Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Genetic Variation: Genotypic differences observed among individuals in a population.Heterozygote: An individual having different alleles at one or more loci regarding a specific character.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Homozygote: An individual in which both alleles at a given locus are identical.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Linkage Disequilibrium: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.HLA-DRB1 Chains: A subtype of HLA-DRB beta chains that includes over one hundred allele variants. The HLA-DRB1 subtype is associated with several of the HLA-DR SEROLOGICAL SUBTYPES.Crosses, Genetic: Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Genetic Association Studies: The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.Asian Continental Ancestry Group: Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.HLA-DQ Antigens: A group of the D-related HLA antigens found to differ from the DR antigens in genetic locus and therefore inheritance. These antigens are polymorphic glycoproteins comprising alpha and beta chains and are found on lymphoid and other cells, often associated with certain diseases.HLA-DR Antigens: A subclass of HLA-D antigens that consist of alpha and beta chains. The inheritance of HLA-DR antigens differs from that of the HLA-DQ ANTIGENS and HLA-DP ANTIGENS.Genes, Lethal: Genes whose loss of function or gain of function MUTATION leads to the death of the carrier prior to maturity. They may be essential genes (GENES, ESSENTIAL) required for viability, or genes which cause a block of function of an essential gene at a time when the essential gene function is required for viability.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Genes, Dominant: Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.European Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Europe.HLA-B Antigens: Class I human histocompatibility (HLA) surface antigens encoded by more than 30 detectable alleles on locus B of the HLA complex, the most polymorphic of all the HLA specificities. Several of these antigens (e.g., HLA-B27, -B7, -B8) are strongly associated with predisposition to rheumatoid and other autoimmune disorders. Like other class I HLA determinants, they are involved in the cellular immune reactivity of cytolytic T lymphocytes.Genes, Recessive: Genes that influence the PHENOTYPE only in the homozygous state.Apolipoprotein E4: A major and the second most common isoform of apolipoprotein E. In humans, Apo E4 differs from APOLIPOPROTEIN E3 at only one residue 112 (cysteine is replaced by arginine), and exhibits a lower resistance to denaturation and greater propensity to form folded intermediates. Apo E4 is a risk factor for ALZHEIMER DISEASE and CARDIOVASCULAR DISEASES.Suppression, Genetic: Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Minisatellite Repeats: Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Heterozygote Detection: Identification of genetic carriers for a given trait.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Risk Factors: An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.HLA-DQ alpha-Chains: Transmembrane proteins that form the alpha subunits of the HLA-DQ antigens.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Genes, Plant: The functional hereditary units of PLANTS.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Epistasis, Genetic: A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Genetic Testing: Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.HLA Antigens: Antigens determined by leukocyte loci found on chromosome 6, the major histocompatibility loci in humans. They are polypeptides or glycoproteins found on most nucleated cells and platelets, determine tissue types for transplantation, and are associated with certain diseases.Apolipoproteins E: A class of protein components which can be found in several lipoproteins including HIGH-DENSITY LIPOPROTEINS; VERY-LOW-DENSITY LIPOPROTEINS; and CHYLOMICRONS. Synthesized in most organs, Apo E is important in the global transport of lipids and cholesterol throughout the body. Apo E is also a ligand for LDL receptors (RECEPTORS, LDL) that mediates the binding, internalization, and catabolism of lipoprotein particles in cells. There are several allelic isoforms (such as E2, E3, and E4). Deficiency or defects in Apo E are causes of HYPERLIPOPROTEINEMIA TYPE III.Genes, Fungal: The functional hereditary units of FUNGI.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.China: A country spanning from central Asia to the Pacific Ocean.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.HLA-A Antigens: Polymorphic class I human histocompatibility (HLA) surface antigens present on almost all nucleated cells. At least 20 antigens have been identified which are encoded by the A locus of multiple alleles on chromosome 6. They serve as targets for T-cell cytolytic responses and are involved with acceptance or rejection of tissue/organ grafts.African Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Africa.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Dinucleotide Repeats: The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.HLA-C Antigens: Class I human histocompatibility (HLA) antigens encoded by a small cluster of structural genes at the C locus on chromosome 6. They have significantly lower immunogenicity than the HLA-A and -B determinants and are therefore of minor importance in donor/recipient crossmatching. Their primary role is their high-risk association with certain disease manifestations (e.g., spondylarthritis, psoriasis, multiple myeloma).Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Cohort Studies: Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Genotyping Techniques: Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Fungal Proteins: Proteins found in any species of fungus.Genes, MHC Class II: Genetic loci in the vertebrate major histocompatibility complex that encode polymorphic products which control the immune response to specific antigens. The genes are found in the HLA-D region in humans and in the I region in mice.Trinucleotide Repeats: Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes.Genes, Suppressor: Genes that have a suppressor allele or suppressor mutation (SUPPRESSION, GENETIC) which cancels the effect of a previous mutation, enabling the wild-type phenotype to be maintained or partially restored. For example, amber suppressors cancel the effect of an AMBER NONSENSE MUTATION.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.

Standardized nomenclature for inbred strains of mice: sixth listing. (1/28798)

Rules for designating inbred strains of mice are presented, along with a list of strains with their origins and characteristics, a table of biochemical polymorphisms, and standard subline designations.  (+info)

Lack of genic similarity between two sibling species of drosophila as revealed by varied techniques. (2/28798)

Acrylamide gel electrophoresis was performed on the enzyme xanthine dehydrogenase in sixty isochromosomal lines of Drosophila persimilis from three geographic populations. Sequential electrophoretic analysis using varied gel concentrations and buffers revealed twenty-three alleles in this species where only five had been described previously. These new electrophoretic techniques also detected a profound increase in divergence of gene frequencies at this locus between D. persimilis and its sibling species D. pseudoobscura. The implications of these results for questions of speciation and the maintenance of genetic variability are discussed.  (+info)

Genetic heterogeneity within electrophoretic "alleles" of xanthine dehydrogenase in Drosophila pseudoobscura. (3/28798)

An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed a total of 37 allelic classes out of the 146 genomes examined where only 6 had been previously revealed by the usual method of gel electrophoresis. This immense increase in genic variation also showed previously unsuspected population differences between the main part of the species distribution and the isolated population of Bogota population. The average heterozygosity at the Xdh locus is at least 72% in natural populations. This result, together with the very large number of alleles segregating and the pattern of allelic frequencies, has implications for theories of genetic polymorphism which are discussed.  (+info)

An overview of the evolution of overproduced esterases in the mosquito Culex pipiens. (4/28798)

Insecticide resistance genes have developed in a wide variety of insects in response to heavy chemical application. Few of these examples of adaptation in response to rapid environmental change have been studied both at the population level and at the gene level. One of these is the evolution of the overproduced esterases that are involved in resistance to organophosphate insecticides in the mosquito Culex pipiens. At the gene level, two genetic mechanisms are involved in esterase overproduction, namely gene amplification and gene regulation. At the population level, the co-occurrence of the same amplified allele in distinct geographic areas is best explained by the importance of passive transportation at the worldwide scale. The long-term monitoring of a population of mosquitoes in southern France has enabled a detailed study to be made of the evolution of resistance genes on a local scale, and has shown that a resistance gene with a lower cost has replaced a former resistance allele with a higher cost.  (+info)

Detailed methylation analysis of the glutathione S-transferase pi (GSTP1) gene in prostate cancer. (5/28798)

Glutathione-S-Transferases (GSTs) comprise a family of isoenzymes that provide protection to mammalian cells against electrophilic metabolites of carcinogens and reactive oxygen species. Previous studies have shown that the CpG-rich promoter region of the pi-class gene GSTP1 is methylated at single restriction sites in the majority of prostate cancers. In order to understand the nature of abnormal methylation of the GSTP1 gene in prostate cancer we undertook a detailed analysis of methylation at 131 CpG sites spanning the promoter and body of the gene. Our results show that DNA methylation is not confined to specific CpG sites in the promoter region of the GSTP1 gene but is extensive throughout the CpG island in prostate cancer cells. Furthermore we found that both alleles are abnormally methylated in this region. In normal prostate tissue, the entire CpG island was unmethylated, but extensive methylation was found outside the island in the body of the gene. Loss of GSTP1 expression correlated with DNA methylation of the CpG island in both prostate cancer cell lines and cancer tissues whereas methylation outside the CpG island in normal prostate tissue appeared to have no effect on gene expression.  (+info)

Identification of DNA polymorphisms associated with the V type alpha1-antitrypsin gene. (6/28798)

alpha1-Antitrypsin (alpha1-AT) is a highly polymorphic protein. The V allele of alpha1-AT has been shown to be associated with focal glomerulosclerosis (FGS) in Negroid and mixed race South African patients. To identify mutations and polymorphisms in the gene for the V allele of alpha1-AT in five South African patients with FGS nephrotic syndrome DNA sequence analysis and restriction fragment length polymorphisms of the coding exons were carried out. Four of the patients were heterozygous for the BstEII RFLP in exon III [M1(Val213)(Ala213)] and one patient was a M1(Ala213) homozygote. The mutation for the V allele was identified in exon II as Gly-148 (GGG)-->Arg (AGG) and in all patients was associated with a silent mutation at position 158 (AAC-->AAT). The patient who was homozygous for (Ala213) also had a silent mutation at position 256 in exon III (GAT-->GAC) which was not present in any of the other four patients. Although the V allele of alpha1-AT is not associated with severe plasma deficiency, it may be in linkage disequilibrium with other genes on chromosome 14 that predispose to FGS. Furthermore, the associated silent mutation at position 158 and the Ala213 polymorphism are of interest, as these could represent an evolutionary intermediate between the M1(Ala213) and M1(Val213) subtypes.  (+info)

The alphaE-catenin gene (CTNNA1) acts as an invasion-suppressor gene in human colon cancer cells. (7/28798)

The acquisition of invasiveness is a crucial step in the malignant progression of cancer. In cancers of the colon and of other organs the E-cadherin/catenin complex, which is implicated in homotypic cell-cell adhesion as well as in signal transduction, serves as a powerful inhibitor of invasion. We show here that one allele of the alphaE-catenin (CTNNA1) gene is mutated in the human colon cancer cell family HCT-8, which is identical to HCT-15, DLD-1 and HRT-18. Genetic instability, due to mutations in the HMSH6 (also called GTBP) mismatch repair gene, results in the spontaneous occurrence of invasive variants, all carrying either a mutation or exon skipping in the second alphaE-catenin allele. The alphaE-catenin gene is therefore, an invasion-suppressor gene in accordance with the two-hit model of Knudsen for tumour-suppressor genes.  (+info)

Correlation between the status of the p53 gene and survival in patients with stage I non-small cell lung carcinoma. (8/28798)

The association of p53 abnormalities with the prognosis of patients with non-small cell lung carcinoma (NSCLC) has been extensively investigated to date, however, this association is still controversial. Therefore, we investigated the prognostic significance of p53 mutations through exons 2 to 11 and p53 protein expression in 103 cases of stage I NSCLC. p53 mutations were detected in 49 of 103 (48%) tumors. Two separate mutations were detected in four tumors giving a total of 53 unique mutations in 49 tumors. Ten (19%) of mutations occurred outside exons 5-8. Positive immunohistochemical staining of p53 protein was detected in 41 of 103 (40%) tumors. The concordance rate between mutations and protein overexpression was only 69%. p53 mutations, but not expression, were significantly associated with a shortened survival of patients (P<0.001). Furthermore, we investigated the correlation between the types of p53 mutations and prognosis. p53 missense mutations rather than null mutations were associated with poor prognosis (P < 0.001 in missense mutations and P=0.243 in null mutations). These results indicated that p53 mutations, in particular missense mutations, rather than p53 expression could be a useful molecular marker for the prognosis of patients with surgically resected stage I NSCLC.  (+info)

*Transmission disequilibrium test

The motivating idea for this modification is the fact that, while the transmissions of both allele from parents to a child are ... These can be represented by the transmitted and the non-transmitted alleles M 1 {\displaystyle M_{1}} and M 2 {\displaystyle M ... the number of times a parent transmits the same allele to both affected children with the number of times a different allele is ... A rewording of this statement would be that the type of the transmitted allele is not, in general, independent of the type of ...

*Stepwise mutation model

These include number of alleles, observed and expected heterozygosity, and allele frequencies. The SMM model takes into account ... Variance in allele sizes are used to make inferences about the genetic distance between individuals or populations. By ... The original model assumes that if an allele has a mutation that causes it to change in state, mutations that occur in ... The SMM is distinguished from the Kimura-Crow model, also known as the infinite alleles model (IAM), in that as the population ...

*Ancestry-informative marker

A person having this allele is thus more likely to have Sub-Saharan African ancestors. Examining a suite of these markers more ... As one example, the Duffy Null allele (FY*0) has a frequency of almost 100% of Sub-Saharan Africans, but occurs very ...

*Tag SNP

... the alleles are assigned so their frequencies agree with the allele frequencies of t. When multiple tagging SNPs have the same ... Allele Specific PCR, Somatic cell hybrids). These methods distinguish which allele is present at which chromosome by separating ... If the alleles at those loci are non-randomly inherited then we say that they are at linkage disequilibrium (LD). LD is most ... The Affymetrix platform prints DNA probes on a glass or silicone chip that hybridize to specific alleles in the sample DNA. The ...

*Pseudodeficiency alleles

A pseudodeficiency allele may indicate a deficiency of the enzyme assay method, or it may reflect incomplete understanding of ... A pseudodeficiency allele or pseudodeficiency mutation is a mutation that alters the protein product or changes the gene's ... Because of pseudodeficiency alleles, the results of enzyme assay testing in one population cannot be generalized to other ... One possible cause of false positive results is a pseudodeficiency allele. Disease may also be present, but at a subclinical ...

*Infinite alleles model

Beyond this number of alleles, the selective advantage of presence of those alleles in heterozygous genotypes would be ... that there were a large enough number of alleles so that any mutation would lead to a different allele (that is the probability ... The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and ... The effective number of alleles n maintained in a population is defined as the inverse of the homozygosity, that is n = 1 F = 4 ...

*Allele

It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that ... An allele (/əˈliːl/) is a variant form of a given gene. Sometimes, different alleles can result in different observable ... The term "wild type" allele is sometimes used to describe an allele that is thought to contribute to the typical phenotypic ... for the mutant allele. It is now appreciated that most or all gene loci are highly polymorphic, with multiple alleles, whose ...

*Null allele

One example of a null allele is the 'O' blood type allele in the human A, B and O blood type system. The alleles for the A- ... Null alleles are difficult to identify because a heterozygous individual for one null allele and one active allele is ... Mice homozygous for a null allele for insulin die 48-72 hours after birth. A microsatellite null allele is an allele at a ... The allele for O blood type, however, is a mutated version of the allele for the A-antigen, with a single base pair change due ...

*Allele age

Estimating allele age based on the allele's frequency is based on the fact that alleles in high frequency are older than ... Allele age (or mutation age) is the amount of time elapsed since an allele first appeared due to mutation. Estimating the time ... Allele age can be estimated based on (1) the frequency of the allele in a population and (2) the genetic variation that occurs ... This same study also used the allele frequency and the Kimura-Ohta model to estimate allele age. This method provided very ...

*Lethal allele

Alleles that need only be present in one copy in an organism to be fatal are referred to as dominant lethal alleles. These ... Lethal alleles (also referred to as lethal genes or lethals) are alleles that cause the death of the organism that carries them ... Lethal alleles may be recessive, dominant, or conditional depending on the gene or genes involved. Lethal alleles can cause ... This was the first documented example of a recessive lethal allele. A pair of identical alleles that are both present in an ...

*Allele frequency

For 3 alleles see Allele § Allele and genotype frequencies) Allele frequency can always be calculated from genotype frequency, ... Beneficial alleles tend to increase in frequency, while deleterious alleles tend to decrease in frequency. Even when an allele ... then the frequency p of the A-allele and the frequency q of the B-allele in the population are obtained by counting alleles. p ... Earth Human STR Allele Frequencies Database VWA 17 Allele Frequency in Human Population (Poster) Allele Frequencies in ...

*Minor allele frequency

... (MAF) refers to the frequency at which the second most common allele occurs in a given population. SNPs ... allele frequency The International HapMap Consortium (2005). "A haplotype map of the human genome". Nature. 437 (7063): 1299- ... MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes) 3. what do those numbers mean?: a. C, is the minor allele for that particular ... with a minor allele frequency of 0.05 or greater were targeted by the HapMap project. It is widely used in population genetics ...

*Allele-specific oligonucleotide

Samples 1 and 4 only have the normal "A" allele, while samples 3 and 5 have both the "A" and "S" alleles (and are therefore ... An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target ... It is designed (and used) in a way that makes it specific for only one version, or allele, of the DNA being tested. The length ... The PCR technique itself has been adapted to detect polymorphisms, as allele-specific PCR. However, the simplicity and ...

*Allele frequency spectrum

The joint allele frequency spectrum (JAFS) is the joint distribution of allele frequencies across two or more related ... In this table, a 1 indicates that the derived allele is observed at that site, while a 0 indicates the ancestral allele was ... However, sometimes the ancestral allele cannot be determined, in which case the folded allele frequency spectrum may be ... is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample. Because an allele ...

*Allele frequency net database

The allele frequency net database is a database containing the allele frequencies of immune genes and their corresponding ... Gonzalez-Galarza, Faviel F; Christmas Stephen; Middleton Derek; Jones Andrew R (Jan 2011). "Allele frequency net: a database ...

*Kompetitive Allele Specific PCR (KASP)

If QC is to be used for mapping population non parental alleles are discarded and alleles for which more than 90% of SNPs are ... Kompetitive Allele Specific PCR (KASP) is a homogenous, fluorescence-based genotyping variant of Polymerase Chain Reaction. It ... In the first round of PCR, a KASP primer mix that contains the two allele-specific forward primers and the single reverse ... In the second round of PCR, the complementary strand to the allele-specific forward primer is generated when the common reverse ...

*Earth Human STR Allele Frequencies Database

Allele Frequency Global Tracking (AFGT) - allows searching for allele frequency distribution at global and regional level. STR ... The Earth Human STR Allele Frequencies Database is a scientific project based on a dynamic web interface and a relational ... the allele frequencies gradient distribution over vast geographical areas. ... EHSTRAFD - Earth Human STR Allele Frequencies Database. c2009 [cited on 14 Jun 2009 - R1]. Available from http://www.ehstrafd. ...

*List of human leukocyte antigen alleles associated with cutaneous conditions

There are many human leukocyte antigen (HLA) alleles associated with conditions of or affecting the human integumentary system ...

*Phenotypic trait

Alleles can be significantly different and produce different product RNAs. Combinations of different alleles thus go on to ... Multiple alleles refers to the situation when there are more than 2 common alleles of a particular gene. Blood groups in humans ... and multiple alleles. Incomplete dominance is the condition in which neither allele dominates the other in one heterozygote. ... The ABO blood group proteins are important in determining blood type in humans, and this is determined by different alleles of ...

*ABO (gene)

Other minor alleles have been found for this gene. There are six common alleles in individuals of European descent. Nearly ... The ABO locus encodes three alleles. The A allele produces α-1,3-N-acetylgalactosamine transferase (A-transferase), which ... Many rare variants of these alleles have been found in human populations around the world. In human cells, the ABO alleles and ... The O allele lacks both enzymatic activities because of the frame shift caused by a deletion of guanine-258 in the gene which ...

*Cis AB

... one allele is AB and other is O When one parent carries a Cis AB allele, the other allele can be any of O, A or B and the ... The second allele is O: children are either AB or O Second allele is A: Children are either AB or A Second allele is B: ... A novel cis AB allele derived from a B allele through a single point mutation. Roubinet F1, Janvier D, Blancher A. Rev Fr ... Other parent is AO and second allele is O: The children are either AB or A or O Other parent is AA and the second allele is O: ...

*Introduction to genetics

If one allele dominates the instructions from another, it is called the dominant allele, and the allele that is overridden is ... In this example you can call the allele for brown "B" and the allele for red "b". (It is normal to write dominant alleles with ... The effects of this mixing depend on the types (the alleles) of the gene. If the father has two copies of an allele for red ... Mutations create new alleles. These alleles have new DNA sequences and can produce proteins with new properties. So if an ...

*MHC class I polypeptide-related sequence B

Fischer G, Pérez-Rodríguez M, Argüello JR, Cox ST, McWhinnie A, Travers PJ, Madrigal JA (Feb 2000). "Three novel MICB alleles ... alleles". Tissue Antigens. 51 (6): 649-52. doi:10.1111/j.1399-0039.1998.tb03008.x. PMID 9694358. Steinle A, Groh V, Spies T ( ...

*Extramacrochaetae

Its Fly Base designation is Dmel_emc, and its location is at 3L:749,406..753,505 [+]. 86 alleles have been reported. The Emc ...

*HLA-A

The A signifies which HLA gene the allele belongs to. There are many HLA-A alleles, so that classification by serotype ... due to the diversity amongst those alleles, it is difficult to classify each and every allele's impact upon immune regulation ... In other words, every single person can only express either one or two of the 2432 known HLA-A alleles. All HLAs are assigned a ... An HLA name looks something like this: HLA-A*02:01:01:02L All alleles receive at least a four digit classification (HLA-A*02:12 ...
Objective: The objective of this study is to identify human leukocyte antigen (HLA) class I and killer-cell immunoglobulin-like receptor (KIR) genotypes associated with different risks for HIV acquisition and HIV disease progression.; Design: A cross-sectional study of a cohort of 468 high-risk individuals (246 HIV-positive and 222 HIV-negative) from outpatient clinics in Lima (Peru).; Methods: The cohort was high-resolution HLA and KIR-typed and analysed for potential differences in single-allele frequencies and allele combinations between HIV-positive and HIV-negative individuals and for associations with HIV viral load and CD4(+) cell counts in infected individuals.; Results: HLA class I alleles associated with a lack of viral control had a significantly higher population frequency than relatively protective alleles (P = 0.0093), in line with a rare allele advantage. HLA-A*02 : 01 and HLA-C*04 : 01 were both associated with high viral loads (P = 0.0313 and 0.0001, respectively) and low CD4(+) ...
The foregoing examples show that the finding of population heterozygote advantage, as in the infectious disease studies cited, does not support an inference of allele-specific overdominance, the condition of primary interest as an immunological hypothesis and a mechanism for the maintenance of MHC diversity. Put another way, population heterozygote advantage may appear due to a combination of the two distinct mechanisms we defined in the Introduction: the protective or detrimental effects of particular alleles (R and S alleles in our model), and the effects of heterozygosity itself. The effects of R and S alleles appear as effects of heterozygosity vs. homozygosity because heterozygotes and homozygotes will in general carry different distributions of S and R alleles; thus, in an analysis that fails to condition on the alleles carried, heterozygosity is confounded with the alleles carried.. One advantage of correctly separating the effects of individual alleles from the effects of heterozygosity ...
Definition of Multiple alleles in the Legal Dictionary - by Free online English dictionary and encyclopedia. What is Multiple alleles? Meaning of Multiple alleles as a legal term. What does Multiple alleles mean in law?
The wormbase gene report ( http://www.wormbase.org/db/gene/allele?name=e996;class=Allele ) suggests there are several other alleles for this gene with Jonathon Hodgkin as the contact see http://www.wormbase.org/db/misc/etree?name=CB;class=Laboratory Anthony m.larsen wrote: , I am working on sup-1 and was wondering if anyone has other alleles ,than e995. , In particular I would be interested in the x-ray induced e995xri. The , reference allele e995 is the only allele available from the CGC, so if anyone , would be able to provide me with additional sup-1 alleles I would be very , greatful. , , Thank you , , Morten K. Larsen , University of Southern Denmark , DK , m.larsen at bmb.sdu.dk , , --- ...
Accurate estimation of allele‐specific expression was achieved by using both specific and common probes, with the intensities of the latter reflecting the total expression of the two alleles (Figure 1B). One main challenge was accounting for off‐target effects. Part of contribution toward hybridization signal of allele‐specific probes comes from their cross‐hybridization with transcripts of the other allele (Figure 1B). Indeed, in most cases, allele‐specific probes have only one nucleotide mismatch with the other allele and show significant hybridization with it. Not accounting for this effect would lead to biased estimation of allele‐specific expression levels. This off‐target effect was accounted for by modeling the probe intensities as noisy observations of weighted sums of the two allelic levels (equation (1)). The weights represent the affinities of the probe with respect to each allele. They are equal for common probes and can differ for specific probes, none being a priori ...
Allelic association methods based on increased transmission of marker alleles will have to be employed for the mapping of complex disease susceptibility genes. However, because the extent of association of single marker alleles with disease is a function of the relative frequency of the allele on disease-associated chromosomes versus non disease-predisposing chromosomes, the most associated marker allele in a region will not necessarily be closest to the disease locus. To overcome this problem we describe a haplotype-based approach developed for mapping of the putative type 1 diabetes susceptibility gene IDDM6. Ten microsatellite markers spanning a 550 kb segment of chromosome 18q21 in the putative IDDM6 region were genotyped in 1708 type 1 diabetic Caucasian families from seven countries. The most likely ancestral diabetogenic chromosome was reconstructed in a step-wise fashion by analysing linkage disequilibrium between a previously defined haplotype of three adjacent markers and the next ...
View Notes - wk2 from LS 4 at UCLA. Application to Punnett Square: IV. Inheritance Patterns Allelic Interactions: Name Description _________ ratio *adds to ____ *seen in ____ Example Genetic
The stepwise mutation model (SMM) is a mathematical theory, developed by Motoo Kimura and Tomoko Ohta, that allows for investigation of the equilibrium distribution of allelic frequencies in a finite population where neutral alleles are produced in step-wise fashion. The original model assumes that if an allele has a mutation that causes it to change in state, mutations that occur in repetitive regions of the genome will increase or decrease by a single repeat unit at a fixed rate (i.e. by the addition or subtraction of one repeat unit per generation) and these changes in allele states are expressed by an integer (. . . A-1, A, A1, .. .). The model also assumes random mating and that all alleles are selectively equivalent for each locus. The SMM is distinguished from the Kimura-Crow model, also known as the infinite alleles model (IAM), in that as the population size increases to infinity, while the product of the Ne (effective population size) and the mutation rate is fixed, the mean number of ...
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental ...
Kawashima Y., Pfafferott K., Frater J., Matthews P., Payne R., Addo M., Gatanaga H., Fujiwara M., Hachiya A., Koizumi H., Kuse N., Oka S., Duda A., Prendergast A., Crawford H., Leslie A., Brumme Z., Brumme C., Allen T., Brander C., Kaslow R., Tang J., Hunter E., Allen S., Mulenga J., Branch S., Roach T., John M., Mallal S., Ogwu A., Shapiro R., Prado J.G., Fidler S., Weber J., Pybus O.G., Klenerman P., Ndungu T., Phillips R., Heckerman D., Harrigan P.R., Walker B.D., Takiguchi M., Goulder P. (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature ...
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details.. Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too.. A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string.. In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. ca) and repeat_count (e.g. 7).. ...
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details.. Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too.. A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string.. In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. ca) and repeat_count (e.g. 7).. ...
function manually one at a time. However, this approach takes too much time to compute allele frequencies for 5,000 SNPs. Recall that allele frequency of A is given by \[ f(A) = p = \frac{2 \times (\text{no. of } AA \text{ individuals}) + 1 \times (\text{no. of } Aa \text{ individuals})}{2 \times \text{total no. of individuals}}. \] We can rewrite this equation into \[ f(A) = p = \frac{(\text{no. of } A \text{ allele in the population})}{2 \times \text{total no. of individuals}}. \] This suggests that all we need is the number of \(A\) allele or reference allele \(a\) for each SNP. The ...
Although single-SNP associations were not significant at pFDR,0.05, several genes were significant in the ARTP analyses. In AA women, significant ARTP gene-level associations included CDH1 with LN+ (pARTP=0.10; multi-allelic OR=1.13, 95% CI 1.07-1.19, pFDR=0.0003) and SIPA1 with ER− breast cancer (pARTP=0.10; multi-allelic OR=1.16, 95% CI 1.02-1.31, pFDR=0.03). In EA women, MTA2 was associated with overall breast cancer risk (pARTP=0.004), regardless of ER status, and with LN− disease (pARTP=0.01). Also significant were SATB1 in ER− (pARTP=0.03; multi-allelic OR=1.12, 95% CI 1.05-1.20, pFDR=0.003) and KISS1 in LN− (pARTP=0.10; multi-allelic OR=1.18, 95% CI 1.08-1.29, pFDR=0.002) analyses. Among LN+ cases, significant ARTP associations were observed for SNAI1, CD82, NME1, and CTNNB1 (multi-allelic OR=1.09, 95% CI 1.04-1.14, pFDR=0.001 ...
4586 A number of studies have shown that HLA-DR, DQ and DP alleles are associated with an increased risk of paediatric acute lymphoblastic leukaemia (ALL), but the significance of these multiple HLA locus/allele associations for the aetiology of childhood ALL remains uncertain. One possibility is that they denote differences in immune responsiveness to a causative infection(s), mediated by the differential antigenic peptide-binding efficiency of HLA class II alleles. We previously reported that B cell precursor ALL [BCP] was associated with HLA-DPB1*0201 and related alleles with glutamic acid (E) at position DPβ169 in the P4 peptide binding pocket (PBP). However, recent studies suggest that DPB1 alleles can be clustered into a small number of functional supertypes based on the shared peptide binding characteristics of several PBP. To determine whether these influence the risk of BCP ALL, we clustered DPB1 alleles into 3 pairs of supertypes, defined by di-allelic polymorphisms at DPβ184, 69 and ...
The Hardy-Weinberg Law states: In a large, random-mating population that is not affected by the evolutionary processes of mutation, migration, or selection, both the allele frequencies and the genotype frequencies are constant from generation to generation. Furthermore, the genotype frequencies are related to the allele frequencies by the square expansion of those allele frequencies. In other words, the Hardy-Weinberg Law states that under a restrictive set of assumptions, it is possible to calculate the expected frequencies of genotypes in a population if the frequency of the different alleles in a population is known.. The genotype frequencies are calculated using the square expansion of the allele frequencies. To illustrate this concept, assume that at some locus, A, you have two alleles, call them A1, and A2. Assume that the frequency of allele A1 is p and the frequency of allele A2 is q. We can write this as:. f(A1) = p f(A2) = q. Under Hardy-Weinberg conditions, the expected genotypic ...
A recessive allele is an allele that will not determine the phenotype unless the genotype is homozygous with that allele.[1] Examples of recessive alleles include the allele for green in the pea Pisum sativum (the subject of Gregor Mendels heredity experiments). In humans, a variety of inherited diseases are recessive, such as Cystic fibrosis and Tay-Sachs. ...
Figure 6 Five alleles in Model II. w, wild-type allele with target genes containing sequence recognized by the nuclease. n, allele with nuclease gene inserted in the middle of the target sequence, protecting the chromosome from being cut but also disrupting the target gene. e, effector gene linked to a target gene in which the recognition sequence has been changed so it is no longer recognized by the nuclease. d, disrupted target gene formed by non-HR of w alleles or by loss of nuclease from n alleles. r, functional target gene that is also resistant to cleavage due to not having the target sequence; can be formed by non-HR of w alleles or by loss of the effector gene of e alleles. Note that other alleles are possible, such as effector with disrupted target gene (e.g., formed by spontaneous mutation of e alleles), or effector with functional target gene with target sequence (e.g., formed by recombination between w and e alleles). These are expected to be rare because they are formed rarely and ...
FERREIRA, Alessandro Clayton Souza et al. Type 1 diabetes susceptibility determined by HLA alleles and CTLA-4 and insulin genes polymorphisms in Brazilians. Arq Bras Endocrinol Metab [online]. 2009, vol.53, n.3, pp.368-373. ISSN 1677-9487. http://dx.doi.org/10.1590/S0004-27302009000300012.. INTRODUCTION:Type 1A diabetes mellitus (T1ADM) is a multifactorial disease in which genetic and environmental aspects are important to its development. The association of genetic variations with disease has been demonstrated in several studies; however, the role of some gene loci has not yet been fully elucidated. OBJECTIVE:To compare the frequency of HLA alleles and polymorphism in CTLA-4 and insulin genes in Brazilians with T1ADM and individuals without the disease, as well as to identify genetic markers that are able to discriminate between diabetic and non-diabetic individuals. METHODS: The presence of HLA DQB1, DQA1 and DRB1 alleles, as well as the -2221 MspI polymorphism in the insulin gene and 49 A/G ...
a , Incomplete lineage sorting can produce discrepancy between the phylogenetic tree for a specific gene or a genomic segment and the overall species-level phylogenetic tree. If an ancestral species is polymorphic (in this case, it is segregating Alleles A and B) and divides into two descendent lineages, then both alleles can be retained in the two daughter lineages. If one of these lineages divides again relatively soon, then all three species lineages may carry both alleles. Over time, each lineage will lose one or the other allele owing to genetic drift or selection. In this case, Species 1 retains Allele A and Species 3 retains Allele B. For this genomic segment, Species 2 will seem to be more closely related to either Species 1 or Species 3 depending on whether it retains Allele A or Allele B. Retention of Allele B would mean that this genomic segment matches the overall species-level phylogenetic tree, but retention of Allele A would lead to discrepancy. Analyses of whole-genome sequences ...
How common is an observed genetic allele in the population?. Simple question, but no simple answers. This is the challenge for all clinical geneticists and translational researchers alike. Current human allele frequency information is simply inadequate for accurate clinical interpretation sequence based tests and rare disease causal variant identification.. What if allele frequencies were readily available for every position in the human genome?. This is a community-based effort to address this need. Registered community members have access to anonymous, pooled allele frequencies computed from across the whole community. All community data is safe, secure and anonymous.. ...
In the present study, we identified and characterized 2 common polymorphisms in the promoter region of the MMP-7 gene that are functional in vitro and seem to influence coronary arterial dimensions in a preliminary study of hypercholesterolemic patients with manifest CAD. Hypercholesterolemic patients carrying the G allele at position −181 had smaller reference luminal diameters before PTCA than did patients homozygous for the A allele. Furthermore, carriers of the T allele at position −153 had smaller reference diameters before PTCA than did patients homozygous for the C allele. In vitro in the human monocyte/macrophage cell line U937, the −81 A/G and the −153 C/T polymorphisms influenced the binding of nuclear proteins. Also, basal promoter activity was higher in promoter constructs harboring the combination of the 2 rare alleles in transient transfection studies.. The finding that the G allele of the −181 A/G and the T allele of the −153 T/C polymorphisms, both of which are ...
The immune response to HIV infection is complex involving multiple interactive pathways and components. These pathways are influenced by both virus and host genetic factors, which determine disease progression, complications and response to treatment. HIV virus evades the antigen specific T-cell immunity by undergoing mutations throughout its entire genome, which at a population level are both positively and negatively associated with particular HLA alleles. The extent to which this adaptation occurs influences viral load. These results provide evidence that host HLA is an important factor imprinting on viral evolution. Host genetic factors are also important predictors of clinical course and complications in established HIV infection. In cross-sectional and longitudinal studies of the WA HIV cohort, we have shown certain HLA and chemokine receptor alleles influence viral load set point. In addition, the presence of certain NK cell KIR genes influence outcome, particularly, in relation to rate ...
With the using modern molecular-genetic methods for the study it was shown that the allele C and genotypes GC and CC of the polymorphic variant G-405C of VEGF gene, allele A and genotypes GA and AA of the polymorphic region G-1154A of VEGF gene, allele C and genotypes ТС and СС of polymorphism T-604C of KDR gene as well as allele A and genotypes СА and GА of polymorphism G-735A of Ang2 gene pr ... ...
from operator import itemgetter from random import random import math import matplotlib.pyplot as plt import nltk import numpy as np def person(): alleles = [] for allele in [a,b,c]: pairs = [] for pair in range(2): pairs.append(allele if random() ,= 0.5 else allele.upper()) alleles.append(.join(sorted(pairs))) return alleles def shuffle_and_choose(counts): shuffled = [x[0] for x in sorted(enumerate([random() for i in range(len(counts))]), key=itemgetter(1))] return counts[shuffled[0]] def compute_mating_likelihood(left, right): left_dominant = get_num_dominant(left) right_dominant = get_num_dominant(right) diff = abs(left_dominant - right_dominant) return math.exp(-diff) def mate(left, right): mated_alleles = [] for i in range(3): child_pairs = [] for lp in left[i]: for rp in right[i]: child_pairs.append(.join(sorted([lp, rp]))) mated_alleles.append(shuffle_and_choose(child_pairs)) return mated_alleles def get_num_dominant(allele): return len([c for c in .join(allele) if c == ...
Looking for fixed allele? Find out information about fixed allele. An allele that is homozygous in all members of a population Explanation of fixed allele
Figure 1. The table should be interpreted as follows: For row 1, the locus is DQ, and the allele is 201. This particular allele codes for alanine at postion 57 of the Beta chain of the MHC II molecule, making the patient susceptible to IDDM. For row 2, allele 302 also codes for alanine and elicits the same result. For row 3, allele 303 in the same locus codes for aspartic acid, conferring immunity on the host, etc (Tisch 1996). It is believed that MHC alleles susceptible to autoantigen specific T cells, particularly Th1 cells specific for B cell islet antigens, mediate IDDM susceptibility. These susceptible cells bind antigens that elicit a primarily Th1 cell response. The resistant alleles, like those of the DR isotype expressing aspartic acid, elicit a primarily Th2 cell response. Studies support this hypothesis, as nonobese diabetic mice (because human testing would be unethical, animal models are used to better understand IDDM. The most common model uses mice infected with IDDM, also known ...
For example, lets take an extremely simple case. Say the frequency of an allele in a population is 0.15 or 15%, while the frequency of another allele is 0.20 or 20%. Based on random assortment or chance, one would predict the two alleles would be found together with a frequency of 0.15 x 0.20 = 0.03 or 3% of the time. However, say in reality the two alleles are found together 15% of the time in the population. So, since 15% is 5.0 times greater than 3%, the two alleles are found together 5.0 times more frequently than expected or predicted by their individual allele frequencies i.e. random assortment or chance. Thus, this disequilibrium suggests linkage of the two alleles on a specific locus or loci which is on, say, chromosome 7 ...
Try again. Im assuming the data in the table is the allele frequency for the three alleles of locus 1 and that each column is one taxon-and here I reveal my ignorance of genetic terms because I dont know for certain what a taxon is and I havent bothered to look up the definition. For the other 10 loci there may be a fewer or greater number of alleles per locus. If the tabulated data are the allele frequencies, then the answer to 3) is just read off the table multiplied by 100 to express the proportion as a percentage. For 1) you should be able to caluclate %P for each column (taxon?) as ((# loci with multiple alleles)/11)X100. For the number of alleles/locus wouldnt that just be (total # of alleles)/11 calculated for each column? The allele frequencies should just be read off the table, I think. Then the %heterozygosity for each locus can be calculated per taxon with Hardy-Weinberg, as above, and the average heterozygosity would be the average of the %heterozygosity per locus calculated for ...
In contrast, monoallelic transcription was restricted to exon 1′ in tumor 26 (Fig. 4 ⇓ , Lane 7). The two alleles were present in approximately the same copy numbers, and transcripts associated with exons Ha, E, and 1 were symmetrically expressed from the two alleles (Fig. 4 ⇓ , Lanes 7-10). For comparison, a sample demonstrating equal copy numbers for both the N and n alleles and symmetrical expression from each of the promoters is shown (T3; Fig. 4 ⇓ , Lanes 11-15).. In a panel of 14 ER-negative tumors, 8 were heterozygous; of these, 5 demonstrated evidence of amplification of one allele. In two samples, the N allele was amplified, whereas in three samples, the n allele was amplified (data not shown), suggesting that ER expression was extinguished after gene amplification had occurred. As expected, when samples were analyzed for allele-specific transcription, no conclusion could be drawn because only low levels of cDNA and, therefore, mRNA were detected.. The observed monoallelic ...
I am running an experiment in which I need to sample all six HLA class I alleles (HLA-A, HLA-B, HLA-C) repeatedly. Is there a dataset online that contains this information? I found this website (http://www.allelefrequencies.net/) but I cannot figure out how to get the data from it in the format that I want. Any help is appreciated. Thank you. EDIT: Sorry, I think the question was a little unclear. What I want to do is have a dataset containing a set of patients, and all 6 of their HLA alleles. Is there such a dataset available somewhere? ...
The distinction between genotype and phenotype is commonly experienced when studying family patterns for certain hereditary diseases or conditions, for example, hemophilia. Humans and most animals are diploid; thus there are two alleles for any given gene. These alleles can be the same (homozygous) or different (heterozygous), depending on the individual (see zygote). With a dominant allele, the offspring is guaranteed to inherit the trait in question irrespective of the second allele.. In the case of an albino with a recessive allele (aa), the phenotype depends upon the other allele (Aa, aA, aa or AA). An affected person mating with a heterozygous individual (Aa or aA, also carrier) there is a 50-50 chance the offspring will be albinos phenotype. If a heterozygote mates with another heterozygote, there is 75% chance passing the gene on and only a 25% chance that the gene will be displayed. A homozygous dominant (AA) individual has a normal phenotype and no risk of abnormal offspring. A ...
Don Bowden bowden at mgrp.bgsm.wfu.edu writes: , This is probably a dumb question, but... we have genotyped a micro- , satellite in a large number of caucasian and african-american samples and , would like to compare the allele frequency distribution to see if they are , different. I did this using a contingency table to calculate chi square , and there is a significant difference. I seem to recall thought that if any , of the cells has less than 5 elements in it, chi square is not the appropriate , way to go. What is the right way to do this, and more importantly, is there , some textbook or other source which would show a simple-minded molecular bio- , logist how to do it? , This is not a dumb question. It is not easy to deal with statistical analysis of loci with lots of alleles, as is typical of micro-satellite repeats. You could look at Bruce Weirs Data Analysis book; there is some stuff on tests involving multiple locus markers. Depending on the number of alleles it may be easy or ...
Supposing we have the genotypes "Aa", "AA", and "aa"... which are not mono-allelic (not imprinted and not X-inactivated). Does the dominance of the "A" allele over "a" allele affect which gene is transcribed, or are both alleles transcribed and the allelic dominance only determines the observed phenotype? Im guessing its the latter, but that makes me confused as to what the concept of allelic dominance would mean for mono-allelic expression, where only one allele is always expressed and observed. ...
The majority of the population specific SNPs had a rather low frequency for the minor allele of less than 20%, but some SNPs with higher frequencies were also identified. 14 SNPs had a minor allele frequency of 19% and less, while only 7 SNPs had a minor allele frequency of 20% and higher. For SNPs with minor alleles in 2 populations, the higher minor frequency value was chosen for this diagram. Some caution should be applied not to overestimate or interpolate our results. Both datasets as well as the work of Stephens et al. (2001) are based on a limited number of individuals for each population group . Hence, alleles with a very low frequency in any one population may have been missed. Therefore it is possible and likely that some of the alleles that were not identified in one population group may be present at low frequencies in these groups, so that many of the SNPs that were included in our analysis as they showed a 0% frequency for the minor allele would have to be excluded as their real ...
Each human has two copies of each gene or a form (allele) thereof, one from each parent. One form (allele) of a given gene may be dominant and, if it is, the other form may be recessive - i.e. it can "hide" or not express itself if a dominant allele of the same gene is present. When a disease is termed "genetic recessive," it only manifests itself if an individual has two copies of the recessive, disease-causing allele. If an individual has one copy of the recessive allele and one copy of the dominant allele, s/he is termed a "carrier" - the disease itself does not show up, but if his or her spouse also has one copy of the recessive allele, their children have a 25% chance of receiving two recessive copies, developing the disease. Tay-Sachs is genetic recessive and kills by age six ...
Results A total of 24 comparative studies were included in this meta-analysis, including 22,682 patients with RA and 23,493 controls. The meta-analysis showed an association between the second allele of rs10818488 and RA in all study subjects (OR 1.170, 95% CI 1.082-1.266, p = 8.2 x 10-6). Analysis after stratification by population indicated that the second allele of rs10818488 were associated with RA in Europeans, but not in Asians (OR 1.229, 95% CI 1.094-1.381, p = 0.001; OR 1.060, 95% CI 0.930-1.335, p = 0.092). The meta-analysis also indicated an association between the second allele of rs3761847 and RA in all study subjects (OR 1.098, 95% CI 1.019-1.184, p = 0.015). The second allele of rs3761847 was associated with RA in Europeans, but not in Asians (OR 1.156, 95% CI 1.006-1.327, p = 0.041; OR 1.049, 95% CI 0.952-1.156, p = 0.333). The meta-analysis revealed an association between the second allele of the rs2900180 polymorphism and the risk of developing RA in all study subjects and ...
A collection of cutting-edge computational tools and experimental techniques to study how genes are regulated, and to reconstruct the regulatory networks through which various cell-types are produced. On the computational side, web-based technologies to localize genes, to access and retrieve data from microarray databases, to conduct comparative genomics, and to discover the potential "codes" in genomic DNA that may control the expression of protein-coding genes. Detailed experimental techniques described include methods for studying chromatin structure and allele-specific gene expression, methods for high-throughput analysis to characterize the transcription factor binding elements, and methods for isolating and identifying proteins that interact with DNA. The protocols follow the successful Methods in Molecular Biologyâ„¢ series format, each offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and ...
... As definições de siglas Allele. As definições de acrónimo Allele. Sigla Allele significa para. Além de encontrar siglas. Encontre o que significam as siglas!
The delta32 allele distribution of the CCR5 gene and its relationship with certain cancers in a Turkish population.: The frequency of the delta32 allele detecte
Wing pattern is controlled by a single gene, which comes in 4 different versions, or alleles.. Pigeons inherit two copies of the pattern gene, one from each parent. The two alleles together make up a bird's genotype. What we see, also called the phenotype, reflects the dominant-most allele in the genotype. 'T-check' is the most-dominant, followed by 'check', 'bar', and finally 'barless', which is recessive to all the others.. While this dominance pattern generally holds up, sometimes the less-dominant allele does have a small effect on the phenotype. For instance, a bird with one t-check allele and one bar allele may have flecks of lighter feathers rather than a solid black wing.. Pattern is a great example that shows the relative aspect of dominance and recessiveness. An allele is never simply "dominant" or "recessive." It is always dominant to or recessive to another.. ...
A plant whose genotype is represented with the alleles TT has the phenotype of a tall plant. Since T represents a tall plant and it is the only type of allele present in the plants genotype, the...
A mathematical equation that can be used to calculate the frequencies of alleles.. It states that in large, randomly mating population, on absences of migration, mutation and selection, the gene pool remains constant. The proportion of dominant and recessive alleles of a particular gene remains ththe same.. it can use the frequency of one allele to predict expected proportions of the genotype in the population. It demonstrates the large amount of recessive alleles in heterozygotes, who are the reservoir of genetic variability.. P^(2) + 2pq+ q^(2)= 1. P is frequency of dominant allele, q is frequency of recessive allele. P + q = q, but the next generation:. PP = p^(2), Pq= 2pq, pp= q^(2). ...
This study will identify variations in the genome of the human immunodeficiency virus (HIV) early after infection and following the development of AIDS. It will analyze genetic material and clinical data from HIV-positive individuals to assess differences in viral epitopes between patients with two different gene alleles (alternative forms of a gene)-B*3501 and B*3503. (An epitope is a molecular region on the surface of an antigen capable of eliciting an immune response and of combining with the specific antibody produced by such a response.). HIV disease in people with the B*3503 allele progresses significantly faster than it does in people with the B*3501 allele. This study might provide information that is potentially useful in developing a successful HIV vaccine.. Blood samples and clinical data for analysis will be obtained from the Johns Hopkins Bloomberg School of Public Health; the University of Pittsburgh; the John H. Stroger, Jr. Hospital of Cook County; the Howard Brown Health Center; ...
This study will identify variations in the genome of the human immunodeficiency virus (HIV) early after infection and following the development of AIDS. It will analyze genetic material and clinical data from HIV-positive individuals to assess differences in viral epitopes between patients with two different gene alleles (alternative forms of a gene)-B*3501 and B*3503. (An epitope is a molecular region on the surface of an antigen capable of eliciting an immune response and of combining with the specific antibody produced by such a response.). HIV disease in people with the B*3503 allele progresses significantly faster than it does in people with the B*3501 allele. This study might provide information that is potentially useful in developing a successful HIV vaccine.. Blood samples and clinical data for analysis will be obtained from the Johns Hopkins Bloomberg School of Public Health; the University of Pittsburgh; the John H. Stroger, Jr. Hospital of Cook County; the Howard Brown Health Center; ...
Correct Response: B. This question requires examinees to demonstrate an understanding of the principles of Mendelian genetics and inheritance and the application of those principles to genotype and phenotype variation in plants. The parent plants in this cross are heterozygous for two traits, which means they each contain a dominant allele and a recessive allele for pod color (Gg) and a dominant allele and a recessive allele for seed shape (Rr), with G and R representing the dominant alleles of each gene. A cross between these two plants can be represented as GgRr × GgRr. According to the principle of independent assortment, each parent plant will produce four types of gametes: GR, Gr, gR, and gr. A Punnett square can be used to determine the number and type of genotypes produced by this cross. When a 4 × 4 Punnett square is constructed by placing one set of gametes on the top of the square and the other set of gametes along the side of the square, the results show a total of 16 possible ...
The Comai laboratory does not work any longer on the REVOLUTA gene. Following our publication in Development we are sometime asked for alleles. The rev-1 allele is available from TAIR. The other alleles described in the paper are no longer available in my laboratory. We distributed seed while available, but the most of these seem to have gone to the great fields in the sky. While still in Seattle (around 2005) we searched the TILLING collection of STP for additional alleles. We collected and grew 28 new alleles, of which 2 showed strong phenotypes. ...
Conventional allele frequency analysis can overlook alleles with relatively rare frequencies. In addition, traditional analysis of HLA population genetics does not account for shared HLA epitopes that allow disparate alleles to present the same antigen. Our analysis found HLA epitopes associated with susceptibility and resistance to disease. In addition, rare alleles were identified because HLA epitopes were first determined at the amino acid level and then the associated alleles identified.. A previous group that used the same dataset from the T1DGC identified a number of susceptible, neutral, and protective HLA-DR-DQ haplotypes associated with type 1 diabetes (9). Instead of analyzing the disease associations by individual loci, the authors looked at specific combinations of DRB1, DQA1, and DQB1 alleles. They established that the most susceptible haplotypes were DRB1*03:01-DQA1*05:01-DQB1*02:01, DRB1*04:05-DQA1*03:01-DQB1*03:02, DRB1*04:01-DQA1*03:01-DQB1*03:02, and ...
The proinflamatory cytokine interleukin-1b (IL-1b) and the interleukin-1 receptor antagonist (IL-1Ra), which is a specific inhibitor of IL-1 activity, have been shown to be induced in vitro byMycobacterium tuberculosis. Moreover patients with tuberculosis present an elevated serum concentration of IL-1Ra and IL-1Ra was identified as a marker of disease activity in tuberculosis (Juffermans et al., 1998). Within the IL-1b gene, two biallelic polymorphisms have been identified at positions −511 and +3953, respectively. An 86-base pair variable number of tandem repeats polymorphism with five different alleles is found in theIL-1Ra gene. Genetic analysis detected that theIL-1Ra VNTR allele A2 was associated with a higher production of IL-1Ra in response to M. tuberculosisinfection. Indeed, individuals with the IL-1Ra A2+ allele produced 1.9-fold more IL-1Ra than patients with IL-1Ra A2- alleles (Wilkinson et al., 1999). The two polymorphisms in IL-1bwere not clearly associated with the level of ...
Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. Thus, any naturally occurring genetic variants that directly affect gene expression and/or protein function would be expected to impact on progression of pathological processes involving tissue remodeling. We scanned a 2-kilobase pair promoter region and all 13 exons of the human MMP-2 gene, from a panel of 32 individuals, and we identified the position, nature, and relative allele frequencies of 15 variant loci as follows: 6 in the promoter, 1 in the 5-untranslated region, 6 in the coding region, 1 in intronic sequence, and 1 in the 3-untranslated region. The majority of coding region polymorphisms resulted in synonymous substitutions, whereas three promoter variants (at -1306, -790, and +220) mapped onto cis-acting elements. We functionally characterized all promoter variants by transient transfection experiments with 293, RAW264.7, and A10
The yolk proteins, denoted as Pa F, correspond to the fraction marked Pr 2 in Tanabe and Ogawa [17]. The number of bands observed for homozygotes was the same as in the mentioned study. However, the five or six bands observed in this subregion of heterozygotes do not correspond to those presented by Tanabe and Ogawa [17]. The phenotype frequencies recorded in this study were similar to those of the same breeds of hens studied in the years 1970 1980. The allele TfB frequency ranged between 0.80 and 1.00, whereas the allele TfC was very rare, and the allele TfA, which had been quite often present during the 1970s in the hens bred in Poland [8], in this study was not observed at all. The frequencies of ovalbumin encoding alleles can be compared to those studied by Stratil [15], Kury [9] and Moiseeva et al. [10]. The frequencies calculated here correspond with those presented by these authors. It should be added, however, that the ovalbumin alleles A and B, as well as the alleles of the remaining ...
Forces that determine the allele frequencies in natural populations include genetic drift, natural selection, migration and mutation
A local barrier to gene flow will delay the spread of an advantageous allele. Exact calculations for the deterministic case show that an allele that is favorable when rare is delayed very little even by a strong barrier; its spread is allowed by a time proportional to log((B/σ)√2S)/S, where B is the barrier strength, σ the dispersal range, and fitnesses are 1:1 + S:1 + 2S. However, when there is selection against heterozytes, such that the allele cannot increase from low frequency, a barrier can cause a much greater delay. If gene flow is reduced below a critical value, spread is entirely prevented. Stochastic simulations show that with additive selection, random drift slows down the spread of the allele, below the deterministic speed of σ√2S. The delay to the advance of an advantageous allele caused by a strong barrier can be substantially increased by random drift and increases with B/(2Sρσ2) in a one-dimensional habitat of density ρ. However, with selection against heterozygotes, ...
Although it is likely that chromosomal deletions occur randomly, those that result in a proliferative advantage or resistance to, e.g., physiological apoptosis could initiate clonal outgrowth. Selection for clones with a specific region of LOH could be related to a somatic or germline loss of a wild-type allele, resulting in hemizygosity for an SNP-encoded, disease-prone allele or a somatic or germline mutated allele (Fig. 1). If the affected area includes promoters of alleles that are differentially silenced (imprinted), deletion can lead to either a gain of imprinting (GOI) or loss of imprinting (LOI). This can result in changes in gene expression. UPD can also lead to the duplication of an imprinted expressed allele or a silenced (methylated), imprinted allele. When the transcription of both alleles is required for normal cellular physiology, deletions can result in pathological haploinsufficiency, and thus LOH is less likely to play a pathogenic role (Fig. 1).. There are similarities and ...
Association analysis: For marker D14S306, for BP2, allele 6...... Association analysis: For marker D14S306, for BP2, allele 6, z-score = 2.05, FBAT P-value = 0.040409, perm P-value = 0.040958; For marker D14S1048, for BP2, allele 10, z-score = -2.044, FBAT P-value = 0.040951, perm P-value = 0.043478; allele 13, z-score = 2.646, FBAT P-value = 0.008151, perm P-value = 0.008258; For marker D14S1068, for BP2, allele 4, z-score = -2.553, FBAT P-value = 0.010674, perm P-value = 0.01256; allele 6, z-score = 2.077, FBAT P-value = 0.03782, perm P-value = 0.037744; allele 7, z-score = 2.443, FBAT P-value = 0.014556, perm P-value = 0.014445; Global FBAT P-value = 0.012825, perm P-value = 0.025058; linkage study: For marker D14S306, for BP2, ASP model, LOD = 0.65 in new pedigrees(N = 16); LOD = 1.9 in all pedigrees(N = 56) More... ...
Adjust the initial allelic frequencies (p,q) and genotype fitnesses (W) to the right:. For best results, begin by setting the fitness values to 1.0, and initial allelic frequencies to 0.5. Then, decrease one or more of the fitness values by a small amount.. Selection against the A allele occurs when WAA,WAa and/or WAA,Waa. The strength of this selection is a function of the differences among the three fitness values. Selection of this type (directional) generally leads to fixation of one of the two alleles.. Selection against the a allele occurs when Waa,WAa and/or Waa,WAA.. Heterozygote advantage occurs when WAA,WAa,Waa. In this case both alleles are preserved in the population. Note that allelic frequencies do not change when WAA=Waa.. Heterozygotes can also be selected against, when WAA,WAa,Waa. Note that allelic frequencies do not change when WAA=Waa.. The population represented to the right posseses 5000 randomly breeding individuals. This large size is chosen to minimize the effects of ...
Alleles of the apolipoprotein E (ApoE) gene are known to modulate the genetic risk for developing late-onset Alzheimers disease (AD) and have been associated with hippocampal volume differences in AD. However, the effect of these alleles on hippocam
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Credit: Douglas Tave and Alison Hutson (USA): Alternate artificial spawning protocol of Rio Grande silvery minnow to minimize genetic. and to maximize the retention of rare alleles. This paper addresses the following topics: Captive Propagation and Genetics, Inbreeding, Effective breeding number, Genetic drift, Allele frequency and Artificial Propagation of Rio Grande Silvery Minnow. [important]Alternate artificial … Continue reading ». ...
Results We identified 4 single-nucleotide polymorphisms (SNP; -572 C , G, -278A, C in the promoter, and 330 T , G, and 334 A , T in exon 2) and a -373 AnTn tract polymorphism in the IL-6 gene. The genotype frequency, -373 A10T11, -278 C, and 334 T allele were significantly associated with SLE (p , 0.001, p = 0.03 and p = 0.005, respectively). Patients with SLE carrying the -572 G allele had anti-dsDNA more frequently (p = 0.007). In addition, thrombocytopenia was significantly more common in patients carrying the -278 C allele (p = 0.006). In the haplotype analysis, patients with SLE had more frequently haplotype HT3 (CA10T11ATA, dominant model, p = 0.012) that was associated with arthritis, leukopenia, anti-dsDNA, and hypocomplementemia. Promoter reporter structures carrying the -278 C allele displayed significantly higher promoter activity than the -278 A allele in Hep3B cells (p , 0.001) and HeLa cells (p , 0.001). ...
With Melting Curve Analysis, different alleles or allele combinations are identified due to the differing interaction strengths they have with the probe. Allele-specific primers or probes are not needed; the same sequence is used for all alleles of an investigated SNP, or can even cover several nearby SNPs. This saves reagent costs and, combined with the LightCycler® 480 Instrument´s high number of available detection channels, enables straightforward reaction multiplexing. As a post-PCR process, melting curve analysis depends neither on the efficiency of the amplification process nor on the cleavage of a substrate (e.g., a dye attached to a probe) and is therefore, very robust. The LightCycler® 480 Genotyping algorithm works by grouping samples with similar melting curve shape either by auto-calling or via included standards of known genotype, and calls genotypes of unknown samples instantly based on their melting profile´s comparison to the identified groups.. ...
If we can identify the individuals in a population that are homozygous for a particular allele of interest we can then calculate the frequency of that allele. If for instance 1/10,000 babies are born with a certain recessive genetic defect we can easily determine the allele frequencies of A & a ...
The GRC currently favors a model in which haplotypic integrity is retained within blocks of linkage disequilibrium (LD) as best possible, every base is found at an MAF ,5% in some population (i.e. no universally rare alleles) and coding alleles are favored over non-coding alleles, so long as they too are not universally rare. However, additional analyses will be performed before any bases changes are made. Examples of genomic regions where the existing reference base is associated with disease (ASPN, PMID:15640800) or non-coding variants (CYP3A5, PMID:11279519) are presented below in Figures 1 and 2. In the former case, the reference base is the minor allele, while in the latter, it is the major allele. We invite you to consider examples such as these as you form your own views of what should be represented in the reference assembly. If you have questions or concerns about base updates for GRCh38, let us know! ...
Discussion. We have detected differences in the association between the CFH gene and exudative AMD in Chinese from Caucasians as well as Japanese, though it was more similar between Chinese and Japanese (Table 2).. SNP rs1061170 (Y402H) has been identified as the major genetic factor for developing AMD in Caucasians. Frequencies of the C allele were between 61-94% in AMD and 34-46% in controls [9-17]. However, the Y402H C allele was low in frequency in our Chinese study population (5.8% in cases and 3.9% in controls). It was not associated with exudative AMD. Actually such low frequency does not allow conclusion of genetic susceptibility in Chinese. In Japanese, the C allele was also at a low frequency and not associated with exudative AMD [24,25]. Dramatic differences may exist in the allele frequencies of individual SNPs across populations [32].. In the present study, three alleles, T, G, C, respectively for SNPs in the promoter (rs3753394), exon 2 (rs800292) and intron 15 (rs1329428) located ...
Figure 2. Mutation analysis of the MYO7A gene in the family. A: Sequencing chromatograms of PCR products of exon 22 from a normal individual and the affected individual IV-4; insertion of an A residue is marked by an arrow. B: Partial nucleotide and amino acid sequences of wild type (normal) and mutant alleles; insertion site of an A residue is marked above by a "pipe" (,) in the wild type allele; a missense run of 18 amino acids are shown in purple in the mutant protein; premature stop codon in exon 23 is shown in red. C: PCR-SSCP analysis of all 13 individuals from the family, note all five affected individuals (IV-1, IV-2, IV-3, IV-4, and IV-6) are homozygous for the mutant allele (M) and their parents (II-1, III-1, III-2, and III-3) are heterozygous for the mutant and the wild type (W) alleles. D: Schematic representation of mutant (above) and normal MYO7A (below) proteins. Note the truncation of MYO7A protein in affected individuals. The normal protein has a head domain with an ATP binding ...
and so forth. The binning with the smallest criterion is then applied to the data. For example, If the second of the three models listed above were used, with the default bin width all observed values between 101 and 102 would be rounded to 101.5. These new values are then rounded to the nearest integer repeat value.. To reduce misclassification errors in binning, a plausible pattern of inheritance of alleles in each family is calculated using a gene dropping algorithm. This algorithm discards and resimulates ibd configurations that are inconsistent with the data, where inconsistency is defined as a greater than cutp*rpt length difference ("*" is multiplication) between an individual allele value and the mean value for the other family members carrying that allele ibd encountered so far. The mean value is binned, and the result used for all those pedigree members inheriting that allele. Any pedigrees where an acceptable ibd configuration cannot be reached are flagged, and set to missing for that ...
Identity by descent Two or more alleles are be identical by descent (IBD) if they have been inherited from the same ancestral allele without recombination events. A common way to identify alleles as identical by descent is usually carried using SNP data. If enough SNPs in two alleles are the observed as the same, then the two alleles are inferred as IBD. See also half-identical region ...
According to our knowledge, our work was the first finding of the assessment polymorphisms A to G in the promoter of FoxP3 gene and its relation to susceptibility to tuberculosis. We observed that the presence of G allele in male and GG genotype in female patients with TB could be an effective marker increasing risk factor to emergence of TB. Several previous studies confirmed that Treg cells play critical roles in the development of TB and their number increases in peripheral blood and disease sites in patient [7-12].Since FoxP3 is the most specific molecular marker for naturally occurring Treg cells, therefore, many studies has been done on FoxP3 gene expression that some of them have shown increased FoxP3 gene expression in patients with TB [27-29]. Our previous reports showed significant higher expression of FoxP3 gene in TB patients. The combination of data from the FoxP3 gene expression and SNP polymorphism provided the surprising finding. Here, our data viewed approximately 5- folds more ...
A subset of CD8+ T cell epitopes within HIV-1 are consistently targeted early after infection. This could explain some of the protective effect of certain HLA class I alleles on HIV-1 disease progression.
HLA A2 allele is associated with age at onset of Alzheimers disease.: The prevalence of the HLA A2 allele was investigated in a group of Italian patients with
A novel DFNB1 deletion allele supports the existence of a distant **cis**-regulatory region that controls **GJB2** and **GJB6** expression ...
function: starting with an observed allele count, it computes an associated threshold filter allele frequency for a variant. Technically, this is the highest disease-specific maximum credible population AF for which the observed AC is not compatible with pathogenicity. More practically, If the filter allele frequency of a variant is above the maximum credible population AF for a condition of interest, then that variant should be filtered (ie not considered a candidate causative variant). The filter allele frequency corresponds to the "filter_AF" annotation in the ExAC dataset. The value in ExAC was computed for a 95% confidence - here the user can choose from a range of thresholds.. Observed population AC - e.g. in ExAC.. Reference population size - we recommend using the number of alleles successfully sequenced at the site (often denoted AN) rather than the full population size. Defaults to 121,412, representing a variant succesfully genotyped in the entire ExAC population.. Confidence - select ...
A quality found in the relationship between two versions of a gene. Individuals receive one version of a gene, called an allele, from each parent. If the alleles are different, the dominant allele will be expressed, while the effect of the other allele, called recessive, is masked. In the case of a recessive genetic disorder, an individual must inherit two copies of the mutated allele in order for the disease to be present.. ...
Use of the NGS to type patients with newly diagnosed type 1 diabetes and control subjects resulted in the following principal findings. First, among the 25 HLA-DRB1 alleles, only 4 (DRB1*03:01:01, DRB1*04:01:01, DRB1*04:04:01, and DRB1*04:05:01) were positively associated with type 1 diabetes. The H-score was used as a way to rank the relative degree of protection. Second, NGS detected nine alleles of DRB3, DRB4, and DRB5, including chromosomes with only nonamplified loci. Only DRB4*01:03:01 and DRB3*01:01:02 were positively associated; the remaining five alleles were negatively associated with the disease. Most importantly, DRB4 was dichotomized in that DRB4*01:03:01 was positively but DRB4*01:01:01 was negatively associated with type 1 diabetes. Similarly, DRB3*01:01:02 was positively but DRB3*02:02:01 was negatively associated with the disease. Because either one of these two alleles may be present on a haplotype containing DRB1*03:01:01, it cannot be excluded that the risk of this allele for ...
Studies containing regions of association that span this marker are shown below. Please note that when making comparisons across studies, that they may vary in terms of size, genotyping platform, and exclusion criteria. If the Odds Ratio is less than 1 then the region is protective (alleles are marked as blue) otherwise it is susceptible (alleles marked as red). ...
Studies containing regions of association that span this gene are shown below. Please note that when making comparisons across studies, that they may vary in terms of size, genotyping platform, and exclusion criteria. If the Odds Ratio is less than 1 then the region is protective (alleles are marked as blue) otherwise it is susceptible (alleles marked as red). ...
Characterization of the pleiotropic effects of ten new putative W locus mutations, nine co-isogenic and one highly congenic with the C57BL/6J strain, reveals a wide variety of influences upon pigmentation, blood formation and gametogenesis. None of the putative alleles, each of which is closely linked to Ph, a gene 0.1 cM from W, gave evidence of complementation with W39, a new allele previously shown to be allelic to Wv. All W/W39 genotypes resulted in black-eyed-white anemics with reduced gametogenic activity. Homozygotes for seven of these mutations are lethal during perinatal life; anemic embryos have been identified in litters produced by intercross matings involving each of these alleles.--Phenotypes of mice of several mutant genotypes provide exceptions to the frequent observation that a double dose of dominant W alleles (e.g., W/Wv or W/W) results in defects of corresponding severity in each of the three affected tissues. One viable homozygote has little or no defect in blood
A team of researchers affiliated with a large number of institutions in the U.S. has found that a subgroup of breast cancers have two PIK3CA mutations, and that such mutations occur on the same allele. In their paper published ...
The Columbian pattern (e) is almost completely dominant to Cornish but is less completely dominant to the Brown Leghorn pattern. The data are insufficient at this time to determine the relationship of the Cornish and Brown Leghorn patterns. The data suggest that these patterns are produced by two alleles at the E locus thus giving a four allele series. It is possible, however, that further investigation may show these two patterns to be produced by a single allele at this locus and that the differences between them is caused by genes modifying the basic black-red pattern and resulting in a three allele series ...
This called the Hardy-Weinberg law. It can easily be extended to cases where there are two or more alleles, but I wont go through the details here.. Now what we have to do is examine the DNA of a particular individual and see how it compares with what is known about the population. Suppose we take one locus to start with, and the individual turns out to be homozygotic: the two alleles at that locus are the same. In the population at large the frequency of that allele might be, say, 0.6. The probability that this combination arises "by chance" is therefore 0.6 times 0.6, or 0.36. Now move to the next locus, where the individual profile has two different alleles. The frequency of one is 0.25 and that of the other is 0.75. so the probability of the combination is "2pq", which is 0.375. The probability of a match at both these loci is therefore 0.36 times 0.375, or 13.5%. The addition of further loci gradually refines the profile, so the corresponding probability reduces.. This is a perfectly bona ...
The difference between the two becomes more pronounced in the case of traits. A trait refers to what you see, so it is the physical expression of the genes themselves. Alleles determine the different versions of the genes that we see. A gene is like a machine that has been put together. However, how it will works will depend on the alleles. ...
LABType HD identifies over 90% of common allele pairs without any ambiguities. The use of over 300 probes allows users to eliminate a significant number of rare alleles and provides a higher resolution typing, distinguishing among known alleles. Since LABType HD uses the same platform, protocol and analysis software as other LABType products, crossover training is minimal. There is also no need to upgrade or purchase new instrumentation.. ...
rs6495446, an intronic SNP in the MTHFS gene, was associated with increased risk for chronic kidney disease based on a study associated with the Framingham Heart Study of ~1,000 Caucasian individuals. The odds ratio rs6495446(C) allele was 1.24 (CI: 1.09-1.41, p=0.001).news 23andMe reports this same information with a different emphasis since the T allele is the minor allele in both European and Asian populations: each T allele lowers the odds of chronic kidney disease by 0.8 times. [PMID 18522750 ...
学位の種類: 博士(医学). 報告番号: 甲第4125号. 学位記番号: 新大院博(医)甲第692号. 学位授与年月日: 平成28年3月23日
Genotypic correlations and regressions can be estimated from multiallelic data sets either by weighting the allelic effects additively or by specifically weighting the genotypic interactions. Both methods can be extended to multiple loci, but they do not fully take into account the joint segregation patterns at the loci. These genotypic statistics have a great importance in sociobiological contexts, as they can be used for genetic descriptions of social structures. In this paper I examine the two estimation methods and show how the genotypic correlation and regression coefficients from genotypic interactions are connected to other statistics of standard population genetics; special emphasis is given to the sample-size correction when intracolony correlations from small samples were estimated. I also show how genotypic correlation and regression can be estimated in subdivided populations, both in continuous populations with isolation by distance and in populations divided into separate ...
Read "Characterization of the dwg mutations: dwg and dwg Bayer are new mutant alleles of the Ggt1 gene, Mammalian Genome" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Ramunno, L.; Cosenza, G.; Rando, A.; Macciotta, N.P.; Pappalardo, M.; Masina, P., 1997: Identification of carriers of the Welsh CASA1 variant using an allele-specific PCR method
VCF file format comes with a lot of interesting QA and statistics fields that can be used for filtering in VarSeq, such as Alternate Allele Frequency
Figure 1. Generation of a Drosophila rugose −/− mutation. The rg locus is located on the X chromosome, and a precise deletion could be generated by remobilization of P-elements. A, Genomic structure of the rg locus. The rg gene is depicted in gray, and the coding sequence (CDS) is shown underneath. Translational start sites of the multiple isoforms are indicated with an arrow and "ATG. " Other genes in this region are indicated in white, and CG numbers are mentioned. The P-elements, PBac(WH)f02898 and PBac(WH)f02325, used to generate the FDD allele of rg, are visualized as triangles and are located within the rg gene and 3′ of the gene, deleting the complete second translational unit, generating the rgFDD null allele. B, Relative rg mRNA levels extracted from adult male fly lysates, measured with qRT-PCR, confirm that the rg alleles generated by Shamloula et al. (2002) are hypomorphic alleles [p , 0.05, t , −10.109, df = 4, Students t test for all mutants except rgP2 compared with w1118 ...
This gene has been identified as an orphan chemoattractant G-protein-coupled receptors (GPCR) pseudogene. Studies have shown that the inactivated gene is present as the predominant allele in the human population. A small fraction of the human population has been found to harbor an intact allele.[provided by RefSeq, Oct 2010 ...
How Are Wizards Made? Being a wizard or a muggle is all decided by genetics All humans including wizards receive one allele from each parent
According to Dr. Crespi and Dr. Badcock (thrilling surname!), epigenetic gene silencing of the fathers versus the mothers genes may tilt a person more toward autism or more toward schizophrenia (NYTs article, Nature essay). Epigenetics is the term that describes changes to the genome that change which genes are expressed but do not change the genome itself. In general, methylation, the adding of a CH3 group to the 5 carbon of the nucleotide cytosine in a promoter, silences the expression of a gene, while demethylation or acetylation (tagging with a -CoCH3 group) increases expression. When a section of a genome is silenced depending on a parents gender, that is called imprinting. As we all carry two alleles (one variant of a specific gene) total, one from each parent, when our sperm or eggs are being made only one of each of our alleles gets put into the sperm or egg. With a few genes, a paternal allele in an egg should be silenced, and a maternal allele in a sperm should be silenced (with ...
I keep saying it because to me it is intuitively obvious and the objections to it make no sense to me, they seem to me to reflect a belief in the ToE and nothing much else. Seems to me it depends on HOW common the alleles that "define a species" were in the original population whether their frequencies will remain the same when the subpopulation is first formed. Of course the alleles that define the main Species, say Cats or Dogs or Bears or Gerbils will remain the same, if those major characteristics are governed by alleles at all, but those for the particular characteristics of the first population are very likely to change, especially in a population that has fairly high genetic diversity. The first population could be characterized by pointy ears, long noses, short tails, brown coat with black markings, but the alleles will nevertheless be present in that population for variations on all those traits, floppy ears or round ears or even pointier ears, short broad noses or longer noses, broad ...
Results.-Polymerase chain reaction-based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRASmutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negativeKRAS result (wild type versus G12C ...
No cell contamination observed with the magnetic wand in Pyrosequencing analysis. A. Representative pyrogram showing the G>A point mutation in the human EGFR gene in a sample with single SW48 cells (positive control). B. Representative pyrogram showing absence of the A allele in single HT-29 cells, transferred with the same unwashed magnetic wand as the SW48 cells. C. Frequency of the A allele in two pierced HT-29 cells (negative control), two pierced SW48 cells (positive control) and 24 pierced HT-29 cells. Single SW48 cells transferred using a clean magnetic wand (positive control) show a mean frequency of A allele (=point mutation) of 50.7%. Pierced single HT-29 cells transferred using an unwashed magnetic wand and analyzed for the presence of SW48 cell contamination showed a similar frequency of A allele when compared to the pierced single HT-29 cells transferred using the clean magnetic wand (negative control), indicating no contamination between the two cell lines, the arrays and the ...
Introduction: Human diseases fall into three broad categories according to our understanding of their origins: genetic, infectious, and indeterminate. While the second category seemed until recently to be shrinking, and the last category is certainly getting smaller, the first is growing rapidly, not due to increased incidence of genetic disease, but due to a fast moving front of new knowledge about disease-associated human alleles. The isolation and characterization of multiple alleles for thousands of other disease-associated genes is on the way. This course is designed to give students an opportunity learn on the some of the many molecular mechanisms of diseases caused by novel alleles, while not losing sight of other causes, in particular emergent infectious agents ...
All DNA from a person, whether collected via saliva, sperm, urine, blood will be the same. Analysts look at 15 different spots on chromosomes where they know our information will be different from each other. First, the DNA is extracted from the collected item and purified. Then they determine how much material is there, whether its weak or concentrated. Then the PCR comes into play where the DNA testing kits use a "primer" to mark the alleles (loci) and make lots of copies of those specifically marked alleles. After that, the material is passed under a special fluorescent light source and the "box cars", the number of repeats occurring for that allele is read. Passing under the light source, gives the program the strength of the signal from the DNA, (the large number on the Electrophermogram) and the number or "tandem repeats" (the small number on the graph) of the box cars. The number of repeats represent the number of copies of that allele/locus. The specific number of tandem repeats at ...
RESULTS The major alleles of rs6717980 and rs2384628 were associated with reduced β-cell function (P ≤ 0.05), with mutual additive effects of each variant (P , 0.01). The minor alleles of rs1049817 and rs6547626 and the major allele of rs780094 were associated with reduced eGFR according to a recessive model (P ≤ 0.03), but with no mutual additive effects of the variants. Additional associations were found between rs780094 and 2-h plasma glucose (P , 0.05) and rs8731 and insulin sensitivity (P , 0.05) and triglycerides (P , 0.05). ...
CSN1S1is one of the major genes encoding milk proteins of mammals. In this study we determined allele frequencies of CSN1S1-5` flanking region as well as exon 17 variants and their effects on milk traits in three indigenous cattle breeds Mazandarani, Golpaygani (Bos indicus) and Sarabi (Bos taurus) and Holstein cattle in Iran. CSN1S1*B variant was nearly fixed in Holstein but ranged from 0.40 to 0.66 in indigenous breeds. CSN1S1*C allele had higher frequency inindigenous breeds, especially inBos indicus. Four genetic variants of the promoter were found in all breeds in different frequencies with allele 2 being the prevalent in all breeds (frequency 0.359 to 0.711) and allele 4 the least frequent (0.074 to 0.011). Allele B of the coding region was found in combination with all four promoter alleles. Allele 4 of the promoter was not found in any cow having the exon 17 allele C in all breeds except Mazandarani. BC / 23 genotype yielded the highest fat percentage (P|0.05) in Holstein but it had no
The magnitude of negative selection on alleles involved in age-specific mortality decreases with age. This is the foundation of the evolutionary theory of senescence. Because of this decrease in negative selection with age, and because of the absence of reproduction after menopause, alleles involved in womens late-onset diseases are generally considered evolutionarily neutral. Recently, genetic and epidemiological data on alleles involved in late onset-diseases have become available. It is therefore timely to estimate selection on these alleles. Here, we estimate selection on BRCA1 alleles leading to susceptibility to late-onset breast and ovarian cancer. For this, we integrate estimates of the risk of developing a cancer for BRCA1-carriers into population genetics frameworks, and calculate selection coefficients on BRCA1 alleles for different demographic scenarios varying across the extent of human demography. We then explore the magnitude of negative selection on alleles leading to a diverse range of
Inherited alpha-1 antitrypsin deficiency (A1ATD) is listed among the three most common genetic disorders in Caucasians. It considerably increases the risk of progressive obstructive lung diseases, mostly chronic obstructive pulmonary disease. Data on the A1ATD prevalence in Poland are scarce, no studies with large enough groups representative for whole Polish population have been performed. Here, we present the preliminary data on the incidence of A1AT main deficiency alleles from the newborn screening in Mazovia (Central Poland) region. Real-time PCR genotyping and A1AT blood concentration measurement by nephelometry were performed from the dry blood spots (DBS) samples of 658 newborns. Deficiency alleles PI*Z i PI*S were present in 28 children, respectively in 2.8% and 1.5%. Their existence corresponded with significantly lower A1AT blood concentration. Estimated incidence of deficiency alleles was 13,7/1000 (95% CI 5.8-21.5) for PI∗Z and 7.6/1000 (95% CI 1.7- 13.5) for PI∗S. The ...
We studied the relationship between JAK2 (V617F) mutant allele burden and clinical phenotype, disease progression and survival in patients with polycythemia vera (PV). The percentage of granulocyte mutant alleles was evaluated using a quantitative real-time polymerase chain reaction-based allelic discrimination assay. Of the 338 patients enrolled in this prospective study, 320 (94.7%) carried the JAK2 (V617F) mutation. Direct relationships were found between mutant allele burden and hemoglobin concentration (P=0.001), white blood cell count (P=0.001), spleen size (P=0.001) and age-adjusted bone marrow cellularity (P=0.002), while an inverse relationship was found with platelet count (P,0.001). During the study period, eight patients progressed to post-PV myelofibrosis (MF) (all carrying ,50% mutant alleles), while 10 patients developed acute myeloid leukemia (AML). The mutant allele burden was significantly related to the risk of developing myelofibrosis (P=0.029) and retained its significant ...
Toda la información sobre las últimas publicaciones científicas de la Clínica Universidad de Navarra. The angiotensin-converting enzyme insertion deletion polymorphism is associated with phagocytic NADPH oxidase-dependent superoxide generation: potential implication in hypertension
We report four novel KIR2DL2 alleles and two novel KIR2DL3 alleles identified from an East African population using sequence-based typing. Sequencing and molecular cloning of exon 4 confirmed that the new 2DL2 alleles were identical to 2DL2*003, except for the following nucleotide differences: 2DL2*00601 had a difference at codon 16 (CGC→CCC), resulting in a coding change from arginine to proline; 2DL2*00602 also had this difference at codon 16, as well as a synonymous difference (GAT→GAC) at codon 31; 2DL2*00303 had a synonymous difference (AAA→AAG) at codon 61; and 2DL2*00304 had a synonymous difference (GGG→GGA) at codon 75. 2DL3*017 was identical to 2DL3*005 except at codon 11 (CGG→CTG, arginine→leucine) and exon 9, codons 297 (CAC→CGC, histidine→arginine) and 321 (TGA→AGA, stop codon→arginine). 2DL3*00104 was identical to KIR2DL3*001 except for a synonymous difference (GAG→GAA) at codon 54. Identification of novel killer cell immunoglobulin-like receptor (KIR) alleles ...
In eastern and southern Africa, there has been a rapid increase in the prevalence of alleles with mutations in the Plasmodium falciparum dihydrofolate reductase gene (dhfr) associated with increased risk of clinical failure of sulfadoxine-pyrimethamine (S/P). Molecular methods for surveillance of these mutations are now widespread, but the usual analysis detects only the most prevalent allele in a polyclonal sample. We used a yeast-expression system to identify rare, highly pyrimethamine-resistant alleles of dhfr in isolates from 5 African countries-Kenya, Tanzania, Malawi, Gabon, and Nigeria. Only the isolates from Nigeria yielded significant numbers of novel resistant alleles, and only 1 of the alleles from any location showed a |3-fold increase in resistance to S/P or to chlorproguanil-dapsone. Overall, these results suggest that dhfr alleles that confer high levels of resistance to antifolates are rare, even in eastern and southern Africa, where pyrimethamine has been intensively used.
Background: Onychomycosis is a fungal infection of one or more units of the nail caused by dermatophytes, or mold and nondermatophytes yeast. Investigations are needed to establish the diagnosis of onychomycosis before starting treatment. Several investigations methods for diagnosing onychomycosis such as microscopic examination with 20% KOH, fungal culture, histopathology examination with PAS staining (Periodic acid Schiff) and PCR (Polymerase Chain Reaction), for culture methods require a long time about 4 weeks to identify fungal that cause onychomycosis. A molecular technology such as PCR is a sensitive and specific test for the diagnosis of a variety of microorganisms including fungal pathogens. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) is a method with the addition of the enzyme after PCR amplification allowing more specific results. Objective: To determine the diagnostic value of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism ...
Saha, N.,Tay, J.S.H.,Basair, J.,Talmud, P.J.,Humphries, S.E. (1996). Lack of association of angiotensin-converting enzyme (ACE). Gene insertion/deletion polymorphism with CAD in two Asian populations. Clinical Genetics 50 (3) : 121-125. [email protected] Repository ...

Data Element: HUMAN LEUKOCYTE ANTIGEN DR ALLELE 1 DONORData Element: HUMAN LEUKOCYTE ANTIGEN DR ALLELE 1 DONOR

HUMAN LEUKOCYTE ANTIGEN DR ALLELE 1 DONOR is the ORGAN OR TISSUE DONORs Human Leukocyte Antigen DR Allele 1, as contained in ...
more infohttps://datadictionary.nhs.uk/data_dictionary/data_field_notes/h/hu/human_leukocyte_antigen_dr_allele_1_donor_de.asp?shownav=0

Why Are Dominant Lethal Genes Rare - portsettpon - dayviews.comWhy Are Dominant Lethal Genes Rare - portsettpon - dayviews.com

... allele,of,a,gene,that,codes,for,the,.,A,common,mistake,is,to,believe,that,if,an,allele,is,dominant,,.In,addition,to,there,being ... alleles,rather,than,dominant,alleles.,Based,on,this,exercise,,can,you,explain,why,a,recessive,lethal,gene,could,.Why,are, ... alleles,,is,,that,,they,,are,,more,,common,,in,,the,,population.,,Explain,,why,,dominant,,alleles,,can,,be,,quite,,rare,,.,,of ... Alleles,,-,,Its,,Instances,,in,,Humans,,,Plants,,and,,.,,Examples,,of,,diseases,,caused,,by,,dominant,,lethal,,allele,,in,,.,,A ...
more infohttp://dayviews.com/portsettpon/524007645/

Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987-2008 - Volume 16, Number 4-April 2010 -...Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987-2008 - Volume 16, Number 4-April 2010 -...

Four of 8 loci showed null alleles and a frequency <44.1%. These loci were distributed among 48.5% of all strains. Overall, ... Especially in VNTR-9 and VNTR-36, the frequency of null alleles was high (31.7% and 44.1%). Although null alleles were reported ... the frequency of null alleles differed markedly. A total of 98 (48.5%) of 202 strains exhibited null alleles in 4 of the 8 VNTR ... Null alleles were also included in the overall number of alleles in a specific VNTR locus. ...
more infohttps://wwwnc.cdc.gov/eid/article/16/4/09-1361_article

Multiple Alleles | Encyclopedia.comMultiple Alleles | Encyclopedia.com

A gene for which at least two alleles exist is said to be polymorphic. ... Multiple Alleles Alleles are alternative forms of a gene, and they are responsible for differences in phenotypic expression of ... Multiple Alleles Genetics Copyright Genetics Society of America. Multiple Alleles. Alleles are alternative forms of a gene, and ... multiple alleles Three or more alternative forms of a gene (alleles) that can occupy the same locus. However, only two of the ...
more infohttps://www.encyclopedia.com/science-and-technology/biology-and-genetics/genetics-and-genetic-engineering/multiple-alleles

collapsing allelescollapsing alleles

... Michael Braverman braver at magnolia.cs.berkeley.edu Tue Jan 3 14:35:55 EST 1995 *Previous message: ... alleles? I have never done it, and would like to learn how to. , ,Thanks! , ,Dean , You may be interested in the following ... This article was inspired by Otts original work on collapsing alleles, but extends his ideas in two important ways (while ...
more infohttp://www.bio.net/bionet/mm/gen-link/1995-January/000503.html

High-throughput allelesHigh-throughput alleles

These are alleles generated through high-throughput, genome-wide projects. Million Mutation Project alleles are placed in a ...
more infohttps://wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/?display_citation=VARIATIONS_HIGH_THROUGHPUT_ALLELES

Alleles and Genes | Physics ForumsAlleles and Genes | Physics Forums

I am trying to get some clarity on the concept of allele. Please let me know if my concepts are correct: Each human cell ( ... Different variants of a gene are called alleles. Thus, each individual has two alleles of every gene. These two alleles can be ... alleles, in some cases only in two. Regardless, every human being always has only two alleles, i.e. two different types of a ... Allele - member of a single gene family. For one trait there can be several sets of alleles, maybe all different, for a ...
more infohttps://www.physicsforums.com/threads/alleles-and-genes.967716/

hy alleles in Nossen background?hy alleles in Nossen background?

... Marc Crepeau ez018859 at bullwinkle.ucdavis.edu Thu Feb 15 20:34:00 EST 1996 *Previous ...
more infohttp://bio.net/bionet/mm/arab-gen/1996-February/004257.html

ApoE4 | allele | Britannica.comApoE4 | allele | Britannica.com

Other articles where ApoE4 is discussed: Alzheimer disease: Genetic variants: …of this gene-APOE2, APOE3, and APOE4-two of which, APOE3 and APOE4, are associated with an increased risk of disease and influence the age of onset of disease.
more infohttps://www.britannica.com/science/ApoE4

Order of allelesOrder of alleles

At a separate gene, the allele sb gives stubby legs while wildtype sb+ allele gives normal legs. At a third gene, the allele w ... Order of alleles. Add. Remove. This content was COPIED from BrainMass.com - View the original, and get the already-completed ... In Drosophila melanogaster, the allele n gives notched wings while the wildtype allele n+ gives normal wings. ... Is the dominant allele the one that occurs most often?. Ive included the queston as an attachment.. Thanks. ...
more infohttps://brainmass.com/biology/genetics/order-of-alleles-388601

Recessive allele - ConservapediaRecessive allele - Conservapedia

A recessive allele is an allele that will not determine the phenotype unless the genotype is homozygous with that allele.[1] ... Examples of recessive alleles include the allele for green in the pea Pisum sativum (the subject of Gregor Mendels heredity ... Retrieved from "http://www.conservapedia.com/index.php?title=Recessive_allele&oldid=865623" ...
more infohttp://www.conservapedia.com/Recessive_allele

New alleles for complex cell labelingNew alleles for complex cell labeling

... By Kristin Lamont Ph.D. Mapping specified cell types at intersections of gene expression ... Of note, Flp- or Dre-deleted alleles derived from RC::RFLTG mice (stock numbers 026931 and 026932 respectively), are available ... Jensens team created a new strain that carries a reporter allele that will label cells defined by the overlapping expression ... To demonstrate the utility of their new intersectional reporter allele, the researchers crossed the reporter-bearing mice with ...
more infohttps://www.jax.org/news-and-insights/2015/december/new-alleles-for-complex-cell-labeling

Allele - WikipediaAllele - Wikipedia

Redirected from Alleles). An allele (/əˈliːl/)[1][2] is a variant form of a given gene.[3] Sometimes, different alleles can ... With three alleles: p. +. q. +. r. =. 1. {\displaystyle p+q+r=1\,}. and. p. 2. +. q. 2. +. r. 2. +. 2. p. q. +. 2. p. r. +. 2. ... Main article: Allele frequency. The frequency of alleles in a diploid population can be used to predict the frequencies of the ... where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, ...
more infohttps://en.m.wikipedia.org/wiki/Alleles

HLA allele frequenciesHLA allele frequencies

... Kevin Mulcahy K.Mulcahy at Sheffield.ac.uk Fri Jul 7 09:51:54 EST 1995 *Previous message: HLA allele ... Can anybody please give me an up-to-date list of all the alleles of the following HLA specificities: HLA-A1, A2, A3, A11, A24, ... In addition, could you also tell me the frequencies of the alleles in the population? Id be most grateful if anybody could ...
more infohttp://www.bio.net/bionet/mm/immuno/1995-July/004622.html

Glossary:Allele CombinationGlossary:Allele Combination

... all allele pairs of a genotype). An allele combination can be composed of one or more allele pairs. ... A designation of the specific alleles present on the two homologous chromosomes for all relevant loci of a mouse (i.e., ...
more infohttp://www.informatics.jax.org/glossary/allele_combination

Glossary:Allele CategoryGlossary:Allele Category

A grouping of MGI allele types on the Phenotypes and Alleles Query Form. Some of the selections in the Categories section of ... the form invoke multiple allele types; for example, chemically induced, all invokes chemically induced (other), and chemically ...
more infohttp://www.informatics.jax.org/glossary/allele_category

Allele
    
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Khan AcademyAllele | Khan Academy

Learn for free about math, art, computer programming, economics, physics, chemistry, biology, medicine, finance, history, and more. Khan Academy is a nonprofit with the mission of providing a free, world-class education for anyone, anywhere.
more infohttps://www.khanacademy.org/tag/allele

AlleleAllele

... An allele (pronounced /əˈliːl/ (US), /ˈæliːl/ (UK)) is a viable DNA (deoxyribonucleic acid) coding that occupies a given ... A wild type allele is an allele which is considered to be "normal" for the organism in question, as opposed to a mutant allele ... where p is the frequency of one allele and q is the frequency of the other allele. Under appropriate conditions, subject to ... An example of multiple alleles is blood type. There are three alleles for blood type, A, B, and O. Because of this, people can ...
more infohttps://www.bionity.com/en/encyclopedia/Allele.html

Alleles - Vancouver MagazineAlleles - Vancouver Magazine

Vancouver magazine is the indispensable playbook to Canadas most exciting city. For over 50 years, this citys influencers have turned to our iconic brand for insightful, informative coverage of the issues, the people, the places and the events that shape Vancouver. From in-depth reporting and analysis of the issues that matter most, to expert fashion and travel guides, reviews of the buzziest new restaurants and the best in wine and spirits, VanMag uncovers what matters now.. 230, 4321 Still Creek Drive, Burnaby, B.C. V5C ...
more infohttp://vanmag.com/tag/alleles/

Codominant allele definition | Drugs.comCodominant allele definition | Drugs.com

Definition of codominant allele. Provided by Stedmans medical dictionary and Drugs.com. Includes medical terms and definitions ...
more infohttps://www.drugs.com/dict/codominant-allele.html

SEMEN ARCHIVES EYES ALLELES CARRIERS - Farmers WeeklySEMEN ARCHIVES EYES ALLELES CARRIERS - Farmers Weekly

Pedigree Flockmasters with rams carrying alleles which fall in categories two, three, four and five of the National Scapie Plan ... SEMEN ARCHIVES EYES ALLELES CARRIERS. PEDIGREE FLOCKMASTERS with rams carrying alleles which fall in categories two, three, ... with 400 semen doses representing each susceptible allele from 11 main breeds and 100 semen doses of each allele for every ... Semen Archive breed liason manager Simon Farmer says the archive is interested in collecting the alleles that make up ...
more infohttp://www.fwi.co.uk/livestock/semen-archives-eyes-alleles-carriers.htm

Chains Of Alice Lyrics - AlleleChains Of Alice Lyrics - Allele

Lyrics to Chains Of Alice by Allele: Sober company to find, / As you walk into a lice / Just the token of divine, / To everyone ...
more infohttp://www.lyricsfreak.com/a/allele/chains+of+alice_21096443.html

Quantification of mutant alleles ... preview & related info | MendeleyQuantification of mutant alleles ... preview & related info | Mendeley

Quantification of mutant alleles in circulating tumor DNA can predict survival in lung cancer. *Yang X ... Yang, X., Zhuo, M., Ye, X., Bai, H., Wang, Z., Sun, Y., … Wang, J. (2016). Quantification of mutant alleles in circulating ... Absolute quantities of plasma EGFR mutant and wild-type alleles were measured by ddPCR. Multi-genes testing was performed using ...
more infohttps://www.mendeley.com/catalogue/quantification-mutant-alleles-circulating-tumor-dna-predict-survival-lung-cancer/

Bio::Variation::Allele - search.cpan.orgBio::Variation::Allele - search.cpan.org

Bio::Variation::Allele - Sequence object with allele-specific attributes. SYNOPSIS $allele1 = Bio::Variation::Allele-,new ( - ... A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length ... List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI ... Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio:: ...
more infohttp://search.cpan.org/dist/BioPerl/Bio/Variation/Allele.pm

Allele (Ruth  Padel)Allele (Ruth Padel)

Allele. The variant. Scripture from a chamber of errors.. The ghost who stalks the body like a shadow. in the mirror, invisible ...
more infohttps://www.lyrikline.org/sl/pesmi/allele-12280?showmodal=de
  • A designation of the specific alleles present on the two homologous chromosomes for all relevant loci of a mouse ( i.e. , all allele pairs of a genotype ). (jax.org)
  • In a diploid organism, one that has two copies of each chromosome, two alleles make up the individual's genotype. (bionity.com)
  • However, this result only holds for the neutral case, and is not necessarily true for the case when some alleles are subject to selection, i.e. more or less fit than others, for example when the fittest genotype is a heterozygote (a situation often referred to as overdominance or heterosis). (wikipedia.org)
  • A wild type allele is an allele which is considered to be "normal" for the organism in question, as opposed to a mutant allele which is usually a relatively new modification. (bionity.com)
  • Absolute quantities of plasma EGFR mutant and wild-type alleles were measured by ddPCR. (mendeley.com)
  • The reason I'm focusing on alleles with selective value is that moments like the settlement of the Americas by a small group of Iberian men and the generation of a mestizo population within a century through hybridization are rare events. (gnxp.com)
  • The ABO system in humans is controlled by three alleles, usually referred to as I A , I B , and I O (the "I" stands for isohaemagglutinin). (encyclopedia.com)
  • The sampling theory of selectively neutral alleles. (nih.gov)
  • These results became important in the formation of the neutral theory, because neutral (or nearly neutral) alleles create no such segregational load, and allow for the accumulation of a great deal of polymorphism. (wikipedia.org)
  • Allele objects that have zero length sequence string. (cpan.org)
  • Function: Sets and returns the sequence of the repeat_unit the allele is composed of. (cpan.org)
  • There can be several variations of this sequence, and each of these is called an allele. (dictionary.com)
  • A pseudodeficiency allele may indicate a deficiency of the enzyme assay method, or it may reflect incomplete understanding of the enzyme's activity. (wikipedia.org)
  • The infinite alleles model is a mathematical model for calculating genetic mutations. (wikipedia.org)
  • Also there are many different types of alleles. (bionity.com)
  • The archive will collect semen from 20 rams of each breed, with 400 semen doses representing each susceptible allele from 11 main breeds and 100 semen doses of each allele for every other breed. (fwi.co.uk)