Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene Frequency”

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.

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

At least 37 records · Page 2Linked to original sources

Variation of female frequency and cytoplasmic male-sterility gene frequency among natural gynodioecious populations of wild radish (Raphanus sativus L.).

In gynodioecious plant populations, sex determination often involves both cytoplasmic male-sterility (CMS) genes and specific nuclear genes that restore male function. How gynodioecy is maintained under the joint dynamics of CMS and restorer genes remains controversial. Although many theoretical models deal with interactions between CMS genes and restorer genes with sexual phenotypes and predict changes in their frequencies, it is difficult to observe the frequencies because no molecular markers have been established for either CMS or restorer genes in well-studied gynodioecious plants. This is the first report of the frequency of a CMS gene determined using a molecular marker in natural populations of a gynodioecious plant. Using a set of CMS gene-specific polymerase chain reaction primers, we compared female and CMS gene frequencies in 18 natural populations of Raphanus sativus. Female frequency was relatively low, ranging from 0 to 0.21. In contrast, the CMS gene frequency was highly variable among populations, ranging from 0 to 1. Estimated restorer gene frequency seemed less variable than observed CMS gene frequency, probably due to higher gene flow than in the CMS gene. Genetic drift may play a role in maintaining high variability of the CMS gene, although other possibilities are not excluded.

DNA Primers↗

The effect of differences in gene frequency on probability of paternity.

Knowledge of gene frequencies in populations is required for the calculation of probability of paternity. The question remains open as to the degree of accuracy of gene frequency estimates required to give accurate probability of paternity figures. This is of special concern in the HLA system, which has haplotype frequencies known to vary in populations. This paper presents computer simulation data comparing probability of paternity calculations using HLA data from California and North Carolina. Comparisons were made between geographic regions, and between blacks and whites within a geographic region. It was found that when the absolute probability of paternity is high, the average differences induced were small, but at lower probabilities the changes can be large. Differences were most pronounced between black and white populations. Examples of individual cases are given to illustrate the huge differences that can be induced in some cases by changing gene frequency.

Child↗

A comparison of disease and gene frequencies of inborn errors of metabolism among different ethnic groups in the West Midlands, UK.

OBJECTIVE: To assess birth and gene frequencies of specific autosomal recessively inborn errors of metabolism (IEM) within different ethnic groups. DESIGN: Retrospective study in a regional centre for investigation and treatment of IEM. SUBJECTS: All children born within the West Midlands NHS Region, UK, during the decade immediately preceding the 1991 National Census. METHODS: Birth frequencies for individual IEM were calculated separately for the main ethnic groups in the West Midlands using data from the West Midlands Neonatal Screening Programme, the regional register of IEM patients, and population frequencies from the National Census. Gene frequencies were calculated using previously documented observations on parental consanguinity rates and inbreeding coefficients. RESULTS: The overall incidence of recorded IEM was tenfold higher among Pakistanis compared to white children (1:318 v 1:3760), whereas only one AfroCaribbean child was identified (incidence 1:16 887). Tyrosinaemia type 1, cystinosis, mucopolysaccharidosis type 1, non-ketotic hyperglycinaemia, and hyperchylomicronaemia all occurred more frequently among Pakistanis. An increased gene frequency was only confirmed for tyrosinaemia. The incidence of phenylketonuria was similar in Pakistani and white children (1:14 452 v 1:12 611), but the gene frequency was significantly lower in Pakistanis (1:713 v 1:112). These results illustrate the interplay between gene frequency and parental consanguinity in determining disease frequencies in different populations, and indicate anticipated disease frequencies in the absence of consanguineous marriage. These figures have implications for the organisation of services for management of inborn errors, for genetic counselling, and for the assessment of gene flow in world populations.

Ethnicity↗

[Gene frequency and haplotypes of the HLA system in the Panamanian population].

The authors determined the frequency of genes and haplotypes of the HLA system in 965 panamanian men and women not related to each other, between 6 and 65 years of age. The HLA-A locus genes with the highest frequency (f) were A2, with f 0.1763; A24, f 0.1584; A30, f 0.1340; A23, f 0.1069; A3, f 0.0774. The other 20 genes each had less than 0.07. The genes with the highest frequency for locus HLA-B were B35, f 0.1946; B44, f 0.0904; B7, f 0.0774; B60 and B61, f 0.0582. For locus HLA-C, the most frequent genes were Cw3 with f 0.1549 and Cw4, f 0.1444. For locus HLA-DR, the most frequent genes were DR2 with f 0.1283; DR3, f 0.0620; DR7, f 0.0409. The most frequent haplotypes in the panamanian population were A2-B35 with f 0.0382; A3-B35, f 0.0191; A24-35, f 0.0287; A24-B61, f 0.0239; A29-B44, f 0.0287; A30-B42, f 0.0239; A23-B44, f 0.0191; A1-B8, f 0.0143. The authors conclude that the panamanian population exhibits a high degree of polymorphism for loci HLA-A, B and C, while for locu HLA-DR the frequency is the median when compared with that in caucasian, negro and oriental groups; and that, according to locus, predominant genes originating from these groups and found, corroborating the multiracial origen of the panamanian population.

Adolescent↗

Germ-line knockout heterokaryons of an essential alpha-tubulin gene enable high-frequency gene replacement and a test of gene transfer from somatic to germ-line nuclei in Tetrahymena thermophila.

The haploid Tetrahymena thermophila genome contains a single alpha-tubulin (ATU) gene. Using biolistic transformation, we disrupted one of the two copies of the ATU gene in the diploid germ-line micronucleus. The heterozygous germ-line transformants were made homozygous in the micronucleus by mating to a star strain containing a defective micronucleus. This mating, known as round 1 genomic exclusion, resulted in two heterokaryon clones of different mating types which have both copies of the ATU gene knocked out in the micronucleus but only wild-type genes in the polycopy somatic macronucleus. When these heterokaryons were mated, the exconjugant progeny cells did not grow because the new somatic macronuclei do not have any alpha-tubulin genes. However, when these conjugants were transformed with a functional marked ATU gene, viable transformants were obtained that contained the transforming ATU gene at the homologous locus in the new macronucleus. The exconjugant progeny could be rescued at a high efficiency (900 transformants per microg of DNA) with a wild-type ATU gene. Unlike previous macronuclear transformation protocols, this strategy should allow introduction of highly disadvantageous (but viable) mutations into Tetrahymena, providing a powerful tool for molecular and functional studies of essential genes. These knockout heterokaryons were used to demonstrate that gene transfer from somatic macronuclei to germ-line micronuclei occurs rarely if at all.

Animals↗

Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells.

In mammalian cells, little is known about the nature of recombination-prone regions of the genome. Previously, we reported that the immunoglobulin heavy chain (IgH) mu locus behaved as a hotspot for mitotic, intrachromosomal gene conversion (GC) between repeated mu constant (Cmu) regions in mouse hybridoma cells. To investigate whether elements within the mu gene regulatory region were required for hotspot activity, gene targeting was used to delete a 9.1 kb segment encompassing the mu gene promoter (Pmu), enhancer (Emu) and switch region (Smu) from the locus. In these cell lines, GC between the Cmu repeats was significantly reduced, indicating that this 'recombination-enhancing sequence' (RES) is necessary for GC hotspot activity at the IgH locus. Importantly, the RES fragment stimulated GC when appended to the same Cmu repeats integrated at ectopic genomic sites. We also show that deletion of Emu and flanking matrix attachment regions (MARs) from the RES abolishes GC hotspot activity at the IgH locus. However, no stimulation of ectopic GC was observed with the Emu/MARs fragment alone. Finally, we provide evidence that no correlation exists between the level of transcription and GC promoted by the RES. We suggest a model whereby Emu/MARS enhances mitotic GC at the endogenous IgH mu locus by effecting chromatin modifications in adjacent DNA.

Animals↗

Time required for gene frequency change in a deterministic model of gene-culture coevolution, with special reference to the lactose absorption problem.

The time required for gene frequency change under natural selection in a deterministic model of gene-culture coevolution is investigated. A discrete generations model is formulated, and its continuous time approximation is derived. In passing to the continuous time limit, it is assumed that the frequency of the culturally transmitted trait does not change under oblique (between generations) transmission. The system of ordinary differential equations thus obtained are solved, and the dependence on the parameters of horizontal (within generations) transmission and natural selection is examined. The time required is found to be substantially longer when the determination of a phenotypic difference subject to natural selection is partly cultural rather than completely genetic. The predictions are relevant to the possibility of the coevolution of lactose absorbers and milk drinkers in some human populations. Alternative hypotheses are briefly discussed in the light of the theoretical results.

Biological Evolution↗

FCGR3B gene frequencies and FCGR3 variants in a Chinese population from Zhejiang Province.

The human neutrophil antigens HNA-1a, -1b and -1c play an important role in immune neutropenia. The frequencies of the coding FCGR3B genes were determined in different populations. New FCGR3B variants were also found in some populations. This study investigated the FCGR3B gene frequencies and FCGR3 variants in a Chinese population compared with the results of Northern Germans and African Blacks (Uganda). Our results show that the gene frequencies in 413 healthy Chinese individuals from Zhejiang Province were 0.565 for FCGR3B*1, 0.430 for FCGR3B*2 and 0.00 for FCGR3B*3. The genotype frequency of FCGR3B(null) was 0.48% (2/413). Sequencing of FCGR3 revealed that in seven out of 19 Chinese individuals, cloned and sequenced DNA fragments that exhibited variants caused by single nucleotide exchanges at one or more of the polymorphic positions 141, 147, 227, 266 and 277 in exon 3 also existed in this Chinese population. From the present study, it is concluded that the FCGR3B*1 gene is more frequent in a Chinese population from Zhejiang Province than the FCGR3B*2 gene, and the FCGR3B*3 gene seems to be absent, which is in contrast to studies in the white populations. Gene variants caused by single nucleotide exchanges were found in addition to the well-known forms, but the reason for this remains unclear.

Alleles↗

PGM1 and Gc subtype gene frequencies in a California Hispanic population.

The gene frequencies of the subtypes of the Gc (group-specific component) protein and PGM1 (phosphoglucomutase) enzyme systems have been determined by means of isoelectric focusing for a California Hispanic population (no. = 404). The Gc subtyping, done by immunofixation on a polyacrylamide gel, gave the following results: 1s = 0.491; 1f = 0.288; 2 = 0.218; variant = 0.0025. The PGM subtyping, done on agarose gel, gave results as follows: 1+ = 0.502; 1- = 0.266; 2+ = 0.128; 2- = 0.104. Because the gene frequencies for Hispanics in both these systems are relatively evenly balanced, the systems are of great value in Hispanic paternity investigations. The average power of exclusion is calculated to be 34.4% (Gc subtyping) and 39.8% (PGM1 subtyping).

Alpha-Globulins↗

Gene frequency clines produced by kin-structured founder effects.

Two mechanisms are commonly invoked to explain geographic gradients in gene frequencies (clines): gene flow and natural selection. Thus gene frequency clines in Europe have been attributed to gene flow because expanding Neolithic farmers from the Near East spread and absorbed resident foragers, a process Cavalli-Sforza and his colleagues labeled demic diffusion. Alternatively, gradients in natural selection can produce the same genetic pattern. A third mechanism to explain European clines has recently been proposed by Barbujani et al. (1995). They found that European allele frequencies were consistent with distributions generated by a simple model of total replacement of foragers by expanding farmers. Clines were produced by repeated founder effects in colonizing farmer groups. Here, I present a simulation model using different population parameters to test the generality of the Barbujani model. Results of the simulation show that steep clines (measured by spatial autocorrelation statistics) can be produced by kin-structured founder effects. The implication of these findings is that several genetic mechanisms are consistent with the allele distributions in Europe. To discriminate among these alternatives, other information, such as better archeological and demographic characterization of interactions between farmers and foragers, is required. In any case, the mere presence of genetic clines does not necessarily validate the demic diffusion model.

Demography↗

Genetic variation in North Amerindian populations: the geography of gene frequencies.

Ten-level synthetic gene frequency maps derived from a principal component analysis of seven polymorphic loci are displayed for a large sample of North Amerindian populations. These maps are useful for assessing population affinities over broad geographical regions and perhaps, as others have argued, for inferring recent migrations. The influence of European admixture is investigated by deleting highly admixed populations and regenerating the maps. In broad outline the resultant geographic patterning, while appearing more homogeneous, preserves many features of the maps that include the highly admixed samples--especially with respect to the Eskimo/non-Eskimo dichotomy. Further, in an effort to evaluate how varying the number of display levels affects patterning as well as interpretation, the maps were replotted at 5 and 20 levels. The 5-level maps are found to accentuate differences between the full data set and the less admixed data set, while the 20-level maps tend to obscure these differences.

Gene Frequency↗

Estimation of milk protein gene frequencies in crossbred cattle by maximum likelihood.

A maximum likelihood method is presented to estimate the fraction of animals misclassified and breed effects for milk protein gene frequencies based on crossbred data. A simulation study indicates that the method provides estimates of gene frequencies that agree closely with the true values. Gene frequencies in the Dutch Black and White and the Dutch Red and White crossbred populations, based on data on 10,151 and 580 animals respectively, were estimated. Dutch Friesian and Holstein-Friesian breeds differ in gene frequencies for beta-casein and beta-lactoglobulin. Estimates for fractions misclassified are zero for alpha s1-casein, .09 for beta-casein and beta-lactoglobulin, and .12 for kappa-casein. Differences between Dutch Red and Whites and Red Holstein-Friesian breeds are small, and estimates for fractions misclassified are high but have high approximate standard errors. Compared with the Black and White breeds, the Red and Whites have a high kappa-casein B gene frequency.

Alleles↗

Perturbation of gene frequencies in a natural population of Drosophila melanogaster: evidence for selection at the Adh locus.

The cellular population of Drosophila melanogaster at the Chateau Tahbilk Winery (Victoria, Australia) was perturbed for alcohol dehydrogenase (Adh) gene frequencies. Phenol oxidase (Phox) frequencies were also perturbed and monitored as a control. Subsequent gene frequency changes, together with information on population structure, indicated that selection acted on the chromosome regions of both loci. Adh gene frequencies returned to preperturbation levels in a predictable manner. A model in which the relative fitness of Adh phenotypes was determined by temperature-dependent specific activities of enzymes of Adh genotypes adequately accounts for the rate of gene frequency change at this locus. Thus temperature behaves as a selective agent in modulating Adh gene frequencies in this cellar environment.

Alcohol Dehydrogenase↗

Gene frequencies of blood groups in Dutch swine breeds.

Gene frequencies of blood groups at 6 loci were estimated within two Dutch breeds of swine, Dutch Landrace and Dutch Large White. At all loci there were significant differences between breeds. The relationship of the two breeds with, respectively, the Germany Landrace breed and the German Large White breed could be confirmed by the gene frequencies.

Animals↗

Gaucher disease: gene frequencies in the Ashkenazi Jewish population.

DNA from over 2,000 Ashkenazi Jewish subjects has been examined for the four most common Jewish Gaucher disease mutations, which collectively account for about 96% of the disease-producing alleles in Jewish patients. This population survey has made possible the estimation of gene frequencies for these alleles. Eighty-seven of 1,528 individuals were heterozygous for the 1226G (N370S) mutation, and four presumably well persons were homozygous for this mutation. The gene frequency for the 1226G allele was calculated to be .0311, and when these data were pooled with those obtained previously from another 593 Jewish subjects, a gene frequency of .032 with a standard error of .004 was found. Among 2,305 normal subjects, 10 were found to be heterozygous for the 84GG allele, giving a gene frequency of .00217 with a standard error of .00096. No examples of the IVS2(+1) mutation were found among 1,256 samples screened, and no 1448C (L444P) mutations were found among 1,528 samples examined. Examination of the distribution of Gaucher disease gene frequencies in the general population shows that the ratio of 1226G mutations to 84GG mutations is higher than that in the patient population. This is presumed to be due to the fact that homozygotes for the 1226G mutation often have late-onset disease or no significant clinical manifestations at all. To bring the gene frequency in the patient population into conformity with the gene frequency in the general population, nearly two-thirds of persons with a Gaucher disease genotype would be missing from the patient population, presumably because their clinical manifestations were very mild.

Base Sequence↗

Autocorrelation of gene frequencies under isolation by distance.

Spatial autocorrelation statistics are used for description of geographic variation of gene frequencies, but the relationship of these indices with the parameters describing the genetic structure of populations is not established. A simple relation is derived here between kinship coefficient and a measure of spatial autocorrelation, Moran's I. The autocorrelation coefficient of gene frequencies at a given distance is a direct function of the kinship at that distance, and an inverse function of the standardized gene frequency variance, Fst. Under isolation by distance, the expected values of Moran's I for any allele may be calculated by means of Malécot-Morton function, which predicts an exponential decline of genetic similarity in space. This allows comparison of observed gene frequency patterns with the patterns that should be caused by interaction of short range migration and random genetic drift.

Alleles↗

[Gene frequency of 5 genetic characters in 6 nationalities in southern Guizhou].

The gene frequency of 5 characters was reported in Buyi, Miao, Shui, Maonan, Dong, and Han nationalities in southern Guizhou, and analyzed for statistical significance among these nationalities. The results showed that: (1) For Hair forms and Nasal profile, the frequency of the dominant gene was lower than that of theirs recessive gene, but the opposite was true for Nostril forms. (2) Among different nationalities, the difference of gene frequency of Mongoloid fold, Nasal profile, Hair forms and Eye fold of the upper eyelid was quite significant, which was followed by that of Nostril forms.

Adolescent↗

Principal axis analysis of gene frequency data.

When a set of populations are compared in respect of gene frequencies, and the chi-square test of heterogeneity is found to be significant, it is pertinent to find out whether the heterogeneity can be explained by a few linear combinations of the gene frequencies, and the total heterogeneity chi-square value can be partitioned as the sum of heterogeneity chi-square values contributed by the linear combinations. The present report describes such a method, and the linear combination that explains the maximum heterogeneity is called the principal axis. An application of this method is presented to find clusters of 31 Mongoloid tribal populations of eastern India using ABO gene frequency data.

ABO Blood-Group System↗