Apolipoprotein A-IV polymorphism in the Finnish population: gene frequencies and description of a rare allele

The apolipoprotein A-IV (apoA-IV) allele frequencies were determined in 387 adult Finns by immunoblotting after isoelectric focusing of serum. The gene frequencies were: A-IV1 = 0.942 and A-IV2 = 0.058. The phenotypes of 147 mother-child pairs studied were in accordance with the two allelic modes of inheritance. In 2 subjects, a rare apoA-IV variant was found.     

OPHN1基因rs492933位点多态性与秦巴山区汉族儿童非特异精神发育迟滞的相关性研究

OPHN1基因编码RhoGTP酶激活蛋白(RhoGAP), 是X连锁的与非特异性精神发育迟滞有关的基因之一。采用PCR-RFLP方法, 对234名陕西秦巴山区正常的汉族儿童以及精神发育迟滞(Mental retardation, MR)患者的OPHN1基因5′非翻译区中的单核苷酸多态位点(Single nucleotide polymorphism, SNP) rs492933的等位基因频率和基因型频率以及是否与非特异精神发育迟滞相关进行分析。结果发现: 这一位点基因频率C为0.826, T为0.174; MR组与对照组之间基因型频率和基因频率没有显著性差异, 边缘组与对照组之间基因型频率和基因频率也没有显著性差异。证明OPHN1基因内SNP rs492933的多态性与秦巴山区汉族儿童精神发育迟滞不存在相关性。     

Acid phosphatase, adenosine deaminase and esterase D polymorphisms in the Spanish Basque population.

The 3 red-cell polymorphic systems acid phosphatase (ACP), adenosine deaminase (ADA) and esterase D (ESD) have been studied in a random sample of 1,112 individuals from the Basque country: The allelic frequencies obtained were ACP*A = 0.275, ACP*B = 0.718 and ACP*C = 0.007; ADA*2 = 0.021, and, ESD*2 = 0.066. The allelic frequencies have been compared with those of other Basque and other European populations. In comparison with Basques, significant differences were detected only for ACP, whereas as regards other Europeans significant differences were obtained with practically all the populations compared for the 3 genetic systems studied. The low values of the less frequent alleles, especially that for the ACP*C allele which is the lowest reported in Europe, are noteworthy.     

Polymorphism of the HFE gene associated with hereditary hemochromatosis in populations of Russia

Expression of hereditary hemochromatosis as well as predisposition to iron overload syndrome and sporadic porphyria cutanea tarda are currently believed to be associated with the inheritance of certain allelic variants of the HFE gene. Allele frequencies of the C282Y (845A) and H63D (187G) mutations in the HFE gene in human populations of different races are remarkably different, and the prevalence of the S65C (193T) mutation is still poorly studied. In the present study we estimated allele frequencies of HFE mutations in Russians and in a number of Siberian ethnic indigenous populations. In Russians, allele frequencies of the C282Y, H63D and S65C mutations were 3.7, 13.3 and 1.7%, respectively. These values were similar to those observed in populations of Europe. The C282Y mutation was not detected in the population samples of Siberian ethnic groups, including Mansis, Khantys (Finno-Ugric group), Altaians, and Nivkhs (Mongoloids), suggesting that the frequency of this allele in the populations examined was lower than 1%. The frequency of the C282Y allele in the Tuvinian and Chukchi samples (Mongoloids) constituted 0.45 and 0.8%, respectively. Furthermore, pedigree analysis of both Chukchi carriers discovered showed that some of their ancestors were from other ethnic groups. Low frequencies of this allelic variant is typical of many Eastern Asian populations, which are also characterized by rather low frequencies of the H63D variant. In contrast, in some ethnic groups of Western Siberia allelic frequency of the H63D mutation is rather high, constituting 8.7% in Altaians, 15.5% in Mansis, and 11.3% in Khantys. The frequency of this allele in Tuvinians, Nivkhs, and Chukchis constituted 5, 4.7, and 0.8%, respectively. These findings make it possible to estimate the proportion of individuals predisposed to iron overload syndrome in different Russian ethnic groups. The HFE allele frequency distribution patterns observed in the populations examined pointed to pre-Celtic appearance of the CY82 allele. It also provides elucidation of the evolutionary genetic relationships between Siberian ethnic groups and the contemporary populations of Eastern and Western Europe.     

Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

Racial differences in selected cytokine allelic and genotypic frequencies among healthy,pregnant women in North Carolina

BACKGROUND: Genetic susceptibility to diseases is likely influenced by common DNA variants in the form of single nucleotide polymorphisms (SNPs). The value of SNPs for linkage and association mapping studies may depend on the distribution of SNP allele frequencies across populations. OBJECTIVES: To establish the SNP allelic frequencies among Caucasian and African American women for tumor necrosis factor (TNF)alpha, transforming growth factor (TGF)beta1, interleukin-10 (IL10), interleukin-6 (IL6), and interferon (IFN)gamma. MATERIALS AND METHODS: DNA was extracted from whole blood from 123 healthy, pregnant women. PCR-based genotyping was performed for the genes encoding TNFalpha (-308G/A), TGFbeta1 (codon 10C/T, codon 25C/G), IL10 (-1082A/G, -819T/C, -592A/C), IL6 (-174C/G) and IFNgamma (874T/A). Allele frequencies were determined by Hardy-Weinberg Equilibrium and Linkage Disequilibrium tests. Differences in the SNP allelic frequencies between Caucasians and African Americans were assessed by the chi(2) of Amitage trend test. RESULTS: SNP allelic and genotypic frequencies for IL6 and IFNgamma, but not for TNFalpha, TGFbeta1, and IL10, differed significantly between the Caucasian and African American women. CONCLUSIONS: Recognition of racial differences in SNP allelic and genotypic frequencies for selected cytokines is important for designing and powering future linkage and association mapping studies investigating the role of cytokines in human disease.     

Study of the most often encountered allele of the HLA-B27 gene in Tuvinian and Russian inhabitants of Western Siberia

HLA-B27 gene frequencies and allelic polymorphism were studied in two Siberian ethnic groups: Russians from Novosibirsk (western Siberia) and Tuvinians from Kyzyl (southern Siberia). The HLA-B27 frequencies were determined by means of serologic typing of HLA antigens in 198 Tuvinians and 288 Russians. Molecular typing was performed via hybridization of oligonucleotide probes with amplified DNAs obtained from 30 HLA-B27-positive Russians and 11 HLA-B27-positive Tuvinians. The HLA-B27 gene frequencies in Tuvinians and Russians were 5.5 and 10.4%, respectively. Molecular variants of the HLA-B27 gene were studied in Tuvinians for the first time. The proportions of the HLA-B2705 and HLA-B2704 alleles were found to be 64 and 36%, respectively, in the population studied. The presence of the HLA-B2704 allele indicates a Mongoloid origin of Tuvinians. In the Russian population of Novosibirsk, the HLA-B2704 allele was not found, whereas the proportions of the HLA-B2705 and HLA-B2702 alleles were 76.2 and 23.8%, respectively, which is characteristic of Caucasoid populations.     

Genotype and allele frequencies of the polymorphic methylenetetrahydrofolate reductase gene in Turkey

The polymorphic methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms C677T and A1298C cause mild hyperhomocysteinemia, not only in homozygotes for C677T, but also in compound heterozygotes for C677T/A1298C. The aim of this study was to determine allelic frequencies of the polymorphic MTHFR gene C677T, A1298C. In this regard, we have investigated the allelic frequencies of C677T and A1298C polymorphisms of the MTHFR gene in 1684 randomized individuals around Turkey. DNA samples isolated from peripheral blood samples of randomized individuals were analysed. The study population consisted of 1004 females and 680 males. The frequency in Turkey of the C677T was 42.9 %; of C677C, 47.4 %; and of T677T, 9.6 %. The frequency in Turkey of A1298C was 43.7 %; of A1298A, 46.3 %; and of C1298C, 10.0 %. The allelic frequencies of the T allele of MTHFR 677 and the C allele of MTHFR 1298 were 33.34 and 33.16 %, respectively. The frequency of C677T/A1298C compound heterozygosity is highest in Turkey (21.6 %), as compared to Canada (15 %), the United States (17 %) and The Netherlands (20 %).     

Five polymorphisms of the apolipoprotein B gene in healthy Bulgarians

Five APOB polymorphisms (I/D in the promoter region, XbaI [codon 24881, MspI [codon 3611], EcoRI [codon 41541, and 3' VNTRs) were studied in a population sample of 147 healthy normolipemic Bulgarians. For all biallelic loci, the observed genotype distributions do not deviate from Hardy-Weinberg equilibrium. In Bulgaria the insertion allele and the MspI+ allele of APOB presented the highest allelic frequencies (0.793 +/- 0.024 and 0.959 +/- 0.012, respectively) among the European population groups studied so far. The allele frequencies of the other two biallelic polymorphisms (XbaI and EcoRI) found in the Bulgarian population are similar to those previously described in other Caucasian populations. Analysis of the 3' VNTR polymorphism revealed 11 different alleles. Like studies in other Caucasian populations, this study found bimodal allele-size distribution and a high level of heterozygosity. The frequency of allele *31 (0.162 +/- 0.022) among Bulgarians is higher than that of any other European population group studied so far. Genetic distances between Bulgarians and each of six populations from southeastern Europe for which 3' VNTR allele frequencies are available showed an increase in the order: Albanians相似文献   

The Maintenance of Single-Locus Polymorphism. IV. Models with Mutation from Existing Alleles

The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.     

Clarification of genetic terms and their use in the management of captive populations

Some of the concepts, terms, and methods used in the genetic management of captive populations have not been defined precisely in the scientific literature and consequently have been misunderstood and misused. The definitions and interrelationships among gene diversity, effective population size, founder genome equivalents, inbreeding, allelic diversity, mean kinship, and kinship value are presented here. It is important to understand what populations and generations are used as the baselines against which losses of genetic variation are measured. Gene diversity and founder genome equivalents are defined relative to a source population from which founders of the captive population were randomly sampled. Inbreeding and allelic diversity are assessed relative to the founders. The potential gene diversity that would result from an equalization of frequencies of founder alleles retained in the population can never be achieved because, among other limitations, the random process of gene transmission will prevent equalization of allele frequencies even if animals are bred optimally. The gene diversity achievable with the population can be determined by iterative production of hypothetical offspring from the pairs with lowest mean kinship. The long-term objective for offspring production from each animal is also thereby generated. Mean kinships should be recalculated with each real or hypothetical birth and death, because offspring objectives based on current mean kinships might correlate poorly with the optimal long-term offspring objectives. © 1995 Wiley-Liss, Inc.     

An ancient bottleneck in the Lost Pines of central Texas

The retreating edge hypothesis for species responding to climate change predicts severe bottlenecks and eventual extinction. The disjunct Lost Pines population at the westernmost edge of the widespread Pinus taeda range is well suited for testing this prediction. The occurrence of one or more genetic bottlenecks in the Lost Pines population was tested using 34 nuclear microsatellite markers and a control sample from the larger, more continuous east Texas P. taeda forests. The Lost Pines population has undergone drastic contractions in effective population size between 3000 and 30 000 years bp. These results were supported by: (i) detection of transient heterozygosity excess, (ii) a mode-shift indicator of allele frequencies, and (iii) a ratio of allele number to allele size range. No bottleneck was detected for the east Texas control using any of the three methods. The distribution of allele frequencies was skewed for the Lost Pines population compared to the control, indicating a loss of rare alleles. However, allelic diversity was similar between the Lost Pines population and its east Texas control; the mean allele number per locus was 5.29 and 5.38, respectively. It is proposed that the Lost Pines population was the western refugium for P. taeda during Pleistocene glaciation and that East Texas P. taeda forests descended from the bottlenecked Lost Pines population.     

haplotypes identified by DNA polymorphisms at the apolipoprotein A-1 and C-III loci and hypertriglyceridaemia

Summary A Japanese group comprising 40 hypertriglyceridaemic and 35 normolipidaemic subjects were genotyped for two intragenic DNA restriction fragment length polymorphisms (RFLPs) at the A-1 and C-III gene loci. An Sst-1 polymorphism is located at the 3 end of the C-III gene and a Msp-1 polymorphism in the third intron of the A-1 gene. The polymorphic restriction sites are 3.8kb apart. The polymorphism with Sst-1 was present at allelic frequencies of 0.67 (S1 allele) and 0.33 (S2 allele), and the polymorphism with Msp-1 was present at allelic frequencies of 0.55 (M1 allele) and 0.45 (M2 allele). The alleles S1, S2, M1, and M2 are in linkage disequilibrium and three haplotypes were identified S1-M1, S1-M2, and S2-M2. Unlike the previously reported association of the S2 allele with hypertriglyceridaemia found in Caucasians there was no difference in the frequency of S2 allele between normolipidaemic and hyperlipidaemic Japanese. However one of the haplotypes S1-M2 was significantly increased in the hypertriglyceridaemic subjects (32% versus 11% P>0.025). Thus in Japanese there is an association with genotypes at this locus and hypertriglyceridaemia but with a different haplotype than in Caucasians.     

Spatiotemporal allozyme divergence caused by aridity stress in a natural population of wild wheat, Triticum dicoccoides, at the Ammiad microsite, Israel

Spatiotemporal diversity at 35 allozyme loci was assayed over 6 years in 1,207 individuals of wild emmer wheat (Triticum dicoccoides)from a microgeographic microsite, Ammiad, north Israel. This analysis used new methods and two additional sample sets (1988 and 1993) and previous allozymic data (1984–1987). This microsite includes four major habitats (North-facing slope, Valley, Ridge, and Karst) that show topographic and ecological heterogeneity. Significant temporal and spatial variations in allele frequencies and levels of genetic diversity were detected in the four subpopulations. Significant associations were observed among allele frequencies and gene diversities at different loci, indicating that many allele frequencies change over time in the same or opposite directions. Multiple regression analysis showed that variation in soil-water content and rainfall distribution in the growing season significantly affected 10 allele frequencies, numbers of alleles at 8 loci, and gene diversity at 4 loci. Random genetic drift and hitchhiking models may not explain such locus-specific spatiotemporal divergence and strong allelic correlation or locus correlation as well as the functional importance of allozymes. Natural ecological selection, presumably through water stress, might be an important force adaptively directing spatiotemporal allozyme diversity and divergence in wild emmer wheat at the Ammiad microsite. Received: 3 July 2000 / Accepted: 1August 2000     

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays

Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.     

Does the geographical gradient of ApoE4 allele exist in China? A systemic comparison among multiple Chinese populations

The allelic frequencies of apolipoprotein E (apoE) vary substantially around the world. There is a conspicuous south-to-north gradient of e4 frequencies in Europe, with the proportion of e4 carriers from only 10–15% in the south to 40–50% in the north. The mechanism may be related to the possibility that e4 carriers are less likely to develop vitamin D deficiency. In addition, Asian populations traditionally have lower e4 frequency than Europeans, which may be attributed in part to the scarce or irregular food supplies in Western world in the recent past. However, whether these geographical distribution gradients exist in China is yet unknown. ApoE genotypes of 200 children from Nanning City were determined by PCR-restriction fragment length polymorphism (RFLP) analysis. Allele frequency data of 18 other populations were collected from published sources and correlated with latitude and longitude information from different geographic resources. In our subjects, the frequencies of apoE genotypes were E3/E3: 73.0%, E3/E2: 15.0%, E4/E3: 5.0%, E4/E4: 5.0%, and E4/E2: 2.0%; the frequencies of apoE alleles were e2: 8.5%, e3: 83.0%, and e4: 8.5%, respectively. The total sample consisted of 3,679 individuals from 19 Chinese populations; the allelic frequencies were e2: 7.6%, e3: 85.5%, and e4: 6.9%, respectively; the proportion of e4 carriers was from 4.9% in Kunming to 17.5% in Harbin. Systemic comparison among multiple Chinese populations revealed that positive correlation existed between the e4 allele frequency distribution and latitude north (r = 0.586, P = 0.008), but no correlation of the e4 allele frequency distribution with longitude east was found (r = −0.018, P = 0.942). We conclude that there is a south-to-north, but not an east-to-west gradient for the apoE4 allele in China.     

Correlations of allele frequencies with physical and environmental variables for populations of largemouth bass, Micropterus salmoides (Lacepede)

Differences in the biochemical genetic structure of each of 90 populations of largemouth bass, Micropterus salmoides (Lacepede), were detected by vertical starch gel electrophoresis. The allele frequencies at each of 28 enzyme loci were tested for correlation with 24 physical and environmental variables determined for each body of water from which the populations were sampled. The allele frequencies at several loci (malate dehydrogenase-B, isocitrate dehydrogenase-B, superoxide dismutase-A, and aspartate aminotransferase-B) were highly significantly correlated ( P ≤0.000l) with several physical and environmental variables (latitude, heating degree-days, cooling degree-days, and the length of the growing season). These correlations are consistent with the hypothesis that allelic differences at specific enzyme loci can confer different degrees of fitness in different thermal environments. Additional laboratory and field studies will be required to determine the extent to which allelic variants at a given enzyme locus contribute to thermal tolerance and thermal preference of largemouth bass.     

Unequal allelic frequencies at the self‐incompatibility locus within local populations of Prunus avium L.: an effect of population structure?

In this paper, we investigated the genetic structure and distribution of allelic frequencies at the gametophytic self-incompatibility locus in three populations of Prunus avium L. In line with theoretical predictions under balancing selection, genetic structure at the self-incompatibility locus was almost three times lower than at seven unlinked microsatellites. Furthermore, we found that S-allele frequencies in wild cherry populations departed significantly from the expected isoplethic distribution towards which balancing selection is expected to drive allelic frequencies (i.e. identical frequency equal to the inverse of the number of alleles in the population). To assess whether this departure could be caused either by drift alone or by population structure, we used numerical simulations to compare our observations with allelic frequency distributions expected : (1) within a single deme from a subdivided population with various levels of differentiation; and (2) within a finite panmictic population with identical allelic diversity. We also investigated the effects of sample size and degree of population structure on tests of departure from isoplethic equilibrium. Overall, our results showed that the observed allele frequency distributions were consistent with a model of subdivided population with demes linked by moderate migration rate.     

Polymorphism of HLA class I loci HLA-A, -B, -C, in the Mandenka population from eastern Senegal]

A sample of 162 Mandenkalu from Eastern Senegal has been typed for three HLA class I loci: HLA-A, -B and -C. The Mandenka population presents a very high genetic variability with 15 alleles for locus A, 24 alleles for locus B, and at least 8 alleles for locus C. The calculated heterozygosities for the three loci A, B, and C are respectively 0.884, 0.944 and 0.829. The Mandenkalu allelic frequencies are close to that found in other sub-Saharan populations. They show, however, some peculiarities like the occurrence of the Bw 56 allele and the high frequencies of both B5 and B35.