Genfrequenzen und Vererbung im Duffy-System

Summary Genotyping in the Duffy-system was carried out using special combined trypsin-antiglobulin-techniques. The heterozygous presence of the third allele Fy was estimated by the single dose of the antigen Fy^a or Fy^b, whereas the homozygous types Fy^aFy^a or Fy^bFy^b gave the double-dosage-effect.Genotyping on 1408 unrelated persons in Hesse gave the following gene frequencies: Fy^a=0.4251; Fy^b=0.5582; Fy=0.0167. Expected and observed values showed a good correspondence (p0.72 for 4 d.f.).In phenotyping of 3768 persons, the very rare type Fy (a-b-) was found only once, which is in good agreement with the calculated gene frequency of Fy.Among those genotyped, family studies were subsequently done on 22 selected propositi. In the 13 cases in which the propositus had the third allele in the heterozygous state, the same third allele was again found at least once in the family where the propositus was a child (7x). Where the propositus was a parent (6x), the third allele was also found three times in the children; this allele was not transmitted in only 3 families with 4 children. In contrast, we did not find a single Fy-gene in the 8 families where the propositus was Fy^aFy^a or Fy^bFy^b.Finally, phenotyping was done in 283 unselected families. In this group, genotyping was restricted to those cases in which the distribution of Duffy-phenotypes suggested the presence of the third allele. In both groups of families not a single case of contradiction against the hereditary rules was observed.The reliability of genotyping is discussed, as well as its importance for anthropological studies and paternity cases.

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Direktor: Profl Dr. W. Spielmann

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Mit Unterstützung durch die Deutsche Forschungsgemeinschaft.     

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F_IS or F_ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F_IS or F_ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker .     

Distribution of hereditary blood groups among Indians in South America. V. In northern Brazil

This paper reports the results of tests made for hereditary antigens in blood samples procured from Indians in northern Brazil. Specimens were procured from 423 putatively full-blood persons of the following tribes: in the province of Roraima from 261 Macuxi, 48 Uaica, 27 Xirixano, 10 Uapixana, 9 Cacarapai and 9 Paramiteri; in Pará from 21 Assurini; and in Amapá from 38 Galibi. Erythrocyte samples were tested for factors in the A-B-O, M-N-S-s, P, Rh-Hr, Lutheran, Kell-Cellano, Lewis, Duffy, Kidd and Diego systems. Serum samples were tested for haptoglobins and transferrins. Hemolysates, prepared from whole blood, were tested for hemoglobin types. The results are presented on appropriate tables as number and per cent of phenotypes for the various blood group anigens and their calculated gene frequencies. Locations from which blood samples were procured are listed in the tables and shown on a map (fig. 1). All the 423 samples except one Macuxi belonged to group O. The Uaica tribe had a low frequency for M (0.534). All others showed the high frequency usually observed in Amerinds. The s allele was high in all except the Galibi in which the frequency was (0.500). Frequencies for P² was higher than for P¹ in all except the Assurini and Galibi, theirs was high for P¹ (1.00) and low for P² (0.00). The frequencies for R¹ (CDe) and R² (cDE) were high and all others in the Rh-Hr system were low or absent. All specimens were positive for Cellano (k) and negative for Kell (K). There was a complete absence of Lewis (Le₁), excepting in the Uaica and Xirixano in which populations Fy^a allele frequencies were higher than 0.500. The distribution of the Jk (a+) phenotype and corresponding ellele frequencies varied widely in Brazilian Indians as did those for Diego (a+). The haptoglobin Hp¹ allele frequencies were in essential agreement with those reported elsewhere for Indians in South America, and all transferrins determined were classified as Tf C. All samples tested for homoglobin types contained homoglobin (A) as a major component, but five members of the Galibi tribe possessed hemoglobin (S) as well.     

Effects of sampling close relatives on some elementary population genetics analyses

Many molecular ecology analyses assume the genotyped individuals are sampled at random from a population and thus are representative of the population. Realistically, however, a sample may contain excessive close relatives (ECR) because, for example, localized juveniles are drawn from fecund species. Our knowledge is limited about how ECR affect the routinely conducted elementary genetics analyses, and how ECR are best dealt with to yield unbiased and accurate parameter estimates. This study quantifies the effects of ECR on some popular population genetics analyses of marker data, including the estimation of allele frequencies, F‐statistics, expected heterozygosity (H_e), effective and observed numbers of alleles, and the tests of Hardy–Weinberg equilibrium (HWE) and linkage equilibrium (LE). It also investigates several strategies for handling ECR to mitigate their impact and to yield accurate parameter estimates. My analytical work, assisted by simulations, shows that ECR have large and global effects on all of the above marker analyses. The naïve approach of simply ignoring ECR could yield low‐precision and often biased parameter estimates, and could cause too many false rejections of HWE and LE. The bold approach, which simply identifies and removes ECR, and the cautious approach, which estimates target parameters (e.g., H_e) by accounting for ECR and using naïve allele frequency estimates, eliminate the bias and the false HWE and LE rejections, but could reduce estimation precision substantially. The likelihood approach, which accounts for ECR in estimating allele frequencies and thus target parameters relying on allele frequencies, usually yields unbiased and the most accurate parameter estimates. Which of the four approaches is the most effective and efficient may depend on the particular marker analysis to be conducted. The results are discussed in the context of using marker data for understanding population properties and marker properties.     

Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F_ST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.     

Distribution of hereditary blood groups among indians in South America. VII. In Argentina

This seventh and last paper in a series on the distribution of blood groups among Indians in South America reports the findings among Amerinds in Argentina. Blood specimens were procured from putative full-bloods of the following tribes: 38 Diaguita (Calchaqui), 230 Mataco, 90 Chiriguano, 142 Choroti, 51 Toba, 120 Chané, 96 Chulupi (Ashluslay), and 178 Araucano (Mapuche). These 945 samples were tested for blood factors in the A-B-O, M-N-S-s, P, Rh-Hr, K-k, Lewis, Duffy, Kidd, and Diego systems. Serum samples were tested for haptoglobins and transferrins. Hemolysates prepared from whole blood were tested for hemoglobin types. The results are presented in tables as phenotype distribution and calculated allele frequencies. Locations of the populations from which blood samples were procured are shown on a map of North and Central Argentina. High frequencies are reported for the O allele. Allele frequencies are high also for M, s, R¹ (CDe), R² (cDE), k, Le^H and Fy. They are usually low or absent for alleles B, N, S, Mi^a, Vw, R^o (cDe), r (cde), K, Le¹, and fy. The Di allele ranged from 0.013 in the Araucano (Mapuche) to 0.192 in the Toba. Allele frequencies aberrant for Indians were observed more often in the Araucano (Mapuche) and Diaguita tribes, due probably to greater inflow of non-Indian genes into their gene pool and perhaps also to genetic drift in small inbred populations. Hp¹ allele frequencies varied from 0.43 in the Choroti to 0.80 in the Diaguita. All samples tested for transferrins except six contained the variant Tf C; the six were B₁ C present in samples from one Mataco and six Araucano persons. All the specimens tested electrophoretically for hemoglobin types contained only (A) as a major component.     

Characterization of pharmacogenetically relevant CYP2D6 and ABCB1 gene polymorphisms in a Portuguese population sample

Differences in metabolism of drugs can lead to severe toxicity or therapeutic failure. In addition to cytochrome P450 2D6, which plays a critical role in drug metabolism, ABCB1 encoded P‐glycoprotein (PGP) is also an important determinant in drug bioavailability. The genes encoding these molecules are highly variable among populations and, given their clinical importance in drug therapy, determining CYP2D6 and ABCB1 allele frequencies in specific populations is very important for useful application in clinical settings. In this study the frequency of the pharmacologically relevant CYP2D6*3, *4, *5, *6 allelic variants and gene duplication, and ABCB1 C1236T and C3435T gene polymorphisms and their haplotypes was determined in a population sample of 100 Portuguese healthy subjects. CYP2D6 allele frequencies were 1.4% (*3), 13.3% (*4), 2.8% (*5), 1.8% (*6) and 6.1% (gene duplication), with 5% of the individuals classified as PM and 8.4% as UM. The frequencies obtained for the non‐functional alleles and for the CYP2D6 gene duplication are in agreement with other South European populations, and reinforce the previously suggested south/north gradient of CYP2D6 duplications. Allelic frequencies for the ABCB1 polymorphisms were 52% (3435C) and 54% (1236C) and the most common haplotype (1236C‐3435C) occurred with a frequency of 45.5%. Although allele and haplotype frequency data for ABCB1 in Southern Europe is limited, some discrepancies were found with other European populations, with possible therapeutic implications for PGP substrate drugs. Copyright © 2009 John Wiley & Sons, Ltd.     

Variants of galactose-1-phosphate uridyl transferase in the Greek populations

Summary The frequency of variants of galactose-1-phosphate uridyl transferase was determined among the nine Greek populations by studying a sample of 1570 unselected individuals. Average frequency of normal allele GALT=0.942, galactosemia gene GALT ^G=0.0021 and the Duarte variant gene GALT ^D=0.0548 were observed. Frequency of galactosemia heterozygotes among Greeks was similar to that in other Caucasian populations, but the frequency of the Duarte variant was considerably higher. With the exception of two populations, one with low (Epirus) and one with high (Thrace) frequencies, the polymorphism of the Duarte variant displays very similar frequencies in the various Greek population groups.Supported by Grants HD 01 974 and GM 15 253 from the U.S. Public Health Service     

Restriction and persistence of polymorphisms of HLA and other blood genetic traits in the Parakanã Indians of Brazil

Results concerning HLA types and 22 other blood genetic systems are reported for the Parakanã Indians of northern Brazil, a tribe that is notable for the light color and pilosity of some of its members. No clear evidence of Caucasoid admixture was found, but the Parkanã show unusual frequencies in the EsD¹, PGM¹₁, Gc², Cp^B, Fy^a, Di^a, and L^M genetic markers. In addition, the very rare Rh allele r^y is present, as well as what seems to be a new PGM₂ variant. There is very limited heterogeneity in the HLA system. All these distinctive features may have arisen through a combination of founder effects and genetic drift. However, low F_is values, as well as higher mean ages in heterozygous as compared to homozygous persons, suggest that an heterotic effect is counteracting these dispersive forces.     

Aspartate aminotransferase allozyme variation in a germplasm collection of the domesticated lentil (Lens culinaris)

Summary Variation at a polymorphic Aspartate aminotransferase locus was assayed in a sample of 298 accessions from the ICARDA germplasm collection of the domesticated lentil (Lens culinaris). Two alleles Aat-1 ^F and Aat-1 ^S were detected with global frequencies of 0.51 and 0.49, respectively. Fifty-nine percent of accessions were polymorphic for both alleles. The frequency of outcrossing was estimated from the observed heterozygosity to be about 1%. This is higher than direct estimates of outcrossing and implicates selection in favour of heterozygous gene combinations. Significant variation in allele frequency and in the occurrence of polymorphic accessions was observed between countries or geographic areas. Significant associations were observed between the allozymes and agronomic characters. In particular high frequency of Aat-1 ^F appeared to be associated with late flowering and maturity and low yield.     

Placental alkaline phosphatase polymorphism in some Italian populations

Summary Gene frequencies of Pl alleles for alkaline phosphatase of human placenta have been studied in the populations of Rome and L'Aquila. The latter represents a mixed sample of descendants from ancient Italic populations which in the last 20 centuries have been free from significant immigratory influx.The Pl gene frequencies in the two Italian populations are significantly different, the Pl ^s ₁ frequency being lower and Pl ^f ₁ frequency higher in the population of L'Aquila as compared to the population of Rome. The gene frequency of the 3 common Pl alleles in the population of Rome are quite similar to that found in some Northern-European populations. The frequency of the Pl ^s ₁ allele observed in the population of L'Aquila is the lowest (and correspondingly that for Pl ^f ₁ allele is the highest) amongst all populations studied so far.     

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F _ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.     

Distribution of blood groups among indians in South America. VI. In Paraguay

This paper on the distribution of hereditary factors in the blood of Indians in South America, reports the results of tests made on samples procured from Paraguayan Indians. Specimens from putatively full-blood persons were obtained from the following tribes: 88 Chamacoco, 36 Moro, 85 Chulupi, 207 Lengua, 100 Toba, 20 Yam Lengua, and 51 Guayaki, These 587 Samples were tested for factors in the A-B-O, M-N-S-s, P. Rh-Hr, Lutheran, Kell-Cellano, Lewis, Duffy, Kidd, and Diego systems. Serum samples were tested for haptoglobins and transferrins. He molysates, prepared from whole blood, were tested for hemoglobin types. The results are presented on appropriate tables as number and per cent of phenotypes for the various blood group antigens and their calculated allele frequencies. Locations of the populations from which blood samples were procured are listed on the tables and shown on a map (fig. 1). Of the 587 samples all except two Chamacoco belonged to group O. High frequencies are reported generally for M, s, P, R¹ (CDe), R² (cDE), k (100%) and Fy alleles in Paraguayn Indians. Low frequencies were generally reported for N, S, r (cde) and R° (cDe) alleles. There was a wide variation in frequencies for Di, Jk, and haptoglobin Hp¹. All tested for transferrins were classified as Tf C and all contained hemoglobin (A) as a major component. The following antigens were completely absent: Mi^a, Vw, p, P^k, r^y (CdE), K, and Le¹. Most notable is the unusual distribution of hereditary blood antigens among the Guayaki and Moro. The Guayaki had 100% P₁ and Fy^a; they were higher in R° (cDe), R¹ (CDe), and Jk^a; and lower in R² (cDE) and Hp¹ genes than other Indians; and Di was absent. The Guayaki differed from the other Indians also in having fair skin. The Moro were lower in the P¹ and Jk gene frequencies than is usually found in Amerinds, and the Di gene was absent. The Chamacoco also had an exceptionally low frequency for the P¹ gene (0.261).     

Geographic pattern of allozyme and inversion polymorphism on chromosome O of Drosophila subobscura and its evolutionary origin

The chromosome O of Drosophila subobscura was studied with respect to genetic variability at three enzyme loci (Odh, Me, and Lap-4) and with respect to inversion polymorphism. Population samples were taken from seven localities along a north-south gradient from Sweden and Scotland to Tunisia.The chromosomal analysis revealed clinal frequency changes for gene arrangements from north to south. With the enzyme loci Odh and Me allele frequencies are similar throughout the distribution range. Both loci are located outside the common inversion complex O₃₊₄. On the other hand, frequency changes parallel to those of the gene arrangements were observed for the alleles of the Lap-locus. Nonrandom associations between Lap-alleles and the superimposed gene arrangements O_ST, O₃₊₄, O₃₊₄₊₈, and O₃₊₄₊₂₃ were found. These gene arrangements differ from each other with respect to allele frequencies at the Lap-locus but for a given gene arrangement the relative frequencies of Lap-alleles remain relatively constant along the north-south gradient. Thus allele frequencies at the Lap-locus can be predicted from inversion frequencies.These observations can be interpreted in such a way that the pattern of allozyme variation within gene arrangements is due to founder effects caused by the unique origin of inversions. The gene blocks in the different inversions seem to represent more or less separated gene pools. In polymorphic populations the coexistence of genetically differentiated inversions presumably gives rise to heterotic interaction.     

Genotype‐free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

Restriction‐site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq‐specific biases remains unexplored. Here we assess in how far genotype‐free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Using the well‐studied pied flycatcher (Ficedula hypoleuca) as a study system, we compare allele frequency estimation and demographic inference from whole genome sequencing data with that from RADSeq data matched for samples using both genotype‐based and genotype free methods. The demographic history of pied flycatchers as inferred from RADSeq data was highly congruent with that inferred from whole genome resequencing (WGS) data when allele frequencies were estimated directly from the read data. In contrast, when allele frequencies were derived from called genotypes, RADSeq‐based estimates of most model parameters fell outside the 95% confidence interval of estimates derived from WGS data. Notably, more stringent filtering of the genotype calls tended to increase the discrepancy between parameter estimates from WGS and RADSeq data, respectively. The results from this study demonstrate the ability of genotype‐free methods to improve allele frequency spectrum‐ (AFS‐) based demographic inference from empirical RADSeq data and highlight the need to account for uncertainty in NGS data regardless of sequencing method.     

Confidence Intervals for Population Allele Frequencies: The General Case of Sampling from a Finite Diploid Population of Any Size

The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (%), a sample size of is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive % confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint % confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a % confidence interval for Jost''s D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management.     

C′3 polymorphism in Italy

Summary C'3 phenotype and gene frequencies observed in two Italian samples are reported. The allele frequencies resemble those reported for other Caucasian populations. Five different rare variants are described.     

Dosage effect of a gene with a regulating effect on anthocyanin synthesis in a trisomic Petunia hybrida

A Petunia hybrida inbred line (W 28) has white flowers with red spots on the corolla. These spots are the result of back mutations of an unstable allele of the gene Anl for anthocyanin synthesis. Among the progeny of a population of selfed plants a primary trisomic with red-spotted white flowers was found. The reversion frequency was more than twice as high as compared with disomic plants of the same family.It was found that the chromosome in triplicate was not the chromosome on which the gene Anl is localized. It can be concluded that there is an independently segregating factor which influences the frequency of back mutations of the Anl locus. Twin spots were found among the flowers of the trisomic. They consisted of two adjacent sectors, one with a spot frequency equal to that of the flowers of disomic plants, and the other with a spot frequency more than twice as high as that of the trisomic. Probably an irregular distribution of the extra chromosome resulted in one sector with the normal diploid number of chromosomes, and an adjacent sector with two extra chromosomes. The reversion frequencies in the sector suggest that the factor which affects the reversion frequency of the unstable alleles of Anl exhibits a dosage effect.     

One step closer to fixing association studies: evidence for age- and gender-specific allele frequency variations and deviations from Hardy-Weinberg expectations in controls

Association studies are the most powerful method available for identifying modest gene effects in complex disorders, but they often produce inconsistent results. With the rapidly growing SNP databases, haplotype maps and high throughput genotyping, the use of association studies is expected to increase; therefore, it is critical and timely that the problems with study design are identified and fixed. We questioned if unrecognized allele and genotype frequency variations in controls could be responsible for some of the inconsistent association findings. We performed a population genetic study of apolipoprotein E (APOE) and cytochrome P450 2D6 (CYP2D6) in 1,748 individuals ranging in age from newborns to centenarians. Although APOE and CYP2D6 are two of the most commonly used candidate genes, this is the first study to examine age- and gender-specific frequency distributions over the entire age spectrum, using a large, ethnically and geographically uniform population. We found significant, previously unrecognized variations in APOE allele frequencies, and deviations from Hardy-Weinberg expectations in CYP2D6 genotype frequencies starting at birth. The allele frequency variations within controls were larger than some reported case-control differences. We demonstrate that unrecognized frequency fluctuations in controls are a serious and potentially common confounder whose impact on association studies has not been appreciated, and one that can be addressed with proper study design. We recommend that population genetic studies be performed on commonly used candidate markers and that rigorous standards be applied for case-control matching.