A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The 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)
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The 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.
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.
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.
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.
Genotypic differences observed among individuals in a population.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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.
Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A 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).
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
Individuals whose ancestral origins are in the continent of Europe.
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.
An individual in which both alleles at a given locus are identical.
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.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
A country spanning from central Asia to the Pacific Ocean.
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.
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.
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.
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
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.
An individual having different alleles at one or more loci regarding a specific character.
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).
Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.
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.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
The 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.
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.
A branch of genetics which deals with the genetic variability in individual responses to drugs and drug metabolism (BIOTRANSFORMATION).
The ratio of two odds. The exposure-odds ratio for case control data is the ratio of the odds in favor of exposure among cases to the odds in favor of exposure among noncases. The disease-odds ratio for a cohort or cross section is the ratio of the odds in favor of disease among the exposed to the odds in favor of disease among the unexposed. The prevalence-odds ratio refers to an odds ratio derived cross-sectionally from studies of prevalent cases.
A 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.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A flavoprotein amine oxidoreductase that catalyzes the reversible conversion of 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. This enzyme was formerly classified as EC
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
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.
Genetic loci associated with a QUANTITATIVE TRAIT.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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 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.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.
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.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Enzyme that catalyzes the movement of a methyl group from S-adenosylmethionone to a catechol or a catecholamine.
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)
Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.
Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome.
The functional hereditary units of BACTERIA.
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).
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
The 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.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Databases devoted to knowledge about specific genes and gene products.
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.
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)
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
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.
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.
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.
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.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The rate dynamics in chemical or physical systems.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Established cell cultures that have the potential to propagate indefinitely.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
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.
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
A 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.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
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.
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).
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.
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)
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.
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.
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).
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.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A 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.
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.
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
Deoxyribonucleic acid that makes up the genetic material of plants.
Ribonucleic acid that makes up the genetic material of viruses.
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.
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.
Proteins found in any species of bacterium.
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 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.
The combined effects of genotypes and environmental factors together on phenotypic characteristics.
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.
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships.
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.
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).
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.
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.
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.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
A 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)
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 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.
Persons living in the United States having origins in any of the black groups of Africa.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The genetic complement of a plant (PLANTS) as represented in its DNA.
Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Tumors or cancer of the human BREAST.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
Inhaling and exhaling the smoke of burning TOBACCO.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Transport proteins that carry specific substances in the blood or across cell membranes.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)
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
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety.
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.
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.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
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.
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.
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.
The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.
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.-.
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.
A specific pair GROUP C CHROMSOMES of the human chromosome classification.
A pyrimidine base that is a fundamental unit of nucleic acids.
Identification of genetic carriers for a given trait.
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.
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 present in neoplastic tissue.
A coordinated international effort to identify and catalog patterns of linked variations (HAPLOTYPES) found in the human genome across the entire human population.
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.
The functional hereditary units of VIRUSES.
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.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The temperature at which a substance changes from one state or conformation of matter to another.
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.
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.
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 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.
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.
The functional hereditary units of PLANTS.
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.
Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)
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.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
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
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A purine base and a fundamental unit of ADENINE NUCLEOTIDES.
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.
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.
A guanine nucleotide containing two phosphate groups esterified to the sugar moiety.

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
TY - JOUR. T1 - Characterization of chromosome arm 20q abnormalities in myeloid malignancies using genome-wide single nucleotide polymorphism array analysis. AU - Huh, Jungwon. AU - Tiu, Ramon V.. AU - Gondek, Lukasz P.. AU - OKeefe, Christine L.. AU - Jasek, Monika. AU - Makishima, Hideki. AU - Jankowska, Ania M.. AU - Jiang, Ying. AU - Verma, Amit. AU - Theil, Karl S.. AU - McDevitt, Michael A.. AU - Maciejewski, Jaroslaw P.. PY - 2010/4. Y1 - 2010/4. N2 - Deletion of the long arm of chromosome 20 is a common abnormality associated with myeloid malignancies. We characterized abnormalities of chromosome 20 as defined by metaphase cytogenetics (MC) in patients with myeloid neoplasms to define commonly deleted regions (CDR) and commonly retained regions (CRR) using genome-wide, high resolution single nucleotide polymorphism array (SNP-A) analysis. We reviewed the MC results of a cohort of 1,162 patients with myeloid malignancies, including myelodysplastic syndromes (MDS), MDS/myeloproliferative ...
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.
YAKUBU, A.; DE DONATO, M. e IMUMORIN, I. G.. Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds. S. Afr. j. anim. sci. [online]. 2017, vol.47, n.2, pp.146-156. ISSN 2221-4062. http://dx.doi.org/10.4314/sajas.v47i2.6.. The DQA1 gene is a member of the highly polymorphic MHC class II locus that is responsible for the differences among individuals in immune response to infectious agents. In this study, the authors performed a comprehensive computational analysis of the functional and structural impact of non-synonymous or amino acid-changing single nucleotide polymorphisms (SNPs) (nsSNPs) that are deleterious to the DQA1 protein in Nigerian goats. A 310-bp fragment of exon 2 of the DQA1 gene was amplified and sequenced in 27 unrelated animals that are representative of three major Nigerian goat breeds (nine each of West African Dwarf, Red Sokoto, and Sahel of both sexes) using genomic DNA. Forty-two nsSNPs were ...
Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage ...
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.
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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.. ...
Novel association of a functional single nucleotide polymorphism in the BTNL2 gene with susceptibility to rheumatoid arthritis and baseline radiographic severity in African-Americans independent of HLA DRB1: Results from the CLEAR registry ...
BNP assays are widely used in the diagnosis and prognosis of left ventricular (LV) dysfunction and heart failure. The functional single nucleotide polymorphism rs198389 in the promoter region of the BNP gene has been associated with higher BNP levels [1-3]. The prevalence of rs198389 in the general US population is unknown. The impact on common assay test characteristics, and cardiovascular and clinical phenotypes is also unknown. The goal of this study was to determine for the first time the prevalence of rs198389 in a US general adult population and its impact on (a) three commonly used BNP assays (BNP levels, diagnostic test performance), and (b) clinical phenotype and disease prevalence. ...
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 ...
Association of carriers of single nucleotide polymorphisms rs1143634 and rs16944 of the Il-1B gene and rs6265 of the BDNF gene with temporal lobe epilepsy
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 (+) ...
Miller, R. D., Phillips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A., Callahan, C. E., Carey, B. J., Conley, C. L., Cyr, J. M., Derohannessian, V., Donaldson, R. A., Elosua, C., Ford, S. E., Forman, A. M., Gelfand, C. A., Grecco, N. M., Gutendorf, S. M., Hock, C. R., Hozza, M. J., Hur, S., In, S. M., Jackson, D. L., Jo, S. A., Jung, S. C., Kim, S., Kimm, K., Kloss, E. F., Koboldt, D. C., Kuebler, J. M., Kuo, F. S., Lathrop, J. A., Lee, J. K., Leis, K. L., Livingston, S. A., Lovins, E. G., Lundy, M. L., Maggan, S., Minton, M., Mockler, M. A., Morris, D. W., Nachtman, E. P., Oh, B., Park, C., Park, C. W., Pavelka, N., Perkins, A. B., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Shah, G. J., Tate, J. M., Varde, S. A., Walters, A., White, J. R., Yoo, Y. K., Lee, J. E., Boyce-Jacino, M. T., Kwok, P. Y. (August 2005) High-density single-nucleotide ...
The single nucleotide polymorphism (SNP) rs1053004 in Signal transducer and activator of transcription 3(STAT3) was recently reported to be associated with chronic hepatitis B (CHB)-related hepatocellular carcinoma(HCC) in a Chinese cohort. This study was aimed at investigating whether the SNP might also contribute toHCC susceptibility in the Thai population. Study subjects were enrolled and divided into 3 groups includingCHB-related HCC (n=211), CHB without HCC (n=233) and healthy controls (n=206). The SNP was genotypedusing allelic discrimination assays based on TaqMan real-time PCR. Data analysis revealed that the distributionof different genotypes was in Hardy-Weinberg equilibrium (P|0.05). The frequencies of allele T (major allele)in HCC patients, CHB patients and healthy controls were 51.4%, 58.6% and 61.4%, respectively, whereas thefrequencies of C allele (minor allele) were 48.6%, 41.4% and 38.6%. The C allele frequency was higher in HCCwhen compared with CHB patients (odds ratio (OR)=1.34, 95%
Adiponectin gene (ADIPOQ) polymorphisms have been shown to affect adiponectin serum concentration and some have been associated with breast cancer (BC) risk. The aims of this study were to describe the frequency of single nucleotide polymorphisms (SNPs) of ADIPOQ in Mexican women with BC and to determine if they show an association with it. DNA samples from 397 patients and 355 controls were tested for the ADIPOQ gene SNPs: rs2241766 (GT) and rs1501299 (GT) by TaqMan allelic discrimination assay. Hardy-Weinberg equilibrium (HWE) was tested. Multiple SNP inheritance models adjusted by age and body mass index (BMI) were examined for the SNP rs1501299. We found that in the frequency analysis of rs1501299 without adjusting the BMI and age, the genotype distribution had a statistically significant difference (P = 0.003). The T allele was associated with a BC risk (OR, 1.99; 95% CI 1.13-3.51, TT vs. GG; OR, 1.53; 95% CI 1.12-2.09, GT vs. GG). The SNP rs2241766 was in HW disequilibrium in controls. In
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
This paper introduces and applies a genome wide predictive study to learn a model that predicts whether a new subject will develop breast cancer or not, based on her SNP profile. We first genotyped 696 female subjects (348 breast cancer cases and 348 apparently healthy controls), predominantly of Caucasian origin from Alberta, Canada using Affymetrix Human SNP 6.0 arrays. Then, we applied EIGENSTRAT population stratification correction method to remove 73 subjects not belonging to the Caucasian population. Then, we filtered any SNP that had any missing calls, whose genotype frequency was deviated from Hardy-Weinberg equilibrium, or whose minor allele frequency was less than 5%. Finally, we applied a combination of MeanDiff feature selection method and KNN learning method to this filtered dataset to produce a breast cancer prediction model. LOOCV accuracy of this classifier is 59.55%. Random permutation tests show that this result is significantly better than the baseline accuracy of 51.52%. Sensitivity
Single nucleotide polymorphism at exon 7 splice acceptor site of OAS1 gene determines response of hepatitis C virus patients to interferon therapy.: Response to
TY - CHAP. T1 - Development of single nucleotide polymorphism (SNP) markers for cereal breeding and crop research. T2 - current methods and future prospects. AU - Schramm, Carly. AU - Shavrukov, Yuri. AU - Anderson, Peter. AU - Kurishbaev, Akhylbek. AU - Jatayev, Satyvaldy. PY - 2019/6/27. Y1 - 2019/6/27. N2 - Modern cereal breeding and research increasingly relies upon the application of molecular genetics. This chapter provides an overview of the development of single nucleotide polymorphism (SNP) markers for use in such breeding and research. Fluorescence detection methods are fully reviewed as this field is experiencing an explosion of interest among plant biologists and crop breeders. More than 20 modern fluorescence-based methods for SNP identification and discrimination are included and the specific advantages and disadvantages of each covered. This variety of approaches gives researchers and industry the freedom to adapt and improve upon existing methods and develop novel techniques to ...
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 ...
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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 ...
The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis. Twenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA). Comparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH
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 ...
Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. All single nucleotide polymorphisms were segregating in this sample population and none deviated (P | 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P | 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P | 0.1). The G allele of LEP-1238 was associated (P | 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer
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 ...
Mechanisms involved in metabolic syndrome (MetS) development include insulin resistance, weight regulation, inflammation and lipid metabolism. Aim of this study is to investigate the association of single nucleotide polymorphisms (SNPs) involved in these mechanisms with MetS. In a random sample of the EPIC-NL study (n = 1886), 38 SNPs associated with waist circumference, insulin resistance, triglycerides, HDL cholesterol and inflammation in genome wide association studies (GWAS) were selected from the 50K IBC array and one additional SNP was measured with KASPar chemistry. The five groups of SNPs, each belonging to one of the metabolic endpoints mentioned above, were associated with MetS and MetS-score using Goemans global test. For groups of SNPs significantly associated with the presence of MetS or MetS-score, further analyses were conducted. The group of waist circumference SNPs was associated with waist circumference (P=0.03) and presence of MetS (P=0.03). Furthermore, the group of SNPs related to
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 ...
Articular cartilage functions in withstanding mechanical loads and provides a lubricating surface for frictionless movement of joints. Osteoarthritis, characterised by cartilage degeneration, develops due to the progressive erosion of structural integrity and eventual loss of functional performance. Osteoarthritis is a multi-factorial disorder; two important risk factors are abnormal mechanical load and genetic predisposition. A single nucleotide polymorphism analysis demonstrated an association of hip osteoarthritis with an Arg324Gly substitution mutation in FrzB, a Wnt antagonist. The purpose of this study was two-fold: to assess whether mechanical stimulation modulates β-catenin signalling and catabolic gene expression in articular chondrocytes, and further to investigate whether there is an interplay of mechanical load and Wnt signalling in mediating a catabolic response. Chondrocytes were pre-stimulated with recombinant Wnt3A for 24 hours prior to the application of tensile strain (7.5%, 1 Hz) for
Single nucleotide polymorphisms 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 ...
BACKGROUND: Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated phi29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. RESULTS: Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray
Background: Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated Φ29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray™ genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. Results: Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray
The MDR1 gene encodes the P-glycoprotein, an efflux transporter with broad substrate specificity. P-glycoprotein has raised great interest in pharmacogenetics because it transports a variety of structurally divergent drugs, including lipid-lowering drugs. The synonymous single-nucleotide polymorphism C3435T and the nonsynonymous single-nucleotide polymorphism G2677T/A in MDR1 have been indicated as potential determinants of variability in drug disposition and efficacy. In order to evaluate the effect of G2677T/A and C3435T MDR1 polymorphisms on serum levels of lipids before and after atorvastatin administration, 69 unrelated hypercholesterolemic individuals from São Paulo city, Brazil, were selected and treated with 10 mg atorvastatin orally once daily for ...
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 ...
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 ...
2020). Single Nucleotide Polymorphism. Salem Press Encyclopedia of Science. Allaby, Michael, ed. (2009). A dictionary of ... 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), amplified fragment length polymorphism (AFLP), and multiplex ... Often though, genotype is used to refer to a single gene or set of genes, such as the genotype for eye color. The genes take ...
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 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 ...
"Single Nucleotide Polymorphisms". Dolan DNA Learning Center. Retrieved 2010-11-23. CS1 maint: discouraged parameter (link) The ... allow researchers to screen an individual's genome for huge numbers of genetic markers called single nucleotide polymorphisms ( ... A SNP occurs when the DNA in two individuals in the population differs by a single nucleotide. For example, one individual may ... Deletions and duplications of greater than 1,000 nucleotides are called copy number variants (CNVs). The Center is equipped ...
... single nucleotide polymorphisms; depletions and duplications of parts of a gene, larger portion of a chromosome, or even an ...
... 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 ...
Mao X, Young BD, Lu Y (June 2007). "The application of single nucleotide polymorphism microarrays in cancer research". Curr ... Dutt A, Beroukhim R (January 2007). "Single nucleotide polymorphism array analysis of cancer". Current Opinion in Oncology. 19 ... "Loss of heterozygosity of chromosome 3 detected with single nucleotide polymorphisms is superior to monosomy 3 for predicting ... primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays". Am J Hum Genet. 81 (1): ...
SNP stands for Single nucleotide polymorphism probes. These probes allow for increased precision and greater diagnostic yield. ...
The Single-nucleotide polymorphism (SNP) was also examined. Y-chromosome SNPs are rare and can be used to separate populations ...
Duran C; Appleby N; Vardy M; Imelfort M; Edwards D; Batley J (May 2009). "Single nucleotide polymorphism discovery in barley ... Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted ... 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 ...
2004). "A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms". Nature. 432 (7018): 717-722. ... The reproductive strategy of this species is best described as facultative polyandry, in that a single female is typically ... Editor). CRC Press (1992), ISBN 978-0-8493-4258-5. International Chicken Polymorphism Map Consortium Wong, GK; et al. ( ...
Clifford, R. (2000). "Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome ... "Bioinformatics Tools for Single Nucleotide Polymorphism Discovery and Analysis". Annals of the New York Academy of Sciences. ... is to discover and catalogue single nucleotide polymorphisms (SNPs) that correlate with cancer initiation and progression. CGAP ... Other gene tools accessible through the CGAP web interface include the Gene Ontology Browser (GO) and the Nucleotide BLAST tool ...
Fairbrother WG, Holste D, Burge CB, Sharp PA (September 2004). "Single nucleotide polymorphism-based validation of exonic ... Changes in the RNA processing machinery may lead to mis-splicing of multiple transcripts, while single-nucleotide alterations ... The nucleotide at the branchpoint is always an A; the consensus around this sequence varies somewhat. In humans the branch site ... A single point mutation may cause a given exon to be occasionally excluded or included from a transcript during splicing, ...
Fairbrother W.G.; Holste D.; Burge C.B.; Sharp P.A. (September 2004). "Single Nucleotide Polymorphism-based Validation of ...
Single Nucleotide Polymorphisms, or SNPs, allow for a wide array of genetic variation among humans as well as pathogens. They ... "What are single nucleotide polymorphisms (SNPs)?". Genetics Home Reference. Retrieved 8 November 2019. Tettelin H, Masignani V ... It has been thought that the total number of genes associated with a single pathogen species may be unlimited, although some ... There is a need to analyze more than a single genome sequence of a pathogen species to understand pathogen mechanisms. ...
Single-nucleotide polymorphism or SNPs are variations of a single nucleotide. SNPs can occur in coding or non-coding regions of ... "What are single nucleotide polymorphisms (SNPs)?". Genetics Home Reference. Retrieved 16 November 2016. Wolf, A. B.; Caselli, R ... Many genetic differences (polymorphisms) have little effect on health or reproductive success but help to distinguish one ... We are able to treat biological traits as manifestations of either a single loci or multiple loci, labeling said biological ...
This single nucleotide polymorphism has been discovered on chromosome 19. This variation of the single nucleotide involving ... Single nucleotide polymorphisms in this gene may be associated with sporadic amyotrophic lateral sclerosis. ... Pathology involving TDP-43 is a result of the single nucleotide polymorphisms in both ALS and FTD. This gene has also been ...
The application of single-nucleotide polymorphism microarrays in cancer research. Curr Genomics. 2007 Jun;8(4):219-28. Gondek ... This is often done using polymorphic markers, such as microsatellites or single-nucleotide polymorphisms, for which the two ... and these positions are called single nucleotide polymorphisms or SNPs. When the genomic copies derived from each parent have ... The single copy cannot be heterozygous at SNP locations and therefore the region shows loss of heterozygosity. Loss of ...
A single-nucleotide polymorphism in this gene causes Proteus syndrome. AKT (now also called AKT1) was originally identified as ...
So far, more than 4580 single nucleotide polymorphisms (SNPs) for this gene have been identified. SLC46A3 is expressed at ... Cite journal requires ,journal= (help) Shen LX, Basilion JP, Stanton VP (July 1999). "Single-nucleotide polymorphisms can cause ... NSP2: A high-throughput Y2H screening of the SARS-CoV ORFeome and host proteins isolated a single-hit interaction between NSP2 ... Nucleotide. "Homo sapiens solute carrier family 46 member 3 (SLC46A3), transcript variant 2, mRNA". NCBI (National Center for ...
Snpstr Short tandem repeat Microsatellite Single-nucleotide polymorphism Agrafioti, I; Stumpf M P H (Jan 2007). "SNPSTR: a ...
At the lowest possible size an allele can be a single nucleotide polymorphism (SNP). At the higher end, it can be up to several ... Meiosis Mendelian error Mendelian inheritance Mitosis Penetrance Polymorphism Punnett square Single-nucleotide polymorphism " ... a database of single nucleotide polymorphisms". Nucleic Acids Research. 28 (1): 352-355. doi:10.1093/nar/28.1.352. ISSN 0305- ... Allelic variation at a locus is measurable as the number of alleles (polymorphism) present, or the proportion of heterozygotes ...
2004). "Single nucleotide polymorphisms in breast cancer". Oncol. Rep. 11 (4): 917-22. doi:10.3892/or.11.4.917. PMID 15010895. ...
Kitts A; Sherry S (2009). "The single nucleotide polymorphism database (dbSNP) of nucleotide sequence variation". National ... The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different ... NCBI (2010). "The single nucleotide polymorphism database (dbSNP) frequently asked questions". National Center for ... Sherry ST, Ward M; Sirotkin, K. (1999). "dbSNP - database for single nucleotide polymorphisms and other classes of minor ...
Only one Single-nucleotide polymorphism within mir-126 has been identified. A change to the 24th base prevents the processing ... "Alteration of processing induced by a single nucleotide polymorphism in pri-miR-126". Biochem Biophys Res Commun. 399 (2): 117- ...
A mutation in this gene occurs through a single-nucleotide polymorphism. When a mutation occurs the gene does not produce a ... January 2008). "ITPKC functional polymorphism associated with Kawasaki disease susceptibility and formation of coronary artery ...
A single nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. The relative mutation rate for an ... mt-SNP is a single nucleotide polymorphism on the mitochondrial chromosome. mt-SNPs are often used in maternal genealogical DNA ... Y-SNP Single-nucleotide polymorphism Short tandem repeat Haplogroup Haplotype Genealogical DNA test. ...
Single-nucleotide polymorphism (SNP) Pharmacogenomics Genetic counseling Genomic counseling Licenses/Accreditations. Retrieved ...
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
More than 36 genes and 80 single nucleotide polymorphisms (SNPs) had been found that contribute to the risk of type 2 diabetes. ... There are a number of rare cases of diabetes that arise due to an abnormality in a single gene (known as monogenic forms of ... The World Health Organization definition of diabetes (both type 1 and type 2) is for a single raised glucose reading with ...
1999). "Characterization of single-nucleotide polymorphisms in coding regions of human genes". Nat. Genet. 22 (3): 231-8. PMID ...
2010). «Identification of fetal and maternal single nucleotide polymorphisms in candidate genes that predispose to spontaneous ... 2009). «Lack of Association of Polymorphisms in Elastin With Pseudoexfoliation Syndrome and Glaucoma». Journal of glaucoma. 19 ...
"Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms". ...
The 308 G/A single nucleotide polymorphism variation in the gene for TNF is associated with an increased risk for acne.[40] ... Acne often resolves completely or is much milder after a 4-6 month course of oral isotretinoin.[1] After a single round of ... dermatologists realized that no single hypothesized factor (sebum, bacteria, or excess keratin) fully accounted for the disease ... "TNF-308 G/A polymorphism and risk of acne vulgaris: a meta-analysis". PLOS One (Systematic Review & Meta-Analysis). 9 (2): ...
Nucleotide diversity measures polymorphisms on the level of nucleotides rather than on level of loci. ... The words homozygous, heterozygous, and hemizygous are used to describe the genotype of a diploid organism at a single locus on ... In some cases the term "zygosity" is used in the context of a single chromosome.[1] ... hemizygous describes a genotype consisting of only a single copy of a particular gene in an otherwise diploid organism, and ...
Single nucleotide polymorphism. T. *Tandem repeat. *Transcription factor. Τ. *Template:Single strand DNA discovery ...
At 4.7 million nucleotides in length, A1::DQ2 is the second longest haplotype identified within the human genome.[1] A1::DQ2 ... June 2004). "Genetic polymorphisms in tumor necrosis factor (TNF)-alpha and TNF-beta in a population-based study of systemic ... but not as a single haplotype. In Kenya two slightly variant HLA-A and B alleles for an A1-B8 haplotype. One possibility is ... At 4.7 million nucleotides in length and ~300 genes the locus had resisted the effects of recombination, either as a ...
The link was a single nucleotide polymorphism of two genes involved in calcium channel signaling with neurons. One of these ... The mutation is a single nucleotide polymorphism (SNP) in an intron of the Myosin heavy polypeptide 4 gene.[38] ... "A novel intronic single nucleotide polymorphism in the myosin heavy polypeptide 4 gene is responsible for the mini-muscle ... The disease is caused by a defect in a single gene on chromosome 12 that codes for enzyme phenylalanine hydroxylase , that ...
has found that individuals with a single nucleotide polymorphism variant in the OR11H7P pseudogene have a lower receptor ... individuals with the semi-functional OR7D4 have two non-synonymous single nucleotide polymorphisms in the OR7D4 pseudogene, ... These individuals are hyperosmic for this single odorant. Another study by Keller et al. has found that people with the intact ... rather than for just a single odorant. There has not been extensive research into environmental causes of hyperosmia, but there ...
"An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays". ... "Nucleotide sequence of bacteriophage λ DNA". Journal of Molecular Biology 162 (4). Arquivado dende o orixinal o 02 de decembro ... "The nucleotide sequence of bacteriophage φX174". Journal of Molecular Biology 125 (2). Arquivado dende o orixinal o 02 de ...
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- ...
Mutation in the CACNA1C gene, the single-nucleotide polymorphism located in the third intron of the Cav1.2 gene,[18] are ...
Gastric cancer is correlated with TATA box polymorphism.[39] The TATA box has a binding site for the transcription factor of ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ... "Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and ... A CAAT box (also CAT box) is a region of nucleotides with the following consensus sequence: 5' GGCCAATCT 3'. The CAAT box is ...
BDNF has several known single nucleotide polymorphisms (SNP), including, but not limited to, rs6265, C270T, rs7103411, ... Local interaction of BDNF with the TrkB receptor on a single dendritic segment is able to stimulate an increase in PSD-95 ... Epilepsy has also been linked with polymorphisms in BDNF. Given BDNF's vital role in the development of the landscape of the ... The polymorphism Thr2Ile may be linked to congenital central hypoventilation syndrome.[98][99] BDNF and IL-6 might be involved ...
O மாற்றுருவை பொறுத்த வரை 6 ஆவது குறியீடு செய்யப்பட்ட மரபணுக் கோர்வை ஒற்றை நியூக்ளியோடைட்டு நீக்கம் (single nucleotide deletion ... Ogasawara K, Bannai M, Saitou N, et al. (1996). "Extensive polymorphism of ABO blood group gene: three major lineages of the ... Seymour RM, Allan MJ, Pomiankowski A, and Gustafsson K (2004) Evolution of the Human ABO Polymorphism by Two Complementary ...
"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. ...
El-Khamisy SF, Saifi GM, Weinfeld M, Johansson F, Helleday T, Lupski JR, Caldecott KW (March 2005). "Defective DNA single- ... the impact of two linked polymorphisms". Hum. Mol. Genet. 13 (20): 2369-76. PMID 15333585. doi:10.1093/hmg/ddh274.. ... "Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III alpha in a cell-cycle- ... "Physical and functional interaction between DNA ligase IIIalpha and poly(ADP-Ribose) polymerase 1 in DNA single-strand break ...
These subclades are also defined by single-nucleotide polymorphisms (SNPs) or unique-event polymorphisms (UEPs). Haplogroup Q- ... Sep 2014). "Genetic polymorphism of 17 Y chromosomal STRs in Kazakh and Uighur populations from Xinjiang, China". Int J Legal ... Nucleotide change: C to T. Position (base pair): 180. Total size (base pairs): 366. Forward 5′→ 3′: aactcttgataaaccgtgctg. ... The subclade (under Q-MEH2) proposed by Sharma (2007), which shows polymorphism (ss4bp, rs41352448) at 72,314 position of human ...
Single-nucleotide polymorphisms. *Identity by descent. *Genetic disorder. Applications. *Personalized medicine. *Predictive ...
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 ...
Caspi, A. (18 July 2003). "Influence of Life Stress on Depression: Moderation by a Polymorphism in the 5-HTT Gene". Science. ... In other words, as a single fertilized egg cell - the zygote - continues to divide, the resulting daughter cells change into ... MicroRNAs (miRNAs) are members of non-coding RNAs that range in size from 17 to 25 nucleotides. miRNAs regulate a large variety ... Direct detection of epigenetic marks in microorganisms is possible with single molecule real time sequencing, in which ...
The single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines. ... So XXY D. melanogaster are female, and D. melanogaster with a single X (X0), are male but sterile. There are some species of ... All single-copy Y-linked genes are hemizygous (present on only one chromosome) except in cases of aneuploidy such as XYY ... 47, XYY syndrome (simply known as XYY syndrome) is caused by the presence of a single extra copy of the Y chromosome in each of ...
Üksiku nukleotiidi polümorfismid ehk üksiknukleotiidsed polümorfismid (inglise single nucleotide polymorphisms; SNPs ( ... "Insertion-deletion polymorphisms (indels) as genetic markers in natural populations" BMC genetics, 9:8 ...
Mendelian (single-gene) inheritance was studied in a number of important disorders such as albinism, brachydactyly (short ... stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and ... Examples of single gene disorders include achondroplasia, cystic fibrosis, Duchenne muscular dystrophy, hereditary breast ... Molecular genetics involves the discovery of and laboratory testing for DNA mutations that underlie many single gene disorders ...
Single-nucleotide polymorphisms (SNPs), which are a big part of genetic variation in the human genome, and copy number ... Single-cell genome (DNA) sequencing[edit]. Single-cell DNA genome sequencing involves isolating a single cell, amplifying the ... "Genome-wide detection of single-nucleotide and copy-number variations of a single human cell". Science. 338 (6114): 1622-6. ... "Genome-wide detection of single-nucleotide and copy-number variations of a single human cell". Science. 338 (6114): 1622-6. ...
Two large genome-wide association studies linking single nucleotide polymorphisms (SNPs) to prostate cancer were published in ... No single gene is responsible for prostate cancer; many different genes have been implicated. Mutations in BRCA1 and BRCA2, ...
... it is likely to be replaced by MLST and Single Nucleotide Polymorphism-analysis (SNP). The pathogenetic pathways of ... The complete nucleotide sequences and characterization of the binding domains". European Journal of Biochemistry / FEBS. 214 (3 ... Lo, Hsueh-Hsia; Cheng, Wei-Shan (2015-01-01). "Distribution of virulence factors and association with emm polymorphism or ...
Several single nucleotide polymorphisms of this gene are known to have a significant correlation with blood uric acid.[12] ... Ethanol also increases the plasma concentrations of hypoxanthine and xanthine via the acceleration of adenine nucleotide ...
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 ...
To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is ... exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small indel mismatches. ... To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is ... Lesions IN Genomes) exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small ...
New biosensor chip detects single nucleotide polymorphism in real time with high sensitivity 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 ... Finland have discovered novel genes and mechanisms that can explain how a genomic variant in a single nucleotide polymorphism ...
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 ...
... are a type of polymorphism involving variation of a single base pair. Scientists are ... Single nucleotide polymorphism is way too many syllables, so you can understand why we just say "snip". And this is really a ... studying how single nucleotide polymorphisms, or SNPs (pronounced "snips"), in the human genome correlate with disease, drug ...
The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population ...
Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters. Mary K. Kuhner, Peter Beerli, Jon ... Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters. Mary K. Kuhner, Peter Beerli, Jon ... Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters. Mary K. Kuhner, Peter Beerli, Jon ... Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters Message Subject (Your Name) has ...
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 ...
Several previously unknown single nucleotide polymorphisms (SNPs) related to diet were discovered. Some were also related to ... Several previously unknown single nucleotide polymorphisms (SNPs) related to diet were discovered. Some were also related to ...
Single Nucleotide Polymorphisms. This specification addresses the need for a standardized data exchange format for Single ... Nucleotide Polymorphisms (SNPs) entities in the Life Sciences domains. As a result of recent advances in SNPs research, a large ... Single Nucleotide Polymorphisms. Acronym:. SNP. Version:. 1.0 Document Status:. formal ⓘ Publication Date:. November 2005. ...
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 ...
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). ...
In genetics, a single-nucleotide polymorphism (SNP /snɪp/; plural /snɪps/) is a germline substitution of a single nucleotide at ... A single-nucleotide variant (SNV) is a variation in a single nucleotide. SNVs differ from SNPs in that a SNV can be somatic and ... "Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on ... Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic ...
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 ...
... 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 ...
Associations of Polymorphism, Single Nucleotide with chemical compounds. *In humans, single nucleotide polymorphisms (SNPs) ... Biological context of Polymorphism, Single Nucleotide. *Our findings show that single-nucleotide polymorphisms (SNPs) in CYP3A5 ... Chemical compound and disease context of Polymorphism, Single Nucleotide. *A single nucleotide polymorphism of dopamine ... Psychiatry related information on Polymorphism, Single Nucleotide. *High impact information on Polymorphism, Single Nucleotide ...
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. ...
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 ...
Xing H, Chen X, Sun H, Han Y, Ding L, Chen X (2019) Association of regenerating gene 1A single-nucleotide polymorphisms and ... Dear, we read the publication on "Association of regenerating gene (*REG) 1A single-nucleotide polymorphisms and nasopharyngeal ... The examples of other genetic polymorphisms that relate to risk of developing NPC are COX-2 gene polymorphism [2] and 5′-UTR ... Guo Z, Wang Y, Zhao Y, Jin Y, An L, Xu H, Liu Z, Chen X, Zhou H, Wang H, Zhang W (2019) A Functional 5-UTR polymorphism of MYC ...
We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora ...
  • To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is PCR-amplified and subjected to heteroduplex formation, followed by CEL I cleavage. (psu.edu)
  • What are single nucleotide polymorphisms (SNPs)? (medlineplus.gov)
  • Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation among people. (medlineplus.gov)
  • They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person's genome. (medlineplus.gov)
  • Single nucleotide polymorphisms (SNPs) are a type of polymorphism involving variation of a single base pair. (genome.gov)
  • Scientists are studying how single nucleotide polymorphisms, or SNPs (pronounced "snips"), in the human genome correlate with disease, drug response, and other phenotypes. (genome.gov)
  • However, one still needs a method to sort through potentially thousands of SNPs, the vast majority of which will have no detectable function, to find those polymorphisms that affect a phenotype. (pnas.org)
  • To accomplish this, an unbiased approach was chosen whereby polymorphisms in relevant genes were identified and the ability of those SNPs to affect a cancer-relevant phenotype, apoptosis, or programmed cell death in response to DNA damage was measured. (pnas.org)
  • Several previously unknown single nucleotide polymorphisms (SNPs) related to diet were discovered. (eurekalert.org)
  • This specification addresses the need for a standardized data exchange format for Single Nucleotide Polymorphisms (SNPs) entities in the Life Sciences domains. (omg.org)
  • Single-nucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. (genetics.org)
  • In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of θ = 0.000997. (genetics.org)
  • Alternatively, discovery of single-nucleotide polymorphisms (SNPs, which include single-base changes and insertion/deletions) in genic sequence would provide a source of markers that can be analyzed via PCR and other approaches. (genetics.org)
  • one of them is the rapid advancement in high‐throughput single nucleotide polymorphisms (SNPs) genotyping technologies which has enabled researchers to comprehensively interrogate the entire human genome. (els.net)
  • We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. (ebscohost.com)
  • Ivec, a major Belgian research center, and Pansonic have unveiled a set of new technologies to make lab-on-chip sensors that can detect Single Nucleotide Polymorphisms (SNPs) in DNA. (medgadget.com)
  • Sequence variation in human genes is largely confined to single-nucleotide polymorphisms (SNPs) and is valuable in tests of association with common diseases and pharmacogenetic traits. (nih.gov)
  • As a case study for single-nucleotide polymorphism (SNP) identification in species for which little or no sequence information is available, we investigated several approaches to identifying SNPs in two passerine bird species: pied and collared flycatchers ( Ficedula hypoleuca and F. albicollis ). (wiley.com)
  • All approaches were successful in identifying sequence polymorphism and over 50 candidate SNPs per species were identified from ≈ 9.1 kb of sequence. (wiley.com)
  • The overall nucleotide diversity of flycatchers was 2.3-2.7 × 10 −3 , which is ≈ 3-6 times higher than observed in recent studies of human SNPs. (wiley.com)
  • We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). (pnas.org)
  • Individualize or personalize etoposide chemotherapy toward small cell lung cancer (SCLC) with maximizing effectiveness via assay single nucleotide polymorphisms (SNPs) of relative etoposide target - topoisomerase II, and minimizing risk via assay single nucleotide polymorphisms (SNPs) of relative etoposide target - CYP4503A4, based on precisely sequencing drug targets' genes. (clinicaltrials.gov)
  • Objective: To determine if single nucleotide polymorphisms (SNPs) in interleukin (IL) IL-1A, IL-1B, IL-1RN, IL-2, IL-9, and IL-9R were associated with chronic beryllium disease (CBD) and beryllium sensitization (BeS). (cdc.gov)
  • We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). (plos.org)
  • Single nucleotide polymorphisms (SNPs) are single nucleotide variations which comprise the most wide spread source of genetic diversity in the genome. (mdpi.com)
  • The aim of this study was to determine whether the known rs12979860 and rs8099917 single nucleotide polymorphisms (SNPs) in interleukin (IL)28B region, influence clinical features and natural history of bronchiolitis. (biomedsearch.com)
  • DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. (asm.org)
  • Each of us carries in our genomes about 10 million genetic variations called single nucleotide polymorphisms (SNPs), which represent a difference of just one letter in the genetic code. (medicalxpress.com)
  • We genotyped the two ADIPOQ SNPs in 140 unrelated T2DM patients and 66 nondiabetic controls using the polymerase chain reaction-restriction fragment length polymorphism assay. (who.int)
  • Recently, SNPs (single nucleotide polymorphism) have become the markers of choice for genetic analyses in rainbow trout as they are highly abundant, cost-effective and are amenable for high throughput genotyping. (frontiersin.org)
  • Several simulation studies have suggested that a high-density single-nucleotide polymorphisms (SNPs) marker set may be as useful as a traditional microsatellites (MS) marker set in performing whole-genome linkage analysis. (harvard.edu)
  • They occur in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. (wellmark.com)
  • SNPs, which are single base-pair variations in the DNA sequence of the genome, have been found to be associated with breast cancer and are common in the population, but confer only small increases in risk. (wellmark.com)
  • We detected deletions as small as 20 kb when covered by at least three single-nucleotide polymorphisms (SNPs) and duplications as small as 150 kb when covered by at least six SNPs, with only one false-positive signal in six patients. (bmj.com)
  • Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. (unl.edu)
  • Single nucleotide polymorphisms (SNPs) in the interleukin (IL)28B locus have been associated with a sustained virological response (SVR) in interferon-ribavirin (IFN-RBV)-treated chronic hepatitis C virus (HCV)-infected patients in European and African populations. (scielo.br)
  • OBJECTIVE: This paper aims at studying the influence of single-nucleotide polymorphisms (SNPs) on cancer risk, tumor recurrence, and survival in head and neck (H&N) cancer patients. (diva-portal.org)
  • In the present work, we used the genotyping-by-sequencing (GBS) approach for genome-wide identification of single nucleotide polymorphisms (SNPs) to assess the level of genetic diversity in a collection of 78 olive cultivars. (ishs.org)
  • 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. (diva-portal.org)
  • Single nucleotide polymorphisms (SNPs) in the Plasmodium falciparum dihydrofolate reductase ( dhfr ), and dihydropteroate synthetase ( dhps ), and chloroquine resistance transporter ( Pfcrt ) genes are used as molecular markers of P. falciparum resistance to sulfadoxine/pyrimethamine and chloroquine. (ajtmh.org)
  • The SSOP-ELISA of all dhfr , dhps , or Pfcrt SNPs on 88 samples can be performed in a single day and provides quick and reproducible results. (ajtmh.org)
  • We searched the Celera Discovery System database for single nucleotide polymorphisms (SNPs) between C57BL/6J (B6) and 129S1/SvImJ in the Ath17 region and found defined blocks of high and low diversity and one polymorphic region of over 4 Mb surrounded by nonpolymorphic regions. (umd.edu)
  • Single nucleotide polymorphisms (SNPs) may act as biological markers, as they can relate to the genes that are associated with various complex diseases such as heart diseases, diabetes, cancer, schizophrenia, blood pressure, migraine, and Alzheimer. (springer.com)
  • Thirty-five single nucleotide polymorphism (SNP) markers with a high minor allele frequency in East African landraces were used. (cambridge.org)
  • 2014) Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity. (plos.org)
  • Single-nucleotide polymorphism Unique-event polymorphism Human Y-chromosome DNA haplogroups List of Y-STR markers Sequence information for 218 M series markers published by 2001 ISOGG Y-DNA SNP Index - 2007 Karafet et al. (wikipedia.org)
  • In addition to being susceptibility markers, several of these polymorphisms are emerging to be important for response to chemotherapy/radiotherapy and survival of patients. (dovepress.com)
  • Therefore, it is hypothesized that single nucleotide polymorphisms will be valuable genetic markers in individual-based prognosis and therapy in future. (dovepress.com)
  • Keim P , Kalif A , Schupp J , Hill K , Travis SE , Richmond K , Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. (cdc.gov)
  • Identification of genes that confer disease susceptibility can be facilitated by studying DNA markers such as single nucleotide polymorphism (SNP) associated with a disease trait. (igi-global.com)
  • We report here two highly reliable ribosomal DNA-based single nucleotide polymorphism (SNP) markers, CxpG2T and CxpA2d, for detecting Cx. (ajtmh.org)
  • Single-nucleotide polymorphism (SNP) molecular markers were identified in DNA sequences from 16 distinct regions of the genome of 24 strains of X. fastidiosa from coffee and citrus plants. (apsnet.org)
  • To this end, 31 single nucleotide polymorphism (SNP) markers were developed for seven bovine chemokine genes. (unl.edu)
  • Accessing genetic variation: genotyping single nucleotide polymorphisms. (springer.com)
  • We used a single-nucleotide polymorphism (SNP) genotyping typing system based on the multilocus sequence type (MLST) database to investigate the epidemiology of CA-MRSA and methicillin-sensitive S. aureus (MSSA) over a 12-month period in three remote Aboriginal communities of Northern Australia. (asm.org)
  • In this report, the United States Single Nucleotide Polymorphism (SNP) Genotyping market is valued at USD XX million in 2016 and is expected to reach USD XX million by the end of 2022, growing at a CAGR of XX% between 2016 and 2022. (rnrmarketresearch.com)
  • Genotyping of polymorphisms was done using polymerase chain reaction. (molvis.org)
  • Rapid, field-deployable method for genotyping and discovery of single-nucleotide polymorphisms associated with drug resistance in Plasmodium falciparum. (broadinstitute.org)
  • This study of 1,103 individuals infected with human immunodeficiency virus assessed the usefulness of genotyping a HCP5 single-nucleotide polymorphism (SNP), rs2395029, in relation to ABC-HSR. (epfl.ch)
  • We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. (asm.org)
  • Dear, we read the publication on "Association of regenerating gene (*REG) 1A single-nucleotide polymorphisms and nasopharyngeal carcinoma (NPC) susceptibility in southern Chinese population" with a great interest and would like to share some ideas on this report. (springer.com)
  • Xing H, Chen X, Sun H, Han Y, Ding L, Chen X (2019) Association of regenerating gene 1A single-nucleotide polymorphisms and nasopharyngeal carcinoma susceptibility in southern Chinese population. (springer.com)
  • Sun N, Wang XQ (2019) Correlation between COX-2 gene polymorphism and susceptibility to nasopharyngeal carcinoma. (springer.com)
  • A common type of genetic variation in the genome, known as single nucleotide polymorphism, has been found to be associated with susceptibility to lung cancer. (dovepress.com)
  • Here we will review some of the most important single nucleotide polymorphisms in the metabolic pathways that may modulate susceptibility, prognosis, and therapy in NSCLC. (dovepress.com)
  • We previously reported that the G/G genotype of a resistin gene promoter single nucleotide polymorphism (SNP) at -420 increases type 2 diabetes susceptibility by enhancing promoter activity. (unboundmedicine.com)
  • The C1858T polymorphism in the Ptpn22 gene is associated with increased susceptibility to several autoimmune disorders including Type 1 Diabetes (T1D). (jimmunol.org)
  • Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions (regions between genes). (wikipedia.org)
  • Overall, the degree of nucleotide polymorphism across these human genes, and orthologous great ape sequences, is highly variable and is correlated with the effects of functional conservation on gene sequences. (nih.gov)
  • The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. (scirp.org)
  • Interestingly, many of these polymorphisms are found in the genes that regulate major pathways of carcinogen metabolism (cytochrome P450 genes), detoxification (glutathione S -transferases), adduct removal (DNA repair genes), cell growth/apoptosis (TP53/MDM2), the immune system (cytokines/chemokines), and membrane receptors (nicotinic acetylcholine and dopaminergic receptors). (dovepress.com)
  • Common diseases or traits in humans are often influenced by complex interactions among multiple genes as well as environmental and lifestyle factors rather than being attributable to a genetic variation within a single gene. (igi-global.com)
  • Researchers at the University of Oulu in Finland have discovered novel genes and mechanisms that can explain how a genomic variant in a single nucleotide polymorphism (SNP) rs11672691 influences prostate cancer aggressiveness. (medicalxpress.com)
  • Recently, single-nucleotide polymorphism (SNP) arrays have been successfully applied to identify cryptic oncogenic lesions harboring genes and gene mutations in malignant hematologic diseases such as acute lymphoblastic or acute myeloid leukemia. (haematologica.org)
  • We identified 26 genes involved in glycosylation and examined 93 single nucleotide polymorphisms (SNP) with a minor allele frequency of ≥0.05 in relation to incident ovarian cancer. (aacrjournals.org)
  • Genome-wide association studies (GWAS) identified a single nucleotide polymorphism (SNP) located on chromosome 19 within an 80-KB region containing the genes encoding the lambda IFNs. (scielo.br)
  • 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. (diva-portal.org)
  • Association of single nucleotide polymorphisms in CAPN1 and CAST genes with beef tenderness from Spanish commercial feedlots. (gc.ca)
  • 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. (nih.gov)
  • Shen W, Lim CL, Gao Z. A ferrofluid-based homogeneous assay for highly sensitive and selective detection of single-nucleotide polymorphisms. (springer.com)
  • SNP mapping arrays are a relatively new technique with the capacity to characterize both copy number and allelic imbalance aberrations in a single assay ( 12 ). (aacrjournals.org)
  • A single nucleotide polymorphism (SNP), a variation at a single site in DNA , is the most frequent type of variation in the genome. (wikipedia.org)
  • Polymorphisms occur within the human genome an average of once every 1,000 nucleotides ( 5 , 6 ). (pnas.org)
  • plural /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome. (wikipedia.org)
  • For example, at a specific base position in the human genome, the C nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations - C or A - are said to be the alleles for this specific position. (wikipedia.org)
  • A single-nucleotide polymorphism ( 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 (or other shared sequence) differs between members of a species or paired chromosomes in an individual. (isogg.org)
  • A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. (springer.com)
  • Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. (springer.com)
  • Higher nucleotide diversity in the avian genome could be due to the relatively older age of flycatcher populations, compared with humans, and/or a higher long-term effective population size. (wiley.com)
  • A single-nucleotide polymorphism ( SNP , pronounced snip ) is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). (medicalxpress.com)
  • The most common variations are single-nucleotide polymorphisms (SNP), which occur approximately once every 100 to 300 bp in the human genome and constitute an immense source of information for unraveling the heterogeneity of human cancer pathogenesis, clinical course, and response to treatment. (aacrjournals.org)
  • Pearson T , Busch JD , Ravel J , Read TD , Rhoton SD , U'Ren JM , Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. (cdc.gov)
  • Ang isang single-nucleotide polymorphism o SNP ay isang pagkakaiba ng sekwensiyang DNA na nangyayari kapag ang isang nucleotide - A, T, C o G sa genome o ibang mga pinagsasaluhang sekwensiya ay magkaiba sa pagitan ng mga kasapi ng isang species o mga magkapares na kromosoma sa tao. (wikipedia.org)
  • Single-nucleotide polymorphism arrays allow for genome-wide profiling of copy-number alterations and copy-neutral runs of homozygosity at high resolution. (haematologica.org)
  • Whole-genome sequence (WGS)-single-nucleotide polymorphism (SNP)-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. (frontiersin.org)
  • A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. (lu.se)
  • We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the Xba I restriction enzyme sites in the genome. (asm.org)
  • In this study, we recovered the nucleotide sequences flanking each Xba I restriction enzyme site in the O157 genome and used these sequences to examine genomic differences across a well-defined strain set of O157 isolates. (asm.org)
  • A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. (nih.gov)
  • Single nucleotides may be changed (substitution), removed ( deletions ) or added ( insertion ) to a polynucleotide sequence. (isogg.org)
  • Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. (scirp.org)
  • No study on the nucleotides sequence of this gene has been reported in Nigeria. (scirp.org)
  • SNP, or single nucleotide polymorphism, is a genetic variation in a person's DNA sequence that occurs when a single nucleotide is replaced by one of the other three nucleotides. (igi-global.com)
  • Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms ( SNP s) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. (plantphysiol.org)
  • Each single nucleotide region is considered independent of each other region when determining the distance between sequences. (scribd.com)
  • Interestingly, polymorphism of microsatellite/intron loci in the source species appeared to be a positive predictor of nucleotide diversity in homologous flycatcher sequences. (wiley.com)
  • A single-nucleotide variant (SNV) is a variation in a single nucleotide. (wikipedia.org)
  • 2017. https://www.tabers.com/tabersonline/view/Tabers-Dictionary/755124/all/single_nucleotide_polymorphism. (tabers.com)
  • But at certain locations there are differences - these variations are called polymorphisms. (snpedia.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)
  • Lesions IN Genomes) exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small indel mismatches. (psu.edu)
  • There were no association between the BCRP C421A polymorphism and clinicopathological or epidemiological factors including age, gender, tumor grade, stage, cigarette smoking, family history of cancer and body mass index. (aacrjournals.org)
  • shows the clinical interrelation for only one variant, the 2022 C/T. The interesting question is whether there is any effect of other genetic polymorphisms that are not studied in the present report. (springer.com)
  • These results suggest that genetic polymorphisms in the glycoslyation process may be novel risk factors for ovarian cancer. (aacrjournals.org)
  • Thus, there is emerging consensus that most of the genetic component of ovarian cancer risk is due to genetic polymorphisms that confer low to moderate risk. (aacrjournals.org)
  • 2004) Selecting a maximally informative set of single‐nucleotide polymorphisms for association analyses using linkage disequilibrium. (els.net)
  • Further analyses on single-gene level are necessary to uncover the mechanisms that are involved in the pathogenesis of myeloproliferative neoplasms. (haematologica.org)
  • In this study, we cloned the full-length open reading frame (ORF) of the leptin-a gene in the orange-spotted grouper, searched for polymorphisms, and performed association analyses between these polymorphisms and seven growth traits. (mdpi.com)
  • Over the greater than 76 kbp, mean nucleotide diversity expressed as Watterson's [theta] was 0.00097. (unl.edu)
  • Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana . (unl.edu)
  • In molecular biology , SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. (wikipedia.org)
  • We demonstrate that our assays (i) identify both known and novel polymorphisms, (ii) detect multiple genotypes indicative of mixed infections, and (iii) distinguish between variants when multiple copies of a locus are present. (broadinstitute.org)
  • Syndrome diagnosis with single-nucleotide polymorphism (SNP) microarray. (edu.au)
  • Hybridization of yeast DNA from a test strain to a microarray with redundant reference DNA simply and rapidly identifies most of the polymorphisms between the two strains. (sciencemag.org)
  • The impact of genetic factors has been studied with great effort leading to the identification of several mutations and gene polymorphisms as risk factors. (molvis.org)
  • Conclusions: Carriers with the C/C genotype of the BCRP C421A polymorphism are at risk of developing non-papillary RCC. (aacrjournals.org)
  • GT polymorphism was significantly associated with body weight (BWT) and body width (BWH), with the AB (TG/GT) genotype showing positive effects on growth traits. (mdpi.com)
  • The most common type of variant is the single nucleotide polymorphism (SNP). (nih.gov)
  • Some genetic studies reported that single nucleotide polymorphism (SNP) involving variant rs1344706 from the ZNF804A gene in human beings is associated with the risk of schizophrenia in several populations. (dovepress.com)
  • The399Ile polymorphism of TLR4 may be responsible for altered immune response to microbial infection in variant carriers and represent a mechanism of triggering overproduction of proinflammatory cytokines and long-term inflammation in jSpA. (sigmaaldrich.com)
  • We have evaluated 31 primary ovarian cancers and matched normal DNA for loss of heterozygosity and copy number alterations using 500K single nucleotide polymorphism arrays. (aacrjournals.org)
  • Association between IL-1A single nucleotide polymorphisms and chronic beryllium disease and beryllium sensitization. (cdc.gov)
  • We studied the association between type 1 diabetes and 4 VDR gene polymorphisms [‎Bb, Ff, Aa and Tt]‎ in an Iranian population. (who.int)
  • 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)
  • 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)
  • Evaluation of interleukin 28B single nucleotide polymorphisms in infants suffering from bronchiolitis. (biomedsearch.com)
  • 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)
  • In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). (springer.com)
  • Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. (springer.com)
  • Deng H, Shen W, Gao Z. Colorimetric detection of single nucleotide polymorphisms in the presence of 10(3)-fold excess of a wild-type gene. (springer.com)
  • Wee EJ, Shiddiky MJ, Brown MA, Trau M. eLCR: electrochemical detection of single DNA base changes via ligase chain reaction. (springer.com)
  • Shen W, Deng H, Teo AK, Gao Z. Colorimetric detection of single-nucleotide polymorphisms with a real-time PCR-like sensitivity. (springer.com)
  • In this work, we measured the primer extension kinetics of the Klenow fragment ( exo -) to achieve rapid detection of single nucleotide polymorphism (SNP). (rsc.org)
  • For example, a single-base mutation in the APOE (apolipoprotein E) gene is associated with a lower risk for Alzheimer's disease. (wikipedia.org)
  • Common and rare SORLA single nucleotide polymorphisms have been associated with the development of Alzheimer's disease. (medicalxpress.com)
  • As the alignment depth was shallow (only four strains), the density of mutations in the promoter of a single gene was correspondingly low. (plantphysiol.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)
  • 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)
  • Some of these polymorphisms have been shown to alter the level of mRNA, and protein structure and function. (dovepress.com)
  • For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. (medlineplus.gov)
  • T polymorphisms showed complete linkage and were analyzed together. (mdpi.com)
  • Single nucleotide polymorphism (SNP) discovery and linkage mapping of" by William M. Grosse, Steven M. Kappes et al. (unl.edu)
  • A single nucleotide polymorphism in TLR4 is linked with the risk of HIV-1 infection. (medworm.com)
  • CONCLUSION: TLR4 (Asp299Gly) gene polymorphism is a risk factor in HIV-1 disease. (medworm.com)
  • Single nucleotide polymorphism of toll-like receptor 4 (TLR4) is associated with juvenile spondyloarthritis in Croatian population. (sigmaaldrich.com)
  • Miserez AR, Muller PY, Barella L, Schwietert M, Erb P, Vernazza PL, Battegay M: A single-nucleotide polymorphism in the sterol-regulatory element-binding protein-1c gene is predictive of HIV-related hyperlipo-proteinemia. (grstiftung.ch)
  • Both the matching and the single-base mismatching targets were used as the primer in the kinetic measurements to identify the single nucleotide polymorphism. (rsc.org)
  • Single Nucleotide Polymorphism and its Application in Mapping Loci Involved in Developing Human Diseases and Traits. (igi-global.com)
  • Using a candidate gene approach based on an N2 × CB4856 recombinant inbred panel in combination with mutant analysis, complementation, and transgenic studies, we show that a single nucleotide polymorphism in tra-3 leads to mutation F96L in the encoded calpain-like protease. (wur.nl)
  • In this population, the analysis of a single SNP, rs12979860, successfully predicts SVR in the IFN-RBV treatment of HCV. (scielo.br)
  • Mutation detection and single-molecule counting using isothermal rolling-circle amplification. (springer.com)
  • This polymorphism codes for an asparagine to aspartic acid substitution at amino acid 40 in the amino-terminus, thereby removing a potential extracellular glycosylation site. (nih.gov)

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