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.
Genotypic differences observed among individuals in a population.
The relationships of groups of organisms as reflected by their genetic makeup.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.
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 proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The variety of all native living organisms and their various forms and interrelationships.
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.
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.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
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 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)
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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 field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)
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.
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.
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.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
Coexistence of numerous distinct ethnic, racial, religious, or cultural groups within one social unit, organization, or population. (From American Heritage Dictionary, 2d college ed., 1982, p955)
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
A group of the D-related HLA antigens found to differ from the DR antigens in genetic locus and therefore inheritance. These antigens are polymorphic glycoproteins comprising alpha and beta chains and are found on lymphoid and other cells, often associated with certain diseases.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
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.
Transmembrane proteins that form the beta subunits of the HLA-DQ antigens.
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.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.
Individuals whose ancestral origins are in the continent of Europe.
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.
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 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 phenomenon of immense variability characteristic of ANTIBODIES. It enables the IMMUNE SYSTEM to react specifically against the essentially unlimited kinds of ANTIGENS it encounters. Antibody diversity is accounted for by three main theories: (1) the Germ Line Theory, which holds that each antibody-producing cell has genes coding for all possible antibody specificities, but expresses only the one stimulated by antigen; (2) the Somatic Mutation Theory, which holds that antibody-producing cells contain only a few genes, which produce antibody diversity by mutation; and (3) the Gene Rearrangement Theory, which holds that antibody diversity is generated by the rearrangement of IMMUNOGLOBULIN VARIABLE REGION gene segments during the differentiation of the ANTIBODY-PRODUCING CELLS.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
Deoxyribonucleic acid that makes up the genetic material of plants.
Antigens determined by leukocyte loci found on chromosome 6, the major histocompatibility loci in humans. They are polypeptides or glycoproteins found on most nucleated cells and platelets, determine tissue types for transplantation, and are associated with certain diseases.
Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.
An individual having different alleles at one or more loci regarding a specific character.
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 country spanning from central Asia to the Pacific Ocean.
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 male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.
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.
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.
An animal or plant species in danger of extinction. Causes can include human activity, changing climate, or change in predator/prey ratios.
The human male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans.
The total genetic information possessed by the reproductive members of a POPULATION of sexually reproducing organisms.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
Genetic loci in the vertebrate major histocompatibility complex that encode polymorphic products which control the immune response to specific antigens. The genes are found in the HLA-D region in humans and in the I region in mice.
Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.
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 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 intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
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 arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
An HLA-DR antigen which is associated with HLA-DRB1 CHAINS encoded by DRB1*03 alleles.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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 splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
The protection, preservation, restoration, and rational use of all resources in the total environment.
Number of individuals in a population relative to space.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
The largest of the continents. It was known to the Romans more specifically as what we know today as Asia Minor. The name comes from at least two possible sources: from the Assyrian asu (to rise) or from the Sanskrit usa (dawn), both with reference to its being the land of the rising sun, i.e., eastern as opposed to Europe, to the west. (From Webster's New Geographical Dictionary, 1988, p82 & Room, Brewer's Dictionary of Names, 1992, p34)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.
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.
Individuals whose ancestral origins are in the continent of Africa.
The collective name for the islands of the central Pacific Ocean, including the Austral Islands, Cook Islands, Easter Island, HAWAII; NEW ZEALAND; Phoenix Islands, PITCAIRN ISLAND; SAMOA; TONGA; Tuamotu Archipelago, Wake Island, and Wallis and Futuna Islands. Polynesians are of the Caucasoid race, but many are of mixed origin. Polynesia is from the Greek poly, many + nesos, island, with reference to the many islands in the group. (From Webster's New Geographical Dictionary, 1988, p966 & Room, Brewer's Dictionary of Names, 1992, p426)
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.
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.
Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.
An independent state, an archipelago in the western Persian Gulf, northwest of Qatar. It comprises low-lying islands of Bahrain (the largest), Muharraq, Sitra, and several islets. It has extensive oil fields. The name comes from the Arabic al-bahrayn, "the two seas", with reference to its lying in the middle of a bay with its "two seas" east and west of it. (From Webster's New Geographical Dictionary, 1988, p107 & Room, Brewer's Dictionary of Names, 1992, p45)
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Individual members of South American ethnic groups with historic ancestral origins in Asia.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
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.
A specific HLA-B surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-B*08 allele family.
Genetic loci associated with a QUANTITATIVE TRAIT.
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 collective genome representative of the many organisms, primarily microorganisms, existing in a community.
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.
Deoxyribonucleic acid that makes up the genetic material of protozoa.
The functional hereditary units of PLANTS.
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.
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
Genetic loci in the vertebrate major histocompatibility complex which encode polymorphic characteristics not related to immune responsiveness or complement activity, e.g., B loci (chicken), DLA (dog), GPLA (guinea pig), H-2 (mouse), RT-1 (rat), HLA-A, -B, and -C class I genes of man.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Computer-based representation of physical systems and phenomena such as chemical processes.
Any of several large carnivorous mammals of the family CANIDAE that usually hunt in packs.
A region, north-central Asia, largely in Russia. It extends from the Ural Mountains to the Pacific Ocean and from the Arctic Ocean to central Kazakhstan and the borders of China and Mongolia.
Animals considered to be wild or feral or not adapted for domestic use. It does not include wild animals in zoos for which ANIMALS, ZOO is available.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
The fluctuation of the ALLELE FREQUENCY from one generation to the next.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.
This single species of Gorilla, which is a member of the HOMINIDAE family, is the largest and most powerful of the PRIMATES. It is distributed in isolated scattered populations throughout forests of equatorial Africa.
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
Biochemical identification of mutational changes in a nucleotide sequence.
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.
The general name for NORTH AMERICA; CENTRAL AMERICA; and SOUTH AMERICA unspecified or combined.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
A specific HLA-A surface antigen subtype. Members of this subtype contain alpha chains that are encoded by the HLA-A*01 allele family.
The ceasing of existence of a species or taxonomic groups of organisms.
A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
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.
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
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.
Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".
The systematic study of the complete DNA sequences (GENOME) of organisms.
A climate which is typical of equatorial and tropical regions, i.e., one with continually high temperatures with considerable precipitation, at least during part of the year. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
The mating of plants or non-human animals which are closely related genetically.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
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)
Proteins found in any species of protozoan.
Statistical interpretation and description of a population with reference to distribution, composition, or structure.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
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 characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)
A family of receptors found on NK CELLS that have specificity for a variety of HLA ANTIGENS. KIR receptors contain up to three different extracellular immunoglobulin-like domains referred to as D0, D1, and D2 and play an important role in blocking NK cell activation against cells expressing the appropriate HLA antigens thus preventing cell lysis. Although they are often referred to as being inhibitory receptors, a subset of KIR receptors may also play an activating role in NK cells.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.
Parliamentary democracy located between France on the northeast and Portugual on the west and bordered by the Atlantic Ocean and the Mediterranean Sea.
The major group of transplantation antigens in the mouse.
A species of protozoa that is the causal agent of falciparum malaria (MALARIA, FALCIPARUM). It is most prevalent in the tropics and subtropics.
Class I human histocompatibility (HLA) antigens encoded by a small cluster of structural genes at the C locus on chromosome 6. They have significantly lower immunogenicity than the HLA-A and -B determinants and are therefore of minor importance in donor/recipient crossmatching. Their primary role is their high-risk association with certain disease manifestations (e.g., spondylarthritis, psoriasis, multiple myeloma).
The geographical area of Africa comprising ANGOLA; BOTSWANA; LESOTHO; MALAWI; MOZAMBIQUE; NAMIBIA; SOUTH AFRICA; SWAZILAND; ZAMBIA; and ZIMBABWE.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
The fusion of a male gamete with a female gamete from the same individual animal or plant.
The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)
Sequential operating programs and data which instruct the functioning of a digital computer.
The genetic complement of MITOCHONDRIA as represented in their DNA.
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 phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.
Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.
The MEDITERRANEAN SEA, the MEDITERRANEAN ISLANDS, and the countries bordering on the sea collectively.
The longterm manifestations of WEATHER. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Databases devoted to knowledge about specific genes and gene products.
A constitution or condition of the body which makes the tissues react in special ways to certain extrinsic stimuli and thus tends to make the individual more than usually susceptible to certain diseases.
The process of leaving one's country to establish residence in a foreign country.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Cultivated plants or agricultural produce such as grain, vegetables, or fruit. (From American Heritage Dictionary, 1982)
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.
The total number of individuals inhabiting a particular region or area.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
A family composed of spouses and their children.
The biological objects that contain genetic information and that are involved in transmitting genetically encoded traits from one organism to another.
Non-native organisms brought into a region, habitat, or ECOSYSTEM by human activity.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The genomic analysis of assemblages of organisms.
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.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
A country consisting of the eastern half of the island of New Guinea and adjacent islands, including New Britain, New Ireland, the Admiralty Islands, and New Hanover in the Bismarck Archipelago; Bougainville and Buka in the northern Solomon Islands; the D'Entrecasteaux and Trobriand Islands; Woodlark (Murua) Island; and the Louisiade Archipelago. It became independent on September 16, 1975. Formerly, the southern part was the Australian Territory of Papua, and the northern part was the UN Trust Territory of New Guinea, administered by Australia. They were administratively merged in 1949 and named Papua and New Guinea, and renamed Papua New Guinea in 1971.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
Diseases of plants.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A group of autosomal recessive disorders marked by a deficiency of the hepatic enzyme PHENYLALANINE HYDROXYLASE or less frequently by reduced activity of DIHYDROPTERIDINE REDUCTASE (i.e., atypical phenylketonuria). Classical phenylketonuria is caused by a severe deficiency of phenylalanine hydroxylase and presents in infancy with developmental delay; SEIZURES; skin HYPOPIGMENTATION; ECZEMA; and demyelination in the central nervous system. (From Adams et al., Principles of Neurology, 6th ed, p952).
Fish-eating carnivores of the family MUSTELIDAE, found on both hemispheres.
A country in northern Africa between ALGERIA and LIBYA. Its capital is Tunis.
Identification of the major histocompatibility antigens of transplant DONORS and potential recipients, usually by serological tests. Donor and recipient pairs should be of identical ABO blood group, and in addition should be matched as closely as possible for HISTOCOMPATIBILITY ANTIGENS in order to minimize the likelihood of allograft rejection. (King, Dictionary of Genetics, 4th ed)
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.
Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations, or by parent x offspring matings carried out with certain restrictions. All animals within an inbred strain trace back to a common ancestor in the twentieth generation.
Seltsam A, Hallensleben M, Kollmann A, Blasczyk R (October 2003). "The nature of diversity and diversification at the ABO locus ... "What are variants, alleles and haplotypes? , Human genetic variation". Retrieved 16 November 2020. ...
Thompson EE, Kuttab-Boulos H, Yang L, Roe BA, Di Rienzo A (2006). "Sequence diversity and haplotype structure at the human ...
2006). "Sequence diversity and haplotype structure at the human CYP3A cluster". Pharmacogenomics J. 6 (2): 105-14. doi:10.1038/ ... Laity JH, Lee BM, Wright PE (Feb 2001). "Zinc finger proteins: new insights into structural and functional diversity". Curr ...
April 2015). "A recent bottleneck of Y chromosome diversity coincides with a global change in culture". Genome Research. 25 (4 ... African admixture in Europe Genetic genealogy Haplogroup D Haplogroup DE Haplogroup Haplotype Human Y-chromosome DNA haplogroup ... Zalloua (2008). "Y-chromosomal diversity in Lebanon is structured by recent historical events". Am J Hum Genet. 82 (4): 873-82 ... Chiaroni, J.; Underhill, P. A.; Cavalli-Sforza, L. L. (2009). "Y chromosome diversity, human expansion, drift, and cultural ...
The Cook Island DQ8 had only one associated DR haplotype suggesting diversity limiting introduction into the region, either via ... A rare haplotype DQA1*0503:DQB1*0302 is detected below 1% of all DQ8 haplotypes in Asia and Mesoamerica. Another rarer ... DQB1*0302 and is found most often in the haplotype DQA1*0301:DQB1*0302, about 10% of the time it is found in the haplotype DQA1 ... DQ8 along with a few other haplotypes appears to be split NW/SE in Eurasia and with the evidence for DQ2.5 and other haplotypes ...
In: Genomic Diversity: Applications in Human Population Genetics. S. S. Papiha, R. Deka and R. Chakraborty (Eds.), Plenum Press ... HLA-DQ haplotypes in 15 different populations. In: The Major Histocompatibility Complex: Evolution, Structure and Function. M ... Microbiome diversity in human saliva. In: Handbook of Microbial Ecology, Volume II: Metagenomics in Different Habitats. F J. de ... "Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern ...
2008). "Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East ... Malyarchuk, Boris A (2011). "Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the ... haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with ... 2014). "Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies". American ...
"Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains". Genome Research. 14 (10a): 1880-1887. doi:10.1101/gr. ... Genetic and haplotype diversity among wild-derived mouse inbred strains. Genome Research, 2004 Oct;14:1880-1887. PMID 15466288 ... She explored genetic diversity through a clear evolutionary framework. Her first work in the lab helped to elucidate the ... She found that deletions are more frequent than insertions and that sequence diversity is about two orders of magnitude higher ...
Haplotype diversity is noted for being higher here than elsewhere. Frequencies of N1a in Yemen are relatively high, with ... Yemen is noted for high haplotype diversity within the population. Elsewhere in the Near East, prevalence of N1a is lower. A ... This supposition is based on the relatively high frequency and genetic diversity of N1a in modern populations of the peninsula ... 2009). "Out of Arabia-the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity" (PDF). ...
Lucotte G, Smets P, Ruffié J (October 1993). "Y-chromosome-specific haplotype diversity in Ashkenazic and Sephardic Jews". ... "seem to be similar in their Y-haplotype patterns, both with regard to the haplotype distributions and the ancestral haplotype ... Lucotte G, David F, Berriche S (June 1996). "Haplotype VIII of the Y chromosome is the ancestral haplotype in Jews". Human ... A set of special markers (called Cohen Modal Haplotype or CMH) was defined as one which is more likely to be present in the ...
This incredible diversity likely reflects the pressure from rapidly evolving viruses. 30 distinct haplotypes have been ... Inheritance of maternal and paternal haplotypes results in further diversity of individual KIR genotype. Group A only has one ... Group B haplotypes encompass all other haplotypes, and therefore have a variable set of genes, including several genes absent ... Because group B has both gene and allelic diversity (compared to just allelic diversity in group A), group B is even more ...
2006). "Sequence diversity and haplotype structure at the human CYP3A cluster". Pharmacogenomics J. 6 (2): 105-14. doi:10.1038/ ...
"Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity". American Journal of Human ... of human diversity exists in a single African population, whereas only about 70% of human genetic diversity exists in a ... Human genetic diversity decreases in native populations with migratory distance from Africa, and this is thought to be due to ... Understanding how genetic diversity in the human population impacts various levels of gene expression is an active area of ...
2012). "Haplotype diversity of 17 Y-str loci in an admixed population from the Brazilian Amazon". Genetics and Molecular ... Chang YM, Swaran Y, Phoon YK, Sothirasan K, Sim HT, Lim KB, Kuehn D (2009). "Haplotype diversity of 17 Y-chromosomal STRs in ... Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T (2016). "Y chromosome haplotype diversity ... Ghada A. Omran et al., "Diversity of 17-locus Y-STR haplotypes in Upper (Southern) Egyptians," Forensic Science International: ...
2008). "Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East ... Malyarchuk, Boris A (2011). "Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the ... haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with ... 2003). "Haplotypes from the Caucasus, Turkey and Iran for nine Y-STR loci". Forensic Science International. 137 (1): 85-93. doi ...
As people moved they have tended to lose haplotypes and in the process lose allelic diversity. On the other hand, on arrival at ... The DQA1*05:01-DQB1*02:01 haplotype is called the DQ2.5 haplotype, and the DQ that results α5β² is the "cis-haplotype" or "cis- ... If a person carries haplotypes -A-B- and -A-b- then they can only make 2 DQ (AB and Ab), but if a person carries haplotypes -A- ... There is other evidence that some haplotypes are linked to disease but show neutral linkage with other particular haplotypes ...
Diversity of mitochondrial DNA haplotypes in ethnic populations of the Volga-Ural region of Russia]" (PDF). Molekuliarnaia ... Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G (January 2000). "Geographic patterns of mtDNA diversity in Europe ...
Haplotype diversity of DQB1*0402 appears to be centered around the Amur River/Japanese Island Chain, and diversity of DQB1*0401 ... The DR*0405 and DR*410 are found specifically associated with these DQ types and there is some haplotype diversity. So that it ... The most common haplotypes in the !Kung (for example Cw-B) that also appear in Eurasia appear to have been associated with the ... There are a number of other A-B haplotypes that suggest a connection between the Ainu and the Meso-American and Andean ...
So far there were only two main haplotype found in the whole population. Comparison of the genetic diversity to its sister ...
Kim U, Wooding S, Ricci D, Jorde LB, Drayna D (2005). "Worldwide haplotype diversity and coding sequence variation at human ...
The first haplotype is seven amino acids in strong linkage disequilibrium. This haplotype is global and seems to be moving ... were interested in the evolution of the innate immune system; specifically, they wished to map the genetic diversity-the ... The second haplotype is restricted to Europe and is not in linkage disequilibrium with the global haplotype. This European ... The authors hypothesize another mutation in the haplotype is what selection is acting on and this deleterious mutation is ...
Low values of haplotype diversity and nucleotide diversity were found for the baiji of the Yangtze River. The analysis of ... 2012). "Considerable MHC Diversity Suggests That the Functional Extinction of Baiji Is Not Related to Population Genetic ... it is likely that much of the low genetic diversity observed was caused by the precipitous decline in the total baiji ...
The lack of diversity of DYS448=19 haplotypes in the Western Balkan also indicate a founder effect. Although it is considered ... found the haplogroups STR haplotypes have the highest diversity in Ukraine, with ancestral STR marker result DYS448=20 ...
Rather, these HGs contain considerable demographic complexity, as implied by their high haplotype diversity. Specifically, they ... 2008), "Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events." Myres et al. (2010), "A major Y- ... 2007), "Y-chromosome diversity characterizes the Gulf of Oman." Mohammad et al. (2009), "Genetic structure of nomadic Bedouin ... 2003), "Excavating Y-chromosome haplotype strata in Anatolia Archived 2006-06-19 at the Wayback Machine." Regueiro M, Cadenas ...
On the other hand, analyses of the Y chromosome and of autosomal diversity have shown a general gradient of genetic similarity ... 2005): "Signature of recent historical events in the European Y-chromosomal STR haplotype distribution". Human Genetics 116: ... Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G (2000): "Geographic patterns of mtDNA diversity in Europe". ... Barbujani G, Goldstein DB (2004): "Africans and Asians abroad: genetic diversity in Europe". Annual Review of Genomics and ...
April 2004). "Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class ... January 2006). "HLA class I diversity among rural rainforest inhabitants in Cameroon: identification of A*2612-B*4407 haplotype ... 2006). "HLA class I diversity among rural rainforest inhabitants in Cameroon: identification of A*2612-B*4407 haplotype". ...
High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North ... A multidisciplinary approach reveals hidden taxonomic diversity in the morphologically challenging Taxus wallichiana complex. ...
"Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population samples". Journal of the ... "Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 ... "Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico". Proceedings of the ... Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals". PLOS Genetics. 10 (9): e1004572. doi:10.1371/ ...
"Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population samples". Journal of the ... Mexican society enjoys a vast array of music genres, showing the diversity of Mexican culture. Traditional music includes ... Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals". PLOS Genetics. 10 (9): e1004572. doi:10.1371/ ... "Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico". Proceedings of the ...
"Animal Diversity Web. Archived from the original on 13 March 2016. Retrieved 19 June 2017.. ... Haplotypes typical of American mallard relatives and Eastern spot-billed ducks can be found in mallards around the Bering Sea.[ ... Mallards of all ages (but especially young ones) and in all locations must contend with a wide diversity of predators including ... allopatric speciation and isolating behaviour have produced today's diversity of mallard-like ducks despite the fact that, in ...
Analysis on the haplotype of some coyotes from Texas also detected the presence of male wolf introgression such as Y ... Wayne, R. & Ostrander, Elaine A. (1999). "Origin, genetic diversity, and genome structure of the domestic dog". BioEssays. 21 ( ... analysis of control region haplotypes of the mitochondrial DNA and sex chromosomes from Mexican wolves, a critically endangered ...
"The diversity of life". Global Biodiversity Strategy: Guidelines for action to save, study and use Earth's biotic wealth ... "A haplotype map of the human genome" (PDF). Nature 437. Páxs. 1299-1320. ...
In most Citrus species, the peel contains a greater diversity and a higher concentration of furanocoumarins than the pulp of ... "Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrusspecies: analysis of chromosome 2" ...
"Croatian national reference Y-STR haplotype database" (PDF). Draganprimorac.com. Retrieved 20 December 2016.. ... In relation to dialect diversity, Romani works in the same way as most other European languages.[211] Cross-dialect ... "Patterns of inter- and intra-group genetic diversity in the Vlax Roma as revealed by Y chromosome and mitochondrial DNA ... "Y-chromosome diversity in modern Bulgarians: new clues about their ancestry". PLoS ONE. 8 (3): e56779. Bibcode:2013PLoSO... ...
a b c LIU Shuhu, NIZAM Yilihamu, RABIYAMU Bake, ABDUKERAM Bupatima, and DOLKUN Matyusup, "A study of genetic diversity of three ... 2013). "Characterization and Haplotype analysis of 11 Y-STR loci in Ecuadorian population". Forensic Sci. Int. Genet. Suppl. ... a b On Henbei, Pengyang, and Heigouliang, Lihongjie, Y-Chromosome Genetic Diversity of the Ancient North Chinese populations, ... Q-MEH2 (MEH2) Was found in Koryaks (at 10.3%), although the level of STR diversity associated with Q-MEH2 is very low, this ...
"Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture". PLOS Genetics. 9 (2): e1003316. doi:10.1371/journal ... "Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes" (PDF). Proceedings ...
A study of haplotypes of the Y-chromosome, published in 2000, addressed the paternal origins of Ashkenazi Jews. Hammer et al.[ ... their higher diversity compared to Middle Easterners stems from the latter's marriage practices, not necessarily from the ... "High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap ... Y-chromosome haplotypes) and for matrilineal markers (mitotypes).[114] Since the middle of the 20th century, many Ashkenazi ...
"Animal Diversity Web. University of Michigan Museum of Zoology.. *^ Ostriches in Australia - and near my home. trevorsbirding. ... Mitochondrial DNA haplotype comparisons suggest that it diverged from the other ostriches not quite 4 mya due to formation of ... "Studies of the population structure and genetic diversity of domesticated and 'wild' ostriches (Struthio camelus)". PhD thesis ...
Cardon LR, Abecasis GR (2003). "Using haplotype blocks to map human complex trait loci". Trends Genet. 19: 135-140. doi:10.1016 ... Short tandem repeats are unique markers that can be used to determine haplotypes and are used in identity testing for maternal ...
Theta-Pi less than Theta-k (Observed,Expected). Fewer haplotypes (lower average heterozygosity) than # of segregating sites. ... Tajima's D is computed as the difference between two measures of genetic diversity: the mean number of pairwise differences and ... Theta-Pi greater than Theta-k (Observed,Expected). More haplotypes (more average heterozygosity)than # of segregating sites. ...
Bradley, DG; MacHugh, DE; Cunningham, P; Loftus, RT (1996). "Mitochondrial diversity and the origins of African and European ... indicus haplotypes, demonstrating their derivation from two geographically and genetically divergent wild populations.[12] A ...
"Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrusspecies: analysis of chromosome 2" ... Organisms Diversity & Evolution. 3 (1): 55-62. doi:10.1078/1439-6092-00058.. ...
... suggesting a high degree of mtDNA diversity. These two individuals from the same cave showed more diversity than seen among ... As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of ...
"Animal Diversity Web. Animaldiversity.ummz.umich.edu. *^ a b Archibald, George W. & Meine, Curt (1996): 7. Sandhill Crane. In: ... Analysis of control region mtDNA haplotype data shows two major lineages. The Arctic and the subarctic migratory population ...
Other haplotypes that early descents of Japanese people were thought to be carried into include C-M8, which is another Y- ... "The New Face of Asian Pacific America: Numbers, Diversity, and Change in the 21st century." San Francisco, CA: Asian Week, 2003 ... chromosome haplotype. Also going back to the Jōmon, that gene is displayed in high frequencies in people of Japanese descent. ... of the mitochondrial component of Japanese American genes of haplogroup M12 shows a direct correlation of Japanese haplotypes ...
"The Eurasian Heartland: A continental perspective on Y-chromosome diversity".. *. Underhill, Peter A; Myres, Natalie M; Rootsi ... "Excavating Y-chromosome haplotype strata in Anatolia" (PDF). Archived from the original (PDF) on 2006-06-19. ... 494-503, and; E. Heyer et al., 2013, "Genetic Diversity of Four Filipino Negrito Populations from Luzon: Comparison of Male and ... See also: Tumonggor, Karafet et al., 2014, "Isolation, contact and social behavior shaped genetic diversity in West Timor", ...
This trait is hypothesized to derive from ancient hybrid haplotypes thought to have links to evolutionary lineages from Africa ... sequences of 32 Africanized honey bees sampled from throughout Brazil to study the effect of this process on genome diversity. ... These observations are largely driven by one large gene‐rich 1.4 Mbp segment on chromosome 11 where European haplotypes are ...
Knut Vikor (2013). Leif Manger (ed.). Muslim Diversity: Local Islam in Global Contexts. Routledge. pp. 92-93. ISBN 978-1-136- ... 2002), around 90% of Fulani individuals from Burkina Faso carried haplotype 24, which corresponds with the E-M2 that is common ... The remainder belonged to haplotype 42/haplogroup E-M132. Both of these clades are today most frequent among Niger-Congo- ... "A Back Migration from Asia to Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes". American ...
Those with the CT haplotype experience a stronger reaction, in the form of anger, to betrayal.[100] ... "Genetic diversity in oxytocin ligands and receptors in New World monkeys". PLOS One. 10 (5): e0125775. Bibcode:2015PLoSO.. ...
2000). Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language. The American ... Geographical-Distribution Gradients of the Major Pku Mutations and the Linked Haplotypes. Hum. Genet. 86, 411-413. ... 2003). Genetic diversity within the R408W phenylketonuria mutation lineages in Europe. Hum. Mutat. 21, 387-393. ... and Cultural Influences on Genetic Diversity: Y-Chromosomal Distribution in Northern European Populations. Mol Biol Evol 18, ...
French and Swiss wolves share the same mtDNA haplotype,[35] a haplotype that has never been found in any other wolf population ... "Ecological and cultural diversities in the evolution of wolf-human relationships", in Ecology and conservation of wolves in a ... The Italian wolf is the only remaining grey wolf subspecies to still possess this haplotype[21] since the extinction of the ... The phylogenetic tree indicated that the haplotypes represented two haplogroups that were separated by five mutational steps. ...
Animal Diversity Web. *Lyle R. Walton and Damien O. Joly. MAMMALIAN SPECIES - Canis mesomelas. No. 715, pp. 1-9, 3 figs. ... 2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803 in 803-19. ...
Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes groups are found in three different lineages: Y3A, the ... "Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa" ...
Haplotypes[edit]. An HLA haplotype is a series of HLA "genes" (loci-alleles) by chromosome, one passed from the mother and one ... Allelic diversity makes it necessary to use broad antigen typing followed by gene sequencing because there is an increased risk ... Diversity of HLAs in the human population is one aspect of disease defense, and, as a result, the chance of two unrelated ... Haplotypes can be obtained by typing family members in areas of the world where SSP-PCR is unable to recognize alleles and ...
A study of married couples found that MHC haplotypes differed between spouses more than chance would dictate.[70] Taking oral ... According to the heterozygotes-advantage hypothesis, diversity within the MHC genotype is beneficial for the immune system due ... hypothesis suggests that diversity in the MHC gene provides a moving target for pathogens, making it more difficult for them to ... "The role of infectious disease, inbreeding and mating preferences in maintaining MHC genetic diversity: an experimental test" ...
Branches are identified by one or more unique markers which give a mitochondrial "DNA signature" or "haplotype" (e.g. the CRS ... Reed, FA; Tishkoff, SA (2006), "Africa human diversity, origins and migrations", Current Opinion in Genetics & Development, 16 ... The Origin of Patrilineal Diversity in Africa", The American Journal of Human Genetics, 88 (6): 814-18, doi:10.1016/j.ajhg. ... "The dawn of human matrilineal diversity", American Journal of Human Genetics, 82 (5): 1130-40, doi:10.1016/j.ajhg.2008.04.002 ...
Genetic variations in MYH9 may be involved in predisposition to chronic kidney disease (CKD). A haplotype of MYH9 (haplotype E1 ... "Human nonmuscle myosin heavy chain mRNA: generation of diversity through alternative polyadenylylation". Proceedings of the ... subsequent studies showed that this association is explained by strong linkage disequilibrium with two haplotypes (haplotypes ...
Kato N (2000). "Genome of human hepatitis C virus (HCV): gene organization, sequence diversity, and variation". Microb. Comp. ... 2012). "The vitamin D receptor gene bAt (CCA) haplotype impairs the response to pegylated-interferon/ribavirin-based therapy in ... Simmonds P, Smith DB (1997). "Investigation of the pattern of diversity of hepatitis C virus in relation to times of ... Subtypes are further broken down into quasispecies based on their genetic diversity. Genotypes differ by 30-35% of the ...
The predominance of West African mitochondrial DNA haplotypes in their maternal gene pool, the major West African Y-chromosome ... that gene flow from multiple sources and sex-specific patterns have been important in the formation of the genomic diversity in ...
... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity ... A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) ... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. Haplotype ... Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of ...
Diversity of Maize Haplotypes.. A cursory inspection of Fig. 1 is enough to reveal the exceptional diversity of haplotypes ... the haplotype diversity uncovered here, like the high sequence diversity at select loci (48, 49), was already present in the ... Origin of the Haplotype Variation.. The haplotypic diversity in maize is staggering. Because retrotransposons do not excise, ... Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Qinghua Wang and Hugo K. ...
... of the samples tested and the overall haplotype diversity of 0.9999. These results, including the haplotype data at 22 Y-STR ... Haplotype diversity of 22 Y-chromosomal STRs in a southeast China population sample (Chaoshan area).. Shi M1, Bai R, Yu X, Lv J ... The haplotype diversity using the classical set of Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, ... For the same population sample, the haplotype diversity using the new sets of 11 novel Y-STRs (DYS461, DYS481, DYS504, DYS505, ...
Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two ... Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global ... gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges ... Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation ...
... "classical haplotype A" frequency, the sum of frequencies for haplotype 1 (haplotype A-1D) and haplotype 2 (haplotype A-2DS4) ... haplotype A-1D had the highest haplotype frequency of 38.8%, while haplotype A-2DS4 had a haplotype frequency of 11.8%. ... Haplotype 1 in Fig. 7⇑ is synonymous with the canonical haplotype A, with the remainder comprising the classical B haplotype. ... 5⇑A, haplotype 1), and the other containing KIR2DS4, designated as haplotype A-2DS4 (Fig. 5⇑A, haplotype 2). In the family ...
The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the ... markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from ... Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation ... The polymorphic information content values revealed by the haplotypes (0.436-0.566) were generally much higher than individual ...
... and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically ... Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in ... Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic ... haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the ...
Major Histocompatibility Complex Class I Haplotype Diversity in Chinese Rhesus Macaques. Julie A. Karl, Patrick S. Bohn, Roger ... Table S1 - MHC class I Mamu-A and Mamu-B haplotypes from Chinese- and Indian-origin rhesus macaques (.xls, 86 KB) ... Table S2 - Summary of MHC class I Mamu-A and Mamu-B haplotypes observed in each macaque (.xls, 101 KB) ...
"Genetic diversity and haplotype analysis of Guizhou Miao identified with 19 X-chromosomal short tandem repeats, International ... Genetic diversity and haplotype analysis of Guizhou Miao identified with 19 X-chromosomal short tandem repeats. Han, Yanyan; He ... Genetic diversity and haplotype analysis of Guizhou Miao identified with 19 X-chromosomal short... Han, Yanyan; He, Guanglin; ... Genetic diversity and haplotype analysis of Guizhou Miao identified with 19 X-chromosomal short tandem repeats. ...
Diversity hot spots in the North? - Unexpected haplotype pattern for the marine bivalve Cerastoderma edule (L.) Krakau, Manuela ... Krakau, M. , Jacobsen, S. and Reise, K. (2007): Diversity hot spots in the North? - Unexpected haplotype pattern for the marine ... Helmholtz Research Programs , MARCOPOLI (2004-2008) , CO2-Coastal diversity - key species and food webs ...
... that marker spacing and frequency profoundly influence observed levels of haplotype diversity; (ii) that the spectrum of ... theory extensive coalescent simulations are used to disentangle the influence of all of these factors on haplotype diversity. ... that so-called haplotype blocks can be generated due by the stochasticity inherent in the recombination process without having ... haplotypes contains information about how exhaustively genetic variation in a region is described by a given marker set; and ( ...
Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies. Ogawa A, Tokunaga K, Lin L, Kashiwase K, Tanaka ... Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies (abs) Tissue Antigens. 1998 Apr;51(4 Pt 1):356- ... Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies.. Ogawa A, Tokunaga K, Lin L, Kashiwase K, ... Thread: Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies (abs) ...
Haplotype diversities for each of four Halichoeres species.Haplotype diversities for each of four Halichoeres species with ... Nucleotide diversities were 0.0022±0.0016 for CO1 and 0.0400±0.0200 for CR. Haplotype diversity and nucleotide diversities by ... Nucleotide diversities were 0.0022±0.0016 for CO1 and 0.0400±0.0200 for CR. Haplotype diversity and nucleotide diversities by ... pone-0038042-g004: Haplotype diversities for each of four Halichoeres species.Haplotype diversities for each of four ...
Further study is needed to confirm these regions with high recombination rate and high haplotype diversity. ... characterize haplotype diversity and identify recombination hotspots on chromosomes 5 and 15 in layer chicken. BEAGLE, DAGPHASE ... and fastPHASE software recognized fewer haplotypes than two other methods. In total, 10 and 2 recombination hotspots were ... The objectives of this study were to compare the performance of different haplotype reconstruction approaches, ...
Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype diversity is given ... the greater the haplotype diversity will be for a particular number of descendants. However, if the haplotype diversity is ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ...
Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype diversity is given ... the greater the haplotype diversity will be for a particular number of descendants. However, if the haplotype diversity is ... BiologyPages/H/Haplotypes.html Kimballs Biology Pages (Creative Commons Attribution 3.0) *^ "haplotype / haplotypes , Learn ...
Diversity of MICA (PERB11.1) and HLA haplotypes in Northeastern Thais A V Romphruk 1 , T K Naruse, A Romphruk, H Kawata, C ... Diversity of MICA (PERB11.1) and HLA haplotypes in Northeastern Thais A V Romphruk et al. Tissue Antigens. 2001 Aug. ... HLA-A, -B, and -DRB1 allele and haplotype diversity in a cohort of Brazilian renal transplant candidates. Ravazzi-Gauch C, ... MICA polymorphisms and haplotypes with HLA-B and HLA-DRB1 in Koreans. Sohn YH, Cha CH, Oh HB, Kim MH, Choi SE, Kwon OJ. Sohn YH ...
Haplotype diversity:. Haplotype diversity was calculated in a manner identical to the calculation of gene diversity (Weir 1996 ... Haplotype diversity:. The mean number of haplotypes present among the 6 soybean genotypes in the 2032 SNP-containing STSs was ... Haplotype diversity:. Among the six genotypes analyzed, just two haplotypes were found in 1502 (73.9%) of the 2032 gene ... There was a mean of 2.31 haplotypes in the 2032 SNP-containing genes. Haplotype diversity in gene fragments that contained two ...
Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China. ... Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, ... alleles and haplotypes varies widely between different ethnic populations and geographic areas. It is meaningful to investigate ... as the most common two-locus haplotypes. Data comparison by neighbor-joining dendrograms and principal component analysis to ...
... chosen because of their 12S gene haplotype and/or geographical origin. Haplotype networks generated by maximum-likelihood and ... Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, ... Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were ... Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and the Middle East. *Antoinette C ...
Haplotype Diversity and LD Decay.. To evaluate the effects of domestication on levels of genetic diversity, haplotype diversity ... Haplotype diversity was calculated as (n/(n − 1))(1 − ∑xi2), where xi is the haplotype frequency of each haplotype and n is the ... Haplotype diversity was evaluated across a range of window sizes (SI Appendix, Fig. S2 and Fig. S5). ... Analyses of haplotype diversity and LD suggest that grape domestication involved a weak bottleneck, because present-day wine ...
Tag: Haplotype Diversity. Haploscope - Visualize Haplotype Diversity. Haploscope. :: DESCRIPTION. Haploscope is a software ... Haplotype Diversity, VisualizeLeave a comment on Haploscope - Visualize Haplotype Diversity ... Haploscope: a tool for the graphical display of haplotype structure in populations.. Genetic Epidemiology, 36: 17-21. doi: ... Haploscope is designed to accept haplotype frequency input directly from output files of fastPHASE (Scheet & Stephens, 2006), ...
The DR region of primate species is generally complex and displays diversity concerning the number and combination of distinct ... Therefore, haplotypes of the family members could be determined by segregation analyses. Furthermore, DRB haplotypes of the 68 ... which are present on the majority of haplotypes. This undocumented high level of DRB region configuration-associated diversity ... resulting in a total of 54 DRB haplotypes. Most of these unreported haplotypes were detected within the group of unrelated ...
A complementary analysis of haplotype blocks (see Materials and Methods) also revealed shared haplotype blocks of megabase size ... The correlation between across-clade and within-clade diversity likely stems from ancestral diversity. This ancestral diversity ... Restricting the analysis of the global P. pacificus diversity to coding regions, we find a mean silent site diversity πsi = 1.4 ... We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. ...
MAPT haplotype diversity in multiple system atrophy.. Labbé C1, Heckman MG2, Lorenzo-Betancor O1, Murray ME1, Ogaki K1, Soto- ... In the present study, we assessed the full MAPT haplotype diversity in MSA patients using six MAPT tagging SNPs. We genotyped a ... 0.9%, p = 0.021). We evaluated the association of MSA subtypes with the common protective H2 haplotype and found a significant ... We identified four significant association signals in our pathologically confirmed cases, two from the protective haplotypes H2 ...
In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races ... Tag SNPs were selected to evaluate the haplotype diversities in the four populations by HaploStats software. APOL1 gene was ... APOL1 coding region showed that two SNP of G1 with higher frequency are actually pull down the haplotype H-1 frequency when ... while other three haplotypes taken an opposite pattern; 3UTR presents several high-frequency variation sites in a short ...
... *778. *Robert A. Scott, Richard H. Wilson, William ...
... Author: Sanna, Mauro; Cires Rodríguez, Eduardo ...
... diversity within breeds, and evolutionary relationships among related species. ... Haplotypes at coat color loci. Haplotypes containing markers at the MC1R, ASIP and STX17 loci on ECA3, 22 and 25, respectively ... Species diversity Is the Subject Area "Species diversity" applicable to this article? Yes. No. ... Genetic diversity, inbreeding, and LD in the domestic horse. Measurements of genetic diversity, inbreeding and LD all reflect ...
Three haplotypes each were observed in all other continents, with the exception of the Americas, where haplotype diversity is ... The dominant haplotype is Ht1. Of 282 chromosomes tested, 248 (88%) were observed to carry this haplotype. Haplotypes 2 and 3 ... haplotype diversity for class I β-tubulin was not observed to be greatest in Africa. Actually, of the six haplotypes, four were ... Haplotypes are defined as follows (the base change defining a new haplotype is underlined): Ht0, ACTGCGC; Ht1, ACCGCGC; Ht2, AT ...
  • We analyzed 1,601 individuals from 19 populations using 765 base pairs of the mitochondrial cytochrome oxidase I ( COI ) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. (cabi.org)
  • In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. (purdue.edu)
  • Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. (purdue.edu)
  • Moreover, the association of these B61 alleles with the DRB1 alleles revealed considerable diversity among the different populations. (skadi.net)
  • Consequently, the frequencies of the B61 alleles varied among the different East Asian populations, but the individual B61 alleles were carried by specific haplotypes often regardless of the ethnic differences. (skadi.net)
  • Interestingly, MICA052, which is a very rare allele in other populations, was prevalent with the allele frequency of 8.2%, mainly on the HLA haplotype carrying HLA-B*13 in this population. (cdc.gov)
  • Previous studies indicate the distribution of major histocompatibility complex class I chain-related genes A ( MICA ) and B (MICB) alleles and haplotypes varies widely between different ethnic populations and geographic areas. (bvsalud.org)
  • Tag SNPs were selected to evaluate the haplotype diversities in the four populations by HaploStats software. (biomedcentral.com)
  • APOL1 coding region showed that two SNP of G1 with higher frequency are actually pull down the haplotype H-1 frequency when considering all populations pooled together, and the diversity among the four populations be widen by the G1 two mutation ( P 1 = 3.33E-4 vs P 2 = 3.61E-30). (biomedcentral.com)
  • The distributions of APOL1 gene variants and haplotypes were significantly different among the different populations, in either regulatory or coding regions. (biomedcentral.com)
  • Compared with other populations, our results indicated that the Han populations in different regions had a similar allelic diversity of HLA -A, -B, and -DRB1 loci. (elsevier.com)
  • In summary, the similarities and differences of the HLA allelic diversity and haplotype structure between the Han population in the Guanzhong region and related populations, regarding HLA genotype distribution, provide basic information for further studies of the HLA heterogeneity and anthropological studies. (elsevier.com)
  • The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. (sciencemag.org)
  • D). An HMM for this purpose formally requires the calculation of two-locus diplotype probabilities, although if the populations are formed with a large number of mating pairs, the two haplotypes within an individual are independent, and so it is sufficient to calculate two-locus haplotype probabilities. (g3journal.org)
  • Recently, we and others made the unexpected finding that V617F JAK2 is not acquired randomly but instead arises preferentially on a specific constitutional JAK2 haplotype, at least in white populations. (bloodjournal.org)
  • While an individual human could exhibit any of 2k different patterns of markers on a single chromosome, in real populations only a small subset of such patterns-haplotypes-are actually observed (Gabriel et al. (psu.edu)
  • The identification of such haplotypes would have significant implications for the understanding of the migration patterns of ancestral populations of humans. (psu.edu)
  • It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. (psu.edu)
  • Sharing of mitochondrial haplotypes by SCA and Canarian goats suggests that goat populations from the Atlantic archipelagos, where Spanish and Portuguese ships en route to the New World used to stow food and supplies, participated in the foundation of SCA caprine breeds. (nih.gov)
  • Hence, for woody perennial plant species, nuclear genes provide little power for discrimination among populations because the majority of their diversity resides within populations [ 9 ]. (hindawi.com)
  • Recent developments in statistical methods have permitted the reconstruction of haplotypes and the estimation of haplotype frequencies in unrelated populations based on SNP data. (aacrjournals.org)
  • We show that the introduced populations have mixed ancestry between south Texas and more northern areas and experienced founder effects and genetic bottlenecks resulting in decreased genetic diversity. (nature.com)
  • To help delimit the regions that likely harbor the disease-causing variants in populations of non-European origin, we studied the haplotype diversity and allelic history of the 9p21.3 region using 938 unrelated individuals from 51 populations (Human Genome Diversity Panel). (beds.ac.uk)
  • For the T2D locus, the TT risk haplotype of SNPs rs10811661 and rs10757283 was present at similar frequencies in all global populations, while a shared 6-SNP haplotype that carries the protective C allele of rs10811661 was found at a frequency of 2.9% in Africans and 41.3% in East Asians and was associated with low haplotype diversity. (beds.ac.uk)
  • The extensive linkage disequilibrium (LD) seen in this genomic region in the CEU HapMap population is diminished in the other HapMap populations of African, Chinese and Japanese ancestry, both for pair-wise LD levels as well as size of the haplotype blocks. (beds.ac.uk)
  • 2011. Characterization of haplotype diversity defined by discontinuous insertions/deletions within the intron 2 of interleukin 2 in different domestic chicken populations. (cgiar.org)
  • We conducted a meta-analysis integrating case- control and haplotype variant studies in multiple ethnic populations to clearly discern the effect of these two variants on SLE. (bvsalud.org)
  • Haplotype network analysis of global PfCSP revealed that global PfCSP clustered into 103 different haplotypes with geographically-separated populations. (springer.com)
  • chromosome 21, scientists have found that the vast majority of human populations around the globe fall into only three haplotypes. (godandscience.org)
  • Hotspots of recombination are now known to be a key component in dictating the structure of diversity in human populations, and recent research suggests they may play a more fundamental role in the evolution of the human genome. (els.net)
  • All except one of the P. mugo populations sampled contained a notable share of private haplotypes. (vdu.lt)
  • AMOVA revealed high intra-specific diversity but low differentiation between the P. mugo populations. (vdu.lt)
  • To test this, we again analyzed the phase 1 data of the 1000 Genomes Project, which includes 338 haplotypes from three African populations. (blogspot.com)
  • This result indicates that African NE1 haplotypes have a longer coalescence and, as such, the presence of the NE1 haplogroup among modern Africans cannot be explained by simple back migration and admixture of Eurasian haplotypes to African populations. (blogspot.com)
  • the African-Eurasian diversity differential can be explained both in terms of loss of diversity in an Out-of-Africa bottleneck and a gain-of-diversity in In-Africa admixture events between divergent populations that must have lived in the large and ecologically diverse continent. (blogspot.com)
  • This scenario explains the presence of NE1 haplotypes (that are similar to the Neandertal haplotype) among modern human populations as well as the deep, distinct lineages observed among African NE1 haplotypes. (blogspot.com)
  • One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. (blogspot.com)
  • Heteromys nelsoni populations have undergone a very recent demographic contraction and the low genetic diversity observed indicates an unfavorable future for the species. (degruyter.com)
  • Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. (le.ac.uk)
  • The larger sample of MSP-3α diversity revealed incongruence between the observed levels of nucleotide polymorphism, which were high in all populations, and the pattern of PCR-RFLP haplotype diversity. (biomedcentral.com)
  • Before achieving the goal of eliminating malarial infection in Hainan Island, it is essential to understand the diversity of autochthonous malaria and to predict the origin and the spread of parasite variants within and between populations. (biomedcentral.com)
  • Killer Ig-like receptor ( KIR ) genes constitute a multigene family whose genomic diversity is achieved through differences in gene content and allelic polymorphism. (jimmunol.org)
  • The term ' haplogroup ' refers to the SNP/ unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (wikipedia.org)
  • [7] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)
  • Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China. (bvsalud.org)
  • Vinifera harbors levels of genetic variation an order of magnitude greater than humans and is comparable in diversity to maize ( 2 , 3 ), with polymorphism that dates back tens of millions of years ( 4 ). (pnas.org)
  • In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. (biomedcentral.com)
  • In this chapter, the definition of several terms such as polymorphism, minor allele frequency (MAF), allele frequency, haplotype, and linkage disequibrium (LD) is clarified. (intechopen.com)
  • What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)? (stackexchange.com)
  • Four of these differed from Japanese haplotypes by one single nucleotide polymorphism (SNP), possibly indicating a recent in situ change. (springer.com)
  • The rs10954213 polymorphism and the haplotype diversity in interferon regulatory factor 5 (IRF5) play a special role in systemic lupus erythematosus (SLE) but with inconclusive results. (bvsalud.org)
  • Relative to the remainder of the genome, the L er and Col-0 RPP5 haplotypes exhibit remarkable intraspecific polymorphism. (plantcell.org)
  • The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. (purdue.edu)
  • In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of θ = 0.000997. (genetics.org)
  • Because SNPs are more abundant than SSRs, they improve the odds of success in a diversity of applications including positional cloning, association analysis, QTL mapping, and the determination of genetic relationships among individuals. (genetics.org)
  • In the present study, we assessed the full MAPT haplotype diversity in MSA patients using six MAPT tagging SNPs. (cdc.gov)
  • 5%), while the remaining three SNPs were found on multiple haplotypes, suggesting a complex history of recombination. (nature.com)
  • Significant associations to a single disease outcome were found for two SNPs and one haplotype in AA. (nature.com)
  • In addition, given the important role played by SDF-1 and CXCR4 in HIV-1/AIDS, we looked for the influence of genetic variation in these SNPs and haplotypes on disease in over 3000 subjects enrolled in five USA-based natural history HIV-1/AIDS cohorts. (nature.com)
  • High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. (frontiersin.org)
  • This topic describes about polymorphisms, SNPs, GWAS, linkage disequilibrium (LD), minor allele frequency, haplotype, method for SNP genotyping, and application of SNPs and genome-wide association study in human diseases and drug development. (intechopen.com)
  • We thus defined two sets of SNPs: (i) the association set and (ii) the diversity set. (sciencemag.org)
  • The diversity set provides SNPs for characterizing genome-wide variation patterns, whereas the association set provides access to more regions of the genome. (sciencemag.org)
  • The single nucleotide polymorphisms (SNPs) associated with these two diseases in Europeans reside on two adjacent haplotype blocks with independent effects on disease. (beds.ac.uk)
  • Interestingly, two SNPs (rs2891168 and rs10757278) tagging this CHD risk haplotype are most strongly associated with CHD disease status according to independent clinical fine-mapping studies. (beds.ac.uk)
  • The additional SNPs were selected to include disease-associated SNPs and haplotype-tagging SNPs that were not present on the 650Y chip. (beds.ac.uk)
  • From the GWAS, the most important discoveries were single-nucleotide polymorphisms (SNPs) located on Chr 1, 2, and 3, which mapped to haplotype blocks providing potential genes for a B toxicity tolerance assay and meriting further investigation. (figshare.com)
  • Shown below are the haplotypes (rows) of a 100 chromosomes assayed at 40 biallelic single nucleotide polymorphisms ( SNPs , columns). (els.net)
  • A haplotype is defined by the nearest 10 SNPs . (els.net)
  • Light colours indicate a 50% chance that two haplotypes, carrying the same derived allele, are identical at the neighbouring 10 SNPs , when sampled at random. (els.net)
  • Shown on the right is a set of haplotypes (rows) typed at SNPs (columns) at which strong positive selection has favoured the red allele at the left‐hand most SNP. (els.net)
  • Using these six SNPs, linkage disequilibrium and haplotype patterns were characterized. (aacrjournals.org)
  • All six SNPs showed a strong linkage disequilibrium pattern and were considered to belong to one haplotype block. (aacrjournals.org)
  • The haplotypes and individual SNPs were not associated with breast cancer risk. (aacrjournals.org)
  • Slope inhabitant Halichoeres claudia had 31 haplotypes for CO1 and 110 haplotypes for CR with 18 and 102 unique haplotypes (observed in single individuals), respectively (Fig. 2a & 3a). (nih.gov)
  • The time usage per marker on chromosome 22 of the WTCCCC Crohn's disease data (top) and the number of unique haplotypes overlapping each marker (bottom). (nih.gov)
  • Of 79 samples analysed, 51 unique haplotypes were identified. (bioone.org)
  • RESULTS Twelve unique haplotypes, labelled A-L, were obtained. (bmj.com)
  • The present data indicate that there was high degree of genetic diversity among P. vivax population in Hainan Province of China during the pre-elimination stage of malaria, with 26 unique haplotypes observed among 27 samples. (biomedcentral.com)
  • By combining the allelic states of the 22 Y-STR loci we could construct highly informative haplotypes that allowed the discrimination of 99.1% (214 out of 216) of the samples tested and the overall haplotype diversity of 0.9999. (nih.gov)
  • These results, including the haplotype data at 22 Y-STR loci in the present study, provide useful information for forensic practice in the Chaoshan population in southeast China. (nih.gov)
  • For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (wikipedia.org)
  • For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you don't know which haplotype you have, e.g. (wikipedia.org)
  • In humans, the number of DRB loci per haplotype varies from one to four and five major region configurations with different gene numbers and content are known (DR8, DR1, DR51, DR52, and DR53), whereas in chimpanzees nine and in rhesus macaques more than 30 region configurations have been defined with up to five and six DRB loci per haplotype, respectively (Mayer et al. (springer.com)
  • 2000 ). In rhesus and cynomolgus macaques, two to three DRB loci per haplotype appear to be expressed. (springer.com)
  • Even though the term draft was introduced in the context of recurrent hitchhiking, we use it here more generally to refer to the effect of linked selection of any kind as it has been shown that the nature of the selected variation is immaterial as long as many loci contribute to fitness diversity ( Neher and Hallatschek 2013 ). (genetics.org)
  • The allele and haplotype frequencies of HLA-A, -B and -DRB1 loci in 10,000 healthy unrelated Han individuals living in the Guanzhong region of the Shaanxi Province were analyzed with the methods of SSO, SSP and SBT. (elsevier.com)
  • Three-loci haplotype analysis revealed that HLA A30- B13- DRB107 (4.11%), A02 -B46 -DRB109 (2.57%) and A33 -B58 -DRB117 (1.32%) were the most common haplotypes in this population. (elsevier.com)
  • Four two-loci haplotypes, including HLA-A30-B43, A30-B53, B43-DRB107 and B73-DRB104 had significant linkage disequilibrium (relative linkage disequilibrium parameter equals to 1). (elsevier.com)
  • Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. (biomedcentral.com)
  • A total of 33 STR loci from across the genome were used to gauge genetic diversity within an individual and across the breed. (ucdavis.edu)
  • The IR value is a measure of genetic diversity within an individual that takes into consideration both heterozygosity of alleles at each STR loci and their relative frequency in the population. (ucdavis.edu)
  • The diversity of alleles at each of the genomic STR loci and their frequency in the population were used to calculate the internal relatedness (IR) of each dog and for the Standard Poodle population as a whole (Fig. 1). (ucdavis.edu)
  • Gene and haplotype frequencies for the loci HLA-A, B and DRB1 in 11755 north Chinese Han bone marrow registry donors]. (openrepository.com)
  • Red (below light colours) indicates greater than half chance and blue (above light colours) indicates that haplotypes are rarely similar in the alleles present at nearby loci. (els.net)
  • METHODS Seven loci across RET were typed and haplotypes formed for HSCR cases, their unaffected parents, and region matched controls. (bmj.com)
  • The microsatellite haplotypes within HG were constructed using 7 STR loci. (blogspot.com)
  • Haplotype and nucleotide diversity were similar among all four species. (nih.gov)
  • Nucleotide diversity was 0.0018±0.0014 for CO1 and 0.0256±0.0135 for CR. (nih.gov)
  • Nucleotide diversity was 0.0011±0.0010 for CO1 and 0.0268±0.0140 for CR. (nih.gov)
  • A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca , chosen because of their 12S gene haplotype and/or geographical origin. (biomedcentral.com)
  • Nucleotide and haplotype diversities reached values of 0.020 +/- 0.00081 and 0.963 +/- 0.0012 respectively. (nih.gov)
  • In that case you could compute the expected difference in nucleotide across haplotypes based on the average number of nucleotide difference conditioned on that H distribution. (stackexchange.com)
  • Isolation of a full-length CC-NBS-LRR resistance gene analog candidate from sugar pine showing low nucleotide diversity. (usda.gov)
  • Nucleotide diversity is the average proportion of nucleotides that differ between two individuals. (wikipedia.org)
  • As of 2004, the human nucleotide diversity was estimated to be 0.1% [10] to 0.4% of base pairs . (wikipedia.org)
  • A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. (els.net)
  • 2001) Haplotype variation and linkage disequilibrium in 313 human genes. (els.net)
  • Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro-" by Hendrik-Jan Megens, Richard PMA Crooijmans et al. (purdue.edu)
  • Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken. (purdue.edu)
  • While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. (purdue.edu)
  • and Groenen, Martien AM, "Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken. (purdue.edu)
  • Assessing the performance of the haplotype block model of linkage disequilibrium. (semanticscholar.org)
  • Linkage disequilibrium analysis further revealed MICB(∗)00502- MICA (∗)019 (13.10%) and MICB(∗)002- MICA (∗)00804 (9.89%) as the most common two-locus haplotypes . (bvsalud.org)
  • High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera , which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. (pnas.org)
  • Well-powered GWA and GS require a genome-wide assessment of genetic diversity, patterns of population structure, and the decay of linkage disequilibrium (LD). (pnas.org)
  • Significantly high linkage disequilibrium was observed in six two-locus haplotypes, with their corresponding relative linkage disequilibrium parameters equal to 1. (openrepository.com)
  • PURPOSE In order to determine if it is the variant per se, a combination thereof, or another locus in linkage disequilibrium which predisposes to HSCR, we looked for association of RET haplotype(s) and disease in HSCR cases compared to region matched controls. (bmj.com)
  • 2001) Haplotype tagging for the identification of common disease genes. (els.net)
  • KIR haplotypes containing a single activating KIR gene ( A -haplotypes), and KIR haplotypes with multiple activating receptor genes ( B -haplotypes) have been described. (jimmunol.org)
  • The DR region of primate species is generally complex and displays diversity concerning the number and combination of distinct types of DRB genes present per region configuration. (springer.com)
  • In previous studies, the number of Mafa - DRB genes was defined to vary from two to four per haplotype (Blancher et al. (springer.com)
  • This SNP genotyping tool will facilitate many genetics applications in equids, including identification of genes for health and performance traits, and compelling studies of the origins of the domestic horse, diversity within breeds, and evolutionary relationships among related species. (plos.org)
  • Distribution of HLA-A, -B and -DRB1 genes and haplotypes in the Tujia population living in the Wufeng Region of Hubei Province, China. (openrepository.com)
  • Allelic and haplotypic diversity of HLA-A, -B, -C, and -DRB1 genes in Koreans defined by high-resolution DNA typing]. (openrepository.com)
  • Whyte also analysed the haplotypes (groups of closely linked genes) carried on mitochondrial DNA, which is inherited only through the female line. (freerepublic.com)
  • Noncolinear haplotypes were also found in a comparison of the z1C zein genomic regions of B73 and BSSS53 ( 5 ), two Corn Belt inbreds extracted from the same population ( 4 ). (pnas.org)
  • Haplotype diversity of 22 Y-chromosomal STRs in a southeast China population sample (Chaoshan area). (nih.gov)
  • Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. (cabi.org)
  • Keywords X-chromosomal STRs Miao population Population genetics Haplotype diversity X-chromosomal short tandem repeats (STRs) with the advan- recognized by the government of the People's Republic of tages of both autosomal and uni-parental biomarkers have China. (deepdyve.com)
  • Population-genetic basis of haplotype blocks in the 5q31 region. (semanticscholar.org)
  • A large variety of three-locus (MICA - HLA-B - HLA-Cw) and six-locus (HLA-DQB1 - HLA-DRB1 - MICA - HLA-B - HLA-Cw - HLA-A) haplotypes were recognized in the northeastern Thai population. (cdc.gov)
  • We provide a refined model of the domestication and breeding history of vinifera by evaluating levels of haplotype diversity, the decay of LD, and patterns of population structure in vinifera and its progenitor, sylvestris . (pnas.org)
  • Haploscope is a software package that facilitates flexible rendering of images to aid interpretation of model-based summaries of population haplotypes. (mybiosoftware.com)
  • Haploscope is designed to accept haplotype frequency input directly from output files of fastPHASE (Scheet & Stephens, 2006), though output from other cluster-based models for population haplotypes could be adapted for input to Haploscope. (mybiosoftware.com)
  • We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. (genetics.org)
  • Related designs include heterogeneous stock and the diversity outcross population. (g3journal.org)
  • To do this, we targeted the 20% of the maize genome that is low-copy ( 4 , 5 ) on a diverse panel of 27 inbred lines (representative of maize breeding efforts and worldwide diversity)―founders of the maize nested association mapping (NAM) population ( 6 )―and used sequencing-by-synthesis (SBS) technology with three complementary restriction enzyme-anchored genomic libraries (figs. S1 and S2A) ( 7 ). (sciencemag.org)
  • Citation Query A new statistical method for haplotype reconstruction from population data. (psu.edu)
  • A new statistical method for haplotype reconstruction from population data. (psu.edu)
  • 2002). Given a meiotic model for the combination of a pair of haplotypes into a genotype during mating, and given a set of observed genotypes in a sample from a human population, it is of great interest to identify the underlying haplotypes (Stephens et al. (psu.edu)
  • The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7]. (psu.edu)
  • The aHt haplotype has found a higher discriminatory potential than minHt haplotype with a better Pd combined value (0.9999936 vs 0.9999836) and has higher average gene diversity per locus (0.7834 vs 0.7518) in Turkish population. (scirp.org)
  • aHt haplotype can be proposed as an alternative to minHt in paternity testing and forensic medicine applications involving Turkish male population. (scirp.org)
  • The present study was undertaken to systematically analyze the effects of anthropogenic activities on the genetic diversity and population structure of S. racemosa and to generate preliminary data for conservation purposes. (hindawi.com)
  • Objective: To detect the diversity of killer Ig-like receptor(KIR) gene content and the combination of haplotypes in Chinese Han population in Shanghai area. (mskcc.org)
  • Conclusion: These findings suggest that there are distinctive frequencies of KIR gene content, haplotype as well as genotype in Chinese Han population in Shanghai area. (mskcc.org)
  • There were seven haplotypes with a frequency of 5% or higher in at least one ethnic group of the study population. (aacrjournals.org)
  • Obviously, this is not enough to evaluate if Chinese wolves have a higher or lower genetic diversity than Middle Eastern wolves and they could by pure chance be unrepresentative of their respective population (for example, closely related, immigrant from another population or an inbred/outcrossed specimen). (biomedcentral.com)
  • In addition, comparisons with other raptors revealed a high degree of genetic diversity in the BJJ population. (bioone.org)
  • A comparative analysis of the two regions in global PfCSP displayed similar patterns of low genetic diversity in global population, but substantial geographic differentiation was also observed. (springer.com)
  • The average similarity of haplotypes carrying the same new (derived) mutation in relation to its frequency in the population and the local recombination rate. (els.net)
  • The standard intra-population diversity indexes were calculated. (vdu.lt)
  • This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. (diva-portal.org)
  • By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. (diva-portal.org)
  • Dienekes' Anthropology Blog: Haplotype that looks Neandertal-introgressed may reflect African population structure (Gokcumen et al. (blogspot.com)
  • Characteristics of autosomal and X-chromosomal haplotypes and application to human population studies. (le.ac.uk)
  • Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas. (le.ac.uk)
  • Characterization of standard population genetic measures of diversity, phylogenetic analysis, and tests for recombination were performed. (biomedcentral.com)
  • Interestingly, these regions are significantly enriched for repeat elements (LTRs and LIN Es) which are known to facilitate accelerated recombination and sequence diversity, key to population fitness and pathogen resistance. (cam.ac.uk)
  • To better understand the genetic information on P. vivax population before elimination of malaria in Hainan Province, the extent of genetic diversity of P. vivax isolates in Hainan Province was investigated using four polymorphic genetic markers, including P. vivax merozoite surface proteins 1, 3α, and 3β ( pvmsp -1, pvmsp - 3α , and pvmsp - 3β ) and circumsporozoite protein ( pvcsp ). (biomedcentral.com)
  • In this study, the population diversity of P. vivax isolates from Hainan Province was evaluated using four polymorphic markers. (biomedcentral.com)
  • Each population has a unique range of haplotypes. (freerepublic.com)
  • From that we have worked out that 56 women came to New Zealand to create the diversity of today s population , she added. (freerepublic.com)
  • The Veterinary Genetics Laboratory (VGL), in collaboration with Dr. Niels C. Pedersen and staff, has developed a panel of short tandem repeat (STR) markers that will determine genetic diversity across the genome and in the Dog Leukocyte Antigen (DLA) class I and II regions. (ucdavis.edu)
  • Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. (els.net)
  • Association between VEGF polymorphisms (936c/t, -460t/c and -634g/c) with haplotypes and coronary heart disease susceptibility. (semanticscholar.org)
  • Haplotypes of RHO polymorphisms and susceptibility to age-related macular degeneration. (semanticscholar.org)
  • We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed 10- to 30-fold variation in recombination rates. (sciencemag.org)
  • Subsequent study revealed an additional haplotype called D (identified with the new polymorphisms found downstream of the ACE transcribed sequences and sharing alleles with haplotype B and A), and this is consistent with a second ancestral 3′ recombination breakpoint ∼16 kb downstream from the intron 5 and exon 8 breakpoint ( 6 ). (diabetesjournals.org)
  • Our results suggest that the currently identified genetic polymorphisms of HER-2 are not associated with an increased risk of breast cancer in Korean women, whereas one haplotype does affect protein expression of the tumor and disease outcome. (aacrjournals.org)
  • Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. (purdue.edu)
  • Estimation of Haplotype Diversity and Recombination Rate on Chromosome" by Ziqing Weng, Anna Wolc et al. (iastate.edu)
  • Further study is needed to confirm these regions with high recombination rate and high haplotype diversity. (iastate.edu)
  • The relationship between the local recombination rate and patterns of genetic diversity. (els.net)
  • A haplotype ( haploid genotype ) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
  • An organism's genotype may not define its haplotype uniquely. (wikipedia.org)
  • These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. (g3journal.org)
  • The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. (wikipedia.org)
  • In this study, we investigated whether haplotype (genotype + phase) information would strengthen the genotype-phenotype relationship for PON1. (aacrjournals.org)
  • Collectively, the genetic (genotype or haplotype) contribution to PON1 enzymatic activity (measured as phenylacetate hydrolysis) was greater in neonates compared with mothers. (aacrjournals.org)
  • Haplotype and genotype frequencies and distributions were compared among these groups using the transmission disequilibrium test and standard case-control statistic. (bmj.com)
  • The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus ( MC1R ) and defining a conserved haplotype of ∼750 kb across all breeds. (plos.org)
  • A fast algorithm for genome-wide haplotype pattern mining. (nih.gov)
  • 7 - 9 This haplotype, which we refer to as 46/1 7 but others have called GGCC, 8 is found in approximately 50% of normal persons and thus is a common, very low penetrance predisposition allele of the type that is typically detected by genome-wide association studies. (bloodjournal.org)
  • This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies. (sciencemag.org)
  • To this end, we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic analyses for the genus. (figshare.com)
  • With the advent of genome‐wide human genetic data, understanding the role of recombination in determining patterns of genetic diversity is more important than ever before. (els.net)
  • Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were either part of the T. g. graeca or of the T. g. ibera clade, suggesting that genetic evidence for the existence of most of the 15 proposed subspecies of T. graeca is weak. (biomedcentral.com)
  • Phylogenetic, haplotype, and network analyses of G. duodenalis based on the bg gene were carried out. (allenpress.com)
  • Based on analysis of microsatellite haplotypes within main Y- chromosomal haplogroups, molecular diversity within monophyletic lineages were calculated and phylogenetic trees for most common haplogroups were reconstructed. (blogspot.com)
  • Evidence of frequent and variable insertion-deletion mutations and recurrent recombination between MSP-3α haplotypes complicated the inference of genetic diversity patterns and reduced the phylogenetic signal. (biomedcentral.com)
  • The new approach use patterns of haplotype diversity in the genome: locally in the genome, the number of observed haplotypes is much smaller than the total number of possible haplotypes. (nih.gov)
  • The frequency of sequence variants in soybean is low due to historical genetic bottlenecks and low sequence diversity in soybean's wild ancestor G. soja (Sieb and Zucc. (genetics.org)
  • 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. (sciencemag.org)
  • Let p s denote the frequency of the AA haplotype at generation F s . (g3journal.org)
  • 2) The frequency of recombinant haplotypes at generation F s is 1 − 2 p s . (g3journal.org)
  • Background: Previous studies indicate that the frequency distributions of HLA alleles and haplotypes vary from one ethnic group to another or between the members of the same ethnic group living in different geographic areas. (openrepository.com)
  • Despite these findings, SP remains a explored emerging lineages of dhps mutant haplotypes in Malawi,theDemocraticRepublicoftheCongo,andTanza- major tool for malaria control when administered as a partner niabyusinganalysesofgeneticmicrosatellitesflankingthe drug with artemisinins and as intermittent preventive therapy dhps locus. (cdc.gov)
  • In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. (g3journal.org)
  • Darvasi and Soller (1995) derived the two-locus haplotype probabilities for the autosome in AIL. (g3journal.org)
  • In this article, I derive the two-locus haplotype probabilities for the autosome and X-chromosome in AIL, HS, and the DO. (g3journal.org)
  • Let us first revisit the two-locus autosomal haplotype probabilities in AIL, as they serve as a simple example of the technique used in these calculations (see also Bulmer 1980 , Ch. 3). (g3journal.org)
  • Gene diversity per locus varied from 0.5788 (DYS388) to 0.8903 (DYS385a/b). (scirp.org)
  • In a departure from these earlier studies, we used three tagging markers (A-5466C, T-3892C, and Ins/Del) at the ACE locus to test for disease haplotype associations. (diabetesjournals.org)
  • However, haplotype analyses revealed a near doubling in the prevalence of the A.T.D risk haplotype in case subjects (0.136) compared with control subjects (0.075) ( P = 0.009), thus providing first evidence for a disease haplotype for advanced diabetic nephropathy at the ACE locus. (diabetesjournals.org)
  • The 28-kb ACE locus is characterized by low haplotype diversity and can be described by three frequent haplotypes: A, B, and C ( 5 ). (diabetesjournals.org)
  • In the present study, we employed a genetic haplotype approach to examine the contribution of common variations at the HER-2 locus to breast cancer risk among Korean women. (aacrjournals.org)
  • Verhoeven KJ and Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. (els.net)
  • To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. (pnas.org)
  • Based on the additional findings (i) that the majority of nonsynonymous variation is eliminated over timescales on the order of the separation between clades, (ii) that diversity is reduced in gene-rich regions, and (iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus . (genetics.org)
  • In addition to reducing neutral genetic diversity, draft results in different patterns of variation that can be used to disentangle the roles of drift and draft. (genetics.org)
  • We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. (sciencemag.org)
  • These two breakpoints are thought to flank the gene interval that harbors most of the genetic variation that determines ACE activity, with haplotypes B, C, and D having higher ACE activity than haplotype A ( 6 ). (diabetesjournals.org)
  • This proposal was principally based on the differential association of class III VNTR-bearing haplotypes, the protective haplotype (PH) and very protective haplotype (VPH) ( 9 ), a phenomenon most easily explained by sequence variation within the VNTR rather than cis effects of SNP alleles on these haplotypes. (diabetesjournals.org)
  • Using this dataset, we found that variation within African NE1 haplotypes is significantly higher than variation within Asian and European NE1 haplotypes (p less than 10-15, Figure 3C, Figure S5). (blogspot.com)
  • But, it is possible that the higher variation within African NE1 haplotypes may reflect introgression of short "Palaeoafrican" variants within the African NE1 haplotypes. (blogspot.com)
  • It is of major interest, therefore, to understand the molecular basis for the evolution of host-pathogen specificity and to characterize intraspecific natural variation at R gene haplotypes. (plantcell.org)
  • The Felupe-Djola and Papel groups exhibit the highest diversity of lineages and harbor the deep-rooting haplogroups A-M91, E2-M75 and E3*-PN2, typical of Sahel's more central and eastern areas. (biomedcentral.com)
  • Complete chIL-2 genomic DNA sequences comprised of these haplotypes are expected to match the major structural lineages and groups within the coding and intronic sequences and to contribute to a deeper understanding of the evolution and function of chIL-2 gene. (cgiar.org)
  • Patterns of inter- and intra-group genetic diversity in the Vlax Roma as revealed by Y chromosome and mitochondrial DNA lineages. (le.ac.uk)
  • Paralogous variants can be used effectively for GWAS and were retained in our association SNP data set, but they pose problems for analyses of diversity and were removed from our diversity SNP data set. (sciencemag.org)
  • The purpose of this study was to investigate the association between common variants of HER-2 and breast cancer risk, HER-2 expression, and survival using a haplotype-based stepwise approach. (aacrjournals.org)
  • The RPP5 haplotypes thus carry dynamic gene clusters with the potential to adapt rapidly to novel pathogen variants by gene duplication and modification of recognition capacity. (plantcell.org)
  • so, unlike autosomal haplotypes, there is effectively not any randomisation of the Y-chromosome haplotype between generations. (wikipedia.org)
  • CONCLUSIONS Our data suggest that genotypes comprising specific pairs of RET haplotypes are associated with predisposition to HSCR either in a simple autosomal recessive manner or in an additive, dose dependent fashion. (bmj.com)
  • The topology of a median-joining network analysis including 286 European, Iberian, Atlantic and SCA mitochondrial sequences was very complex, with most of the haplotypes forming part of independent small clusters. (nih.gov)
  • 2001) Blocks of limited haplotype diversity revealed by high‐resolution scanning of human chromosome 21. (els.net)
  • It is thought that identifying these statistical associations and few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (wikipedia.org)
  • In 545 Pseudomonas aeruginosa strains, mainly collected from patients with cystic fibrosis, SpeI-DraI macrorestriction fragment length diversity was scanned for using probes of known map position on the P. aeruginosa PAO chromosome. (nih.gov)
  • The Guinea-Bissau Y chromosome pool is characterized by low haplogroup diversity (D = 0.470, sd 0.033), with the predominant haplogroup E3a*-M2 shared among the ethnic clusters and reaching a maximum of 82.2% in the Mandenka people. (biomedcentral.com)
  • Recombination and haplotype structure over a 3‐Mb region of human chromosome 20. (els.net)
  • Six or five haplotypes were present at frequencies greater than 5% in AA or EA, respectively. (nature.com)
  • PCR-RFLP of three intergenic regions revealed five haplotypes. (usda.gov)
  • Allele frequencies, gene diversities and haplotype frequencies were analyzed. (scirp.org)
  • Haplotype frequencies were analyzed with the EM algorithm implemented in PLINK. (beds.ac.uk)
  • HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. (openrepository.com)
  • begingroup$ No, unless you have the distribution of haplotype frequencies. (stackexchange.com)
  • Conversely, we found a prominent cluster including Canarian, Chilean, Argentinian and Bolivian mitochondrial haplotypes. (nih.gov)
  • Zhang K, Calabrese P, Nordborg M and Sun F (2002) Haplotype block structure and its applications to association studies: power and study designs. (els.net)
  • Haplotype networks generated by maximum-likelihood and neighbor-joining analyses of both the separate and the combined sequence data sets suggested the existence of two main clades of Testudo graeca , comprising Testudo graeca from northern Africa and Testudo graeca from the Turkey and the Middle East, respectively. (biomedcentral.com)
  • According to sequence analyses of the bg gene region, all isolates were identified as G. duodenalis assemblage B. Haplotype analyses revealed 2 known and 8 novel haplotypes for G. duodenalis assemblage B. This study provides first prevalence and genetic and haplotype diversity data on G. duodenalis assemblage B from cats in Turkey. (allenpress.com)
  • Similar to H. claudia, CO1 minimum spanning networks for H. ornatissimus show a star like pattern dominated by a single haplotype (Fig. 2b). (nih.gov)
  • Finally, in a previous study (Additional file 2), Spanish wolves had the largest number (5) of haplotypes with greatest similarity to the SDH whereas Israeli wolves had only a single haplotype closely related to the SDH. (biomedcentral.com)
  • 2) Frequencies of KIR gene haplotypes: there were 13 haplotypes detected in 87 Han individuals, among them, the most frequent one was type 2 (haplotypeA-2DS4). (mskcc.org)
  • In patients with at least one copy of haplotype I (the most common haplotype), HER-2 expression was 1.5 times higher ( P = 0.009) and the prognosis was worse ( P = 0.032) compared with patients without having that haplotype. (aacrjournals.org)
  • Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, with a calculated divergence time in the early or middle Pleistocene. (biomedcentral.com)
  • For these collections, intra-individual haplotype divergence is typically less than 2%, but for 3% of. (usda.gov)
  • Two probes from the auxotroph-poor region detected a broad size range for the SpeI fragment, suggesting extensive genomic diversity in these regions. (nih.gov)
  • Haplotype diversities for each of four Halichoeres species.Haplotype diversities for each of four Halichoeres species with error bars. (nih.gov)
  • This undocumented high level of DRB region configuration-associated diversity most likely represents a species-specific strategy to cope with various pathogens. (springer.com)
  • Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. (genetics.org)
  • Maize is an important crop species of high genetic diversity. (sciencemag.org)
  • Radiations of species into underused habitats are a basic generator of biological diversity, and their results can be observed at all evolutionary depths and in most groups of living organisms ( 1 , 2 ). (sciencemag.org)
  • For scyphozoan and cubozan species, the medusa stage is usually the life stage chosen for investigating global patterns of abundance, distribution, and diversity (Dawson et al. (thefreelibrary.com)
  • 1 This limited degree of genetic diversity was unexpected for a species that, from an evolutionary viewpoint, had its origins millions of years ago. (godandscience.org)
  • The aims of the present study were to examine genetic differences between BJJ and BJT , determine the genetic structure of the Eastern Buzzard, and assess genetic diversity within each subspecies. (bioone.org)
  • Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. (pnas.org)
  • These differences accompany human-specific evolution of the A and B haplotypes that are under balancing selection and differentially function in defense and reproduction. (prolekare.cz)
  • Sun X, Stephens JC and Zhao H (2004) The impact of sample size and marker selection on the study of haplotype structures. (els.net)
  • Haplotype diversity is controlled by a variety of processes, including mutation, recombination, marker ascertainment and demography. (semanticscholar.org)
  • Thus, an environmentally sustainable grape-growing industry will rely on accessing and using the grape's tremendous genetic diversity to develop improved disease-resistant grape cultivars through marker-assisted breeding ( 5 ). (pnas.org)
  • Using 800 bp of the non-coding chloroplast marker accD-rbcL, we compared 21 Japanese haplotypes with 46 US samples from 11 states, 2 Canadian samples, and 6 European samples from 4 countries, in order to investigate if there were repeated introductions from Asia. (springer.com)
  • Whereas the high genetic diversity of msp-3α makes it a promising marker for some epidemiological applications, the ability of msp-3α PCR-RFLP analysis to accurately track parasites is limited. (biomedcentral.com)
  • Daly MJ, Rioux JD, Schaffner SF, Hudson TJ and Lander ES (2001) High‐resolution haplotype structure in the human genome. (els.net)
  • At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. (purdue.edu)
  • The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. (edu.sa)
  • The aim of this study was to elucidate the introduction history of P. mugo in the unique landscape of the Lithuanian seaside spit of Kursiu Nerija by assessing its genetic structure and the genetic diversity. (vdu.lt)
  • Genetic variability and structure of SNP haplotypes in the DMPK gene in Yakuts and other ethnic. (deepdyve.com)
  • BEAGLE, DAGPHASE, and fastPHASE software recognized fewer haplotypes than two other methods. (iastate.edu)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • Therefore, given a set of possible haplotype resolutions, these methods choose those that use fewer different haplotypes overall. (wikipedia.org)
  • 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. (sciencemag.org)
  • rotundata morphotype was assessed based on the haplotype frequencies by hierarchical AMOVA, GST/RST test, UPGMA clustering and PCA methods. (vdu.lt)
  • The objectives of this study were to compare the performance of different haplotype reconstruction approaches, characterize haplotype diversity and identify recombination hotspots on chromosomes 5 and 15 in layer chicken. (iastate.edu)
  • Analysis of further MPL -positive, V617F-negative cases confirmed an excess of 46/1 (n = 176, P = .002), but no association between MPL mutations and MPL haplotype was seen. (bloodjournal.org)
  • An ancestral 5′ recombination event in the chromosomal region between intron 5 and exon 8 has been advocated to explain the origin of haplotype C, which resembles haplotype A at the polymorphic sites in the 5′ region of the gene and resembles the B haplotype in the 3′ region ( 5 ). (diabetesjournals.org)
  • This meta-analysis suggests that the A allele of rs10954213 and TCA haplotype (rs2004640-rs2070197-rs10954213) in IRF5 is associated with the increased risk of SLE in different ethnic groups , and its prevalence is ethnicity dependent. (bvsalud.org)
  • To be useful in genetic analysis, the haplotype should be shorter than a typical block. (els.net)
  • In view of the complexities modulating ACE expression, the case for a thorough haplotype analysis of ACE for association with diabetic nephropathy cannot be underscored. (diabetesjournals.org)
  • In a similar analysis performed with 12 BJT individuals, three haplotypes were detected. (bioone.org)
  • To corroborate this conclusion, we estimated the coalescence of NE1 haplotypes through network analysis (Figure S6) and found a coalescence time of between ~437 K and ~993 K years before present (YBP) for African NE1 haplotypes and ~134 K YBP and ~304 K YBP for European NE1 haplotypes. (blogspot.com)
  • The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. (psu.edu)
  • Already a critical source of food, fuel, feed, and fiber, the addition of genomic information allows maize to be further improved through plant breeding that exploits its tremendous genetic diversity ( 1 - 3 ). (sciencemag.org)
  • A list of projects and resources related to maize diversity is available here . (maizegdb.org)
  • Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. (wikipedia.org)
  • Genotypes comprising pairs of haplotypes were formed for cases and controls. (bmj.com)