Analysis of heterogeneity in Fanconi's anemia patients of different ethnic origin

Summary Complementation studies based on mitomycin C sensitivity were performed on somatic cell hybrids between cells of a German patient with Fanconi's anemia and a Turkish, Arab, and Black African proband, respectively. Though the underlying genetic defects are expected to go back to different mutational events, the high rate of induced chromosomal aberrations in the hybrids clearly points to allelic mutations.     

Genetic structure of Eurasian otter (Lutra lutra,Carnivora: Mustelidae) populations from the western Baltic sea region and its implications for the recolonization of north‐western Germany

We analysed 229 Eurasian otters from eastern and north‐western Germany, Denmark and southern Sweden based on sequences of the mtDNA control region and genotypes at 12 polymorphic nuclear microsatellite loci. The main focus of the study lay on the north‐west German otters from Schleswig‐Holstein, which represent a newly established and expanding population recolonizing a formerly inhabited region, thereby closing the distributional gap between the large eastern population and the long‐isolated and genetically depleted Danish population. As found before in this species, mtDNA variability was very low but we identified a hitherto unknown haplotype in Sweden. Expected heterozygosities were between 0.46 and 0.69 and thus within the range known from the literature. There were only weak signs of a founder effect in the Schleswig‐Holstein otters with respect to allelic diversity (but not heterozygosity). Nevertheless, there was a statistically significant bottleneck signal based on deviations from mutation‐drift equilibrium in Schleswig‐Holstein. All statistical approaches (amova s, factorial correspondence analysis, assignment tests and Bayesian structure analysis) unequivocally showed that north‐western Germany has so far been predominantly recolonized by otters of east German origin, but we also found evidence of admixture through immigration from Denmark. Both the Danish and the north‐west German otter population will benefit from further exchange in the wake of the ongoing range expansion.     

Microsatellite profiles reveal an unexpected genetic relationship between Asian populations

Allelic frequencies for up to five short tandem repeat systems (HumTH01, HumVWA, HumF13B, HumCD4, HumD21S11) were analyzed in seven population samples from Asia using the polymerase chain reaction and gel electrophoresis. No deviations from Hardy-Weinberg equilibrium were observed. Two new alleles of the CD4 and TH01 loci were detected, and sequenced and their molecular structure is presented. A phylogenetic tree based on Thai, Han Chinese (from the northeast of China), Japanese, German and Ovambo allelic frequencies was constructed and demonstrates the close relationship of the Asian populations. Additionally, allelic frequency data for the VWA and TH01 systems were determined for the south Chinese minorities Bai, Dai and Qiang and for Koreans and compared with the above data. The Bai and Dai populations were clear outliers of the cluster of all other Asians, indicating an unexpected pattern of genetic heterogeneity of the Chinese nation. Two clusters of Asian populations could be established: the Koreans and Japanese together with the Han and Qiang Chinese, and, forming a separate cluster, the Bai and Dai populations. Received: 10 June 1997 / Accepted: 15 March 1998     

Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites

Genetic relationships among six populations of Merino sheep were investigated using microsatellites. The history of the six populations is relatively well documented, with all being derived from the Spanish Merino breed within the last 400 years. Genetic variation was highest amongst the Spanish and Portuguese populations, although the preservation of genetic diversity within the other populations was high. By a variety of different statistical tests the French Mutton, German Mutton and New Zealand Merino populations could be differentiated from each other and the Iberian Merinos, indicating that microsatellites are able to track relatively recent changes in the population structure of sheep breeds. The dendrograms constructed on the basis of microsatellite allelic frequencies showed that populations that have shared selection criteria (meat vs. wool) tend to cluster together.     

Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta)

We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.     

Dimorphic markers for the human apolipoprotein CII gene locus

Two restriction-site polymorphisms (RSP) have been detected when using a human apolipoprotein CII (apoCII) cDNA clone as a hybridization probe. These include a BanI and a TaqI RSP. Frequencies of the more common allele have been determined in a German population of 100 individuals and are 0.66 (BanI RSP) and 0.56 (TaqI RSP). Corresponding polymorphic information content (PIC) values are 0.36 and 0.37 for individual sites, and 0.58 for the BanI-TaqI pair of sites, making this locus a very informative (PIC-rich) marker for this region of chromosome 19. Haplotype studies also indicate the presence of allelic association (linkage disequilibrium) at the human apoCII gene locus.     

Genetic diversity,introgression and relationships among West/Central African cattle breeds

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups – African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.     

New genetic evidence for involvement of the dopamine system in migraine with aura

In order to systematically test the hypothesis that genetic variation in the dopamine system contributes to the susceptibility to migraine with aura (MA), we performed a comprehensive genetic association study of altogether ten genes from the dopaminergic system in a large German migraine with aura case-control sample. Based on the genotyping results of 53 variants across the ten genes in 270 MA cases and 272 controls, three genes—DBH, DRD2 and SLC6A3—were chosen to proceed to additional genotyping of 380 MA cases and 378 controls. Four of the 26 genotyped polymorphisms in these three genes displayed nominally significant allelic P-values in the sample of 650 MA patients and 650 controls. Three of these SNPs [rs2097629 in DBH (uncorrected allelic P value = 0.0012, OR = 0.77), rs7131056 in DRD2 (uncorrected allelic P value = 0.0018, OR = 1.28) and rs40184 in SLC6A3 (uncorrected allelic P value = 0.0082, OR = 0.81)] remained significant after gene-wide correction for multiple testing by permutation analysis. Further consideration of imputed genotype data from 2,937 British control individuals did not affirm the association with DRD2, but supported the associations with DBH and SLC6A3. Our data provide new evidence for an involvement of components of the dopaminergic system—in particular the dopamine-beta hydroxylase and dopamine transporter genes—to the pathogenesis of migraine with aura. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. U. Todt and C. Netzer contributed equally to this work.     

Genetics in genealogical research--reconstruction of a family tree by means of Y-haplotyping

In societies, in which surnames are inherited patrilinearly, surnames and certain Y-chromosome STR allelic patterns, so-called Y-haplotypes, correlate. In order to reconstruct the relationship between three different family lines with the surname Zierdt, a total of 34 German and US-American males with this surname was selected. Among those test candidates several family branches could be identified on the basis of written records. However, the relationship between those family lines was as yet unknown as the necessary documents had not been available. By haplotyping in two family lines the same Y-haplotype could be recognised, thus belonging to the same paternal lineage. As the third family line revealed a deviant Y-haplotype, its relationship could be excluded. Four cases of non-paternity could be revealed and put into historical context.     

Transformation of QTL genotypic effects to allelic effects

The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist.     

The lingering enigma of the allelic exclusion mechanism

B lymphocytes produce diverse antibody specificities by "randomly" assembling antibody genes from germline segments. Yet, though each B lymphocyte has multiple allelic loci for the different antibody chains, each clonally derived mature B lymphocyte expresses a single species of antibody with a unique specificity via a process termed allelic exclusion. Despite some progress, the precise mechanism of allelic exclusion remains an enigma.     

The Qa-1 alloantigens. III. Biochemical analysis of the structure and extent of polymorphism of the Qa-1 allelic products

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to examine and compare the products of the Qa-1 locus. Analysis of Qa-1 isolated from detergent lysates of surface labeled cells indicated this molecule was a slightly acidic 48,000 to 50,000 dalton glycoprotein that displayed little charge heterogeneity on resting lymphocytes. The level of expression and degree of charge heterogeneity were both increased on activated lymphocytes. Direct comparison of the Qa-1b, Qa-1c, and Qa-1d allelic products by 2-D PAGE revealed that these three molecules could be distinguished from one another on the basis of isoelectric point, indicating that they were distinct at the molecular level. Comparison of Qa-1 isolated from several Qa-1b strains did not detect additional polymorphism. Removal of asparagine-linked oligosaccharides by treatment with endoglycosidase F indicated that carbohydrate contributed 10,000 to 12,000 to the m.w. of these allelic products. Comparative 2-D PAGE analysis could not distinguish between the deglycosylated Qa-1b, Qa-1c, and Qa-1d allelic products, implying that these molecules have similar primary structures. Peptide mapping supported this conclusion. Proteolytic digestion of the deglycosylated Qa-1b and Qa-1c allelic products resulted in identical peptide map patterns; such treatment of the deglycosylated Qa-1d allelic product produced a slightly different pattern. Peptide mapping analysis also demonstrated that the Tlaa and Qa-1a allelic products were distinct from one another, as well as being very different from the other three Qa-1 allelic products.     

Seven novel KIT mutations in horses with white coat colour phenotypes

White coat colour in horses is inherited as a monogenic autosomal dominant trait showing a variable expression of coat depigmentation. Mutations in the KIT gene have previously been shown to cause white coat colour phenotypes in pigs, mice and humans. We recently also demonstrated that four independent mutations in the equine KIT gene are responsible for the dominant white coat colour phenotype in various horse breeds. We have now analysed additional horse families segregating for white coat colour phenotypes and report seven new KIT mutations in independent Thoroughbred, Icelandic Horse, German Holstein, Quarter Horse and South German Draft Horse families. In four of the seven families, only one single white horse, presumably representing the founder for each of the four respective mutations, was available for genotyping. The newly reported mutations comprise two frameshift mutations (c.1126_1129delGAAC; c.2193delG), two missense mutations (c.856G>A; c.1789G>A) and three splice site mutations (c.338-1G>C; c.2222-1G>A; c.2684+1G>A). White phenotypes in horses show a remarkable allelic heterogeneity. In fact, a higher number of alleles are molecularly characterized at the equine KIT gene than for any other known gene in livestock species.     

人类基因组STR等位基因阶梯的研制

研究建立一种制备STR等位基因阶梯标准的新方法。以单一来源的DNA链为模板,采用槽式PCR扩增法,并经过PAGE胶回收纯化制备等位基因阶梯标准。结果：该方法适合等位基因阶梯标准的制备,所制备的等位基因阶梯基本无杂带,效果较理想。     

Comparative PRNP genotyping of U.S. cattle sires for potential association with BSE

The recent discovery of significant associations between bovine spongiform encephalopathy (BSE) susceptibility in German cattle and the frequency distributions of insertion/deletion (indel) polymorphisms within the bovine PRNP gene prompted an evaluation of 132 commercial U.S. artificial insemination (AI) sires from 39 breeds. Forward primer sequences from published primer sets targeting indels within the putative bovine PRNP promoter, intron 1, and the 3 UTR (untranslated region) were synthesized with unique 5 fluorescent labels and utilized to develop a rapid multiplexed PCR assay for identifying BSE-associated indels as well as facilitating polymorphism analyses and/or marker-assisted selection. Significant differences (p < 0.05 all tests) were detected between the frequencies of bovine PRNP promoter alleles for 48 healthy German cattle previously described and 132 commercial U.S. cattle sires. The frequency of the 23-bp promoter allele observed for commercial U.S. cattle sires strongly resembled that recently described for 43 BSE-affected German cattle. No significant difference (p=0.051) was detected between the distributions of promoter genotypes for healthy German cattle and our panel of commercial U.S. cattle sires. Interestingly, significant differences (p < 0.01; p < 0.02) were also noted between the frequencies and distributions of intron 1 alleles and genotypes, respectively, for BSE-affected German cattle and our panel of U.S. cattle sires. No significant allelic or genotypic differences were detected for the 14-bp 3 UTR indel for any given comparison between German cattle and commercial U.S. cattle sires.     

Monozygotic twins reveal germline contribution to allelic expression differences

Variation in the level of gene expression is a major determinant of a cell's function and characteristics. Common allelic variants of genes can be expressed at different levels and thus contribute to phenotypic diversity. We have measured allelic expression differences at heterozygous loci in monozygotic twins and in unrelated individuals. We show that the extent of differential allelic expression is highly similar within monozygotic twin pairs for many loci, implying that allelic differences in gene expression are under genetic control. We also show that even subtle departures from equal allelic expression are often genetically determined.     

Large-scale profiling and identification of potential regulatory mechanisms for allelic gene expression in colorectal cancer cells

Allelic variation in gene expression is common in humans and this variation is associated with phenotypic variation. In this study, we employed high-density single nucleotide polymorphism (SNP) chips containing 13,900 exonic SNPs to identify genes with allelic gene expression in cells from colorectal cancer cell lines. We found 2 monoallelically expressed genes (ERAP2 and MYLK4), 32 genes with an allelic imbalance in their expression, and 13 genes showing allele substitution by RNA editing. Among a total of 34 allelically expressed genes in colorectal cancer cells, 15 genes (44.1%) were associated with cis-acting eQTL, indicating that large portions of allelically expressed genes are regulated by cis-acting mechanisms of gene expression. In addition, potential regulatory variants present in the proximal promoter regions of genes showing either monoallelic expression or allelic imbalance were not tightly linked with coding SNPs, which were detected with allelic gene expression. These results suggest that multiple rare variants could be involved in the cis-acting regulatory mechanism of allelic gene expression. In the comparison with allelic gene expression data from Centre d'Etude du Polymorphisme Humain (CEPH) family B cells, 12 genes showed B-cell specific allelic imbalance and 1 noncoding SNP showed colorectal cancer cell-specific allelic imbalance. In addition, different patterns of allele substitution were observed between B cells and colorectal cancer cells. Overall, our study not only indicates that allelic gene expression is common in colorectal cancer cells, but our study also provides a better understanding of allele-specific gene expression in colorectal cancer cells.     

Evidence for positive selection at the pantophysin (Pan I) locus in walleye pollock, Theragra chalcogramma

Nucleotide polymorphism at the pantophysin (Pan I) locus in walleye pollock, Theragra chalcogramma, was examined using DNA sequence data. Two distinct allelic lineages were detected in pollock, resulting from three amino acid replacement mutations in the first intravesicular domain of the protein. The common Pan I allelic group, comprising 94% of the samples, was less polymorphic (pi = 0.005) than the uncommon group (pi = 0.008), and nucleotide diversity in both was higher than for two allelic lineages in the related Atlantic cod, Gadus morhua. Phylogenetic analyses of Pan I sequences from these two species did not clearly resolve orthology among allelic groups, in part because of recombination that has occurred between the two pollock lineages. Conventional tests of neutrality comparing polymorphisms within and between homologous regions of the Pan I locus in walleye pollock and Atlantic cod did not detect the effects of selection. This result is likely attributed to low levels of synonymous divergence among allelic lineages and a lack of mutation-drift equilibrium inferred from nucleotide mismatch frequency distributions. However, the ratio of nonsynonymous to synonymous substitutions per site (dN/dS) exceeded unity in two intravesicular domains of the protein and the influence of positive selection at multiple codon sites was strongly inferred through the use of maximum-likelihood analyses. In addition, the frequency spectrum of linked neutral variation showed indirect effects of adaptive hitchhiking in pollock resulting from a selective sweep of the common allelic lineage. Recombination between the two allelic classes may have prevented complete loss of the older, more polymorphic lineage. The results suggest that recurrent sweeps driven by positive selection is the principle mode of evolution at the Pan I locus in gadid fishes.     

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.