Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Genotypic differences observed among individuals in a 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.
A genus of plant viruses in the family FLEXIVIRIDAE, that cause mosaic and ringspot symptoms. Transmission occurs mechanically. Potato virus X is the type species.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
Viruses parasitic on plants higher than bacteria.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
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.
Individuals whose ancestral origins are in the continent of Europe.
Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.
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.
Viral proteins that facilitate the movement of viruses between plant cells by means of PLASMODESMATA, channels that traverse the plant cell walls.
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).
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Genetic loci associated with a QUANTITATIVE TRAIT.
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.
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.
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.
Individuals whose ancestral origins are in the continent of Africa.
Viruses whose genetic material is RNA.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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.
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.
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.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
The functional hereditary units of PLANTS.
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.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."
Viruses which produce a mottled appearance of the leaves of plants.
Computer-based representation of physical systems and phenomena such as chemical processes.
Membrane-like channels of cytoplasm connecting adjacent plant cells. Plasmodesmata connect through pores in the CELL WALL and associate with the CYTOSKELETON machinery. They are essential for intercellular transport and communication.
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.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)
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.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A family composed of spouses and their children.
A specific pair GROUP C CHROMSOMES of the human chromosome classification.
A plant species of the genus SOLANUM, family SOLANACEAE. The starchy roots are used as food. SOLANINE is found in green parts.
Proteins found in any species of virus.
An individual having different alleles at one or more loci regarding a specific character.
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.
An individual in which both alleles at a given locus are identical.
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.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
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.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
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.
A coordinated international effort to identify and catalog patterns of linked variations (HAPLOTYPES) found in the human genome across the entire human population.
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
Diseases of plants.
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)
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
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)
Transmembrane proteins that form the beta subunits of the HLA-DQ antigens.
Sequential operating programs and data which instruct the functioning of a digital computer.
The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.
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)
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.
A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.
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.
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.
The total number of individuals inhabiting a particular region or area.
Interruption of NEURAL CONDUCTION in peripheral nerves or nerve trunks by the injection of a local anesthetic agent (e.g., LIDOCAINE; PHENOL; BOTULINUM TOXINS) to manage or treat pain.
One of the two pairs of human chromosomes in the group B class (CHROMOSOMES, HUMAN, 4-5).
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.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.
An ethnic group with historical ties to the land of ISRAEL and the religion of JUDAISM.
Genes that influence the PHENOTYPE only in the homozygous state.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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.
A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.
The genetic complement of a plant (PLANTS) as represented in its DNA.
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.
Biochemical identification of mutational changes in a nucleotide sequence.
Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.
Identification of genetic carriers for a given trait.
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).
Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)
Ribonucleic acid that makes up the genetic material of viruses.
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.
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.
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.
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.
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)
The functional hereditary units of VIRUSES.
The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.
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)
An HLA-DR antigen which is associated with HLA-DRB1 CHAINS encoded by DRB1*03 alleles.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
A country spanning from central Asia to the Pacific Ocean.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A specific pair of GROUP B CHROMOSOMES of the human chromosome classification.
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.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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.
A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Impaired conduction of cardiac impulse that can occur anywhere along the conduction pathway, such as between the SINOATRIAL NODE and the right atrium (SA block) or between atria and ventricles (AV block). Heart blocks can be classified by the duration, frequency, or completeness of conduction block. Reversibility depends on the degree of structural or functional defects.
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.
Persons or animals having at least one parent in common. (American College Dictionary, 3d ed)
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).
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.
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.
The mating of plants or non-human animals which are closely related genetically.
Number of individuals in a population relative to space.
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.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
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.
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)
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)
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
Databases devoted to knowledge about specific genes and gene products.
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.
The study of chance processes or the relative frequency characterizing a chance process.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
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.
A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
The magnitude of INBREEDING in humans.
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.
Persons living in the United States having origins in any of the black groups of Africa.
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.
A social group consisting of parents or parent substitutes and children.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
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)
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.
A specific HLA-B surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-B*08 allele family.
An enzyme that catalyzes the conversion of alpha D-glucose 1-phosphate to alpha D-glucose 6-phosphate. EC
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.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
Deoxyribonucleic acid that makes up the genetic material of plants.
The biological objects that contain genetic information and that are involved in transmitting genetically encoded traits from one organism to another.
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)
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).
Transmembrane proteins that form the beta subunits of the HLA-DP antigens.
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.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
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.
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.
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.
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)
A specific pair of GROUP C CHROMSOMES of the human chromosome classification.
A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.
The fluctuation of the ALLELE FREQUENCY from one generation to the next.
A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
Statistical interpretation and description of a population with reference to distribution, composition, or structure.
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.
A species of sheep, Ovis aries, descended from Near Eastern wild forms, especially mouflon.
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
The parts of the gene sequence that carry out the different functions of the GENES.
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.
Groups of individuals whose putative ancestry is from native continental populations based on similarities in physical appearance.
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.
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.
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)
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
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.
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.
A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
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.
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.
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.
The ratio of two odds. The exposure-odds ratio for case control data is the ratio of the odds in favor of exposure among cases to the odds in favor of exposure among noncases. The disease-odds ratio for a cohort or cross section is the ratio of the odds in favor of disease among the exposed to the odds in favor of disease among the unexposed. The prevalence-odds ratio refers to an odds ratio derived cross-sectionally from studies of prevalent cases.
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).
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.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
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).
Visualisation of linkage disequilibrium, haplotype estimation and haplotype tagging (Homepage). HelixTree - Haplotype analysis ... A software package for analyses of haplotype block structure. Haploscribe - Reconstruction of whole-chromosome haplotypes based ... "Facts & Genes. Volume 7, Issue 3". Archived from the original on May 9, 2008. Arora, Devender; Singh, Ajeet; Sharma, Vikrant; ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ...
2003). "The structure of haplotype blocks in the human genome". Science. 296 (5576): 2225-2229. doi:10.1126/science.1069424. ... 2003). "Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans". ... Another tool, gene view reports the location of the variation within a gene (if it is in a gene), the old and new codon, the ... The dbSNP is also linked to many other NCBI resources including the nucleotide, protein, gene, taxonomy and structure databases ...
... heart failure after investigations into the heat shock protein HSPB7 showed that the CLCNKA gene was in linkage disequilibrium ... "Common genetic variants and haplotypes in renal CLCNKA gene are associated to salt-sensitive hypertension". Hum. Mol. Genet. 16 ... Markovic S, Dutzler R (2007). "The structure of the cytoplasmic domain of the chloride channel ClC-Ka reveals a conserved ... Treatment for the SNP associated hyperreninemia involves drugs to block the Renin-Angiotensin-Aldosterone system to relieve the ...
The most commonly used approach, block-based method, exploits the principle of linkage disequilibrium observed within haplotype ... Unlike the block-based approach, a block-free approach does not rely on the block structure. The SNP frequency and ... LD is most commonly caused by physical linkage of genes. When two genes are inherited on the same chromosome, depending on ... This measure is suitable only for haplotype blocks with limited haplotype diversity and it is not clear how to use it for large ...
In the linkage study that has been released, the unique structure of the NAM population, described in the previous section, ... and is performed by scanning a genome for SNPs in linkage disequilibrium with a trait of interest. Association mapping has ... These observations led the authors to propose a model of "Common genes with uncommon variants" to explain flowering time ... November 2009). "A first-generation haplotype map of maize". Science. 326 (5956): 1115-7. doi:10.1126/science.1177837. PMID ...
... the presence of a block of strong linkage disequilibrium might indicate a 'recent' selective sweep near the centre of the block ... Selective sweeps can be detected by measuring linkage disequilibrium, or whether a given haplotype is overrepresented in the ... Gene selection acts directly at the level of the gene. In kin selection and intragenomic conflict, gene-level selection ... A famous example of a vestigial structure, the eye of the blind mole-rat, is believed to retain function in photoperiod ...
Haploview[14] - Visualisation of linkage disequilibrium, haplotype estimation and haplotype tagging (Homepage). ... A software package for analyses of haplotype block structure.. *Haploscribe[13] - Reconstruction of whole-chromosome haplotypes ... "Facts & Genes. Volume 7, Issue 3". Archived from the original on May 9, 2008.. ... is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ...
... the presence of a block of strong linkage disequilibrium might indicate a 'recent' selective sweep near the centre of the block ... Selective sweeps can be detected by measuring linkage disequilibrium, or whether a given haplotype is overrepresented in the ... Gene selection acts directly at the level of the gene. In kin selection and intragenomic conflict, gene-level selection ... Kuhn, Thomas S. (1996). The Structure of Scientific Revolutions (3rd ed.). Chicago, IL: University of Chicago Press. ISBN 978-0 ...
Genetic studies can use this admixture linkage disequilibrium to search for disease alleles with fewer markers than would be ... Cardon LR, Abecasis GR (2003). "Using haplotype blocks to map human complex trait loci". Trends Genet. 19 (3): 135-140. ... Mendelian (single-gene) inheritance was studied in a number of important disorders such as albinism, brachydactyly (short ... Goldstein DB, Chikhi L (2002). "Human migrations and population structure: what we know and why it matters". Annu Rev Genom Hum ...
From the extent of linkage disequilibrium, it was estimated that the last Neanderthal gene flow into early ancestors of ... Although less parsimonious than recent gene flow, the observation may have been due to ancient population sub-structure in ... The introgressive haplotypes were positively selected in only East Asian populations, rising steadily from 45,000 years BP ... and dividing it into non-recombining short sequence blocks-to estimate genome-wide maximum-likelihood under different models, ...
... thus microsatellites can differentiate alleles within a SNP-defined linkage disequilibrium block of interest. Thus, ... Li YC, Korol AB, Fahima T, Nevo E (June 2004). "Microsatellites within genes: structure, function, and evolution". Molecular ... Klintschar M, Dauber EM, Ricci U, Cerri N, Immel UD, Kleiber M, Mayr WR (October 2004). "Haplotype studies support slippage as ... They are also used in genetic linkage analysis to locate a gene or a mutation responsible for a given trait or disease. ...
One explanation for the mixed results is the possibility of other variants which are in linkage disequilibrium with the 118A>G ... Newer approaches shift away from analysis of specific genes and regions, and are based on an unbiased screen of genes across ... Naltrexone, a μ-opioid receptor antagonist, also blocks the euphoric effects of opioids by occupying the opioid receptor, but ... cell structure determination, and RNA, DNA, and protein handling/modifying. While over 100 variants have been identified for ...
Sinha R, Cloninger CR, Parsian A (Aug 2003). "Linkage disequilibrium and haplotype analysis between serotonin receptor 1B gene ... Furthermore, blocking 5-HT1B receptor signalling increases the number of osteoblasts, bone mass, and the bone formation rate.[ ... Available structures. PDB. Ortholog search: PDBe RCSB List of PDB id codes. ... 5-hydroxytryptamine receptor 1B also known as the 5-HT1B receptor is a protein that in humans is encoded by the HTR1B gene.[5][ ...
... thus microsatellites can differentiate alleles within a SNP-defined linkage disequilibrium block of interest. Thus, ... 2003). "Microsatellites within genes: structure, function and evolution". Mol. Biol. Evol. 21 (6): 991-1007. doi:10.1093/molbev ... 2004). "Haplotype studies support slippage as the mechanism of germline mutations in short tandem repeats". Electrophoresis. 25 ... They are also used in genetic linkage analysis to locate a gene or a mutation responsible for a given trait or disease. ...
linkage (See Table) DQA1 and DQB1 Linkage disequilibrium exists for many DR-DQ types. Nomenclature issues. Some older studies ... Das HK, Lawrance SK, Weissman SM (1983). "Structure and nucleotide sequence of the heavy chain gene of HLA-DR". Proc. Natl. ... Klitz W, Maiers M, Spellman S, Baxter-Lowe LA, Schmeckpeper B, Williams TM, Fernandez-Vina M (2003). "New HLA haplotype ... Rosenstein Y, Burakoff SJ, Herrmann SH (1990). "HIV-gp120 can block CD4-class II MHC-mediated adhesion". J. Immunol. 144 (2): ...
Methods based on linkage disequilibrium decay or methods inferring ancestry tracts can be used to date recent admixture or ... Theoretical models on hybrid zones suggest that the breakdown of ancestry blocks through recombination is suppressed near genes ... "Inference of population structure using dense haplotype data". PLOS Genetics. 8 (1): e1002453. doi:10.1371/journal.pgen.1002453 ... in addition to altering gene products if inserted into a gene, also alter promoter activity for genes if inserted upstream of ...
Tatiana M Karafet et al., "Coevolution of genes and languages and high levels of population structure among the highland ... With this reference point, the linkage disequilibrium in the Ashkenazi Jewish population was interpreted as "matches signs of ... "seem to be similar in their Y-haplotype patterns, both with regard to the haplotype distributions and the ancestral haplotype ... The study also investigates how shared autosomal DNA, and longest block values vary by strength-of-relationship for each study ...
Researchers used this information to conclude that the linkage disequilibrium block of the FTO gene acts upon IRX3. These ... The epigenetic variations involved with diabetes can change chromatin structure as well as gene expression. Regardless of ... that created CpGs across the haplotype. Within this 7.7 kb, haplotype-specific methylation area, a highly conserved non-coding ... risk for Type 2 Diabetes and obesity have a highly methylated 7.7 kb region in the linkage disequilibrium block of the FTO gene ...
With new bioinformatics tools there is a possibility of investigating population structure, gene flow and gene migration by ... Linkage disequilibrium (LD), a term used in population genetics, indicates non-random association of alleles at two or more ... Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F (May 2004). "Haplotype block partitioning and tag SNP selection using ... A tag SNP is a representative single-nucleotide polymorphism in a region of the genome with high linkage disequilibrium (the ...
... linkage disequilibrium locus A specific, fixed position on a chromosome where a particular gene or genetic marker resides. LOD ... repressor A DNA-binding protein that decreases the expression of one or more genes by binding to the operator and blocking the ... These network structures also represent functional relationships by approximating the rate at which genes are transcribed. ... haploinsufficiency haplotype A set of alleles in an individual organism that were inherited together from a single parent. ...
Association mapping Genetic association Genetic linkage Genome-wide association study Identity by type Linkage disequilibrium ... utilized geographic structure of IBD segments to estimate dispersal within Eastern Europe during the last centuries. Using the ... IBD mapping can be seen as a new form of association analysis that increases the power to map genes or genomic regions ... Another application of IBD is genotype imputation and haplotype phase inference. Long shared segments of IBD, which are broken ...
Haploview[14] - Visualisation of linkage disequilibrium, haplotype estimation and haplotype tagging (Homepage). ... A software package for analyses of haplotype block structure.. *Haploscribe[13] - Reconstruction of whole-chromosome haplotypes ... Facts & Genes. Volume 7, Issue 3 Archived 2008-05-09 at the Wayback Machine. ... is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ...
Ochi H, Miki D, Hayes CN, Abe H, Hayashida Y, Kubo M, Chayama K (June 2014). "IFNL4/IL-28B haplotype structure and its impact ... High linkage disequilibrium between marker SNPs (e.g., rs12979860) and candidate explanatory genetic variants (e.g., IFNL4-ΔG/ ... As the gene then known as IL28B was the closest known gene at the time, these genetic variants were called 'IL28B variants' and ... June 2017). "IFN-λ4 potently blocks IFN-α signalling by ISG15 and USP18 in hepatitis C virus infection". Scientific Reports. 7 ...
This evidence of linkage disequilibrium supports the hypothesis that most, if not all, CCR5 Δ32 alleles arose from a single ... Information from NCBI Gene Database Crystal Structure of the CCR5 Chemokine Receptor A rotatable, zoomable 3-D image from rcsb. ... Blocking CCR5 with Maraviroc (a drug approved for HIV) may enhance recovery after stroke. In the developing brain, chemokines ... Jun 1998). "Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes". American Journal of ...
The authors concluded that the structure of the modern dog gene pool was contributed to from ancient Siberian wolves and ... concluded that dogs originated in Central Asia because dogs from there exhibit the lowest levels of linkage disequilibrium. In ... 2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803-819. ... All three skeletal remains were found sprayed with red hematite powder and covered with large 20 cm thick basalt blocks. The ...
June 2002). "The structure of haplotype blocks in the human genome". Science. 296 (5576): 2225-9. Bibcode:2002Sci...296.2225G. ... Populations in Africa tend to have lower amounts of linkage disequilibrium than do populations outside Africa, partly because ... Gene flow and admixture[edit]. Main article: Gene flow. Gene flow between two populations reduces the average genetic distance ... "The structure of haplotype blocks in the human genome". Science. 296 (5576): 2225-29. Bibcode:2002Sci...296.2225G. doi:10.1126/ ...
"Linkage disequilibrium, haplotype and association studies of a chromosome 4 GABA receptor gene cluster: candidate gene variants ... The various subunit isoforms seen in the GABA-A receptor structure has an effect on its function. GABRA2 is most often seen as ... Besides giving GABA receptors an extra inhibitory punch, alcohol substrates bind to glutamate receptors, which blocks its ... "GABRA2 gamma-aminobutyric acid type A receptor alpha2 subunit [Homo sapiens (human)]". Gene - NCBI. "Entrez Gene: GABRA2 gamma- ...
... the presence of a block of strong linkage disequilibrium might indicate a 'recent' selective sweep near the centre of the block ... Selective sweeps can be detected by measuring linkage disequilibrium, or whether a given haplotype is overrepresented in the ... Gene selection acts directly at the level of the gene. In kin selection and intragenomic conflict, gene-level selection ... Kuhn, Thomas S. (1996). The Structure of Scientific Revolutions (3rd ed.). Chicago, IL: University of Chicago Press. ISBN 978-0 ...
... Kaori Nakamoto; Shuang Wang; Robert ... Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Archie Digital Collections. ... Here we report a genetic approach for an extensive analysis on linkage disequilibrium (LD) blocks and haplotype structures of ... Comparative LD patterns and haplotype block structure was defined across all test populations.CONCLUSION:A constant genetic ...
Here we report a genetic approach for an extensive analysis on linkage disequilibrium (LD) blocks and haplotype structures of ... Comparative LD patterns and haplotype block structure was defined across all test populations. A constant genetic structure in ... The LD patterns and haplotype blocks of CYP7A1 gene were defined in Africans, Caucasians, and Asians using genotyping data ... Genetic variations in the CYP7A1 gene have been associated with metabolic disorders of cholesterol and bile acids, including ...
Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also ... Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also ... As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies ... As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies ...
This study aimed to investigate the association of complement pathway genes with susceptibility to DR. Eight haplotype-tagging ... A haplotype AA defined by the major alleles of rs17611 and rs1548782 was significantly predisposed to PDR with increased risk ... Linkage disequilibrium (LD) structure of the C5 locus for DR (a), NPDR (b), and PDR (c). LD was measured using data from all ... The haplotype block was defined by the confidence interval method implemented in the Haploview software. The LD (. ) between ...
Haplotype diagram depicting the linkage disequilibrium structure between the SNPs in IL6ST gene. Nine SNPs fall into one block ... The analysis program Haploview (version 3.2) was used to calculate and visualize linkage disequilibrium and haplotype-block ... Based on the available SNP and linkage disequilibrium data from public databases, we selected 11 SNPs covering the whole gene, ... A haplotype comprised of the four SNPs with positive single-point association as part of the overall haplotype block also ...
Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Retrieved from " ...
"Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene," BMC Genetics, vol. 18, pp. 7-29, 2006. ... CYP7A1 Gene Polymorphism Located in the 5′ Upstream Region Modifies the Risk of Coronary Artery Disease. Tomasz Iwanicki,1 Anna ... J. Wang, D. J. Freeman, S. M. Grundy, D. M. Levine, R. Guerra, and J. C. Cohen, "Linkage between cholesterol 7α-hydroxylase and ... P. Niemiec, I. Zak, and K. Wita, "The 242T variant of the CYBA gene polymorphism increases the risk of coronary artery disease ...
... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity ... A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) ... 2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493. ... Zhang K, Calabrese P, Nordborg M and Sun F (2002) Haplotype block structure and its applications to association studies: power ...
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC Genomics. 2014;15(Suppl 7):S6. doi: ... We found one common gene for LM, 37 common genes for LF, 15 common genes for BFT and 12 genes for REA (gene ids at Additional ... After quality control filters we retained genotypes of 449,203 SNPs for linkage disequilibrium and haplotype block analysis, ... Haplotype block summary per autosome (BTA). (XLSX 6 kb). Additional file 4:(296K, pdf). Figure S3. Haplotype block ...
To capture the largest amount of haplotypes possible, we determined the haplotype block structure of the TBX1 locus and ... 1993) Testing linkage disequilibrium between a disease gene and marker loci (abstract). Am. J. Hum. Genet. 53:1107.Google ... 2002) The structure of haplotype blocks in the human genome. Science 296:2225-9.CrossRefGoogle Scholar ... Linkage disequilibrium (LD) at the TBX1 locus and location of SNPs. The genomic organization of the TBX1 gene is shown above. ...
WallJD, PritchardJK (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 4: 587-597. ... 2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229. ... significantly reducing the effect of long haplotype blocks within these important genes. Together, this enabled us to identify ... a haplotype block was identified as a region with a low recombination rate (Figure S4). These linkage blocks were used to show ...
Recent data suggest that linkage disequilibrium is highly structured into conserved blocks of sequence that are separated by ... Haplotype Analysis of the Polymorphic Human Vascular Endothelial Growth Factor Gene Promoter. Adam Stevens, Joanne Soden, Paul ... b, diagram of VEGF gene haplotypes A (A), B (B), and C (C; wild type). The relationship between the polymorphisms identified is ... MCF7 cells were transfected with pGL3-luc constructs containing the VEGF gene haplotypes A (A), B (B), or wild-type (C) for ...
Knowledge of haplotype structure and linkage disequilibrium is essential in mapping the genetic loci associated with disease ... Inversion, duplication, or deletion* of whole genes or gene-sized blocks of non-coded DNA.. • *Chromosomal inversion.*. • * ... Linkage*: certain gene loci and alleles stay together during meiosis and are inherited together.. • *Linkage map*: genetic map ... Haplotype blocks are separated by preferred sites (hotspots) of recombination.. • Haplotype-based methods offer a powerful ...
... population structure-demographic history combined with restricted gene flow can produce large blocks of linkage disequilibrium ... and so we designate it as haplotype group Ia. The haplotype group I sequences also maximize the linkage disequilibrium and the ... The observation of a valley of minimal heterozygosity and maximal haplotype structure, coupled with the retention of haplotype ... In addition, this region showed strong haplotype structure, with a high-frequency haplotype group containing very little ...
... receptor gene cluster, we identified haplotype block structures in 270 Black and 368 White (n = 638) participants, from the ... genomic region has been associated with nicotine dependence in Black and White Americans.By conducting linkage disequilibrium ... that exploration of gene x gene and gene x craving interactions in future, larger studies may provide mechanistic insights into ... versus other haplotypes (24.0%; p = .028). In Whites, the GTG haplotype (vs. other haplotypes) was associated with lifetime ...
The haplotypes spanning this block are shown above the linkage disequilibrium plot, with the thickness of the blue line ... Haplotype structure.. To evaluate the haplotype structure of the IDE gene at high density, we first downloaded data for 35 SNPs ... 10), haplotypes were reconstructed from the SNPs based on the linkage disequilibrium structure in the reference panel. We ... High-Density Haplotype Structure and Association Testing of the Insulin-Degrading Enzyme (IDE) Gene With Type 2 Diabetes in ...
Germline mutations in this gene have been described in families presenting syndromic diffuse gastric cancer ... The CDH1 gene plays an important role during carcinogenesis and craniofacial morphogenesis. ... The LD pattern and the structure of haplotype blocks across the CDH1 gene were determined using genotype data from the HapMap ... Linkage disequilibrium between markers of the CDH1 gene in the control samples ...
... "linkage disequilibrium" (LD)] across one or a few gene regions. These studies have generally concluded that linkage ... With an average block size of 11 to 22 kb and three to five haplotypes per block, our data suggest that fully powered haplotype ... C and D) Summary of haplotype diversity across all blocks. The number of common (≥5%) haplotypes per block (C) and fraction of ... Relation of linkage disequilibrium to physical distance within haplotype blocks, as assessed by the mean value of the ...
10 Due to limited genetic variation and haplotype structure and a high level of linkage disequilibrium within small regions of ... Bayesian mixture modeling of gene-environment and gene-gene interactions. Genet Epidemiol In press. ... Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001;294:1719-23. ... of GSTM1 gene versus having at least one copy of the gene. Recent studies were also able to assess gene dosage effects (ie, ...
Rare mutations in the CHEK2 gene are involved in familial breast cancer. This large study among Swedish women did not find an ... and we therefore treated the whole gene as a single haplotype block in our subsequent haplotype reconstruction. We identified a ... 2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229. * View Article ... Linkage Disequilibrium Characterization and TagSNP Selection. To characterize the linkage disequilibrium (LD) pattern, we ...
This study aimed to evaluate the association of polymorphisms in three linkage disequilibrium (LD) blocks of the IGF-1 on the ... Haplotype in the LD block 3 was analyzed using two tag single nucleotide polymorphisms (SNPs), rs6220 and rs7136446. Cancer- ... the haplotype in the LD block 3 was significantly associated with cancer-specific survival (P = 0.0003). When the sum of the ... especially a haplotype in the LD block 3, are assumed to be genetic markers predicting the outcome of metastatic PCa. ...
The structure and linkage disequilibrium (LD) plot of VPS4A genes. (A) The structure of the VPS4A gene was generated from the ... Haplotype blocks were generated through method solid spine of the LD. The whole VPS4A gene was involved in a single haplotype ... The same haplotype block was constructed in 8,358 ALSPAC individuals, and the same haplotype phases were acquired with similar ... Gene Manipulation in Drosophila.. Vps4 is the highly conserved, sole ortholog of two mammalian VPS4 genes (26), and the fly ...
Figure 1 shows the pairwise linkage disequilibrium and haplotype block structure among these SNPs. The association of single ... Genome-wide search for type 2 diabetes/impaired glucose homeostasis susceptibility genes in the Chinese: significant linkage to ... Pairwise linkage disequilibrium was computed from the combined data of case and control subjects by calculating D′ and r2 in ... Linkage disequilibrium patterns of the 15 typed SNPs in the Chinese population. ...
... structure of the PPARδ gene, and the localization of included SNPs are shown above the LD values and haplotype blocks. Circled ... Linkage disequilibrium (LD) estimates of genetic variants encompassing the PPARD gene. SNPs with minimum allele frequency ≥5% ... PPARδ structure and function. PPARδ forms a heterodimer with the RXR and regulates the transcription of genes harboring a PPAR ... Numbers in squares designate the degree of LD (R2) between any two markers, and the LD estimates and haplotype blocks were made ...
The aim of this study was to investigate potential associations of genetic variants in the MRC1 gene with sarcoidosis. Nine ... These results suggest that MRC1 is an important candidate gene for sarcoidosis. This is the first study to imply that genetic ... single nucleotide polymorphisms (SNPs), encompassing the MRC1 gene, were genotyped in a total of 605 Japanese consisting of 181 ... Haplotype Block. *Mannose Receptor. *Linkage Disequilibrium Structure. *Epithelioid Cell Granuloma. Background. Sarcoidosis is ...
Good review of linkage disequilibrium mapping of disease genes. Collins A (2000) Mapping in the sequencing era. Human Heredity ... The haplotype structure for a human chromosome established using 24047 SNPs. The first whole‐chromosome LD maps may not be far ... 2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proceedings of the ... Techniques and Tools in Clinical Genetics , Gene and Genome Structure and Organisation , DNA Structure and Function , ...
C) Two haplotype blocks were constructed based on the strength of LD in each gene region. The R2 values of each SNP pair are ... Rs3853839 was in low linkage disequilibrium (LD) with other SNPs in the region. To minimize missing any other common ... A) TLR7 and TLR8 gene structure. (B) Eleven TLR7 SNPs and 12 TLR8 SNPs were genotyped in 1,434 SLE cases and 1,591 healthy ... We next performed a haplotype-based association test using Haploview 4.03 software. The "GAACAC" haplotype formed by rs2897827 ...
We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the ... Expected number of genes in and between haplotype blocks. The expected number of genes in and between the haplotype blocks of ... the wild soybean haplotype block structure is characterized by much smaller blocks. In terms of haplotype diversity, the three ... Haplotype map and haplotype block structure among wild, landrace, and N. Am. cultivar populations. The total number of ...
The structure of haplotype blocks in the human genome. Science. 2002. 296:2225-2229. View this article via: PubMed CrossRef ... Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 1999. 22:139-144. ... since very few SNP markers from each of these linkage disequilibrium blocks will be required to screen the entire genome (94). ... haplotype blocks). It has also been shown that in Europeans and Americans of European descent there is very little haplotype ...
These data document the generality of hotspots, a block-like structure of linkage disequilibrium and low-haplotype diversity, ... Hina grain hardness genes: adaptive SNP polymorphism Hina genes in wild barley are one of two known genes related to grain ... showed novel aspects of structure and linkage disequilibrium. Likewise, recombination rates vary systematically around and ... single genes, multilocus structures, candidate genes, and the entire genome organization and sequencing in natural populations ...
  • 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). (
  • 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). (
  • This study aimed to investigate the association of complement pathway genes with susceptibility to DR. Eight haplotype-tagging SNPs of SERPING1 and C5 were genotyped in 570 subjects with type 2 diabetes: 295 DR patients (138 nonproliferative DR [NPDR] and 157 proliferative DR [PDR]) and 275 diabetic controls. (
  • We genotyped nine tag SNPs in this sample but did not observe significant differences in allele or haplotype frequencies in any of the analyzed groups (all affected, schizophrenia and schizoaffective disorder, schizophrenia alone, and bipolar disorder and major depressive disorder) compared with the control group. (
  • These are primarily due to the clonal population structure, and generally limited recombination within bacteria, which make the causal SNPs indistinguishable from other linked SNPs, effectively creating very large haplotype blocks [14] , [15] . (
  • Various groups have explored the role of the common genetic variation of IDE on insulin resistance and reported associations of various single nucleotide polymorphisms (SNPs) and haplotypes on both type 2 diabetes and glycemic traits. (
  • Fourth, several association studies have reported nominal association of IDE single nucleotide polymorphisms (SNPs) or haplotypes with type 2 diabetes and/or glycemic traits ( 8 - 10 ). (
  • The aim of this study was to evaluate the association between nucleotide variants of CDH1 and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). Six single nucleotide polymorphisms (SNPs) of the CDH1 gene (rs16260, rs9929218, rs7186053, rs4783573, rs16958383, and rs1801552) were genotyped using the TaqMan SNP genotyping assays in 250 patients with NSCL/P and 540 controls from the Polish population. (
  • We therefore selected tagging SNPs spanning the HNF1 β gene and performed a case-control study in a Chinese Han population. (
  • We analyzed 14 common SNPs spanning 52 kilobases (kb) of the CHEK2 gene in 92 Swedish women. (
  • Haplotype in the LD block 3 was analyzed using two tag single nucleotide polymorphisms (SNPs), rs6220 and rs7136446. (
  • Nine single nucleotide polymorphisms (SNPs), encompassing the MRC1 gene, were genotyped in a total of 605 Japanese consisting of 181 sarcoidosis patients and 424 healthy controls. (
  • Half of the SNPs and SN indels but only one of seven longer rearrangements found in classical laboratory strains were useful for haplotype mapping in the wild-derived M. m. domesticus . (
  • We also found two major haplotypes among the four novel SNPs. (
  • In 946 subjects (350 healthy controls, 352 patients with BD, and 244 with SPR), nine single nucleotide polymorphisms (SNPs) in the EGR2 gene region were genotyped. (
  • Further, we evaluated the relationship between SNPs of SPP1 gene and response to a standardized 3-month GC treatment protocol with prospectively collected outcome data. (
  • Fontanesi L., Scotti E., Russo V. (2010): Analysis of SNPs in the KIT gene of cattle with different coat colour patterns and perspectives to use these markers for breed traceability and authentication of beef and dairy products. (
  • CGTS integrates the information of the LD association and the genotype diversity using the site graphs, discards redundant SNPs using the algorithm based on these graph structures. (
  • Recent studies show that the abundance of single nucleotide polymorphisms (SNPs) and haplotypes can provide the most complete information for genome-wide association studies. (
  • Through the analysis of SNPs and haplotypes, most of the genetic variations among different people can be discovered. (
  • These tagSNPs can represent associated SNPs in long distance without the block restriction, but may lose some important information contained in the rest SNPs and fail to distinguish all haplotypes in a LD cluster. (
  • To examine whether single-nucleotide polymorphisms (SNPs) in key pharmacokinetic genes were associated with risk of hematological or gastrointestinal toxicity, we analyzed 78 SNPs in ABCB1, ABCC1 and ALDH1A1 in 882 breast cancer patients enrolled in the SWOG trial S0221 and treated with cyclophosphamide and doxorubicin. (
  • Our findings provide evidence that SNPs in pharmacokinetic genes may have an impact on the development of chemotherapy-related toxicities. (
  • In this study, we analyzed 78 tagging single-nucleotide polymorphisms (SNPs) in ABCB1 , ABCC1 and ALDH1A1 that were selected to comprehensively capture germline genetic variations in these key pharmacokinetic genes for cyclophosphamide and doxorubicin, among 882 breast cancer patients enrolled in a cooperative group clinical trial SWOG S0221. (
  • We examined potential associations of single SNPs and haplotypes with risk of high-grade hematological and gastrointestinal toxicities induced by doxorubicin and cyclophosphamide. (
  • Three non-synonymous SNPs in exon 1 of the encoding MBL2 gene and three upstream SNPs form common 'secretor haplotypes' that can predict circulating levels. (
  • the 'secretor haplotypes' lie on a restricted number of extended haplotypes, which could include additional linked SNPs, which might also have possible functional implications. (
  • Although no individual SNPs were associated with ER-positive tumors, two haplotypes (GGTC in 2% of controls and AATT in 7% of controls) showed significant and consistent associations with increased risk for these tumors when compared with the common haplotype (GATT in 46% of controls): 1.71 (1.27-2.32) and 1.26 (1.03-1.54), respectively. (
  • Association testing was performed with both SNPs and reconstructed haplotypes. (
  • Halldorsson BV et al (2004) Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. (
  • C) Haploview output showing three block structures and related ht-SNPs (indicated with up arrowheads). (
  • In the present study, we analysed the linkage disequilibrium (LD) structure encompassing the TSHR, to identify LD 'blocks' and SNPs, which capture the majority of intra-block haplotype diversity. (
  • The haplotype tagging SNPs, plus all common SNPs reported in previous studies were genotyped in 1059 AITD Caucasian cases and 971 Caucasian controls. (
  • The transferability study was carried out using SNPs dispersed over four genomic regions: the PTPN22, HMGCR, VDR and CETP genes. (
  • Here, we have extensively analysed both LRP5 and its flanking three genes, spanning 269 kb, for single nucleotide polymorphisms (SNPs), and we present a comprehensive SNP map comprising 95 polymorphisms. (
  • In particular, methods for haplotype estimation, identification of haplotype blocks, measures of linkage disequilibrium and methods 487-41-2 manufacture for capturing most of the genetic variation in a gene through tag SNPs are discussed. (
  • Single nucleotide polymorphisms (SNPs) were screened and identified in the HGF gene region with denaturing high-performance liquid chromatography, and their linkage disequilibrium pattern was established in a Han Chinese population ( n = 150). (
  • Haplotype and diplotype of these linked SNPs were associated with hematologic toxicities. (
  • We first conducted a case-control study of 234 bladder cancer cases and 253 cancer-free controls, using the haplotype-based tagging single nucleotide polymorphism (SNP) approach involving 13 common SNPs initially identified in 100 control subjects. (
  • In both populations the effects of single SNPs and haplotypes were studied and a gene environment analysis with passive smoke exposure was performed using SAS/Genetics. (
  • Our results suggest that SNPs in genes encoding NF-κB inhibitors may contribute to the development and clinical phenotype of GD. (
  • Objective: Our objective was to search for obesity-related genes using a large number of gene-based single-nucleotide polymorphisms (SNPs). (
  • We sequenced an approximately 300-kb genomic region around rs3764220 and discovered SNPs for haplotype analyses. (
  • Results: Twelve SNPs in the SCG3 gene including rs3764220 were in almost complete linkage disequilibrium and significantly associated with an obesity phenotype. (
  • 32 SNPs in 19 circadian clockwork related genes were analyzed using DNA from 76 individuals with comorbid depression and AUD, 446 individuals with AUD and 517 healthy controls with no psychiatric diagnosis. (
  • The SNPs of importance for this suggestive association were rs2412646 and rs11240 indicating location of the functional variation in the block downstream rs2412648. (
  • If SNPs exist in coding regions of a gene, they can be synonymous or nonsynonymous mutations. (
  • A nonsynonymous mutation can be more impactful, because in this situation, one of the SNPs alter the three base pair codon, and encode for a different amino acid that can change the structure and function of the resultant protein. (
  • If this occurs during meiosis, during gamete formation, the organism that develops from the recombined gametes inherits blocks of SNPs. (
  • The difference between lengths of DNA that travel with SNPs is ultimately what is linkage disequilibrium. (
  • The authors of that study took about 526,000 SNPs and 400 copy number variations (the differences in the number of copies of a gene in the genomes of different people) found in 485 people from about 30 different populations. (
  • A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. (
  • Attempts have been made to take this clonal structure into account in association analyses [16] , [17] , but strong linkage disequilibrium will always restrict the resolution of the approach. (
  • Haplotype-based methods are expected to outperform single-SNP analyses because (i) common genetic variation can be structured into haplotypes within blocks of strong linkage disequilibrium and (ii) the functional properties of a protein are determined by the linear sequence of amino acids corresponding to DNA variation on a haplotype. (
  • We previously reported that two risk haplotypes, each in strong linkage disequilibrium (LD) with an allele of READ1, a polymorphic compound short tandem repeat within intron 2 of risk gene DCDC2 , are associated with RD and LI. (
  • Linkage of genes for a complex disease relies on having a priori knowledge of linkage disequilibrium (LD) blocks and haplotype structure to identify polymorphisms that are associated with the disease. (
  • Polymorphisms at cholesterol 7 α -hydroxylase, apolipoproteins B and E and low density lipoprotein receptor genes in patients with gallbladder stone disease," World Journal of Gastroenterology , vol. 10, no. 10, pp. 1508-1512, 2004. (
  • Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. (
  • The human vascular endothelial growth factor ( VEGF ) gene is unusually polymorphic,and there is evidence for inheritance of conserved haplotypes.One haplotype, carrying polymorphisms at −460/+405, is associated with enhanced production of VEGF in vitro . (
  • Whether common polymorphisms in this gene influence breast cancer risk remains unknown. (
  • In this study, we aimed to assess the importance of common CHEK2 variants on population risk for breast cancer by capturing the majority of diversity in the gene using haplotype tagging single nucleotide polymorphisms (tagSNPs). (
  • Notwithstanding the involvement of the CHEK2 gene in breast cancer aetiology, we show that common polymorphisms do not influence postmenopausal breast cancer risk. (
  • This study aimed to evaluate the association of polymorphisms in three linkage disequilibrium (LD) blocks of the IGF-1 on the survival of metastatic PCa patients. (
  • The cytosine-adenine ( CA ) repeat polymorphism and rs12423791 were selected as representative polymorphisms in the LD blocks 1 and 2, respectively. (
  • Polymorphisms in the IGF-1 , especially a haplotype in the LD block 3, are assumed to be genetic markers predicting the outcome of metastatic PCa. (
  • We therefore speculated that the MRC1 gene may be an excellent candidate for susceptibility to sarcoidosis, and tested for associations between MRC1 polymorphisms and the development of sarcoidosis in our Japanese case-control analysis. (
  • The First Report of Polymorphisms and Genetic Features of the prion-like Protein Gene (PRND) in a Prion Disease-Resistant Animal, Dog. (
  • Case-controlled studies in several species, including humans and cattle, indicated a potent association of prion protein gene ( PRNP ) polymorphisms in the progression of prion disease. (
  • However, to date, polymorphisms of the dog PRND gene have not been reported, and the genetic linkage between the PRNP and PRND genes has not been examined thus far. (
  • Gene map and polymorphisms identified in the dog prion-like protein gene ( PRND ) on chromosome 24. (
  • Effects of vitamin A and D receptor gene polymorphisms/haplotypes on immune responses to measles vaccine. (
  • We assessed the association between polymorphisms in the vitamin A receptors [retinoic acid receptor α, retinoic acid receptor β (RARB), and retinoic acid receptor γ] and vitamin D receptor (VDR)/retinoid X receptor α (RXRA) genes and interindividual variations in immune responses after two doses of measles vaccine in 745 children. (
  • Using a tag single nucleotide polymorphism (SNP) approach, we genotyped 745 healthy children for the 391 polymorphisms in vitamin A receptor and VDR genes. (
  • We hypothesized the pro-inflammatory cytokine, osteopontin (OPN), may be associated with variability of response to glucocorticoids (GCs) in patients with MG. A cohort of 250 MG patients treated with standardized protocol of GCs was recruited, and plasma OPN and polymorphisms of its gene, secreted phosphoprotein 1 ( SPP1 ), were evaluated. (
  • Genetic polymorphisms have been identified that are associated with therapeutic response to GCs in other autoimmune and inflammatory conditions ( 8 ), and we recently identified a single nucleotide polymorphism (SNP) in the GC receptor gene as an independent factor associated with short-term GC responsiveness among patients with MG ( 9 ). (
  • We hypothesized that plasma OPN may be a marker of treatment responsiveness and that genetic variations (polymorphisms) in the secreted phosphoprotein 1 ( SPP1 ) gene, which encodes OPN, are associated with differences in GC responsiveness of patients with MG. (
  • Li X., Ekerljung M., Lundstrom K., Lunden A. (2013): Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color, marbling and water holding capacity in meat from beef cattle populations in Sweden. (
  • These complimentary approaches have demonstrated that polymorphisms in the carnosinase 1 gene on chromosome 18q, the adiponectin gene on 3q, and the engulfment and cell motility gene on 7p are likely associated with susceptibility to diabetic nephropathy. (
  • We genotyped a total of 13 polymorphisms in the carboxylesterase 2 ( CES2 ) gene, the cytidine deaminase ( CDD ) gene, the thymidine phosphorylase ( TP ) gene, the thymidylate synthase ( TS ) gene, and the dihydropyrimidine dehydrogenase ( DPD ) gene in 130 patients treated with capecitabine. (
  • The aim of the present study was to investigate the relationship between capecitabine-induced HFS and polymorphisms in genes of the capecitabine metabolic pathway ( CES2 , CDD , TP , and DPD ) and target gene ( TS ). (
  • Four tag single-nucleotide polymorphisms (SNP) in GATA3 and its 3′ flanking gene FLJ4598 were genotyped in two case control studies in Norway and Poland (2,726 cases and 3,420 controls). (
  • Carlson C, Eberle MA et al (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. (
  • We characterized variation in HSD17B1 by resequencing and dense genotyping a multiethnic sample and identified haplotype-tagging single nucleotide polymorphisms (htSNP) that capture common variation within a 33.3-kb region around HSD17B1 . (
  • Background The ability to digest lactose after weaning, namely, lactase persistence (LP), is encoded by polymorphisms in the MCM6 gene and varies widely in frequency among different human populations. (
  • Do NeuroD Gene Polymorphisms Predict the Risk of Heroin Dependence or Mediate the Association between Personality Traits and Heroin Dependence? (
  • In this genetic case-control study, we aimed to investigate whether NeuroD gene polymorphisms associate with the occurrence of HD and the specific personality traits of patients with HD. (
  • The present study provides a rationale for analyzing associations of KIR polymorphisms by taking into account the complex LD structure of the KIR region. (
  • Association of CTLA-4 but not CD28 gene polymorphisms with systemic lupus erythematosus in the Japanese population. (
  • Technical note: linkage disequilibrium and disease-associated CTLA4 gene polymorphisms. (
  • To investigate the association of high myopia with polymorphisms in the hepatocyte growth factor ( HGF ) gene, a potential candidate for myopia development. (
  • There are at least 253 single nucleotide polymorphisms (SNP) of the MDM2 gene reported in the dbSNP database, 5 of which the vast majority are intronic and few in the exons and promoter regions. (
  • Association between VEGF polymorphisms (936c/t, -460t/c and -634g/c) with haplotypes and coronary heart disease susceptibility. (
  • Haplotypes of RHO polymorphisms and susceptibility to age-related macular degeneration. (
  • By resequencing all the exons and part of the introns of the porcine CGA gene, 22 polymorphisms in total were identified in this study. (
  • Breed-specific haplotypes were found and a map of the porcine CGA polymorphisms' evolution history was inferred. (
  • Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. (
  • We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. (
  • Comparative and functional analyses showed that the human GIP gene encodes a cryptic glucose-dependent insulinotropic polypeptide (GIP) isoform (GIP55S or GIP55G) that encompasses the SNP and is resistant to serum degradation relative to the known mature GIP peptide. (
  • Human studies have used both association and linkage analyses to evaluate the role of candidate genes in the etiology of CL/P. Association mapping is the identification of nonrandom correlations (associations) between alleles at two loci in a population. (
  • Recent genome-wide linkage scans have identified several chromosomal regions that likely contain diabetic nephropathy susceptibility genes, and association analyses have evaluated positional candidate genes under these linkage peaks. (
  • These analyses confirm the location of a QTL affecting tick burden on BTA10 and position it close to the ITGA11 gene. (
  • Analyses of pooled data suggested a reduced risk of breast cancer associated with two intronic variants in GATA3 in linkage disequilibrium (rs3802604 in intron 3 and rs570613 in intron 4). (
  • Logistic regression analyses found no associations between breast cancer and any htSNPs or haplotypes in IGF1, IGFBP1, or IGFBP3. (
  • Stat.TestingAndEstimatingAssociation Modelling genotypic information This section discusses more advanced topics on structuring genotypic information beyond single-marker analyses. (
  • Haplotype analyses suggested a minor effect of the ADAM33 haplotype H4 on asthma (p = 0.033) but not on BHR. (
  • JMP Genomics also supports more complex expression analyses, such as screening for allele-specific expression, filtering intensities or counts, performing batch normalization, and applying sample and gene filters to quickly reanalyze subsets of your data. (
  • JMP Genomics provides exceptional tools for statistical geneticists, from simple case-control association and linkage disequilibrium analyses to complex linear models supporting covariates, interactions and random effects. (
  • As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. (
  • When the sum of the risk genetic factors in each LD block (19-repeat allele, C allele of rs12423791, or C-T haplotype) was considered, patients with all the risk factors had significantly shorter cancer specific-survival than those with 0-2 risk factors ( P = 0.0003). (
  • Interestingly, most variation was associated with the M470 allele, while the V470 allele showed an 'extended haplotype homozygosity' (EHH). (
  • The A allele of the G1733A polymorphism of the AR gene has been associated with increased risk of prostate cancer. (
  • Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele. (
  • Carriers of rs11728697*T allele (allele definition: one of two or more alternative forms of a gene) were more frequent in the poorly GC responsive group compared to the GC responsive group indicating an association of rs11728697*T allele with GC non-responsiveness. (
  • Linkage disequilibrium and marginal allele freqs. (
  • Under this model, haplotypes are clustered according to their similarity, in terms of marker-SNP allele matches, which is used as a proxy for recent shared ancestry. (
  • 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. (
  • Most studies have focused on a single nucleotide polymorphism (SNP) in the promoter region of the CYP7A1 gene. (
  • These effects include decreased polymorphism, increased linkage disequilibrium, and an increased frequency of derived variants. (
  • It is well recognized that common variants of genes that cause monogenic forms of diabetes may also have a role in common type 2 diabetes susceptibility, such as P12A polymorphism in PPARG , E23K polymorphism in KCNJ11 , and common variants in the promoter region of HNF4A ( 7 - 9 ). (
  • These data established a functional polymorphism in type I IFN pathway gene TLR7 predisposing to SLE, especially in Chinese and Japanese male subjects. (
  • By using a candidate gene approach, we report herein that a functional polymorphism in 3′UTR of TLR7 is associated with SLE in Chinese and Japanese populations, with a stronger effect in male than female subjects. (
  • Genetic polymorphism and heterozygosity in nature are structured nonrandomly on a massive scale. (
  • The term 'haplogroup' refers to the SNP/unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (
  • A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. (
  • 3. The SPC map of claim 1, wherein the coincidence of each said polymorphism of said subset with each other polymorphism of said subset is calculated according to a parameter selected from the group consisting of a pairwise C value, C* value, a r.sup.2 linkage disequilibrium value, a A linkage disequilibrium value, a .delta. (
  • We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%-3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. (
  • The LD was studied at two levels of polymorphism: the structural level (presence or absence of KIR genes) and the allelic level (between alleles of KIR genes). (
  • CTLA-4 gene polymorphism in promoter and exon-1 regions in Chinese patients with systemic lupus erythematosus. (
  • Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery using a 30K Unigene Pepper GeneChip. (
  • Multilocus analysis of single-nucleotide-polymorphism (SNP) haplotypes may provide evidence of association with disease, even when the individual loci themselves do not. (
  • I employ a Bayesian partition model to describe the correlation between marker-SNP haplotypes and causal variants at the underlying functional polymorphism(s). (
  • Haplotypes within a cluster are then assigned the same probability of carrying a causal variant at the functional polymorphism(s). (
  • This is the first study reporting the association of an HGF gene polymorphism with high myopia. (
  • The study thereby identified functional polymorphism of SLC31A1 that modulates miRNA-3ʹUTR interaction and gene expression as potential pharmacogenetic biomarker for clinical outcomes of platinum-based chemotherapy in NSCLC patients. (
  • We found that the C1797G polymorphism in the MDM2 promoter region is an important SNP because its homozygous variant genotype, but none of the haplotypes, was associated with risk of bladder cancer. (
  • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. (
  • HLAE gene polymorphism associated with susceptibility to kawasaki disease and formation of coronary artery aneurysms. (
  • Furthermore, there was a trend toward higher plasma levels of soluble HLA-E in KD patients with the CT and TT genotypes of the HLA-E gene polymorphism. (
  • Our results suggest that the HLA-E gene polymorphism may play a role in the pathogenesis of KD. (
  • 13. A method according to claim 1, wherein the at least one genetic marker known to reside in an LD block is selected from the group consisting of a single nucleotide polymorphism (SNP), a haplotype, a microsatellite (simple tandem repeat STR, simple sequence repeat SSR), a restriction fragment length polymorphism (RFLP), an amplified fragment length polymorphism (AFLP), and an insertion-deletion polymorphism (INDEL). (
  • The gene genealogy for these recombining regions may be represented as a graph, called the ancestral recombination graph (ARG). (
  • Graph of the linkage disequilibrium map in the TAP2 region oriented from pter to qter (a) and meiotic recombination (b). (
  • Verhoeven KJ and Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. (
  • We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. (
  • The presence of recombination hot and cold spots has a bearing on efforts to map disease genes and for the understanding of the biological properties of chromosome location. (
  • We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. (
  • The number of SDPs is indirectly proportional to haplotype blocks, regions limited by historical recombination. (
  • Estimates of linkage disequilibrium across MBL2 indicate that it is divided into two blocks, with a probable recombination hot spot in the 3′ end. (
  • TagSNP transferability from the HapMap dataset to admixed populations is of uncertain value due population structure, admixture, drift and recombination effects. (
  • Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene. (
  • Patterns of linkage disequilibrium (LD) in the human genome are beginning to be characterized, with a paucity of haplotype diversity in "LD blocks," interspersed by apparent "hot spots" of recombination. (
  • The identification of hot spots in between these LD blocks provides additional evidence that LD blocks are separated by areas of higher recombination. (
  • Eight haplotypes and two recombination sites were identified within a conserved 40.09 Mb linkage-disequilibrium block on the X chromosome. (
  • Haplotype diversity is controlled by a variety of processes, including mutation, recombination, marker ascertainment and demography. (
  • Often they are inherited in long blocks, and that's because of a unique phenomenon called homologous recombination. (
  • Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also has potential application in finding disease-predisposing genetic variants. (
  • In our previous studies, genetic variants in the CFH and CFB genes, both involved in complement alternative pathway, have been evaluated and identified as susceptibility genes for DR [ 18 ]. (
  • The excess of high-frequency-derived variants should therefore be diagnostic of a region with partial linkage to a swept site. (
  • The relatively long branches between swept and recombined alleles should produce an excess of linkage disequilibrium, due to the large number of polymorphic variants that are fixed between the haplotype groups ( P rzeworski 2002 ). (
  • Due to the impact of genetic variants of this gene in rodents and the function of its protein product, it has been proposed as a candidate gene for type 2 diabetes. (
  • We sought to characterize the haplotype structure of IDE in detail and replicate the association of common variants with type 2 diabetes, fasting insulin, fasting glucose, and insulin resistance. (
  • We therefore investigated common variants across the HNF1 β gene in a Chinese population. (
  • Rare inherited variants in two genes, BRCA1 and BRCA2, are responsible for the high breast cancer risk in most of these "breast cancer families. (
  • These factors could, for example, be common variants in many different genes, each of which on their own cause only a moderately raised risk (although more common variants of the BRCA1 and BRCA2 genes do not seem to be associated with breast cancer). (
  • However, the 1100delC variant of CHEK2 is rare, and scientists want to know whether more common variants of the gene were associated with breast cancer. (
  • The aim of this study was to investigate potential associations of genetic variants in the MRC1 gene with sarcoidosis. (
  • This study investigated if KLF15 gene variants were associated with LVH in type 2 diabetes. (
  • This study aimed to evaluate the impact of selection on the genome structure of beef cattle through identification of selection signatures reflecting the breeding standard of each breed and to discover potential functional genetic variants to improve performance traits. (
  • 96 DNA single base variants in 13 different genes were genotyped with MALDI-TOF and a bead array system. (
  • The structure can be revealed with the use of any data set of genetic variants from a particular locus. (
  • Haplotype-tagging SLC10A2 gene variants were identified in the Hapmap database and genotyped using PCR-based 5' exonuclease assays with fluorescent dye-labelled probes. (
  • Common variants of the SLC10A2 gene are not associated with sporadic or familial CRC. (
  • We first established the LD structure at the IL6ST and LEPR loci to select htSNPs comprehensively capturing genetic variability at these loci then we evaluate whether genetic variants at IL6ST and LEPR loci can modulate metabolic and inflammatory traits in two healthy population, one from Padova (PD, n=630) the other from San Giovanni Rotondo (SGR, n=553). (
  • The IL6ST study points to some genetic variants as possible determinants of impaired glucose metabolism and other abnormalities of the metabolic syndrome, while the LEPR study, by finding that variability in the gene is a significant predictor of CRP and fibrinogen levels, lends further support to the hypothesis that leptin has a physiological influence on inflammatory and prothrombotic traits. (
  • The colonies derive from a limited pool of ancestral haplotypes resembling those found in inbred strains: over 95% of sequence variants segregating in outbred populations are found in inbred strains. (
  • A flexible Bayesian framework for modeling haplotype association with disease, allowing for dominance effects of the underlying causative variants. (
  • We hypothesize that genetic variants in the MDM2 gene are associated with risk of bladder cancer. (
  • Select from an extensive set of rare variant association methods to group rare SNP variants within genes, pathways or positional groups, or identify genomic regions shared identical by state (IBS) between related or unrelated individuals. (
  • The tree-based association approach finds multiple sub-regions where the case haplotypes are more genetically related than the control haplotypes, and that there may be one or multiple disease-predisposing loci. (
  • Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype mapping of mouse quantitative trait loci (QTL). (
  • Both are genetically complex traits, which has limited the ability to identify disease loci or genes. (
  • For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (
  • For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you don't know which haplotype you have, e.g. (
  • The early growth response gene 2 (EGR2) is located at chromosome 10q21, one of the susceptibility loci in bipolar disorder (BD). (
  • Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation. (
  • Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci (QTLs), low linkage disequilibrium between markers to obtain accurate mapping resolution, and an absence of population structure to prevent false positive associations. (
  • Specific loci and genes underlying common phenotypic variation among Chinese domestic pig breeds have not yet been studied. (
  • Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci evaluation for capsaicinoid content in Capsicum. (
  • Fallin D, Schork NJ Accuracy of Haplotype Frequency Estimation for Biallelic Loci, by way of the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data. (
  • The quantitative trait loci (QTL) near their common glycoprotein alpha(A) subunit gene ( CGA ) have been reported inconsistently. (
  • Indicative of this limited resolution is the frequent use of the term "mosaic genes" to describe pneumococcal resistance alleles [7] . (
  • Linkage mapping looks for the cosegregation of alleles for genetic markers with a disease phenotype in a family. (
  • A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. (
  • First, it is used to mean a collection of specific alleles (that is, specific DNA sequences) in a cluster of tightly linked genes on a chromosome that are likely to be inherited together-that is, they are likely to be conserved as a sequence that survives the descent of many generations of reproduction. (
  • It is thought that identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (
  • Results We found that lactase non-persistence (LNP)-related alleles and haplotypes were predominantly present in the examined population. (
  • Conclusions Our study provided a first report of LP-associated alleles and haplotypes in the Tunisian population. (
  • In a comprehensive PPV/NPV-based LD analysis within the KIR cluster, robust tag markers were found that can be used to identify which genes are concomitantly present or absent and to further identify groups of associated KIR alleles. (
  • Okay, I'm sure you understand the importance… For any given gene, a sequence of DNA that is transcribed there could exist more than one variant or alleles. (
  • 2001) Blocks of limited haplotype diversity revealed by high‐resolution scanning of human chromosome 21. (
  • Mutations in 'reading disorder' genes include DCDC2 on chromosome 6 and ROBO1 on chromosome 3 together represent 20% of cases of dyslexia. (
  • Its gene IDE is located on chromosome 10, in an area with suggestive linkage to type 2 diabetes and related phenotypes. (
  • Third, the human IDE gene is located on chromosome 10q23-24, within 4-30 Mb from markers that have shown suggestive linkage for type 2 diabetes and related phenotypes in a number of whole-genome linkage studies ( 4 - 7 ). (
  • Although translocated X chromosome segment in Yaa may contain as many as 16 genes, the major gene for causation of the autoimmune phenotypes was identified to be TLR7 ( 7 ), making it a potential susceptibility gene for SLE. (
  • To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype map of a 250-kb region of the t -complex on chromosome 17 containing the Hybrid sterility 1 ( Hst1 ) gene. (
  • so, unlike autosomal haplotypes, there is effectively not any randomisation of the Y-chromosome haplotype between generations. (
  • Dawson E, Abecasis G et al (2002) A first-generation linkage disequilibrium map of human chromosome 22. (
  • A large, family based genome-wide search of late onset cases reported linkage to the tau locus on chromosome 17q, 1 and, while no tau gene mutations have been found in typical Parkinson's disease, mutations have been reported in cases of fronto-temporal dementia with parkinsonism on chromosome 17 (FTDP-17). (
  • Human MDM2 gene is located on chromosome 12q14.3 to 15.0 with a genomic length of 34 kb, consisting of 12 exons, and it has three different promoters, of which the second and third ones are responsive to p53 ( 7 - 9 ). (
  • We enrolled unrelated subjects in this case-control study to search for susceptibility genes to sarcoidosis. (
  • Familial aggregation of DN has since been demonstrated to be independent from family size, the number of relatives affected with diabetes and hypertension, socioeconomic status, and inadequate access to health care ( 5 ), strongly suggesting the existence of DN-susceptibility genes. (
  • Given the important role of the NF-κB transduction pathway in immune responses, NF-κB related genes are interesting candidates for susceptibility genes in autoimmune disorders. (
  • Comparative LD patterns and haplotype block structure was defined across all test populations.CONCLUSION:A constant genetic structure in CYP7A1 gene and its surrounding sequences was found that may lead to a better design for association studies of genetic variations in CYP7A1 gene with cholesterol and bile acid metabolism. (
  • Comparative LD patterns and haplotype block structure was defined across all test populations. (
  • The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. (
  • Heterozygous mutation of the HNF1 β gene was identified in an autosomal dominant, early-onset subtype of diabetes known as maturity-onset diabetes of the young type 5 (MODY5) in Caucasian, Japanese, and Chinese populations ( 4 - 6 ). (
  • Various forms of natural selection, primarily through the mechanisms of spatiotemporally varying environments and epistasis as well as balancing, directional, diversifying, frequency - dependent and purifying selection regimes are massively involved in genetic structure and divergence of populations (Nevo, 1998), including small populations (Nevo et al. (
  • In the present study, genetic differentiation and linkage disequilibrium pattern in the methylenetetrahydrofolate reductase (MTHFR) locus was examined in the populations of Russians, Tuvinians, and Northern and Southern Kyrgyzes. (
  • in the populations of Russians, Tuvinians, and Northern Kyrgyzes two blocks were detected. (
  • Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. (
  • Southern Europeans and Middle Eastern populations are known to have inherited a small percentage of their genetic material from recent sub-Saharan African migrations, but there has been no estimate of the exact proportion of this gene flow, or of its date. (
  • The accuracy of standard imputation techniques strongly depends on the similarity of linkage disequilibrium (LD) patterns in the study and reference populations. (
  • Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. (
  • Biologists and breeders can employ linkage mapping and QTL analysis for experimental populations, and complex association methods for diversity populations to identify markers for pest and pathogen resistance. (
  • The first was, " Proportionally more deleterious genetic variation in European than in African populations ," and the second was, " Genotype, haplotype and copy-number variation in worldwide human populations . (
  • The first of the papers that I wanna focus in on is Nature 's " Genotype, haplotype and copy-number variation in worldwide human populations . (
  • Previously described patterns of intraspecific variation in three tandemly arranged, testes-expressed genes ( janusA , janusB , and ocnus ) in Drosophila simulans included all three of these features. (
  • These syndromes often have simple Mendelian inheritance patterns and are thus amenable to gene identification. (
  • GATA-binding protein 3 (GATA3) is a transcription factor that is highly expressed in normal breast luminal epithelium and the luminal A tumor subtype that has been defined in studies of gene expression patterns ( 1 - 5 ). (
  • The observed nucleotide and haplotype patterns of variation were then compared with those of several African, European, and Mediterranean human groups for which comparable data were publicly available. (
  • Linkage disequilibrium and haplotype patterns were characterized in the regions surrounding IGF1 and the genes coding for two of its binding proteins, IGFBP1 and IGFBP3. (
  • You can also analyze patterns of linkage disequilibrium, correct for population structure and discover SNP-SNP interactions. (
  • Not to be outdone by Nature , Science also published a very important paper on large scale human population genetic structure, " Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation . (
  • proposed to use haplotype maps to narrow down the region of interest in positional and quantitative trait locus (QTL) cloning experiments. (
  • Thus, the structure of linkage disequilibrium in the MTHFR locus demonstrated population-specific pattern. (
  • Gene density is estimated to be 1 locus per 7.5 Kb (compared with 9 Kb in fruit fly and 100 Kb in human). (
  • Our data should form the basis for conducting MBL2 candidate gene association studies using a locus-wide approach. (
  • Here, we reconstructed haplotypes of the SLC10A2 gene locus and tested for association with non-syndromic familial and sporadic CRC compared to 'hyper-normal' controls who displayed no colorectal polyps on screening colonoscopy. (
  • In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. (
  • Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. (
  • Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. (
  • The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear. (
  • In these circumstances, the knowledge of the structure of the locus can be essential for understanding the effect of CNV on phenotype. (
  • At the locus, each DEFA1A3 repeat unit can be occupied by one of two α-defensin genes, either DEFA1 or DEFA3 , adding additional complexity. (
  • Morton, Newton E(Dec 2007) Blocks of Limited Haplotype Diversity. (
  • Bioinformatics analyzed allozyme and DNA diversity at both coding and noncoding genomic regions permitting precise gene homologous alignment across taxa, the unraveling of gene and genome structure, expression, function, regulation, evolution, and the potential determination of the genetic basis of speciation and adaptation. (
  • These methods do not need prior block partitioning or limited haplotype diversity, but their performances are limited by the restrictions such as the fixed number of tagSNPs and the definitions of the informativeness . (
  • Unlike the previous methods, our method integrates the information of the LD association and the genotype diversity using the site graphs without the information loss and the limit of block partition. (
  • The proposed algorithm uses the information of the linkage disequilibrium association and the haplotype diversity to reduce the information loss in tagSNP selection, and has no limit of block partition. (
  • We surveyed 66 colonies for inbreeding, genetic diversity, and linkage disequilibrium, and we demonstrate that some have haplotype blocks of less than 100 Kb, enabling gene-level mapping resolution. (
  • Background Chinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits have not been explored. (
  • In the absence of an analytical theory extensive coalescent simulations are used to disentangle the influence of all of these factors on haplotype diversity. (
  • Since haplotypes from case individuals are genetically more closely related to each other at the site of a disease-predisposing mutation, their haplotypes would appear to cluster together in the marginal ancestral tree at the site of the mutation. (
  • Previous investigation has established a role for the CHEK2 gene in breast cancer aetiology, but studies have largely been limited to the rare 1100delC mutation. (
  • However it is unknown whether this is an independent occurrence of the mutation, as genotyping of linkage markers to reveal the mutation's haplotype background in the two cases was unable to be performed. (
  • All three findings of the fibrinogen Dunedin mutation were identified on the same haplotype background, suggesting a founder effect for this mutation in New Zealand. (
  • In humans, MDM2 expression levels seem to be critical for regulating p53 in response to DNA damage, and p53 activation is often caused by a point mutation in the MDM2 gene in sporadic tumors, including bladder cancer ( 10 ). (
  • A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. (
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (
  • The approaches applied were based on an assumption that selection leads to linkage disequilibrium or to a decrease of genetic variability in genomic regions containing genotypes connected with favourable phenotypes. (
  • Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. (
  • To confirm these associations, we collected genotypes of 17 SNP from BTA10, including three obtained by sequencing part of the ITGA11 ( Integrin alpha 11 ) gene. (
  • The 185delAG and 5382insC containing haplotypes, determined from the family based genotypes, are indicated with gray (haplotype 2) and blue background (haplotype 1), respectively. (
  • Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure. (
  • The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. (
  • Additional genes that seem to be of importance in renal phenotypes include manganese superoxide dismutase and angiotensin 1-converting enzyme, with nitric oxide synthase implicated in albuminuria. (
  • Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest. (
  • Four htSNPs, including the previously studied SNP rs605059 ( S312G ), were genotyped to tag five common haplotypes in all cases and controls. (
  • We found no evidence of association between common HSD17B1 haplotypes or htSNPs and overall risk of breast cancer. (
  • Stepanov, V. 2008-10-16 00:00:00 Investigation of linkage disequilibrium block architecture in human genome is modern, intensely investigated field of molecular genetics. (
  • Recent insights into the complex mechanisms underlying human innate immunity suggest that genetic variability in the genes encoding immune system components plays a role in the development of chronic inflammatory diseases. (
  • Through this survey the CFTR has become the most exhaustively studied gene for its coding sequence variability and, though to a lesser extent, for its noncoding sequence variability as well. (
  • Thus, the selection signatures were analysed based on Wright's F ST index, distribution of runs of homozygosity segments in the beef genome and determination of linkage disequilibrium variability between breeds. (
  • Genetic analysis of genes involved in the metabolism of anticancer drugs is becoming more and more important for elucidating the interpatient pharmacodynamic variability of anticancer drugs. (
  • A gene genealogy describes relationships among haplotypes sampled from a population. (
  • The concept of the gene genealogy has been useful in the estimation of population genetic parameters. (
  • Consequently, it is thought that the gene/s responsible for the psychiatric manifestations of 22q11DS also contribute to the genetic etiology of nonsyndromic schizophrenia in the general population. (
  • We found a strong association between the cancer predisposing gene CDH1 and the risk of NSCL/P in the Polish population. (
  • We genotyped these six tagSNPs in 1,577 postmenopausal breast cancer cases and 1,513 population controls, but found no convincing association between any common CHEK2 haplotype and breast cancer risk. (
  • The real situation is much more complicated than the simplifying assumptions allow, and several of these assumptions are either biased in favour of the conclusion or are contrary to the data: crossing over is not random, population structure exists at all scales, and population admixture and gene conversion overly complicate the models. (
  • Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. (
  • Each population presented different levels of prediction per gene. (
  • We uncovered population structures among Chinese indigenous pigs, along with selection and domestication signatures associated with body size and temperature-related adaptations. (
  • Abburi L Linkage disequilibrium and population structure analysis among Capsicum annuum L. cultivars for use in association mapping. (
  • Here, I propose a flexible Bayesian framework for modeling haplotype association with disease in population-based studies of candidate genes or small candidate regions. (
  • As in the general population, the SNP in exons 12, 21, and 26 were frequent (16, 17.3, and 22.2% for the variant homozygous genotype, respectively) and exhibited incomplete linkage disequilibrium. (
  • To test the new method, study and reference haplotypes were simulated and gene trees were inferred under the basic coalescent and also considering population growth and structure. (
  • Explicit consideration of population growth and structure, even if present, did not practically improve accuracy. (
  • Create, compress and easily integrate relationship matrices into association tests to simultaneously correct for population structure and relatedness with Q-K mixed model analysis. (
  • Population-genetic basis of haplotype blocks in the 5q31 region. (
  • In last week's issue of Nature , we saw two really important papers on large scale human population genetic structure be published. (
  • Before I get into the thick of it, I wanna give a quick run down on a basic population genetic concept, linkage disequilibrium, because it is screened in all of these papers. (
  • Grouping of markers according to their interdependence needs to account for the actual population structure in order to allow proper inference in genome-based evaluations. (
  • As the choice of tagSNPs is a consequence of grouping, it is also influenced by the underlying population structure. (
  • The objective of this paper is to exploit the family structure of a population for specifying groups of associated markers. (
  • Results were compared to the commonly used population-LD approach which ignores family structure. (
  • 2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. (
  • Weiss KM and Clark AR (2002) Linkage disequilibrium and the mapping of complex human traits. (
  • Zhang K, Calabrese P, Nordborg M and Sun F (2002) Haplotype block structure and its applications to association studies: power and study designs. (
  • Gabriel SB, Schaffner SF et al (2002) The structure of haplotype blocks in the human genome. (
  • Haploinsufficiency of the TBX1 gene has been shown to be sufficient to cause the core physical malformations associated with 22q11DS in mice and humans and via abnormal brain development could contribute to 22q11DS-related and isolated psychiatric disease. (
  • Pritchard J (2001) Linkage disequilibrium in humans: models and data. (
  • 2001) Haplotype variation and linkage disequilibrium in 313 human genes. (
  • Haplotype C (the wild-type promoter) was found to contain no sequence variation compared with the published sequence. (
  • We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. (
  • More particularly, it discloses novel insights into the overall structure of genetic variation in all living species. (
  • We comprehensively examined the association between common genetic variation in the IGF1, IGFBP1, and IGFBP3 genes in relation to circulating IGF-I and IGFBP-3 levels and breast cancer risk within the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). (
  • Here, we report a comprehensive study of the contribution of genetic variation in six genes encoding the β-catenin destruction complex ( APC, AXIN1, AXIN2, CSNK1D, CSNK1E , and GSK3B ) to breast cancer using a Mayo Clinic Breast Cancer Case-Control Study. (
  • Genetic association of sequence variation in exon 3 of the swine leukocyte antigen-DQA gene with piglet diarrhea in Large White, Landrace, and Duroc piglets. (
  • The FOCM is essential in regulation of the epigenome, which controls genes in ways beyond nucleotide sequence. (
  • Fibrinogen Perth results from the deletion of a single cytosine (heterozygous) at nucleotide 4841 of the α gene, predicting a frame shift and the incorporation of 23 new amino acids before termination after residue 517. (
  • Daly MJ, Rioux JD, Schaffner SF, Hudson TJ and Lander ES (2001) High‐resolution haplotype structure in the human genome. (
  • Goldstein DB (2001) Islands of linkage disequilibrium. (
  • 2001) Haplotype tagging for the identification of common disease genes. (
  • Daly MJ et al (2001) High-resolution haplotype structure in the human genome. (
  • Johnson G, Esposito L et al (2001) Haplotype tagging for the identification of common disease genes. (
  • These genealogical relationships will also affect the haplotype structure among sampled chromosomes. (
  • The haplotypes of t -chromosomes differed from all non- t Mmmu and Mmd haplotypes. (
  • The lengths of the haplotype blocks deduced from 36 domesticus chromosomes were in tens of kilobases, suggesting that the wild-derived Mmd strains are suitable for fine interval-specific mapping. (
  • The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. (
  • The present invention provided a method for predicting a phenotype in a bovine animal, the method comprising analysing a nucleic acid sample from said animal for the presence of at least one genetic marker known to reside in an Linkage Disequilibrium (LD) block in any one of bovine chromosomes BTA-I to BTA-29, wherein said LD block is associated with said phenotype. (
  • Also provided is a linkage disequilibrium unit (LDU) map of any one or more of bovine chromosomes BTA-I to BTA-29, the map comprising a plurality of chromosomal regions, and the regions defined by their co-inheritance across generations substantially as entire linkage disequilibrium (LD) blocks. (
  • 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. (
  • To be useful in genetic analysis, the haplotype should be shorter than a typical block. (
  • Linkage disequilibrium structure analysis revealed two haplotype blocks. (
  • Lin Z, Altman R (2004) Finding haplotype tagging SNP by use of principle component analysis. (
  • We report here the results from an analysis of HSD17B1 haplotypes and breast cancer risk from a large, collaborative study (The Breast and Prostate Cancer Cohort Consortium, or BPC3), which includes data from five cohorts from the United States and Europe ( 10 ). (
  • These findings could not be confirmed after haplotype analysis and Bonferroni corrections for multiple comparisons. (
  • Replication and meta-analysis Sections about replication and meta-analysis discuss strategies for scientifically meaningful replication of a gene association finding and for combining data and statistical inference across association studies. (
  • Haplotype analysis substantiated these results and suggested that exons 26 and 21 SNP may be associated with tacrolimus dose requirements. (
  • Point-and-click workflows simplify gene and exon expression, and RNA-seq analysis for new users. (
  • 14. A method according to claim 1, wherein the step of analysing the nucleic acid sample for the presence of at least one genetic marker known to reside in an LD block comprises random amplified polymorphic DNA (RAPD), ligase chain reaction, insertion/deletion analysis or direct sequencing of the gene. (
  • The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle. (
  • These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. (
  • The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality. (
  • However, high-resolution haplotype mapping of mouse traits is precluded by high LD within the classical laboratory strains. (
  • This study suggests that the NeuroD gene may neither contribute to the risk of HD nor mediate the relationship between specific personality traits and HD. (
  • 16 Genetic association study is currently regarded as the most powerful approach to mapping the genes underlying such complex traits. (
  • The aim of this study was to dissect potential genetic factors for these unstable results and validate the association or linkage relationship of CGA gene with growth and carcass traits. (
  • SNP C-925T and SNP A+15599G could be useful linkage markers and SNP C-925T may also be a candidate causative SNP for the corresponding traits. (
  • Considering the extensive effects of the glycoprotein hormones, especially TSH, their common CGA gene shows to be a promising candidate gene for economic important traits. (
  • Germline mutations in this gene have been described in families presenting syndromic diffuse gastric cancer and orofacial clefts. (
  • Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. (
  • only the 70 with MAF ≥ 0.05 in Ashkenazi Jews are shown in B-D. A) Scale representation of the ~650 kb region studied, indicating the BRCA1 gene, founder mutations, and genome sequence gap of unknown true size. (
  • In addition, tau aggregation-sometimes in the absence of Lewy body pathology-has been demonstrated in autosomal recessive Parkinson's disease caused by parkin gene mutations. (
  • Somatic mutations that inactivate the p53 gene have been found in at least half of all human solid tumors, highlighting a crucial role of the p53 protein in carcinogenesis ( 2 ). (
  • 2 3 The HGP demonstrated that a relatively limited number of genes could be identified in the human genome, which substantiated the theory that complex biological processes were regulated on other levels than DNA sequence alone. (
  • Not only that, it's nonsynonomous, which means that it's in a position to change the structure and therefore function of the biochemical which the sequence is ultimately coding for. (
  • BACKGROUND:Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. (
  • From the genomic point of view, the presence of several hundred genes having higher sequence similarity with Drosophila melanogaster and Caenorhabditis elegans than with vertebrates [ 14 ], as well as the small gene number, are indicative of species ancestry. (
  • Haplotype-based tests identified significant associations between specific haplotypes in APC and AXIN2 ( P ≤ 0.03) and breast cancer risk. (
  • Additionally, the insights are useful for the development of algorithms and computer programs that convert genotype data into the constituent haplotypes that are laborious and costly to derive in an experimental way. (
  • Novel designs are needed for studying genes and the environment jointly, and with proper meta-analytic methods, the heterogeneity in the phenotype definitions and measurements and strengths of association may be addressed. (
  • however, this lethal phenotype is rescued by the knockout of both p53 and MDM2 genes, suggesting that the primary function of MDM2 is to regulate the functions of p53 whose functions can be compensated by other proteins such as p63 and p73 ( 5 ). (
  • Data on human haplotypes and LD across the human genome are of interest in whole-genome association studies. (
  • One risk haplotype (AGTACT) was identified associated with GC non-responsiveness compared with GC responsive MG group. (
  • Additionally, we showed a non-additive genetic interaction between READ1 and KIAHap, a previously reported risk haplotype in risk gene KIAA0319 , and that READ1 binds the transcriptional regulator ETV6. (
  • A common feature in this wide range of interactions is modulation of host-cell proliferation, which sometimes leads to the formation of tumour-like structures in which the bacteria can grow. (
  • Clade here refers to a set of haplotypes sharing a common ancestor. (
  • One common approach is based on the haplotype blocks partitions. (
  • These methods delimit the human genome into a set of discrete blocks, where only a small set of common haplotypes exist. (
  • Some of the common haplotypes with the largest sample sizes explained between 1.3% and 1.5% of the residual variance in tick burden. (
  • Each LD block comprised over 80% common haplotypes, concurring with a previous study of 14 genes that showed that common haplotypes account for at least 80% of all haplotypes. (
  • These results suggest that MRC1 is an important candidate gene for sarcoidosis. (
  • Furthermore, candidate gene approaches have identified important roles for IRF6 and MSX1 . (
  • Thus, because of the proximal location and similar structure of the PRNP gene among the prion gene family, the prion-like protein gene ( PRND ) was noted as a novel candidate gene that contributes to prion disease susceptibility. (
  • The androgen receptor (AR) has been proposed as a candidate gene for several cancers (breast, prostate, uterine endometrium, colon, and esophagus). (
  • This section also presents the current methods for solving the problem in both candidate gene studies and in genome-wide association studies. (
  • ADAM33 , the first asthma candidate gene identified by positional cloning, may be associated with childhood asthma, lung function decline and bronchial hyperresponsiveness. (
  • The 17β-hydroxysteroid dehydrogenase 1 gene ( HSD17B1 ) encodes 17HSD1, which catalyzes the final step of estradiol biosynthesis. (
  • The 17β-hydroxysteroid dehydrogenase 1 gene ( HSD17B1 [MIM 109684]) encodes 17HSD1, whose primary function is to catalyze the final step of estradiol biosynthesis, converting estrone to the more biologically active estradiol ( 1 ). (
  • The NeuroD gene encodes a neuroge nic differentiation factor, and its expression is essential for the development of the central nervous system. (
  • The Pun1 gene for pungency in pepper encodes a putative acyltransferase. (
  • The murine double minute 2 ( MDM2 ) gene encodes a protein that is a key component in the p53 signaling pathway. (
  • All haplotypes with an estimated frequency of at least 1% are displayed (h1 to h11), with individual frequencies and sums indicated to the right of the blocks. (
  • Both the T/G genotype of rs882605 and the frequency of haplotype T-T (rs882605 and rs1104760) were higher in patients than in controls and were statistically significant. (
  • OMIM no. 300365) and its functionally related gene TLR8 (OMIM no. 300366) encode proteins that play critical roles in pathogen recognition and activation of innate immunity ( 4 ). (
  • Although tissue distribution and transcriptional regulation of these two genes are significantly different, the two proteins are functionally equivalent in vivo ( 7 ). (
  • We previously implemented an MCMC algorithm to sample from an approximation to the distribution of the gene genealogy conditional on haplotype data. (
  • Haplotypes were reconstructed using the PHASE algorithm. (
  • The purpose of this review is to summarize recent progress of human genetic studies in identifying causal genes for isolated or nonsyndromic cleft lip with or without cleft palate. (
  • We assessed linkage disequilibrium, selected single-marker and multimarker tags, and genotyped these markers in several case-control and family-based samples totalling 4,206 Caucasian individuals. (
  • The RARB haplotype (rs6800566/rs6550976/rs9834818) was significantly associated with variations in both measles antibody (global, P=0.013) and cytokine secretion levels, such as interleukin (IL)-10 (global, P=0.006), interferon (IFN)-α (global, P=0.008), and tumor necrosis factor-α (global, P=0.039) in the Caucasian subgroup. (
  • At the other end of the spectrum, haplotype GG for rs6550978/rs6777544 was associated with lower antibody levels (t-statistic: -2.32, P=0.020) in the Caucasian subgroup. (
  • Haplotype block structure of the RARB gene region in the Caucasian subjects. (
  • Sun X, Stephens JC and Zhao H (2004) The impact of sample size and marker selection on the study of haplotype structures. (
  • So far, no DNA marker or haplotype has shown a consistent effect across different breeds for the number of ticks that animals carry. (
  • Testing for single-marker associations as well as for haplotypes, interactions and model selection procedures are discussed in this section. (
  • Hence, there is need to promote measures of marker dependence which takes into account the particular family structure. (
  • disruption of complement regulation can lead to several distinct downstream inflammatory actions en route to the pathogenesis of DR [ 14 , 15 ]. (
  • Several lines of evidence implicate the IDE gene in the pathogenesis of type 2 diabetes. (
  • There is good evidence implicating the tau gene (MAPT) in the pathogenesis of Parkinson's disease. (
  • To the best of our knowledge, this was the first genetic study of the PRND gene in a prion disease-resistant animal, a dog. (
  • Haplotype block structure study of the CFTR gene. (
  • This study investigated the genetic association of the EGR2 gene with BD and schizophrenia (SPR) in Korea. (
  • The large size of this study enables us to detect modest genetic effects, explore gene-environment interactions, and examine potentially important subclasses of tumors, such as those defined by stage or hormone receptors. (
  • An extensive family-based study of linkage disequilibrium (LD) in the killer cell immunoglobulin-like receptors (KIR) cluster was performed. (
  • The results of a detailed simulation study demonstrate that there is minimal cost associated with modeling these dominance effects, with substantial gains in power over haplotype-based methods that do not incorporate clustering and that assume a multiplicative model of disease risks. (
  • The reference haplotypes that first coalesced with study haplotypes were used as templates for genotype imputation. (
  • In a simulation study, we observed that sensitivity and specificity of a genome-based association study improved if selection of representative markers took family structure into account. (
  • Representative markers can be exploited, for instance, for dimension reduction prior to a genome-based association study or the grouping structure itself can be employed in a grouped penalization approach. (
  • In C. intestinalis , these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5 . (
  • We aimed to describe the LD structure in the KIR gene cluster using a sample of 418 founder haplotypes identified by segregation in a group of 106 families from Northern Ireland. (
  • Although rs7136446 had no significant association with survival, the haplotype in the LD block 3 was significantly associated with cancer-specific survival ( P = 0.0003). (
  • Pathway diagram of genes tested for association. (
  • Here, we tested whether genes encoding for key components of the β-adrenergic signaling pathway are associated with human longevity. (
  • Because the VEGF promoter is so highly polymorphic, haplotypes were established and analyzed. (
  • Recently, the SNP309 (rs2279744) in the intronic p53 -responsive promoter of the MDM2 gene was shown to increase the affinity of the transcriptional activator Sp1, resulting in higher levels of MDM2 mRNA and protein ( 13 ). (
  • In mice, SAA represents the predominant APP, whereas CRP is a minor APP, potentially caused by the limited responsiveness of the gene to inflammatory cytokine signals ( 9 ). (