Allele frequencies with genic selection

The structure of the limit point process of the ordered allele frequencies in the stationary distribution of a K-allele diffusion model with mutation and genic selection is studied. This leads to a formula for expectations of functions of the allele frequencies in terms of expectations in the neutral infinite alleles model.     

Allele frequencies in a multidimensional Wright-Fisher model with general mutation

A formula is obtained for the probability that two genes at a single locus, sampled at random from a population at time t, are of particular types. The model assumed is a diffusion approximation to a neutral Wright-Fisher model in which mutation is general and not necessarily symmetric. An example is given of a population in which one allele has a high mutation rate, and the others have an equal, low mutation rate. The matrix Q, with elements given by the probability of sampling two alleles of particular types, is calculated exactly and approximately for this case. A formula is given for the distribution of the number of segregating sites occurring in two randomly sampled finite sequences of completely linked sites, with general mutation at a site and identical mutation structure between sites.     

Allele frequencies in multidimensional Wright-Fisher models with a general symmetric mutation structure

The diffusion form of a multiple-allele Wright-Fisher model of allele frequencies of types A₁,…,A_K at a neutral locus where there are general symmetric mutation rates of M_ij (=M_ji) from A_i → A_j is studied. A convenient recurrence relationship for the moments of linear forms in the allele frequencies is found. A formula is derived for the expected homozygosity in the transient and stationary models, which is applied to general stepwise mutation models where mutation over more than one step is possible. The probability that two randomly chosen genes are j steps apart at time t in the stepwise mutation model is found to have a reasonably simple form if conditioning is on the initial allele frequencies arranged in order of magnitude. Of interest is a new geometric charge state model, mutation over several steps roughly corresponding to independent charge changes. The expected homozygosity and expected distance between two randomly chosen genes is tabulated in this model.     

Allele and genotype frequencies of CYP2B6 in a Turkish population

Increasing interest in cytochrome P450 2B6 (CYP2B6) genetic polymorphism was stimulated by revelations of a specific CYP2B6 genotype significantly affecting the metabolism of various drugs in common clinical use in terms of increasing drug efficacy and avoiding adverse drug reactions. The present study aimed to determine the frequencies of CYP2B6*4 CYP2B6*5, CYP2B6*6, CYP2B6*7 and CYP2B6*9 alleles in healthy Turkish individuals (n = 172). Frequencies of three single nucleotide polymorphisms were 516G>T (28 %), 785A>G (33 %), and 1459C>T (12 %). The frequencies of CYP2B6*1, *4, *5, *6, *7, and *9 alleles were 54.3 (95 % CI 49.04–59.56), 6.4 % (95 % CI 3.81–8.99), 11 % (95 % CI 7.69–14.31), 25.3 % (95 % CI 20.71–29.89), 0.87 % (95 % CI ?0.11–1.85) and 2.0 % (95 % CI 0.52–3.48), respectively. Allele *6 was more frequent (25.3 %) than the other variant alleles in Turkish subjects. The frequencies of CYP2B6*4, *5, *6, *7, and *9 alleles were similar to European populations but significantly different from that reported for Asian populations. This is the first study to document the frequencies of the CYP2B6*4, *5, *6, *7, *9 alleles in the healthy Turkish individuals and our results could provide clinically useful information on drug metabolism by CYP2B6 in Turkish population.     

Allele frequencies in multigene families. II. Coalescent approach

Shimizu's model for the evolution of multigene families, subject to gene conversion and mutation, is studied. The probability distribution for the allelic configuration of two chromosomes is found, by using "coalescent" methods. For the two chromosomes, moments are found for the number of alleles they have in common and for their total number of alleles, together with the probability that there is only one allele present. Some numerical examples are given.     

Allele frequencies of hereditary hemochromatosis gene mutations in a local population of west Brittany

Hereditary hemochromatosis (HH) gene mutations, C282Y and H63D, have been screened in a cohort of 254presumably healthy persons originating from a western region of France.The carrier frequencies of these mutations and the incidence of HH have been estimated and compared with those of other studies. This cohort contains two C282Y/C282Y genotypes and has the highest C282Y heterozygosity frequency (17.46%) ever reported. Received: 25 May 1997 / Accepted: 19 November 1997     

Allele frequencies in a domestic cat population in a country area of northern Moravia,Czechoslovakia

The frequencies of alleles responsible for colour of cat fur were studied by method of house-to-house survey in a population of domestic cats in northern Moravia, Czechoslovakia.Of the total of 249 adult cats examined, 114 animals were males and 135 females, the sex ratio being 0.458. The following allelic frequencies were recorded: 0=0.016, a=0.646, t^b=0.288 and S=0.237. No other alleles were recorded in the phenotype. The results are compared with other populations in Czechoslovakia and other European countries.     

Allele frequencies in multigene families. I. Diffusion equation approach

Simulation studies by Ohta, and theoretical studies by Shimizu, indicated that the alleles in one chromosome multigene family follow Ewens' sampling distribution at stationarity. The reasons for this are explored, and the theory is extended to obtain transient and stationary results for the sampling distribution. Expressions are obtained for the amount of variation of numbers of alleles across the chromosomes in a population. The population model includes mutation, and gene conversion, but not recombination.     

Allele frequencies of alpha-1-antitrypsin (PI) in the Balkans

The phenotype and allele frequencies of alpha-1-antitrypsin has been studied by an IEF technique (pH 4.2-4.9) in ten population samples from the Balkans. The allele frequencies varied from 0.6667 to 0.7361 (*M1), 0.1100 to 0.1793 (*M2), 0.0992 to 0.1700 (*M3), 0 to 0.0105 (*S), 0 to 0.0078 (*Z) and 0 to 0.0172 (others). The results were compared with data from South and Middle European populations from the literature. Most of the populations form a cluster with small genetic distances, and a weak relationship to geographical distributions. In contrast, the samples from Southern France, the Iberian Peninsula and Madeira form a clearly separated cluster. The differences are mainly based on high frequencies of PI*S in the latter populations.     

Allele frequencies for candidate genes in atherosclerosis and diabetes among Trinidadian neonates

Trinidadians of South Asian origin have a high prevalence of cardiovascular disease and diabetes compared to Trinidadians of African origin. The degree to which these differences are related to genetic and/or environmental factors is unclear. To determine whether there might be a genetic basis for this difference in prevalence of deleterious phenotypes we examined allele frequencies for candidate genes in atherosclerosis and diabetes. We genotyped 81 consecutive neonates of African origin and 103 consecutive neonates of South Asian origin. We evaluated common polymorphisms in 11 candidate genes for atherosclerosis and diabetes. We found differences between the two subpopulations in the allele frequencies of several candidate genes, including APOE, LIPC, APOC3, PON1, PON2, and PPP1R3. However, the differences in the allele frequencies were not all consistent with the pattern of CHD expression between these two ethnic groups in adulthood. Thus, differences in genetic architecture alone may not explain the wide disparities in disease prevalence between these two subpopulations. It is very likely that environmental factors, or unmeasured genetic factors, influence the genetic susceptibility to disease in these subpopulations.     

Allele frequencies of the human platelet antigen-1 in the Egyptian population

Background

We report the expression pattern of 5S rDNA in the eggs of water frogs Rana lessonae, Rana ridibunda and Rana esculenta using the quantitative real-time PCR. This kind of research had never been performed before.

Results

5S rDNA relative expression of the Rana ridibunda oocytes is approximately six times higher in comparison to the Rana lessonae oocytes. The oocytes of the investigated Rana esculenta frogs, in respect of 5S rDNA relative expression ratio, were very similar to the Rana ridibunda oocytes.

Conclusion

We suggest the possibility of using 5S rDNA as the internal control gene, in the studies of relative mRNA quantitative assays in water frog oocytes, because of its characteristic specific expression pattern in the Rana lessonae, Rana ridibunda and Rana esculenta oocytes.     

Allele and genotype frequencies of metabolic genes in Native Americans from Argentina and Paraguay

Interethnic differences in the allele frequencies of CYP2D6, NAT2, GSTM1 and GSTT1 deletions have been documented for Caucasians, Asians, and Africans population. On the other hand, data on Amerindians are scanty and limited to a few populations from southern areas of South America. In this report we analyze the frequencies of 11 allele variants of CYP2D6 and 4 allele variants of NAT2 genes, and the frequency of GSTM1 and GSTT1 homozygous deleted genotypes in a sample of 90 donors representing 8 Native American populations from Argentina and Paraguay, identified as Amerindians on the basis of their geographic location, genealogical data, mitochondrial- and Y-chromosome DNA markers. For CYP2D6, 88.6% of the total allele frequency corresponded to *1, *2, *4 and *10 variants. Average frequencies for NAT2 *4, *5, *6 and *7 alleles were 51.2%, 25%, 6.1%, and 20.1%, respectively. GSTM1 deletion ranged from 20% to 66%, while GSTT1 deletion was present in four populations in less than 50%. We assume that CYP2D6 *2, *4, *10, *14; NAT2 *5, *7 alleles and GSTM1 and GSTT1 *0/*0 genotypes are founder variants brought to America by the first Asian settlers.     

Allele frequencies of the major milk proteins in the Finnish Ayrshire and detection of a new K-casein variant

A total of 20990 Finnish Ayrshire cows were phenotyped for the major milk proteins by isoelectric focusing in polyacrylamide gels. The predominant alleles in the Finnish Ayrshire were α_S1-casein B (0.999), α_S2-casein A (0.991), β-casein A₁ (0.509) and α₂ (0.490), α₂₂-casein A (0.612) and β-lactoglobulin B (0.716). The K-casein E allele (0.307) was also rather common in the Finnish Ayrshire. A new K-casein variant (K-casein F) was demonstrated in two Finnish Ayrshire cows, a dam and a daughter.     

Allele frequencies of apolipoprotein A-I and A-II gene locus DNA polymorphisms in Boston-based whites

Allele frequencies for four restriction fragment length polymorphisms of the apolipoprotein A-I gene locus and one restriction fragment length polymorphism of apolipoprotein A-II gene locus were determined in more than 100 North American whites and are reported herein.     

Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds

Single‐nucleotide polymorphisms (SNPs) are useful markers for biodiversity assessment, linkage analysis, traceability and paternity testing. To date, there are no available SNPs for goat in the NCBI dbSNP database and only a few are reported in the literature. Within the European Union Econogene project, we characterized 27 SNPs in goats using a targeted‐gene approach. Polymorphisms were identified in a panel of 16 unrelated individuals belonging to eight different goat breeds selected throughout Europe. Genotypes of 30 goats from each of the eight breeds were determined for all the SNPs characterized and diversity measures were estimated. The caprine SNPs described will be a useful complement to the available genome markers.     

Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor

Multilocus surveys of sequence variation can be used to identify targets of directional selection, which are expected to have reduced levels of variation. Following a population bottleneck, the signal of directional selection may be hard to detect because many loci may have low variation by chance and the frequency spectrum of variation may be perturbed in ways that resemble the effects of selection. Cultivated Sorghum bicolor contains a subset of the genetic diversity found in its wild ancestor(s) due to the combined effects of a domestication bottleneck and human selection on traits associated with agriculture. As a framework for distinguishing between the effects of demography and selection, we sequenced 204 loci in a diverse panel of 17 cultivated S. bicolor accessions. Genomewide patterns of diversity depart strongly from equilibrium expectations with regard to the variance of the number of segregating sites, the site frequency spectrum, and haplotype configuration. Furthermore, gene genealogies of most loci with an excess of low frequency variants and/or an excess of segregating sites do not show the characteristic signatures of directional and diversifying selection, respectively. A simple bottleneck model provides an improved but inadequate fit to the data, suggesting the action of other population-level factors, such as population structure and migration. Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model.     

Allele frequencies of single nucleotide polymorphisms in the second exon of the myoglobin gene among the Japanese

The difference in the allele frequencies of two single nucleotide polymorphisms (SNPs) in the second exon of the myoglobin gene between Japanese and other populations is reported. These SNPs are the substitutions of (A79G) and (T109C), and they were investigated by a single polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis followed by direct sequencing. The substitutions were always linked and two alleles were found in the samples used: the A-T allele with no substitution at positions (79A) and (109T) and the G-C allele with substitutions of (79G) and (109C). The frequencies of these alleles were 0.755 and 0.245, respectively, and they were found to be in Hardy-Weinberg equilibrium. The distribution of alleles in the Japanese population was significantly different from that reported among whites, blacks, and Hispanics (p < 0.0001).     

Allele frequencies of 6 autosomal STR loci in the Xibo nationality with phylogenetic structure among Chinese populations

In the present study, we investigated the genetic polymorphisms of 6 autosomal STR loci Hum-CSF1PO, D13S317, D5S818, D16S539, TH01, and TPOX in the Xibo population of Liaoning, northeastern China as well as its genetic relationships with other populations in China. No significant deviations from Hardy-Weinberg equilibrium could be found for all loci. Allele frequencies in the Xibo population ranged from 0.001 to 0.507. Among all the 6 loci, D16S539 had the highest polymorphism (PIC = 0.8632), whereas TPOX had the lowest (PIC = 0.5179). A phylogenic tree was constructed using Poptree 2 software. In the phylogenic tree, Xibo population has a distant relationship with the other populations.     

Allele frequencies and linkage disequilibrium of polymorphic DNA markers of the Huntington disease region in the German population

Allele frequencies of 14 different restriction fragment length polymorphisms from 12 DNA markers within the Huntington disease (HD) region were evaluated in the German population. No significant differences from published data of allele frequencies from chromosomes of Caucasian ancestry were found. The analysis of eight DNA polymorphisms in 87 HD families of German origin revealed significant non-random association with the HD locus and the D4S95 locus (p674/AccI/MboI), a result that is consistent with all other published studies. These results are confirmed by the fact that the HD gene maps to this region.