SEARCH · Search PubMed

Results for “common variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources

PubMed1999

Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure.

Chloroplast DNA (cpDNA) sequence variation is currently the most widely used tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than coding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many of these studies is that intraspecific cpDNA variation is either absent or low and therefore will not interfere with the reconstruction of interspecific relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspecific cpDNA sequence variation. These levels were compared to levels of interspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoides, and intraspecific differences were often larger than interspecific differences. cpDNA haplotype relationships were explored using a maximum parsimony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the presumed evolutionary history of cpDNA haplotypes. A combined effect of cpDNA introgression and complex lineage sorting was inferred to explain the pattern of cpDNA variation found in D. aizoides. Our results suggest that intraspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships among closely related taxa.

Brassicaceae↗

PubMed2001

The expression of NA antigens in people with unusual Fcgamma receptor III genotypes.

BACKGROUND: The Fcgamma receptor IIIb (FcgammaRIIIB) genes that encode neutrophil-specific antigens NA1 and NA2 differ at 5 nucleotides (nts); in 4, the result is an amino acid (AA) difference between the two alleles. The role of each of these differences in antigen expression is not known. Persons with FcgammaRIIIB genes that differ from NA1-FcgammaRIIIB and NA2-FcgammaRIIIB by 1 nt have been described. This study compared NA1 and NA2 expression on granulocytes in persons with variant FcgammaRIIIB genes and in healthy blood donors. STUDY DESIGN AND METHODS: Reactions of NA1- and NA2-specific MoAbs and alloantibodies with granulocytes were assessed by flow cytometry in 74 healthy blood donors and 6 persons with known variant FcgammaRIIIB genes. The granulocytes were tested with 1 NA1-specific MoAb, 1 NA2-specific MoAb, 4 NA1-specific alloantibodies, and 4 NA2-specific alloantibodies. RESULTS: Analysis of granulocytes from persons with variant NA genotypes found that single-base substitutions in FcgammaRIIIB at 141 and at 349 are important in NA1 expression and those at 227 and 277 are important in NA2 expression. Among blood donors, neither age, sex, nor race affected the expression of NA1 or NA2. The NA2-specific MoAb reacted more intensely with granulocytes from NA2-double-dose cells than with those from NA-single-dose cells, but this was not true for the NA2-specific alloantibodies. There was no difference in the reactions of the NA1-specific MoAbs and alloantibodies with donor samples of known NA1-double-dose or NA-single-dose cells. The intensity of reactions of both the NA1- and NA2-specific MoAbs and alloantibodies were strongly correlated on double-dose cells but not on single-dose cells. In fact, granulocytes from 7 healthy blood donors, phenotyped as NA-single-dose with the MoAbs, were phenotyped as NA2-double-dose with the alloantibodies. Variations in FcgammaRIIIB are common in blacks, but 5 of the 6 donors were white. These results suggest that FcgammaRIIIB variations may be common in both whites and blacks. CONCLUSIONS: NA2 expression is affected by polymorphisms in FcgammaRIIIB 227 and FcgammaRIIIB 277, both of which are involved in an FcgammaRIIIb N-glycosylation site. Polymorphisms in FcgammaRIIIB at 141 and 349 appear more important to NA1 expression.

Adolescent↗

PubMed2003

Liability to substance use disorders: 1. Common mechanisms and manifestations.

Variation in the risk for and severity of substance use disorders (SUD) in the population is caused by multiple organismic (genetic, biochemical, psychological) and environmental factors. Whereas drug- or drug-class-specific liability mechanisms exist, a substantial proportion of variance in the risk is shared between specific liabilities, reflecting mechanisms that determine common liability to SUD. Data from epidemiologic, clinical, psychological, physiological, biochemical, and family and genetic studies reviewed in this paper indicate the existence of mechanisms and characteristics shared in common by liabilities to SUD related to different drugs. These mechanisms can be conceptualized as common liability to SUD, a latent trait accounting for a substantial portion of variation in SUD risk and severity and determined by all factors influencing the probability of SUD development. An accompanying paper describes an approach to the quantitative estimation of this trait.

Brain Chemistry↗

PubMed2000

No evidence for association between the KCNQ3 gene and susceptibility to idiopathic generalized epilepsy.

Idiopathic generalized epilepsy (IGE) comprises a heterogeneous group of disorders, in which a high genetic predisposition and a complex mode of inheritance have been suggested. Recent identification of ion channel gene mutations in Mendelian epileptic disorders suggests genetically driven neuronal hyperexcitability as one important factor in epileptogenesis. Mutations in two neuronal voltage-gated potassium channel genes (KCNQ2 and KCNQ3) have already been shown to cause epilepsy (BFNC), and we now tested the hypothesis that genetic variation in the KCNQ3 gene confers liability to common IGE subtypes. Length variation of two intragenic polymorphic markers (D8S558 and D8S1835) were therefore assessed in 71 nuclear families ascertained for an affected child. However, the transmission-disequilibrium-test did not show significant differences between the transmitted and non-transmitted parental alleles. Thus, our findings do not provide evidence that genetic variation in the KCNQ3 gene exerts a relevant effect in the etiology of common IGE subtypes.

Alleles↗

PubMed1999

The geography of behaviour: an evolutionary perspective.

Traditional approaches to the study of behaviour have typically assumed that behavioural patterns, especially elements of reproductive behaviour, are invariant within species. Recent research on a diversity of behavioural traits in a wide array of taxa provides evidence that genetically based geographic variation in behaviour is common. Comparisons of populations that display geographic variation in behaviour can offer substantial insight into mechanisms of adaptive divergence and constraining or generative roles of gene flow, initial stages of speciation, and the roles of phenotypic plasticity and ontogeny in determining patterns of behavioural evolution.

Journal Article↗

PubMed2004

Surface amplification of invasive cleavage products.

A major focus of current efforts in genomics is to elucidate the genetic variations extent within the human population, and to study the effects of these variations upon the human system. The most common type of genetic variations are the single nucleotide polymorphisms (SNPs), which occur every 500-1000 nt in the genome. Large-scale population association studies to study the biological or medical significance of such variations may require the analysis of hundreds of thousands of SNPs on thousands of individuals. We are pursuing development of an approach to large-scale SNP analysis that combines the specificity of invasive cleavage reactions with the parallelism of high density DNA arrays. A surface-immobilized probe oligonucleotide is specifically cleaved in the presence of a complementary target sequence in unamplified human genomic DNA, yielding a 5' phosphate group. High sensitivity detection of this reaction product on the surface is achieved by the use of rolling circle amplification, with an approximate concentration detection limit of 10 fM target DNA. This combination of very specific surface cleavage and highly sensitive surface detection will make possible the rapid and parallel analysis of genetic variations across large populations.

DNA↗

PubMed2001

[CSNP discovery by two-dimensional gene scanning (TDGS)].

Challenges in the post-genomic era are to use genetic information in correlating individual gene variations (SNPs; single nucleotide polymorphisms, the most common form of genetic variation) with medically important parameters, such as disease susceptibility, individual responses to drugs and prognostic variables. What is missing is a high-throughput technology to identify all possible SNPs in essentially all human genes in population-based studies with high accuracy and speed in a cost-effective manner. Most tests advocated for their high throughput at low cost are actually SNP screening tests. That is, they screen samples for the presence of one or multiple previously identified SNPs. Such screening methods are only useful when all relevant SNPs in the genes of interest are known, which is presently not the case. Moreover, the usefulness of any one SNP varies enormously from population to population. Indeed, for the Korean population, where no information on possible sequence variation is available, a mutational scanning method, capable to detect all possible gene variations will be most useful. Two-Dimensional Gene Scanning (TDGS) is a high-throughput platform that enables to detect all possible SNPs in an entire gene in one gel under one set of conditions, with high sensitivity and specificity. TDGS is based on automated two-dimensional (2-D) DNA electrophoresis according to size and base pair sequence to detect DNA fragments containing all possible variations. Because the 2-D format permits the analysis of as many as 40 fragments of 250 bp on average in parallel, TDGS allows extensive multiplex PCR (megaplex PCR), i.e. up to 26 fragments in one single reaction, resulting in a significant cost reduction. TDGS tests are designed using a computer program to optimally position PCR primers around the relevant target sequences (exons). A simple automated 2-D instrument allows scanning all exons of a large gene in 8 different samples well within 3 hours. Using three different fluorophores this provides a throughput.

BRCA1 Protein↗

PubMed2005

Prevention programs for reducing adolescent problem behaviors: Implications of the co-occurrence of problem behaviors in adolescence.

PURPOSE: To examine the correlations between multiple risk behaviors in adolescent populations to document the extent to which problem behaviors are intercorrelated and to identify factors associated with variations in these correlations. METHODS: Studies from 1977 through the end of 1999 that included two or more problem behaviors in adolescents were identified by literature searches using the PsychLit database, Social Sciences Citation Index, manual journal searches and "ancestry" approaches. The behaviors studied were alcohol use, marijuana use, illicit drug use, cigarette smoking, general deviant behavior, and sexual activity. Included studies reported correlation coefficients between variables. RESULTS: Across all studies, the mean correlation between any two pairs of problem behaviors was 0.35, with a standard deviation of 0.28. This suggests that, on average, about two-thirds of the variation in problem behavior is the result of unique rather than common causes. The magnitude of the correlations varied as a function of the age of the adolescent, with lower correlations being evident for older adolescents. In addition, the magnitude of the correlation varied as a function of when the study was conducted, with studies of past generations showing stronger connections between risk behaviors than current generations. CONCLUSIONS: The data suggest that there is considerably more unique variation in classic adolescent problem behaviors than common variation.

Adolescent↗

PubMed1979

Temporal variation in suicide and homicide.

In this study of all of the violent deaths in the US over two years, clear monthly and daily variations were found. Suicide peaked in the Spring and Fall; homicide in July and December. Suicide was more common on Mondays; homicide on Saturdays and Sundays. Homicide was more common on national holidays, while suicide tended to be less common. No lunar variation was found.

Holidays↗

PubMed1990

Clinical assessment of osteoarthritis of the knee.

The repeatability of physical signs used to assess osteoarthritis of the knee has not been systematically examined. The within and between observer variation of 10 commonly used physical signs to determine osteoarthritis of the knee has been assessed here. The results obtained show variation in the repeatability of these signs. For those examining the tibiofemoral joints the repeatability was greater than for those examining the patellofemoral joint. It would therefore seem vital to take note of the repeatability of physical signs in determining the number of subjects to be studied in epidemiological studies and therapeutic studies in osteoarthritis.

Female↗

PubMed1999

Single-nucleotide polymorphisms can cause different structural folds of mRNA.

Single-nucleotide polymorphisms (SNPs) are the most common type of genetic variation in man. Genes containing one or more SNPs can give rise to two or more allelic forms of mRNAs. These mRNA variants may possess different biological functions as a result of differences in primary or higher order structures that interact with other cellular components. Here we report the observation of marked differences in mRNA secondary structure associated with SNPs in the coding regions of two human mRNAs: alanyl tRNA synthetase and replication protein A, 70-kDa subunit (RPA70). Enzymatic probing of SNP-containing allelic fragments of the mRNAs revealed pronounced allelic differences in cleavage pattern at sites 14 or 18 nt away from the SNP, suggesting that a single-nucleotide variation can give rise to different mRNA folds. By using phosphorothioate oligodeoxyribonucleotides complementary to the region of different allelic structures in the RPA70 mRNA, but not extending to the SNP itself, we find that the SNP exerts an allele-specific effect on the accessibility of its flanking site in the endogenous human RPA70 mRNA. This further supports the allele-specific structural features identified by enzymatic probing. These results demonstrate the contribution of common genetic variation to structural diversity of mRNA and suggest a broader role than previously thought for the effects of SNPs on mRNA structure and, ultimately, biological function.

Alanine-tRNA Ligase↗

PubMed2003

A common polymorphism in the promoter of UCP2 contributes to the variation in insulin secretion in glucose-tolerant subjects.

It was reported that the common -866G/A polymorphism in the promoter of the human uncoupling protein-2 (UCP2) gene, which enhances its trascriptional activity, is associated with increased mRNA levels in human adipocytes and reduced risk of obesity. Studies in knockout mice and beta-cells indicate that UCP2 may play a role in beta-cell function. In this study, we addressed the question of whether the common -866G/A polymorphism in UCP2 gene contributes to the variation of insulin secretion in humans by genotyping 301 nondiabetic subjects who underwent an oral glucose tolerance test. Glucose-stimulated insulin secretion estimated by several indexes of beta-cell function was significantly lower in carriers of the -866A/A genotype compared with -866A/G or -866G/G according to the dosage of the A allele (P = 0.002-0.05). To investigate directly whether the UCP2 -866G/A polymorphism affects human islet function, pancreatic islets isolated from two -866G/G homozygous, seven -866G/A heterozygous, and one -866A/A homozygous nondiabetic donors were studied. Islets from -866A/A homozygous had lower insulin secretion in response to glucose stimulation as compared with -866G/G and -866G/A carriers. These results indicate that the common -866G/A polymorphism in the UCP2 gene may contribute to the biological variation of insulin secretion in humans.

Adult↗

PubMed2004

Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico.

Cloud forests are distributed in the Neotropics, from northern Mexico to Argentina, under very specific ecological conditions, namely slopes with high humidity input from clouds and mist. Its distribution in Mesoamerica is highly fragmented, similar to an archipelago, and taxa are thus frequently represented as sets of isolated populations, each restricted to particular mountain ranges and often showing a high degree of divergence, both morphologically and genetically. The common bush-tanager (Chlorospingus ophthalmicus, Aves: Thraupidae) inhabits cloud forests from eastern and southern Mexico south to northwestern Argentina. Here we use 676bp of mtDNA (around the ATPase 8 gene) to explore the genetic variation and phylogeographic structure of the Mexican populations of C. ophthalmicus. Phylogenetic analyses of mtDNA sequences indicate deep genetic structure. Five major clades, which segregate according to geographic breaks, are identified (starting from the deepest one in the phylogeny): (1) Southern Chiapas and Northern Central America, (2) Tuxtlas massif, (3) Sierra Madre del Sur, (4) Eastern Oaxaca and Northern Chiapas, and (5) Sierra Madre Oriental. The long history of isolation undergone by each clade, as suggested by the phylogeny, implies that the species status of each of them should be revised.

Animals↗

PubMed1997

The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population.

The amounts of nucleotide variation within and between allelic classes were studied. The expectation and variance of the number of segregating sites and the expectation of the average number of pairwise differences among a sample of DNA sequences were obtained by using the theory of gene genealogy with no recombination. When the ancestral allelic class is unknown, it was found that the amount of variation within an allelic class increases with its frequency in the sample, while the amount of variation between two allelic classes is the largest when the two allelic classes exist equally. On the other hand, if we know the ancestral allelic class, as the frequency of the mutant allelic class increases, the amounts of variation within the mutant allelic class and between two allelic classes increase and the amount of variation within the ancestral allelic class decreases. As an example, we analyzed the polymorphism in the ND5 gene of Drosophila melanogaster and constructed the common ancestral sequence with high confidence, suggesting that the pattern of polymorphism within species gives useful information to know the ancestral sequence of the species.

Alleles↗

PubMed2002

Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes.

Genetic variations have been associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification and pharmacogenetics. Commonly used gel electrophoresis-based genotyping methods for known polymorphisms include polymerase chain reaction (PCR) coupled with restriction fragment-length polymorphism analysis, allele-specific amplification, and oligonucleotide ligation assay. Fluorescent dye-based DNA fragmentation has been extensively used for high-throughput microsatellite or short tandem-repeat genotyping. TaqMan and molecular beacon genotyping are commonly used homogeneous solution hybridization technologies. Because of the ease of experimental assay design, single nucleotide polymorphism (SNP) genotyping methods based on single-base extension are in rapid development, such as fluorescence homogenous assays, pyrosequencing and mass spectrometry. Non-PCR based genotyping assays such as Invader trade mark assays are promised to genotype directly from genomic DNA without the requirement of PCR amplification. The DNA microarray is a solid phase genotyping format that is rapidly developing for parallel genotyping of a large number of SNPs simultaneously. Advanced technologies to identify genetic polymorphisms rapidly, accurately, and cost effectively will fundamentally change the practice of medicine by allowing physicians to prescribe medicine based on a patient's genetic make-up.

Alleles↗

PubMed2002

Global and regional estimates of cancer mortality and incidence by site: II. Results for the global burden of disease 2000.

BACKGROUND: Mortality estimates alone are not sufficient to understand the true magnitude of cancer burden. We present the detailed estimates of mortality and incidence by site as the basis for the future estimation of cancer burden for the Global Burden of Disease 2000 study. METHODS: Age- and sex- specific mortality envelope for all malignancies by region was derived from the analysis of country life-tables and cause of death. We estimated the site-specific cancer mortality distributions from vital records and cancer survival model. The regional cancer mortality by site is estimated by disaggregating the regional cancer mortality envelope based on the mortality distribution. Estimated incidence-to-mortality rate ratios were used to back calculate the final cancer incidence estimates by site. RESULTS: In 2000, cancer accounted for over 7 million deaths (13% of total mortality) and there were more than 10 million new cancer cases world wide in 2000. More than 60% of cancer deaths and approximately half of new cases occurred in developing regions. Lung cancer was the most common cancers in the world, followed by cancers of stomach, liver, colon and rectum, and breast. There was a significant variations in the distribution of site-specific cancer mortality and incidence by region. CONCLUSIONS: Despite a regional variation, the most common cancers are potentially preventable. Cancer burden estimation by taking into account both mortality and morbidity is an essential step to set research priorities and policy formulation. Also it can used for setting priorities when combined with data on costs of interventions against cancers.

Africa↗

PubMed2002

Robustness of the Chen-Dougherty-Bittner procedure against non-normality and heterogeneity in the coefficient of variation.

Chen, Dougherty, and Bittner [Y. Chen, E. R. Dougherty, and M. L. Bittner, J. Biomed. Opt. 2(4), 364-374 (1997)] provided the derivation of a probability density function (PDF) for a signal ratio from a DNA microarray. This PDF is potentially useful for testing whether a pair of signals from the same gene has a common mean. The derivation of the PDF assumes the normality of all signal distributions and a common coefficient of variation (CV) for all signals within a microarray. The testing procedure requires the calculation of a common confidence interval for a microarray, based on a maximum likelihood estimator of the "common" CV, and the determination of whether or not a ratio for a particular gene falls within this interval. This study used Monte Carlo techniques and demonstrated that the procedure is robust to violations of normality and also to constancy in the coefficients of variation. A closer examination of the dynamics of the procedure found that the robustness was the result of offsetting effects. The size of the confidence interval was increased as a result of higher estimates of the common CV, as the actual CV pattern became heterogeneous. This effect mitigated the inflation in the size of the ratio as a result of increasing CV heterogeneity. These findings suggest that the Chen-Dougherty-Bittner procedure may be used even if underlying assumptions do not hold.

Analysis of Variance↗

PubMed1991

Immunohistopathology of variations of human olfactory mucosa.

The characteristics of the human olfactory mucosa were studied immunohistologically. Regular, zonal distribution of the supporting cells, multilayered olfactory receptor cells and basal cells was commonly found in the olfactory mucosa of the human fetus. In contrast, most of the olfactory mucosa in the adult varied to some extent. In the relatively thick, slightly degenerated olfactory mucosa, olfactory marker protein positive receptor cells were arranged irregularly. The most common evidence for variation was the decrease or disappearance of the olfactory receptor cells. Serous-type lactorferrin-containing glandular acini were characteristically found beneath degenerated epithelium. Islands of respiratory epithelium were also seen. The ductules of the Bowman's glands were distended and the openings of these ductules were wide. There was invagination or epithelial cell processes into the glandular lumina. These findings suggest that the epithelial cells of Bowman's glands play an important role in the regeneration of the human olfactory mucosa.

Adult↗