Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Linkage Disequilibrium: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Genetic Variation: Genotypic differences observed among individuals in a population.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genetic Association Studies: The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Asian Continental Ancestry Group: Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Amino Acid Sequence: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Adenine NucleotidesEuropean Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Europe.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Homozygote: An individual in which both alleles at a given locus are identical.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Risk Factors: An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.Guanine NucleotidesChina: A country spanning from central Asia to the Pacific Ocean.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Cloning, Molecular: 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.Genotyping Techniques: Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Heterozygote: An individual having different alleles at one or more loci regarding a specific character.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Purine Nucleotides: Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.Sequence Homology, Nucleic Acid: 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.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Sequence Alignment: 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.Pharmacogenetics: A branch of genetics which deals with the genetic variability in individual responses to drugs and drug metabolism (BIOTRANSFORMATION).Odds Ratio: The ratio of two odds. The exposure-odds ratio for case control data is the ratio of the odds in favor of exposure among cases to the odds in favor of exposure among noncases. The disease-odds ratio for a cohort or cross section is the ratio of the odds in favor of disease among the exposed to the odds in favor of disease among the unexposed. The prevalence-odds ratio refers to an odds ratio derived cross-sectionally from studies of prevalent cases.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Methylenetetrahydrofolate Reductase (NADPH2): A flavoprotein amine oxidoreductase that catalyzes the reversible conversion of 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. This enzyme was formerly classified as EC 1.1.1.171.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Cohort Studies: Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics.JapanDNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Guanine Nucleotide Exchange Factors: Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.Amplified Fragment Length Polymorphism Analysis: The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR amplification of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Nucleotides, CyclicEscherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Catechol O-Methyltransferase: Enzyme that catalyzes the movement of a methyl group from S-adenosylmethionone to a catechol or a catecholamine.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Pyrimidine Nucleotides: Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.Genetic Testing: Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Risk: The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome.Genes, Bacterial: The functional hereditary units of BACTERIA.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Minisatellite Repeats: Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Aryl Hydrocarbon Hydroxylases: A large group of cytochrome P-450 (heme-thiolate) monooxygenases that complex with NAD(P)H-FLAVIN OXIDOREDUCTASE in numerous mixed-function oxidations of aromatic compounds. They catalyze hydroxylation of a broad spectrum of substrates and are important in the metabolism of steroids, drugs, and toxins such as PHENOBARBITAL, carcinogens, and insecticides.Glutathione Transferase: A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Xeroderma Pigmentosum Group D Protein: A DNA helicase that is a component of TRANSCRIPTION FACTOR TFIIH. It plays an essential role in NUCLEOTIDE EXCISION REPAIR, and mutations in this protein are associated with XERODERMA PIGMENTOSUM.Diabetes Mellitus, Type 2: A subclass of DIABETES MELLITUS that is not INSULIN-responsive or dependent (NIDDM). It is characterized initially by INSULIN RESISTANCE and HYPERINSULINEMIA; and eventually by GLUCOSE INTOLERANCE; HYPERGLYCEMIA; and overt diabetes. Type II diabetes mellitus is no longer considered a disease exclusively found in adults. Patients seldom develop KETOSIS but often exhibit OBESITY.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Kinetics: The rate dynamics in chemical or physical systems.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Korea: 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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Epistasis, Genetic: A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Age of Onset: The age, developmental stage, or period of life at which a disease or the initial symptoms or manifestations of a disease appear in an individual.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.High-Throughput Nucleotide Sequencing: 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.Glutathione S-Transferase pi: A glutathione transferase that catalyzes the conjugation of electrophilic substrates to GLUTATHIONE. This enzyme has been shown to provide cellular protection against redox-mediated damage by FREE RADICALS.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Peptidyl-Dipeptidase A: A peptidyl-dipeptidase that catalyzes the release of a C-terminal dipeptide, -Xaa-*-Xbb-Xcc, when neither Xaa nor Xbb is Pro. It is a Cl(-)-dependent, zinc glycoprotein that is generally membrane-bound and active at neutral pH. It may also have endopeptidase activity on some substrates. (From Enzyme Nomenclature, 1992) EC 3.4.15.1.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Logistic Models: Statistical models which describe the relationship between a qualitative dependent variable (that is, one which can take only certain discrete values, such as the presence or absence of a disease) and an independent variable. A common application is in epidemiology for estimating an individual's risk (probability of a disease) as a function of a given risk factor.Bacterial Proteins: Proteins found in any species of bacterium.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Gene-Environment Interaction: The combined effects of genotypes and environmental factors together on phenotypic characteristics.Transcription Factor 7-Like 2 Protein: A transcription factor that takes part in WNT signaling pathway. The activity of the protein is regulated via its interaction with BETA CATENIN. Transcription factor 7-like 2 protein plays an important role in the embryogenesis of the PANCREAS and ISLET CELLS.Ethnic Groups: A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Arylamine N-Acetyltransferase: An enzyme that catalyzes the transfer of acetyl groups from ACETYL-COA to arylamines. It can also catalyze acetyl transfer between arylamines without COENZYME A and has a wide specificity for aromatic amines, including SEROTONIN. However, arylamine N-acetyltransferase should not be confused with the enzyme ARYLALKYLAMINE N-ACETYLTRANSFERASE which is also referred to as SEROTONIN ACETYLTRANSFERASE.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Adenosine Diphosphate: Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.African Americans: Persons living in the United States having origins in any of the black groups of Africa.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Breast Neoplasms: Tumors or cancer of the human BREAST.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Chi-Square Distribution: A distribution in which a variable is distributed like the sum of the squares of any given independent random variable, each of which has a normal distribution with mean of zero and variance of one. The chi-square test is a statistical test based on comparison of a test statistic to a chi-square distribution. The oldest of these tests are used to detect whether two or more population distributions differ from one another.Smoking: Inhaling and exhaling the smoke of burning TOBACCO.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Quantitative Trait, Heritable: A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.DNA Fingerprinting: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Guanosine Triphosphate: Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Serotonin Plasma Membrane Transport Proteins: Sodium chloride-dependent neurotransmitter symporters located primarily on the PLASMA MEMBRANE of serotonergic neurons. They are different than SEROTONIN RECEPTORS, which signal cellular responses to SEROTONIN. They remove SEROTONIN from the EXTRACELLULAR SPACE by high affinity reuptake into PRESYNAPTIC TERMINALS. Regulates signal amplitude and duration at serotonergic synapses and is the site of action of the SEROTONIN UPTAKE INHIBITORS.Receptors, Calcitriol: Proteins, usually found in the cytoplasm, that specifically bind calcitriol, migrate to the nucleus, and regulate transcription of specific segments of DNA with the participation of D receptor interacting proteins (called DRIP). Vitamin D is converted in the liver and kidney to calcitriol and ultimately acts through these receptors.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Breeding: The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.IndiaEndonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.EuropeChromosomes, Human, Pair 6: A specific pair GROUP C CHROMSOMES of the human chromosome classification.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Heterozygote Detection: Identification of genetic carriers for a given trait.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.DNA, Neoplasm: DNA present in neoplastic tissue.HapMap Project: A coordinated international effort to identify and catalog patterns of linked variations (HAPLOTYPES) found in the human genome across the entire human population.Loss of Heterozygosity: The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.Genes, Viral: The functional hereditary units of VIRUSES.Colorectal Neoplasms: Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.GuanineBase Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Transition Temperature: The temperature at which a substance changes from one state or conformation of matter to another.Molecular Epidemiology: 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.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Dinucleotide Repeats: The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Valine: A branched-chain essential amino acid that has stimulant activity. It promotes muscle growth and tissue repair. It is a precursor in the penicillin biosynthetic pathway.Genes, Plant: The functional hereditary units of PLANTS.Publication Bias: The influence of study results on the chances of publication and the tendency of investigators, reviewers, and editors to submit or accept manuscripts for publication based on the direction or strength of the study findings. Publication bias has an impact on the interpretation of clinical trials and meta-analyses. Bias can be minimized by insistence by editors on high-quality research, thorough literature reviews, acknowledgement of conflicts of interest, modification of peer review practices, etc.Thymine Nucleotides: Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Cytosine Nucleotides5' Flanking Region: The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.Glucuronosyltransferase: A family of enzymes accepting a wide range of substrates, including phenols, alcohols, amines, and fatty acids. They function as drug-metabolizing enzymes that catalyze the conjugation of UDPglucuronic acid to a variety of endogenous and exogenous compounds. EC 2.4.1.17.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.Prognosis: A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

Ancestral origins and worldwide distribution of the PRNP 200K mutation causing familial Creutzfeldt-Jakob disease. (1/26608)

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

Linkage disequilibrium at the ADH2 and ADH3 loci and risk of alcoholism. (2/26608)

Two of the three class I alcohol dehydrogenase (ADH) genes (ADH2 and ADH3) encode known functional variants that act on alcohol with different efficiencies. Variants at both these genes have been implicated in alcoholism in some populations because allele frequencies differ between alcoholics and controls. Specifically, controls have higher frequencies of the variants with higher Vmax (ADH2*2 and ADH3*1). In samples both of alcoholics and of controls from three Taiwanese populations (Chinese, Ami, and Atayal) we found significant pairwise disequilibrium for all comparisons of the two functional polymorphisms and a third, presumably neutral, intronic polymorphism in ADH2. The class I ADH genes all lie within 80 kb on chromosome 4; thus, variants are not inherited independently, and haplotypes must be analyzed when evaluating the risk of alcoholism. In the Taiwanese Chinese we found that, only among those chromosomes containing the ADH3*1 variant (high Vmax), the proportions of chromosomes with ADH2*1 (low Vmax) and those with ADH2*2 (high Vmax) are significantly different between alcoholics and controls (P<10-5). The proportions of chromosomes with ADH3*1 and those with ADH3*2 are not significantly different between alcoholics and controls, on a constant ADH2 background (with ADH2*1, P=.83; with ADH2*2, P=.53). Thus, the observed differences in the frequency of the functional polymorphism at ADH3, between alcoholics and controls, can be accounted for by the disequilibrium with ADH2 in this population.  (+info)

Variegate porphyria in Western Europe: identification of PPOX gene mutations in 104 families, extent of allelic heterogeneity, and absence of correlation between phenotype and type of mutation. (3/26608)

Variegate porphyria (VP) is a low-penetrance, autosomal dominant disorder characterized clinically by skin lesions and acute neurovisceral attacks that occur separately or together. It results from partial deficiency of protoporphyrinogen oxidase encoded by the PPOX gene. VP is relatively common in South Africa, where most patients have inherited the same mutation in the PPOX gene from a common ancestor, but few families from elsewhere have been studied. Here we describe the molecular basis and clinical features of 108 unrelated patients from France and the United Kingdom. Mutations in the PPOX gene were identified by a combination of screening (denaturing gradient gel electrophoresis, heteroduplex analysis, or denaturing high-performance liquid chromatography) and direct automated sequencing of amplified genomic DNA. A total of 60 novel and 6 previously reported mutations (25 missense, 24 frameshift, 10 splice site, and 7 nonsense) were identified in 104 (96%) of these unrelated patients, together with 3 previously unrecognized single-nucleotide polymorphisms. VP is less heterogeneous than other acute porphyrias; 5 mutations were present in 28 (26%) of the families, whereas 47 mutations were restricted to 1 family; only 2 mutations were found in both countries. The pattern of clinical presentation was identical to that reported from South Africa and was not influenced by type of mutation. Our results define the molecular genetics of VP in western Europe, demonstrate its allelic heterogeneity outside South Africa, and show that genotype is not a significant determinant of mode of presentation.  (+info)

Multi-forms of human MTH1 polypeptides produced by alternative translation initiation and single nucleotide polymorphism. (4/26608)

The human MTH1 gene for 8-oxo-7,8-dihydrodeoxyguanosine triphosphatase, produces seven types (types 1, 2A, 2B, 3A, 3B, 4A and 4B) of mRNAs. The B-type mRNAs with exon 2b-2c segments have three additional in-frame AUGs in their 5' regions. We report here that these transcripts produce three forms of MTH1 polypeptides (p22, p21 and p18) in in vitro translation reactions. Three polypeptides were also detected in extracts of human cells, using western blotting. B-type mRNAs with a polymorphic alteration (GU-->GC) at the beginning of exon 2c that converts an in-frame UGA to CGA yielding another in-frame AUG further upstream, produced an additional polypeptide (p26) in vitro. Substitution of each AUG abolished the production of each corresponding polypeptide. Cell lines from individuals with the GC allele contain more B-type mRNAs than do those of GT homozygotes, and the former produce all of four polypeptides but the latter lack p26. Amounts of each polypeptide reflected copy number of the GC allele in each cell line. There is an apparent linkage dis-equilibrium between the two polymorphic sites, GT/GC at exon 2c and Val83/Met83 at codon 83 for p18.  (+info)

Is selection responsible for the low level of variation in the last intron of the ZFY locus? (5/26608)

DNA variability was investigated in the last intron of the Y-chromosome-specific zinc finger gene, ZFY, and its X homolog on Xp21.3, ZFX. No polymorphisms were found in the 676-bp ZFY segment in a sample of 205 world-wide-distributed Y chromosomes, other than a solitary nucleotide variant in one individual (nucleotide diversity pi = 0.0014%). In contrast, 10 segregating sites (pi = 0.082%) were identified within 1,089 bp of the ZFX sequence in a sample of 336 X chromosomes. Four of these polymorphisms, which contributed most of the diversity, were located within an Alu insert disrupting the ZFY-ZFX homology (pi Alu = 0.24%). The diversity in the homologous portion of the ZFX intron, although higher than that in ZFY, was lower than that found in genomic segments believed to evolve neutrally; interspecies divergence in both segments was also reduced. Although this suggests that the evolution of both ZFY and ZFX homologs may not be entirely neutral, both Tajima and HKA tests did not reject neutrality. The lack of statistical significance may be attributed to a lack of power in these tests (the low divergence and variability values reduce the power of the HKA and Tajima tests, respectively); furthermore, Homo sapiens has recently undergone a rapid population growth, and selection is more difficult to detect in an expanding population. Therefore, the failure to reject neutrality does not necessarily indicate the absence of selection. In this context, the phylogenetic argument was given more weight in out interpretations. The high level of sequence identity in ZFY and ZFX segments, in spite of their separation 80-130 MYA, reflects a lower mutation rate as compared with other segments believed to undergo unconstrained evolution. Thus, the possibility of weak selection contributing to the low level of nucleotide diversity in the last ZFY intron cannot be excluded and should be kept in mind in the population genetics studies based on Y chromosome variability.  (+info)

Spectrum of hSNF5/INI1 somatic mutations in human cancer and genotype-phenotype correlations. (6/26608)

The hSNF5/INI1 gene which encodes a member of the SWI/SNF chromatin ATP-dependent remodeling complex, is a new tumor suppressor gene localized on chromosome 22q11.2 and recently shown to be mutated in malignant rhabdoid tumors. We have searched for hSNF5/INI1 mutations in 229 tumors of various origins using a screening method based on denaturing high-performance liquid chromatography. A total of 31 homozygous deletions and 36 point alterations were identified. Point mutations were scattered along the coding sequence and included 15 nonsense, 15 frameshift, three splice site, two missense and one editing mutations. Mutations were retrieved in most rhabdoid tumors, whatever their sites of occurrence, indicating the common pathogenetic origin of these tumors. Recurrent hSNF5/INI1 alterations were also observed in choroid plexus carcinomas and in a subset of central primitive neuroectodermal tumors (cPNETs) and medulloblastomas. In contrast, hSNF5/INI1 point mutations were not detected in breast cancers, Wilms' tumors, gliomas, ependymomas, sarcomas and other tumor types, even though most analyzed cases harbored loss of heterozygosity at 22q11.2 loci. These results suggest that rhabdoid tumors, choroid plexus carcinomas and a subset of medulloblastomas and cPNETs share common pathways of oncogenesis related to hSNF5/INI1 alteration and that hSNF5/INI1 mutations define a genetically homogeneous family of highly aggressive cancers mainly occurring in young children and frequently, but not always, exhibiting a rhabdoid phenotype.  (+info)

DNA transport by a micromachined Brownian ratchet device. (7/26608)

We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50-mer agree with theoretical predictions, and the DNA diffusion constant agrees with previous experiments. This type of micromachine could provide a generic pump or separation component for DNA or other charged species as part of a microscale lab-on-a-chip. A device with reduced feature size could produce a size-based separation of DNA molecules, with applications including the detection of single-nucleotide polymorphisms.  (+info)

Direct sequencing of bacterial and P1 artificial chromosome-nested deletions for identifying position-specific single-nucleotide polymorphisms. (8/26608)

A loxP-transposon retrofitting strategy for generating large nested deletions from one end of the insert DNA in bacterial artificial chromosomes and P1 artificial chromosomes was described recently [Chatterjee, P. K. & Coren, J. S. (1997) Nucleic Acids Res. 25, 2205-2212]. In this report, we combine this procedure with direct sequencing of nested-deletion templates by using primers located in the transposon end to illustrate its value for position-specific single-nucleotide polymorphism (SNP) discovery from chosen regions of large insert clones. A simple ampicillin sensitivity screen was developed to facilitate identification and recovery of deletion clones free of transduced transposon plasmid. This directed approach requires minimal DNA sequencing, and no in vitro subclone library generation; positionally oriented SNPs are a consequence of the method. The procedure is used to discover new SNPs as well as physically map those identified from random subcloned libraries or sequence databases. The deletion templates, positioned SNPs, and markers are also used to orient large insert clones into a contig. The deletion clone can serve as a ready resource for future functional genomic studies because each carries a mammalian cell-specific antibiotic resistance gene from the transposon. Furthermore, the technique should be especially applicable to the analysis of genomes for which a full genome sequence or radiation hybrid cell lines are unavailable.  (+info)

Table_2_Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates.xlsx
The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of
Henry, RJ, Bundock, PC, Pacey-Miller, T, Kennedy, BG, Ablett, GA, Waters, DLE & Jin,QS 2003, Single nucleotide polymorphism analysis in support of plant breeding, paper presented to the 12th Australasian Plant Breeding Conference, Perth, WA, 15-20 September.. ...
The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference. The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection. We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 ...
Read "Associations between three common single nucleotide polymorphisms (rs266729, rs2241766, and rs1501299) of ADIPOQ and cardiovascular disease: a meta-analysis, Lipids in Health and Disease" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Recent technological progress has permitted the efficient performance of genome-wide association studies (GWAS) to map genetic variants associated with common diseases. Here, we analyzed 2,893 single nucleotide polymorphisms (SNPs) that have been identified in 593 published GWAS as associated with a disease phenotype with respect to their genomic location. In absolute numbers, most significant SNPs are located in intergenic regions and introns. When compared to their representation on the chips, there is essentially overrepresentation of nonsynonymous coding SNPs (nsSNPs), synonymous coding SNPs, and SNPs in untranscribed regions upstream of genes among the disease associated SNPs. A Gene Ontology term analysis showed that genes putatively causing a phenotype often code for membrane associated proteins or signal transduction genes.. ...
Pharmacological potency, side effect, and kinetics in body are influenced by single nucleotide polymorphisms of genes encoding key proteins controlling drugs
In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers ...
Coronary Heart Disease (CHD) is one of the leading causes of death in the world with a projected global 82 million DALYs by 2020. Genetic and environmental factors contribute to CHD development. Here, the authors investigate the association between CHD risk and three Single Nucleotide Polymorphisms (SNPs) in the AdipoQ gene (rs3774261, rs1063537 and rs2082940); and the interaction of this association with environmental factors, in Northeast Han Chinese population. Using a case-control study design, 1514 participants (754 cases and 760 controls) were investigated. Three variants in the AdipoQ gene (rs3774261, rs1063537 and rs2082940) were selected and genotyped. The online SNPstats program and SPSS 21.0 software were used for data analyses. The authors found that the rs3774261G allele is associated with the risk of CHD but that the rs2082940T allele protects against CHD. No significant association was found between rs1063537 and CHD risk. The study also found significant interactions between triglyceride
We questioned the significance of haplotype structure in gene regulation by testing whether individual single nucleotide polymorphisms (SNPs) within a gene promoter region [interleukin-1-beta (IL1B)] might affect promoter function and, if so, whether function was dependent on haplotype context. We sequenced genomic DNA from 25 individuals of diverse ethnicity, focusing on exons and upstream flanking regions of genes of the cluster. We identified four IL1B promoter region SNPs that were active in transient transfection reporter gene assays. To substantiate allelic differences found in reporter gene assays, we also examined nuclear protein binding to promoter sequence oligonucleotides containing different alleles of the SNPs. The effect of individual SNPs on reporter gene transcription varied according to which alleles of the three other SNPs were present in the promoter construct. The SNP patterns that influenced function reflected common haplotypes that occur in the population, suggesting ...
Genome‐wide association studies have successfullyidentified many novel genetic loci for various human complex diseases and quantitative traits
TABLE-US-00003 TABLE 3 SNPs associated with adolescent idiopathic scoliosis Case Control Allele1/2 Genotype count Genotype count Odds ratiob dbSNP ID Risk Study 11 12 22 RAF 11 12 22 RAF P valuea (95% CI) Pheic rs11190870 T/C GWAS 449 470 114 0.662 479 728 266 0.572 1.27.E-10 1.46 (1.30-1.65) T Replication 152 148 26 0.693 3129 4809 1883 0.563 5.13.E-11 1.75 (1.48-2.07) Combinedd 601 618 140 0.670 3608 5537 2149 0.565 1.24.E-19 1.56 (1.41-1.71) 0.0881 rs625039 G/A GWAS 533 424 76 0.721 600 695 178 0.643 4.75.E-09 1.43 (1.27-1.62) G Replication 172 135 19 0.735 1297 4579 3947 0.635 1.69.E-07 1.59 (1.34-1.90) Combinedd 705 559 95 0.724 1475 5274 4547 0.636 4.30.E-15 1.49 (1.35-1.65) 0.341 rs11598564 A/G GWAS 297 508 228 0.533 310 724 439 0.456 9.40.E-08 1.36 (1.22-1.53) G Replication 107 156 63 0.567 2107 4837 2879 0.461 8.82.E-08 1.54 (1.31-1.80) Combinedd 404 664 291 0.542 2417 5531 3318 0.46 5.98.E-14 1.42 (1.30-1.56) 0.226 Allele 1 represents major allele. Allele 1/2 is shown according to (+) ...
Novel Single Nucleotide Polymorphisms and Combinations of Novel and Known Polymorphisms for Determining the Allele-Specific Expression of the IGF2 Gene - diagram, schematic, and image 42 ...
Introduction: Inherited susceptibility to lung cancer risk in never-smokers is poorly understood. The major reason for this gap in knowledge is that this disease is relatively uncommon (except in Asians), making it difficult to assemble an adequate study sample. In this study we conducted a genome-wide association study on the largest, to date, set of European-descent never-smokers with lung cancer. Methods: We conducted a two-phase (discovery and replication) genome-wide association study in never-smokers of European descent. We further augmented the sample by performing a meta-analysis with never-smokers from the recent OncoArray study, which resulted in a total of 3636 cases and 6295 controls. We also compare our findings with those in smokers with lung cancer. Results: We detected three genome-wide statistically significant single nucleotide polymorphisms rs31490 (odds ratio [OR]: 0.769, 95% confidence interval [CI]: 0.722-0.820; p value 5.31 x 10(-16)), rs380286 (OR: 0.770, 95% CI: ...
BACKGROUND Non-synonymous single nucleotide polymorphisms (SNPs) within vital DNA repair genes may cause reduction of activity leaving the genome unrepaired resulting in genomic instability and cancer. MATERIALS AND METHODS The present endeavour involved study on the association of the SNP rs13181 (Lys751Gln/A18911C) in the Nucleotide Excision Repair (NER) pathway gene ERCC2 (excision repair cross-complementing rodent repair deficiency, complementation group 2) with the risks of Squamous Cell Carcinomas of the Head and Neck (SCCHN) and Breast cancer using a case-control based association study among 685 (400 controls and 285 SCCHN-affected cases) and 395 (227 normal healthy female controls and 168 breast cancer cases) ethnically-matched samples, respectively from north India using Polymerase Chain Reaction followed by Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. RESULTS Results showed significant association of rs13181 homozygous mutant (CC) [Odds Ratio (OR) 4.412, 95% Confidence
Objective: The objective of this study is to determine the associations among genetic variations in the P2X7 receptor gene, decreased bone mineral density (BMD), and the risk of osteoporosis in patients aged older than 50 years with ankle fractures. Methods: Patients were genotyped for 15 nonsynonymous single-nucleotide polymorphisms (SNPs) in the P2X7 gene. The sample was divided into two groups according to the bone densitometry results: an intervention group with osteopenia (T scores between -1.0 and -2.5) or osteoporosis (T scores ≤ -2.5) and a control group with values within the normal range (T scores ≥ -1). A total of 121 patients were evaluated: 65 in the intervention group and 56 in the control group. Results: The results suggested that SNPs 1, 4, 11, 13, 14, and 15 were loss-of-function (LOF) variants. SNP 12 was also associated with LOF in our population, but its RNA expression has not been analyzed to date. Conclusions: In conclusion, we demonstrate that functional polymorphisms ...
Detecting causal single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) has been focusing on measuring the statistical power of single SNPs, which have a relatively small effect on predicting disease susceptibility and ignore prior biological information about the target disease. Especially in complex diseases such as type 2 diabetes (T2D), the effect of each single SNP is too small to explain the disease association significantly.. To enhance the statistical power, we propose considering combinations of SNPs. Yang et al. discovered that estimates of variance explained by genome-wide SNPs are unbiased with the proportion of SNPs used to estimate genetic relationships in human height [1]. Although SNPs with relatively low statistical power are considered together, the statistical power is not significantly affected. In addition, Park et al. compared the discriminatory power of the risk models in Crohns disease and prostate and colorectal (BPC) cancer and found that a ...
TY - JOUR. T1 - An investigation of modifying effects of single nucleotide polymorphisms in metabolism-related genes on the relationship between peripheral nerve function and mercury levels in urine and hair. AU - ​Wang, ​Yi AU - Goodrich, Jaclyn M.. AU - Werner, Robert. AU - Gillespie, Brenda. AU - Basu, Niladri. AU - Franzblau, Alfred. PY - 2012/2/15. Y1 - 2012/2/15. N2 - Mercury (Hg) is a potent neurotoxicant. We hypothesized that single nucleotide polymorphisms (SNPs) in genes coding glutathione-related proteins, selenoproteins and metallothioneins may modify the relationship of mercury biomarkers with changes in peripheral nerve function. Dental professionals (n = 515) were recruited in 2009 and 2010. Sensory nerve function (onset latency, peak latency and amplitude) of the median, ulnar and sural nerves was recorded. Samples of urine, hair and DNA were collected. Covariates related to demographics, nerve function and elemental and methyl-mercury exposure were also collected. Subjects ...
A number of previous studies suggested the presence of deleterious amino acid altering nonsynonymous single-nucleotide polymorphisms (nSNPs) in human populations. However, the proportions of deleterious nSNPs among rare and common variants are not known. To estimate these, ,77?000 SNPs from human protein-coding genes were analyzed. Based on two independent methods, this study reveals that up to 53% of rare nSNPs (minor allele frequency (MAF),0.002) could be deleterious in nature. The fraction of deleterious nSNPs declines with the increase in their allele frequencies and only 12% of the common nSNPs (MAF,0.4) were found to be harmful. This shows that even at high frequencies significant fractions of deleterious polymorphisms are present in human populations. These results could be useful for genome-wide association studies in understanding the relative contributions of rare and common variants in causing human genetic diseases ...
The vast majority of drugs act through binding to their protein targets. Prediction of the interaction between small molecules and these receptors is a key elem...
Researchers believe there are some 10 million common SNPs in the human genome. Scanning the genomes of large numbers of patients for such a large number of variants would be prohibitively expensive. Fortunately, a major shortcut has been discovered that reduces the workload about 30-fold. When the International HapMap Project was completed in October 2005, the researchers demonstrated that the 10 million variants cluster into local neighborhoods, called haplotypes, and that they can be accurately sampled by as few as 300,000 carefully chosen SNPs. New technological systems allow these SNPs to be systematically studied in high-throughput facilities that dramatically lower the cost.. In genome-wide association studies, researchers compare the genomes of people with an illness, who are referred to as cases, to unaffected people, who are referred to as controls. Through this comparison, it becomes possible to identify the genetic differences between sick and healthy people, even when the genetic ...
TY - JOUR. T1 - Association of single nucleotide polymorphisms in SOD2, XRCC1 and XRCC3 with susceptibility for the development of adverse effects resulting from radiotherapy for prostate cancer. AU - Burri, Ryan J.. AU - Stock, Richard G.. AU - Cesaretti, Jamie A.. AU - Atencio, David P.. AU - Peters, Sheila. AU - Peters, Christopher A.. AU - Fan, Grace. AU - Stone, Nelson N.. AU - Ostrer, Harry. AU - Rosenstein, Barry S.. PY - 2008/7. Y1 - 2008/7. N2 - The objective of this study was to determine whether an association exists between certain single nucleotide polymorphisms (SNPs), which have previously been linked with adverse normal tissue effects resulting from radiotherapy, and the development of radiation injury resulting from radiotherapy for prostate cancer. A total of 135 consecutive patients with clinically localized prostate cancer and a minimum of 1 year of follow-up who had been treated with radiation therapy, either brachytherapy alone or in combination with external-beam ...
To the Editors:. Asthma is a complex disease characterised by inflammation and remodelling of the airways. Over the past few decades enormous progress has been made to understand which genes are associated with asthma development and several interactions between genes and environmental factors have been elucidated. Investigations into genetic and gene expression profiling, as well as single nucleotide polymorphism analyses, have helped to better understand the underlying molecular mechanisms of asthma. However, the recent identification of novel regulatory functions for transposable and transposed genetic elements (TEs) may be an important and new key to help understand the genetics that cause the heterogeneous manifestations of the asthma pathology.. Approximately 45% of the human genome is made of TEs [1]. The vast majority of TEs originate from retrotransposition of genetic elements known as short and long interspersed nuclear elements, long terminal repeat-superfamilies and direct ...
... One of the most significant outcomes of the Human Genome Project has been the iden- tification of large numbers of single nucleotide polymorphisms (SNPs) [1-3]. The ap-plication ...
Çfarë janë SNP-te - single nucleotide polymorphisms? Polimorfizmi i një nukleotidi te vetëm, te quajtur shpesh SNP (single nucleotide polymorphisms) janë lloji i variacionit me i shpeshte midis njerezve. Çdo SNP përfaqëson një diference ne një njësi te vetme te ADN-së, te quajtur nukleotid. Për shembull, një SNP mund te zevendesoje nukleotidin citozinë (C) me…
Beth Robb awarded the Stephen J. OBrien Award for the best student paper published in the Journal of Heredity for the paper Robb, E.A., C.L. Gitter, H. Cheng and M.E. Delany. 2011. Single nucleotide polymorphism analysis of chicken genetic resources: Variation within and among MHC-congenic lines and mapping of developmental mutations. J. Heredity 102:141-156. (cover art ...
Single nucleotide polymorphisms, frequently called SNPs are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block called a nucleotide. SNPs occur normally throughout a persons DNA. They occur in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in a disease by affecting the genes function. It has been proposed that SNPs may help predict an individuals response to certain drugs, susceptibility to environmental factors such as toxins and risk of developing particular diseases such as cancer.. SNPs, which are single base-pair variations in the DNA sequence of the genome, have been found to be associated with breast cancer ...
OLIVEIRA, Martha Maria de et al. Single Nucleotide Polymorphisms (SNPs) of the TNF-a (-238/-308) gene among TB and nom TB patients: susceptibility markers of TB occurrence?. J. bras. pneumol. [online]. 2004, vol.30, n.4, pp.371-377. ISSN 1806-3713. https://doi.org/10.1590/S1806-37132004000400012.. BACKGROUND: Host genetic factors may play a role in the susceptibility to active tuberculosis (TB), and several polymorphisms in different cytokine coding genes have been described and associated with diseases to date. OBJECTIVES: To investigate whether polymorphisms within the promoter region of the TNF-a (-238/-308) coding genes are associated to the occurrence of active TB. METHODS: SNPs within the TNF-a gene were analyzed by PCR-RFLP among two groups of individuals: patients with TB (n = 234, and patients non TB (n = 113). RESULTS: In this study, the presence of the -238A allele was associated with susceptibility to TB disease occurrence and severity (p = 0,00002; OR = 0,15; IC = 0,06-0,36. On the ...
A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n = 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B*57:03 [odds ratio (OR) = 5.1; P= 3.4 × 10(-18)] and B*81:01 (OR = 4.8; P= 1.3 × 10(-9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P = 1.2 × 10(-21)) and explains ...
Purpose: MicroRNAs regulate gene expression by binding to the 3′‐untranslated region (UTR) of target genes. Single‐nucleotide polymorphisms of critical genes may affect their regulation by microRNAs. We have identified a single nucleotide polymorphism within the miR‐502 seed binding region in the 3′‐UTR of the SET8 gene. SET8 methylates TP53 and regulates genome stability. We investigated the role of this SET8 single nucleotide polymorphism and in concert with the TP53 codon72 single nucleotide polymorphism in the propensity for onset of breast cancer.. Experimental Design: We measured the SET8 single nucleotide polymorphisms in a case‐control study on 1110 breast cancer cases and 1097 controls.. Results: The SET8 CC and TP53 GG genotypes were independently associated with an earlier age of breast cancer onset in an allele‐dose‐dependent manner (for SET8, 52.2 years for TT, 51.4 for TC, and 49.5 for CC; and for TP53, 53.1 years for CC, 51.5 for GC, 50.7 for GG). Individuals ...
IL-33, an IL-1-like cytokine, is a ligand for IL1RL1, which is an important effector molecule of type 2 T helper responses. Although IL-33/IL1RL1 interaction has been suggested to be important in the development of atherosclerosis, genetic influences of the polymorphisms of IL33 in human ischemic stroke are unclear. The aim of this study was to examine whether the single nucleotide polymorphisms in IL33 are associated with ischemic stroke in Northern Chinese population. We used a nested case-control study involving 90 ischemic stroke patients and 270 age-matched, sex-matched and blood pressure-matched non-ischemic stroke controls from a rural population and determined the genotypes of four polymorphisms (rs1929992, rs10975519, rs4742170, rs16924159) in IL33 by Snapshot SNP genotyping assays to assess any links with ischemic stroke. Univariate analysis showed two single nucleotide polymorphisms (rs1929992, rs4742170) in IL33 were associated with ischemic stroke in additive, dominant, and recessive model.
Background and Purpose: Ischemic stroke (IS) shares many common risk factors with coronary artery disease (CAD). We hypothesized that genetic variants associated with myocardial infarction (MI) or CAD may be similarly involved in the etiology of IS. To test this hypothesis, we evaluated whether single-nucleotide polymorphisms (SNPs) at 11 different loci recently associated with MI or CAD through genome-wide association studies were associated with IS.. Methods: Meta-analyses of the associations between the 11 MI-associated SNPs and IS were performed using 6865 cases and 11 395 control subjects recruited from 9 studies. SNPs were either genotyped directly or imputed; in a few cases a surrogate SNP in high linkage disequilibrium was chosen. Logistic regression was performed within each study to obtain study-specific βs and standard errors. Meta-analysis was conducted using an inverse variance weighted approach assuming a random effect model.. Results: Despite having power to detect odds ratio of ...
Background Polymorphisms in nitric oxide synthase genes (NOS1, NOS2, and NOS3) have been suggested to have a major impact on fraction of exhaled nitric oxide (FENO), a biomarker of airway inflammation. However, the genetic contribution of NOS polymorphisms to FENO is not fully understood. The aim of this study was to investigate comprehensively the association between single nucleotide polymorphisms (SNPs) in all three NOS genes and FENO in an adult population, and to assess whether such associations are modified by asthma or atopy.. Method In 1737 adults from a Swedish general population sample, FENO was measured and genetic variation in the NOS genes was assessed using 49 SNPs. The genetic effect of NOS polymorphisms on FENO, asthma, and atopy was estimated using multiple regression methods.. Results In a multi-SNP model based on stepwise regression analysis, two SNPs in NOS2 and one in NOS3 showed independent associations with levels of FENO. For NOS2 SNP rs9901734, subjects had 5.3% (95% CI ...
Single nucleotide polymorphisms (SNPs) are single nucleotide variations which comprise the most wide spread source of genetic diversity in the genome. Currently, SNPs serve as markers for genetic predispositions, clinically evident disorders and diverse drug responses. Present SNP diagnostics are primarily based on enzymatic reactions in different formats including sequencing, polymerase-chain reaction (PCR) and microarrays. In these assays, the enzymes are applied to address the required sensitivity and specificity when detecting SNP. On the other hand, the development of enzyme-free, simple and robust SNP sensing methods is in a constant focus in research and industry as such assays allow rapid and reproducible SNP diagnostics without the need for expensive equipment and reagents. An ideal method for detection of SNP would entail mixing a DNA or RNA target with a probe to directly obtain a signal. Current assays are still not fulfilling these requirements, although remarkable progress has been
Heres the definition of an SNP …. "Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.. SNPs occur normally throughout a persons DNA. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the genes function.. Most SNPs have no effect on health or development. Some of these genetic differences, however, have proven to be very important in the study ...
The increasing interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) emphasis the need for high-throughput and cost effective scoring methods. Pyrosequencing is a novel method for screening SNPs. In this study we examine breed specific SNPs in the pig melanocortin I receptor gene (MC1R), some causing coat color phenotypes. A total of fifteen pigs representing eight breeds and crosses were analyzed by pyrosequencing. In addition to nine previously known SNPs, we also detected one new missense mutation by pyrosequencing. We here show that the SNPs were readily scored using standard reaction conditions. Insertions as well as substitutions were unambiguously detected and all genotypes were resolved in terms of homo- and heterozygozity.. ...
A Single Nucleotide Polymorphism or SNP (pronounced snip) is a DNA sequence variation, occurring when a single nucleotide: adenine (A), thymine (T), cytosine (C) or guanine (G) - in the genome is altered. A variation must occur in at least 1% of the population to be considered a SNP. SNPs make up 90% of all human genetic variations, and occur every 100 to 300 bases along the human genome. Two of every three SNPs substitute Cytosine (C) with Thymine (T). Variations in the DNA sequences of humans can affect how humans handle diseases, bacteria, viruses, chemicals, drugs, etc. SNPs are of great value to biomedical research and in developing pharmacy products. Because SNPs do not change much from generation to generation, following them during population studies is straightforward. SNPs are generally considered to be a form of point mutation that has been evolutionarily successful enough to recur in a significant proportion of a species population. ...
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mers potential for protein binding in a specific cell type and how this may be changed by sequence variants. Therefore, Sasquatch uses an unbiased approach, independent of known transcription factor binding sites and motifs. Sasquatch only requires a single DNase-seq data set per cell type, from any genotype, and produces consistent predictions from data generated by different experimental procedures and at
BackgroundThe Bcl-2-associated X protein (Bax) is a proapoptotic member of the Bcl-2 family known to be activated and upregulated during apoptosis. Single nucleotide polymorphisms (SNPs) in Bax promoter may participate in the process of carcinogenesis by altering its own expression and the cancer related genes. Bax-248G|A polymorphism has been implicated to alter the risk of cancer, but the listed results are inconsistent and inconclusive. In the present study, we performed a meta-analysis to systematically summarize the possible association of this polymorphism with the risk of cancer. MethodologyWe conducted a search of case-control studies on the associations of Bax-248G|A polymorphism with susceptibility to cancer in Pub Med, Science Direct, Wiley Online Library and hand search. Data from all eligible studies based on some key search terms, inclusion and exclusion criteria were extracted for this meta-analysis. Hardy-Weinberg equilibrium (HWE) in controls, power calculation, heterogeneity analysis
DUGi: Viewing Item from repository Recercat: Delta-like 1 homolog (DLK1) gene encodes a transmembrane protein containing epidermal growth factor-like repeats that promotes the induction of mesenchymal cells but prevents chondrocyte, preadipocytes and osteoblast maturation and differentiation. Rs1802710 polymorphism situated in the fifth exon of DLK1, shows a significant parent-of-origin effect reflecting the known silencing of the maternally inherited copy by imprinting. In humans, a more frequent paternal transmission of the paternal allele in the rs1802710 polymorphism of DLK1 on obese children has been noticed. We aimed to study the single nucleotide polymorphism (SNP) rs1802710 of the DLK1 gene and its effects on early life development. Due to the known imprinting effect surrounding the DLK1 locus, we wanted to analyze whether these changes were different depending on the parental origin of the transmitted rs1802710 variant T allele. Therefore, a longitudinal study has been done from the beginning
Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.). Topics covered include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; controlling population admixture (genomic control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate ...
We appreciate the interest of Dr Frau et al1 in our genome-wide association analysis of blood pressure response to the angiotensin II receptor antagonist, candesartan, in which single nucleotide polymorphism associations were validated by demonstrating opposite direction associations with blood pressure response to the thiazide diuretic, hydrochlorothiazide.2 In lieu of multiple, independent same-race candesartan-treated samples available for replication analyses, this approach to single nucleotide polymorphism validation was motivated by the observation that all known predictors of blood pressure response to inhibitors of the renin-angiotensin system (eg, plasma renin activity, race, and age) have opposite direction associations with blood pressure response to diuretics.3 Although some methodological differences could conceivably account for nonreplication of the opposite direction associations for 6 lead single nucleotide polymorphisms tested by Dr Frau et al, our statistical analysis was ...
In most existing genetic variant association studies, "common trait, common variants", which asserts that common genetic variants contribute to most of traits (disease susceptibilities), serves as the central assumption. Researchers have successfully identified some significant associations between common single nucleotide polymorphisms (SNPs) and disease traits [1]. However, despite the enormous efforts expended on association studies of complex traits, common genetic variants only show a moderate influence on different phenotypes in many reported disease associations and consequently have limited diagnostic value [2, 3]. While the identification of common variants creates a dilemma, known as "common trait, rare variants", an alternative hypothesis, which asserts that multiple rare variants with moderate to high penetrances may collectively influence disease susceptibilities, has been suggested in some literatures [3-5]. Rare variants are defined as those whose minor allele frequencies (MAF) ...
We have conducted a pathway-based analysis of genome-wide single-nucleotide polymorphism (SNP) data in order to identify genetic susceptibility factors for cervical cancer in situ. Genotypes derived from Affymetrix 500k or 5.0 arrays for 1076 cases and 1426 controls were analyzed for association, and pathways with enriched signals were identified using the SNP ratio test. The most strongly associated KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were Asthma (empirical P=0.03), Folate biosynthesis (empirical P=0.04) and Graft-versus-host disease (empirical P=0.05). Among the 11 top-ranking pathways were 6 related to the immune response with the common denominator being genes in the major histocompatibility complex (MHC) region on chromosome 6. Further investigation of the MHC revealed a clear effect of HLA-DPB1 polymorphism on disease susceptibility. At a functional level, DPB1 alleles associated with risk and protection differ in key amino-acid residues affecting peptide-binding motifs ...
Purpose : Glaucoma is a serious eye disease that often leads to blindness. Glaucoma is often described as a degenerative optic neuropathy that is associated with elevated intraocular pressure. Primary glaucoma is a hereditary disease that affects both human and canines. But the genetic mutations association with glaucoma is not fully investigated. Methods : Previously, we have shown a specific association of two single nucleotide polymorphisms (SNPs) with glaucoma in Shiba-Inus and Shih-Tzus. In this study, we screened polymorphisms within SRBD1 and CYP1B1 genes that have been shown to be associated with Glaucoma in several dog breeds. 77 healthy dogs and 135 cases dogs were recruited from the Centre Hospitalier Veterinaire Saint-Martin (France), and from the REOVVA member (European Network in Veterinary Ophthalmology and Vision in Animals). All Dogs were clinically evaluated before taking blood samples for direct sequencing Analysis. Results : Two new SNPs (rs9172407 and rs22115601) within ...
Polymorphic markers at bovine gene loci facilitate the integration of cattle genetic maps with those of humans and mice. To this end, 31 single nucleotide polymorphism (SNP) markers were developed for seven bovine chemokine genes. Loci were amplified from bovine genomic DNA by the polymerase chain reaction, and candidate amplicons were sequenced to determine their identity. Amplified loci from 24 founding parents and select progeny from a beef cattle reference population were sequenced and analyzed for SNPs. SNP haplotype alleles were determined by examining segregation patterns and used to establish the locus position on the bovine linkage map. Loci for growth-related proteins (GRO3, GRO1, and GROX) were clustered with the related CXC chemokine genes, interleukin (IL) 8, and epithelial cell inflammatory protein 1, at 84 cM from the centromeric end of the bovine chromosome (BTA) 6 linkage group. Bovine loci for a cluster of IL8 receptors, a stromal cell-derived factor 1, interferong, and tumor necrosis
A team led by the University of California San Diego has developed a chip that can detect a type of genetic mutation known as a single nucleotide polymorphism (SNP) and send the results in real time to a smartphone, computer, or other electronic device. The chip is at least 1,000 times more sensitive at detecting an SNP than current technology.. The advance, published July 9 in Advanced Materials, could lead to cheaper, faster and portable biosensors for early detection of genetic markers for diseases such as cancer.. An SNP is the change in a single nucleotide base (A, C, G or T) in the DNA sequence. It is the most common type of genetic mutation. While most SNPs have no discernible effect on health, some are associated with increased risk of developing pathological conditions such as cancer, diabetes, heart disease, neurodegenerative disorders, autoimmune and inflammatory diseases.. Traditional SNP detection methods have several limitations: they have relatively poor sensitivity and ...
from June 26-30, 2017. The goal of the course is to teach course participants both theory and application of methods for population based association analysis, with a concentration on the analysis of exome and whole genome sequence and genotype data.Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.). Topics covered include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; controlling population admixture (genomic control, principal components analysis, etc); imputing ...
Background: Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. Results: The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant ...
Main article: Single nucleotide polymorphism. A single nucleotide polymorphism (SNP) is a difference in a single nucleotide ... Single nucleotide polymorphisms[edit]. DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/T ... As of 2017[update], the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed 324 million ... a haplogroup is a group of similar haplotypes that share a common ancestor with a single nucleotide polymorphism (SNP) mutation ...
dbSNP: single nucleotide polymorphism. *Gene:[3] gene-centered information. *HomoloGene: eukaryotic homology groups ... All databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to ... Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single ...
... single nucleotide polymorphism, SNP), or a long one, like minisatellites. ... Some of the methods used to study the genome or phylogenetics are RFLP, Amplified fragment length polymorphism (AFLP), RAPD, ... A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change ( ... molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or ...
Duran C; Appleby N; Vardy M; Imelfort M; Edwards D; Batley J (May 2009). "Single nucleotide polymorphism discovery in barley ... Although DNA and RNA nucleotide bases are more similar to each other than are amino acids, the conservation of base pairs can ... Dot plots can also be used to assess repetitiveness in a single sequence. A sequence can be plotted against itself and regions ... The dot plots of very closely related sequences will appear as a single line along the matrix's main diagonal. ...
Single nucleotide polymorphism rs1045642Edit. This section is empty. You can help by adding to it. (November 2017) ... nucleotide binding. • transporter activity. • ATPase activity. • protein binding. • hydrolase activity. • ATP binding. • ... Although polymorphisms and haplotypes of ABCB1 have been associated with alterations in drug disposition and drug response, ... A 2015 review of polymorphisms in ABCB1 found that "the effect of ABCB1 variation on P-glycoprotein expression (messenger RNA ...
"Y CHROMOSOME SINGLE NUCLEOTIDE POLYMORPHISMS TYPING BY SNaPshot MINISEQUENCING" (PDF). Bjmg.edu.mk. Retrieved 20 December 2016. ... Genetic research published in European Journal of Human Genetics "has revealed that over 70% of males belong to a single ... Genetic findings appear to confirm that the Romani "came from a single group that left northwestern India about 1,500 years ago ... "The genetic structure of the Slovak population revealed by Y-chromosome polymorphisms (PDF Download Available)". Researchgate. ...
"High-Throughput Genotyping with Single Nucleotide Polymorphisms". Genome Research. 11 (7): 1262-1268. doi:10.1101/gr.157801 ( ... Single-linkage on density-based clusters. 20 clusters extracted, most of which contain single elements, since linkage ... DeLi-Clu,[15] Density-Link-Clustering combines ideas from single-linkage clustering and OPTICS, eliminating the ε. {\ ... Purity: Purity is a measure of the extent to which clusters contain a single class.[36] Its calculation can be thought of as ...
Specific single nucleotide polymorphisms (SNP) can be identified using this technique. The gold nanoparticles facilitate the ... Nie, S; Emory, SR (1997). "Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering". Science. ... Le Ru, Eric C.; Meyer, Matthias; Etchegoin, Pablo G. (2006). "Proof of Single-Molecule Sensitivity in Surface Enhanced Raman ... Blackie, Evan J.; Le Ru, Eric C.; Etchegoin, Pablo G. (2009). "Single-Molecule Surface-Enhanced Raman Spectroscopy of ...
"Single-nucleotide polymorphisms in the p53 pathway regulate fertility in humans". Proceedings of the National Academy of ... "Married Vs Single: What Science Says Is Better For Your Health". medicaldaily.com. 2 April 2015.. ... As of 2009[update], the record for lifespan extension in C. elegans is a single-gene mutation which increases adult survival by ... Early life forms on Earth, starting at least 3.7 billion years ago,[2] were single-celled organisms. Such organisms ( ...
"Non-Invasive Prenatal Detection of Trisomy 21 Using Tandem Single Nucleotide Polymorphisms". PLoS ONE. 5 (10): e13184. doi: ... These mutations include single base pair deletions, insertions, duplications, and amino acid changes.[7] ...
Lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions. N.p., n.d. Web. 03 June 2014. ...
Single-nucleotide polymorphism (SNP). ReferencesEdit. *^ a b Nomenclature for Incompletely Specified Bases in Nucleic Acid ... Main article: Nucleotide. Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of ... Each codon consists of three nucleotides, usually representing a single amino acid. ... The possible letters are A, C, G, and T, representing the four nucleotide bases of a DNA strand - adenine, cytosine, guanine, ...
"Novel single nucleotide polymorphisms of organic cation transporter 1 (SLC22A1) affecting transport functions". Biochemical and ... Schinkel AH, Jonker JW (November 2002). "Polymorphisms affecting function of the human organic cation transporter hOCT1 ( ...
These changes are known as single-nucleotide polymorphisms or SNPs. The actual number of genes that contribute to eye color is ... "A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation". Am. J. Hum. ... The polymorphisms may be in an OCA2 regulatory sequence, where they may influence the expression of the gene product, which in ... The same DNA sequence in the region of the OCA2 gene among blue-eyed people suggests they may have a single common ancestor.[44 ...
A more technical example to illustrate genotype is the single nucleotide polymorphism or SNP. A SNP occurs when corresponding ... terminal restriction fragment length polymorphism (t-RFLP),[4] amplified fragment length polymorphism (AFLP),[5] and multiplex ... Several common genotyping techniques include restriction fragment length polymorphism (RFLP), ... "SoftGenetics Application Note - GeneMarker® Software for Terminal-Restriction Fragment Length Polymorphism (T-RFLP) Data ...
"Single nucleotide polymorphism heritability of behavior problems in childhood: genome-wide complex trait analysis". Journal of ...
"Characterization of single-nucleotide polymorphisms in coding regions of human genes". Nature Genetics. 22 (3): 231-8. doi: ... "In vivo single branch axotomy induces GAP-43-dependent sprouting and synaptic remodeling in cerebellar cortex". Proceedings of ...
"Common single nucleotide polymorphisms in immunoregulatory genes and multiple myeloma risk among women in Connecticut". ...
The rs11571288 C/G Single-nucleotide polymorphism (SNP) variant[20] of DP2 has been associated with an increase in the ... "The single nucleotide polymorphism CRTh2 rs533116 is associated with allergic asthma and increased expression of CRTh2". ... "Genetic impact of functional single nucleotide polymorphisms in the 3'-UTR region of the chemoattractant receptor expressed on ... G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger. • chemotaxis. • positive ...
1999). "Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis". Nat. Genet. 22 (3): 239 ... Polymorphism in ADD1 is associated with hypertension. GRCh38: Ensembl release 89: ENSG00000087274 - Ensembl, May 2017 GRCm38: ... 1997). "Polymorphisms of alpha-adducin and salt sensitivity in patients with essential hypertension". Lancet. 349 (9062): 1353- ...
The human single-nucleotide polymorphism (SNP) map has revealed large regional variations in heterozygosity, more so than can ... Kendal WS (2003) An exponential dispersion model for the distribution of human single nucleotide polymorphisms. Mol Biol Evol ... A map of human genome variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933. ... a software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, ...
Graf J, Hodgson R, van Daal A (March 2005). "Single nucleotide polymorphisms in the MATP gene are associated with normal human ... Yuasa I, Umetsu K, Watanabe G, Nakamura H, Endoh M, Irizawa Y (December 2004). "MATP polymorphisms in Germans and Japanese: the ... Zühlke C, Criée C, Gemoll T, Schillinger T, Kaesmann-Kellner B (June 2007). "Polymorphisms in the genes for oculocutaneous ... "Distinctive distribution of AIM1 polymorphism among major human populations with different skin color". Journal of Human ...
"Single Nucleotide Polymorphism-based Validation of Exonic Splicing Enhancers". PLoS Biol. 2 (9): E268. doi:10.1371/journal.pbio ...
"Single Nucleotide Polymorphism-based Validation of Exonic Splicing Enhancers". 》PLoS Biol.》 2 (9): E268. PMC 514884. PMID ...
Ang isang single-nucleotide polymorphism o SNP ay isang pagkakaiba ng sekwensiyang DNA na nangyayari kapag ang isang nucleotide ... Kinuha mula sa "https://tl.wikipedia.org/w/index.php?title=Single-nucleotide_polymorphism&oldid=1650137" ... Ang molekulang DNA 1 ay iba mula sa molekulang DNA 2 sa isang lokasyong isang baseng pares (isang C/T polymorphism). ... "Non-Synonymous Polymorphisms in the FCN1 Gene Determine Ligand-Binding Ability and Serum Levels of M-Ficolin". PLoS ONE 7 (11 ...
大多數對於人類遺傳變異的研究集中在單一核苷酸多型性(single nucleotide polymorphisms;SNPs),也就是DNA中的個別鹼基變換。科學家分析估計,在人類的真染色質(富含基因的染色質)中,平均每100到1000個鹼基會出現1個 ... 2006年一篇發表在《自然》的研究報告中[12],研究人員發現在人類與其他哺乳類DNA序列中的拷貝數
Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin ... LA-MRSA Staphylococcus aureus whole genome sequence (WGS) single nucleotide polymorphism (SNP) typing phylogenetic analysis ... Table_2_Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated ... This study applied whole genome sequencing and single nucleotide polymorphism (SNP) typing to compare the population structure ...
A single-nucleotide polymorphism in the fetal catechol-o-methyltransferase gene is associated with spontaneous preterm birth in ... A single-nucleotide polymorphism in the fetal catechol-o-methyltransferase gene is associated with spontaneous preterm birth in ... A single-nucleotide polymorphism in the fetal catechol-o-methyltransferase gene is associated with spontaneous preterm birth in ... A single-nucleotide polymorphism in the fetal catechol-o-methyltransferase gene is associated with spontaneous preterm birth in ...
A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the ... Zheng, Hai-Tao (2005). "Loss of heterozygosity analyzed by single nucleotide polymorphism array in cancer". World Journal of ... LaFramboise, T. (1 July 2009). "Single nucleotide polymorphism arrays: a decade of biological, computational and technological ... Sato-Otsubo, Aiko; Sanada, Masashi; Ogawa, Seishi (February 2012). "Single-Nucleotide Polymorphism Array Karyotyping in ...
Single nucleotide polymorphism analysis, Single nucleotide polymorphism gentotyping Categories. Genotyping assay → Single ... Single nucleotide polymorphism sampling at OHSU. Definition. A genotyping technique that interrogates SNPs by hybridizing ...
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in people. Learn more about SNPs and what ... Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation ... called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain ... They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a persons ...
The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population ...
Detection of functional single-nucleotide polymorphisms that affect apoptosis. Sandra L. Harris, German Gil, Harlan Robins, ... Detection of functional single-nucleotide polymorphisms that affect apoptosis. Sandra L. Harris, German Gil, Harlan Robins, ... Detection of functional single-nucleotide polymorphisms that affect apoptosis. Sandra L. Harris, German Gil, Harlan Robins, ... Detection of functional single-nucleotide polymorphisms that affect apoptosis Message Subject (Your Name) has sent you a ...
A Single Nucleotide Polymorphism is also known as a SNP or snp (pronounced snip). [These and other terms are briefly defined ... Retrieved from "https://www.SNPedia.com/index.php?title=Single_Nucleotide_Polymorphism&oldid=672287" ... But at certain locations there are differences - these variations are called polymorphisms. Polymorphisms are what make ... Many polymorphisms are likely to have either no effect at all, or to have such subtle effects that it will be many years before ...
A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide adenine ... Single nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic ... This is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms. There are variations between human ... "a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms" ...
tags: single-nucleotide polymorphism x neuroscience x The Scientist. » single-nucleotide polymorphism and neuroscience ...
Their goal is the anonymization of single nucleotide polymorphisms (SNPs) in DNA sequences through the use of generalization ... Previous proposals to anonymize DNA have concentrated on single nucleotide polymorphism (SNP) regions for privacy protection. ... The first step of the DNALA algorithm is to identify single nucleotide variable regions (SN V R) in the DNA. We refer to these ... The single nucleotide generalization lattice model assumes that variation occurs in small sized regions (i.e. 1-3 residues). ...
Alternatively, discovery of single-nucleotide polymorphisms (SNPs, which include single-base changes and insertion/deletions) ... Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli et al., 2003 Single-nucleotide polymorphisms in ... Kanazin, V., H. Talbert, D. See, P. DeCamp, E. Nevo et al., 2002 Discovery and assay of single-nucleotide polymorphisms in ... Marth, G. T., I. Korf, M. D. Yandell, R. T. Yeh, Z. Gu et al., 1999 A general approach to single-nucleotide polymorphism ...
Marth, G. T., I. Korf, M. D. Yandell, R. T. Yeh, Z. Gu et al., 1999 A general approach to single-nucleotide polymorphism ... Lambreghts, R., M. Shi, W. J. Belden, D. Decaprio, D. Park et al., 2009 A high-density single nucleotide polymorphism map for ... Single nucleotide polymorphisms (SNPs) can be converted into genetic markers that are scored in mapping populations using ... High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing. Sanzhen Liu, Hsin D. Chen, ...
... label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single- ... Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat Genet. 2000;26(2):233-6.CrossRef ... Deng H, Shen W, Gao Z. Colorimetric detection of single nucleotide polymorphisms in the presence of 10(3)-fold excess of a wild ... Single-nucleotide polymorphism Branched rolling circle amplification reaction Terpyridine-Zn(II) Fluorometry ...
The single nucleotide polymorphism A118G alters functional properties of the human mu opioid receptor.. Kroslak T1, Laforge KS ... The most common single nucleotide polymorphism in the coding region of the human mu opioid receptor gene is the A118G variant, ... an adenine to guanine transition at nucleotide position 118 of the coding sequence of the gene. This polymorphism codes for an ...
... in which the prevalence of overt disease depends mainly on the frequency of a single common single-nucleotide polymorphism ... Contribution of a common single-nucleotide polymorphism to the genetic predisposition for erythropoietic protoporphyria.. Gouya ... Contribution of a Common Single-Nucleotide Polymorphism to the Genetic Predisposition for Erythropoietic Protoporphyria ... Contribution of a Common Single-Nucleotide Polymorphism to the Genetic Predisposition for Erythropoietic Protoporphyria ...
The aim of the present study was to determine the influence of single nucleotide polymorphism (SNP) of ,i,CYP4F2,/i, (rs1558139 ... H. Q. Yan, Y. Yuan, P. Zhang, Z. Huang, L. Chang, and Y. K. Gui, "CYP4F2 gene single nucleotide polymorphism is associated with ... The aim of the present study was to determine the influence of single nucleotide polymorphism (SNP) of CYP4F2 (rs1558139) and ... Single nucleotide polymorphisms were determined using TaqMan® Drug Metabolism assays (Thermo Scientific). The genotyping was ...
... Keum-Ju Lee ... Keum-Ju Lee, Hye-Mi So, Byoung-Kye Kim, et al., "Single Nucleotide Polymorphism Detection Using Au-Decorated Single-Walled ...
Study on Single-nucleotide-polymorphism in Idiopathic Membranous Nephropathy. The safety and scientific validity of this study ... Genome-wide single-nucleotide-polymorphism of IMN patients treated by the Comprehensive Treatment Regimen or conventional ... Screening for single-nucleotide-polymorphism as the prognostic factor for the TCM intervention of IMN patients. ...
A single-nucleotide polymorphism, often abbreviated to SNP (/snɪp/; plural /snɪps/), is a variation in a single nucleotide that ... A somatic single-nucleotide variation (e.g., caused by cancer) may also be called a single-nucleotide alteration. Single- ... A single-nucleotide variant (SNV) is a variation in a single nucleotide without any limitations of frequency and may arise in ... "Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on ...
The most common type of variant is the single nucleotide polymorphism (SNP). We present a low-cost, high throughput assay for ... Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping Cytometry. 2000 Jun 1;40(2):102-8. ...
... KU Chee Seng, National University of Singapore, ... Keywords: single nucleotide polymorphisms; high‐throughput genotyping technologies; illumina; affymetrix; genome coverage ... Chee Seng, KU, Katherine, KASIMAN, and Kee Seng, CHIA(Sep 2009) High‐Throughput Single Nucleotide Polymorphisms Genotyping ... 2004) Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage ...
Fetal and Maternal Candidate Single Nucleotide Polymorphism Associations With Cerebral Palsy: A Case-Control Study. Michael E. ... Fetal and Maternal Candidate Single Nucleotide Polymorphism Associations With Cerebral Palsy: A Case-Control Study ... Fetal and Maternal Candidate Single Nucleotide Polymorphism Associations With Cerebral Palsy: A Case-Control Study ... Fetal and Maternal Candidate Single Nucleotide Polymorphism Associations With Cerebral Palsy: A Case-Control Study ...
Study of seven single-nucleotide polymorphisms identified in East Asians for association with obesity in a Taiwanese population ... Effects of polymorphisms in APOA5 on the plasma levels of triglycerides and risk of coronary heart disease in Jilin, northeast ...
Using a Single Nucleotide Polymorphism (SNP) to Predict Bitter Tasting Ability Kit. 9 Items Using a Single Nucleotide ... The 2 alleles differ by a single nucleotide, so restriction digestion of the amplified product followed by gel electrophoresis ... They then use safe saline mouthwash and Chelex® extraction to obtain a sample of their own DNA and amplify a 221-nucleotide ... They then use safe saline mouthwash and Chelex® extraction to obtain a sample of their own DNA and amplify a 221-nucleotide ...
  • To assess whether the increased incidence of preterm birth (PTB) among AA women is associated with single-nucleotide polymorphism (SNP) in the COMT gene, we examined variations in maternal and fetal COMT genes and their association with pregnancy outcomes (term vs preterm pregnancies) using 4 functional SNPs: rs4633, rs4680, rs4818, and rs6269 in both AA and Cau. (utmb.edu)
  • We aimed at investigating association and function of the missense single nucleotide polymorphism (SNP), rs201802880 (here denoted NCF1-339) in NCF1 with systemic lupus erythematosus (SLE). (diva-portal.org)
  • OBJECTIVE-A recent meta-analysis demonstrated a nominal association of the ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) K→Q missense single nucleotide polymorphism (SNP) at position 121 with type 2 diabetes. (harvard.edu)
  • The research team of the Department of Periodontology, together with Professor Koichiro Yoshiura of the Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University, analyzed the relationship between the polymorphisms in TLR4 gene and chronic periodontitis. (nagasaki-u.ac.jp)
  • We employ a concept generalization lattice to determine the distance between two residues in a single nucleotide region, which provides the most similar generalized concept for two residues (i.e. adenine and guanine are both purines). (scribd.com)
  • The single nucleotide polymorphism A118G alters functional properties of the human mu opioid receptor. (nih.gov)
  • Introduction and Objective: Breast cancer resistance protein (BCRP), the second member of the ATP-binding cassette membrane transporter family, has a single nucleotide polymorphism, C421A (resulting in Q141K), that has been shown to be of functional importance. (aacrjournals.org)
  • Functional gene polymorphisms of these MMPs such as MMP1 −1607 1G/2G (rs1799750), MMP2 −1306 C/T (rs243865), MMP2 −1575 G/A (rs243866), and MMP9 Q279R (rs17576) are thus plausible candidates as risk factors for open angle glaucomas. (molvis.org)
  • Based upon the importance of IFN-γ in protective immunity against Mycobacterium tuberculosis, and the functional role of the IFN-γ + 874T/A single nucleotide polymorphism in IFN-γ production, we genotyped 93 Brazilian tuberculosis patients and 266 asymptomatic health care workers, including 150 individuals with a positive tuberculin skin test, and analyzed the possible association of the +874A low IFN-γ producer allele with tuberculosis occurrence. (ovid.com)
  • Despite the mixed ethnicity observed in Brazilian populations, the present data agree with observations reported in other populations and thus demonstrate that the functional +874T/A IFN-γ gene polymorphism is associated with tuberculosis in different populations. (ovid.com)
  • Our results demonstrate that several polymorphisms in the leptin-a gene are associated with growth traits and can be used for marker-assisted selection (MAS) in orange-spotted grouper populations. (mdpi.com)
  • Nous avons génotypé les deux polymorphismes mononucléotidiques du gène ADIPOQ chez 140 patients atteints de DNID sans lien de parenté et 66 témoins non diabétiques en recourant à l'analyse du polymorphisme de longueur des fragments de restriction par réaction en chaîne de polymérase. (who.int)
  • The prevalence of VDR polymorphisms in 4 restriction fragment length polymorphism sites including BsmI, FokI, ApaI and TaqI were analysed in patients and controls. (who.int)
  • The SSOP-ELISA compared well with a standard PCR-restriction fragment length polymorphism procedure, and gave identical positive results in more than 90% of the P. falciparum slide-positive samples tested. (ajtmh.org)
  • With regard to chromosomal abnormalities known from conventional cytogenetic analysis, the most frequent observed abnormalities were deletions in 20q11-q13 (n=10), gain of 9p/trisomy 9 (n=6), partial or total gain of 1q (n=4), and trisomy 8 (n=4), followed by loss of 5q11-q13 and 13q12-q21 in single cases ( Table 1 ). (haematologica.org)
  • Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the Xba I sites polymorphic between strains rather than single-nucleotide polymorphisms in the Xba I sites themselves. (asm.org)
  • 27 ]). While prior sequencing has provided a useful starting point for detecting polymorphic loci in potato, the polymorphisms that can be defined at present are restricted to the genotypes sequenced to date and the depth of sequencing performed. (biomedcentral.com)
  • The finding that diabetic autoimmunity can be defined by a single polymorphic residue has not been previously documented. (diabetesjournals.org)
  • Then statistical analysis will be pursued for single marker analysis, haplotype analysis and for the construction of genetic risk model based on the multivariate analysis. (bioportfolio.com)
  • In this population, the analysis of a single SNP, rs12979860, successfully predicts SVR in the IFN-RBV treatment of HCV. (scielo.br)
  • These tissue samples appeared to contain 3-4 allelic variants of B. anthracis , based on a single variable-number tandem repeat (VNTR) marker ( vrrA ), which suggests that the material contained multiple strains of this species ( 4 ). (cdc.gov)
  • Significant associations were observed for raw meat for the Charolais between shear force and the CAPN1 marker ( P = 0.019), as well as between the CAST polymorphism and shear force ( P = 0.027) in the Limousin. (gc.ca)
  • RESULTS: A single nucleotide polymorphism marker (rs12014762) located in the genetic region of CLDN2 was significantly associated to CD (case-control allelic OR = 1.98, 95% CI: 1.17-3.35, P = 0.007). (diva-portal.org)