.0088 respectively). (elsevier.com)
  • In 5 cases, CNVs located were in strong linkage disequilibrium with tag SNPs, either within or adjacent to the same haplotype block. (usda.gov)
  • Genome-wide complex trait analysis in two large cohorts showed that the additive variance explained by common SNPs was not significantly different from zero, but polygenic risk scores, weighted using linkage information, significantly predicted extraversion scores in an independent cohort. (springer.com)
  • in other words, the SNPs within a microhaplotype are so close that they cannot be assumed to be in linkage disequilibrium and we must take into account their mutual dependencies. (r-project.org)
  • Here, we leverage the strong haplotype-specific expression of MAPT exon 3 to investigate the functionality of SNPs that fall within this H1 haplotype region of linkage disequilibrium. (ox.ac.uk)
Variants4
  • As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal variants at associated loci lies in distinguishing among the many closely correlated variants due to LD. (ucla.edu)
  • OCTN variants were in tight linkage disequilibrium with the extended IBD5 risk haplotype D′ 0.79 and 0.88, and r 2 = 0.62 and 0.72 for IGR2096 and 3096, respectively. (bmj.com)
  • The MAPT risk variants fall within a large 1.8 Mb region of high linkage disequilibrium, making it difficult to discern the functionally important risk variants. (ox.ac.uk)
  • This work demonstrates an integrated approach to characterise the functionality of risk variants in large regions of linkage disequilibrium. (ox.ac.uk)
Patterns4
  • Implications of inter-population linkage disequilibrium patterns on the approach to a disease association study in the human MHC class III. (ox.ac.uk)
  • These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. (pacb.com)
  • However, most large-scale GWA studies have been conducted on predominantly European populations 23 , with results that often do not translate to other populations due to differences in allele frequencies and linkage disequilibrium patterns 24 - 26 . (researchsquare.com)
  • These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome. (princeton.edu)
Populations2
  • RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. (ox.ac.uk)
  • La comparaison des distances génétiques a mis en évidence un schéma plus proche de la population caucasienne que des populations mongoliennes, orientales ou afro-américaines. (who.int)
Loci2
  • LD analysis showed that there was certain extent linkage disequilibrium between SNP loci. (hnxb.org.cn)
  • Nous décrivons la fréquence et la répartition des antigènes de la classe I du complexe majeur d'histocompatibilité présents dans les loci A, B et C en fonction des données obtenues auprès de 200 sujets sains n'ayant aucun lien de parenté et originaires de différentes parties du Liban. (who.int)
Analyses2
  • By haplotype and linkage-disequilibrium analyses in Finnish carriers of a putative founder mutation, the critical region was narrowed to 250 kb, of which we sequenced, assembled, and annotated 207 kb. (cell.com)
  • Many chromosomal regions have shown linkage to bipolar disorder, but meta-analyses of microsatellite marker-based linkage studies have not provided consistent findings of susceptibility regions. (medscape.com)
Allele frequencies1
  • We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. (ox.ac.uk)
Polymorphisms2
  • Linkage disequilibrium between any set of polymorphisms can be estimated by initially filtering a genotype dataset and then using this function. (github.io)
  • A follow-up study also pointed to the SLC22A16 (organic cation/carnitine transporter) gene at 6q21,[19] the results of which were corroborated by a linkage study with high-density, single-nucleotide polymorphisms. (medscape.com)
Genes3
  • The development of linkage disequilibrium (LD) maps is very important for understanding the nature of non-linear association between phenotypes and genes, as LD can be defined as the non-random segregation of a pair of alleles at polymorphic sites. (sidalc.net)
  • Linkage disequilibrium (LD) is defined as "the occurrence of some genes (or alleles, or DNA segment) near one another on the same chromosome, more often than would be expected by chance alone. (genewhisperer.com)
  • Unless they are in linkage disequilibrium, different genes are independently inherited. (cdc.gov)
Genotype1
  • The major advantages of GWA over biparental linkage mapping lie in the much wider variability in phenotype and genotype made accessible, a history of multiple rounds of recombination in many different lineages and the inclusion of germplasm of direct relevance to crop improvement. (biomedcentral.com)
Markers3
  • Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers. (uchicago.edu)
  • Background: The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. (houstonmethodist.org)
  • More over, when DNA markers are in linkage disequilibrium things get even more complicated. (r-project.org)
Homozygosity1
  • Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density. (ox.ac.uk)
Estimation1
  • Estimation of linkage disequilibrium, persistence of phase and effective population size of Brazilian Hereford and Braford breeds. (sidalc.net)
Alleles1
  • D'\) is the standardized disequilibrium coefficient, a useful statistic for determining whether recombination or homoplasy has occurred between a pair of alleles. (github.io)
Mapping4
  • Linkage mapping or association mapping approaches are suitable methods for the discovery of QTL. (frontiersin.org)
  • Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. (ox.ac.uk)
  • linkage disequilibrium mapping and dating an ancestral mutation. (medscape.com)
  • 2003). Dense linkage disequilibrium mapping in the 15q11-q13 maternal expression domain yields evidence for association in autism. (bvsalud.org)
Analysis2
  • Association Analysis on Source Sink-related Traits in Rice Based on Linkage Disequilibrium[J]. Journal of Nuclear Agricultural Sciences, 2015, 29(4): 674-684. (hnxb.org.cn)
  • 20. Scapoli C, Trombelli L, Mamolini E, Collins A. Linkage disequilibrium analysis of case-control data: an application to generalized aggressive periodontitis. (bvsalud.org)
Gene1
  • Using S.A.G.E./SIBPAL 2, we identified a linkage with TG at the marker 'ATTT' located within intron 6 of the LPL gene (P = 0.0095). (elsevier.com)
Population1
  • RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding. (pacb.com)
Reveals1
  • Heritability partitioning with linkage disequilibrium score regression (LDSC) reveals a significant enrichment of schizophrenia heritability in conserved genomic regions, promoters, and enhancers. (biomedcentral.com)
Results1
  • Calculates linkage disequilibrium (LD) and runs an interactive Java visualizer for LD results. (github.io)
Global1
Approach1
  • Performance of a blockwise approach in variable selection using linkage disequilibrium information. (revolutionanalytics.com)
State1
  • These are systems that are in a constant state of disequilibrium, as they are always evolving. (lse.ac.uk)
Browsing by Subject Linkage Disequilibrium
Browsing by Subject "Linkage Disequilibrium" (extranet.who.int)
Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci | Parasites & Vectors | Full Text
Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci | Parasites & Vectors | Full Text (parasitesandvectors.biomedcentral.com)
Frontiers | Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis
Frontiers | Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis (frontiersin.org)
Posterior Polymorphous Corneal Dystrophy Workup: Laboratory Studies, Imaging Studies, Other Tests
Posterior Polymorphous Corneal Dystrophy Workup: Laboratory Studies, Imaging Studies, Other Tests (emedicine.medscape.com)
Open problems in human trait genetics | Genome Biology | Full Text
Open problems in human trait genetics | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Genes | Free Full-Text | Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow
Genes | Free Full-Text | Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow (mdpi.com)
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass | Nature
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass | Nature (nature.com)
Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium |...
Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium |... (link.springer.com)
Hermansky-Pudlak Syndrome: Background, Pathophysiology, Epidemiology
Hermansky-Pudlak Syndrome: Background, Pathophysiology, Epidemiology (medscape.com)
New Endemic Legionella pneumophila Serogroup I Clones, Ontario, Canada - Volume 16, Number 3-March 2010 - Emerging Infectious...
New Endemic Legionella pneumophila Serogroup I Clones, Ontario, Canada - Volume 16, Number 3-March 2010 - Emerging Infectious... (wwwnc.cdc.gov)
(researchgate.net)
Association of Genetic Variants of BMP4 with Type 2 Diabetes Mellitus and Clinical Traits in a Chinese Han Population
Association of Genetic Variants of BMP4 with Type 2 Diabetes Mellitus and Clinical Traits in a Chinese Han Population (hindawi.com)
Worldwide patterns of human epigenetic variation | Nature Ecology & Evolution
Worldwide patterns of human epigenetic variation | Nature Ecology & Evolution (nature.com)
Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture | Nature Genetics
Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture | Nature Genetics (nature.com)
Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular...
Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular... (bmcgenomics.biomedcentral.com)
The Polygenic Risk Score Knowledge Base: A Centralized Online Repository for Calculating and Contextualizing Polygenic Risk...
The Polygenic Risk Score Knowledge Base: A Centralized Online Repository for Calculating and Contextualizing Polygenic Risk... (researchsquare.com)
Genome-wide association study followed by trans-ancestry meta-analysis identify 17 new risk loci for schizophrenia | BMC...
Genome-wide association study followed by trans-ancestry meta-analysis identify 17 new risk loci for schizophrenia | BMC... (bmcmedicine.biomedcentral.com)
Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision...
Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision... (nature.com)
From Genetics to Treatment of Eosinophilic Esophagitis
From Genetics to Treatment of Eosinophilic Esophagitis (medscape.com)
PDF] An empirical approach to demographic inference with genomic data. | Semantic Scholar
PDF] An empirical approach to demographic inference with genomic data. | Semantic Scholar (semanticscholar.org)
Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics | Nature Communications
Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics | Nature Communications (nature.com)
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility | Nature...
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility | Nature... (nature.com)