A PvuII restriction fragment length polymorphism of the glucose-6-phosphate dehydrogenase gene is an African-specific marker

Summary The site of a PvuII restriction fragment length polymorphism (RFLP) of the human glucose-6-phosphate dehydrogenase (G6PD) gene has been located in intron V, 60 bp upstream of G6PD exon VI. A population survey shows this RFLP to be specific for African populations, with frequencies of the rarer allele (PvuII type 2 site present) of 0.32–0.40 in Kenyans, Nigerians, Zambians, and West Indians. This allele has not been found in the European, Asian and Middle Eastern populations studied. Such population-specific markers may be useful in the study of population affinities and may provide insight into prehistoric migrations of peoples.     

The extent of linkage disequilibrium caused by selection on G6PD in humans

The gene coding for glucose-6-phosphate dehydrogenase (G6PD) is subject to positive selection by malaria in some human populations. The G6PD A- allele, which is common in sub-Saharan Africa, is associated with deficient enzyme activity and protection from severe malaria. To delimit the impact of selection on patterns of linkage disequilibrium (LD) and nucleotide diversity, we resequenced 5.1 kb at G6PD and approximately 2-3 kb at each of eight loci in a 2.5-Mb region roughly centered on G6PD in a diverse sub-Saharan African panel of 51 unrelated men (including 20 G6PD A-, 11 G6PD A+, and 20 G6PD B chromosomes). The signature of selection is evident in the absence of genetic variation at G6PD and at three neighboring loci within 0.9 Mb from G6PD among all individuals bearing G6PD A- alleles. A genomic region of approximately 1.6 Mb around G6PD was characterized by long-range LD associated with the A- alleles. These patterns of nucleotide variability and LD suggest that G6PD A- is younger than previous age estimates and has increased in frequency in sub-Saharan Africa due to strong selection (0.1 < s < 0.2). These results also show that selection can lead to nonrandom associations among SNPs over great physical and genetic distances, even in African populations.     

Red cell glucose 6 phosphate dehydrogenase genotypes of the population of two West African villages

Summary Blood samples from 1109 individuals, residents of two villages in The Gambia, West Africa, have been examined for red cell G6PD. Using both starch gel electrophoresis and a spectrophotometric assay, preliminary phenotypes were assigned to the 519 males and 590 females. The G6PD genotypes were established by reference to the family trees of the two village populations. In addition to the G6PD alleles B⁺, A⁺ and A^-, a fourth allele, representing a new variant of human G6PD was discovered. A significant difference in the frequency of G6PD deficiency was discovered between the two villages, despite their being of the same tribal origin and only five miles apart.     

Distribution of G6PD phenotypes in red blood cells of Southern African Negroids: Evidence for somatic selection

Summary In a recent population study, we observed a striking deficit of G6PD heterozygotes among Southern African Negroid females. This finding was interpreted tentatively as evidence for a small number of hematopoetic stem cells in man. In a follow-up study we examined peripheral blood and cord blood in 547 mothers and in their newborn offspring. In mothers and sons, the frequencies of the G6PD alleles are apparently quite different. When the allele frequencies determined in sons are used for calculation of the expected phenotype frequencies in mothers and daughters, there is a large deficit of maternal G6PD AB phenotypes, and an equivalent surplus of G6PD homozygotes. However, no relevant heterozygote deficit is observed in newborn daughters. This discrepancy may be explained by the assumption that in peripheral blood of heterozygotes carrying the Gd^A- allele, G6PD-deficient cells progressively become eliminated during development from birth to adulthood. In other words, the large heterozygote deficit observed in adult females may be due to somatic selection rather than to a small pool of hematopoetic cells at the time of X differentiation.H-.H.R. is supported by the Deutsche Forschungsgemeinschaft     

The Y-associated XY275 low allele is not restricted to indigenous African peoples.

The level of linkage disequilibrium between the XY275 MspI polymorphism and the X and Y boundaries was investigated in 21 different southern African populations. A full range of frequencies of the high allele was observed on the 1,013 X chromosomes studied, in keeping with published data. In previous studies fixation of the high allele on the Y chromosome was observed in all but two groups--a Pygmy and a Tsumkwe San population. However, in the present study of 673 Y chromosomes, the low allele was found to be associated with the Y chromosome in several different Bantu-speaking negroid groups, the Khoisan-speaking negroid Dama, the Khoisan, two groups of mixed ancestry, and the South African Asiatic-Indian population. The discovery of the low allele on Y chromosomes of caucasoid individuals suggests that more than one class of Y chromosome gave rise to the present-day non-African population. The data also fail to provide support for the theory that Africa is the site of origin of Homo sapiens, but they equally do not exclude it.     

Some Mexican glucose-6-phosphate dehydrogenase variants revisited

Summary Glucose-6-phosphate dehydrogenase (G6PD) deficiency appears to be fairly common in Mexico. We have now examined the DNA of three previously reported electrophoretically fast Mexican G6PD variants, — G6PD Distrito Federal, G6PD Tepic, and G6PD Castilla. All three of these variants, believed on the basis of biochemical characterization and population origin to be unique, have the GA transition at nucleotide 202 and the AG transition at nucleotide 376, mutations that we now recognize to be characteristic of G6PD A —. Two other Mexican males with G6PD deficiency were found to have the same mutation. All five have the (NlaIII/ FokI/PvuII/PstI) haplotype characteristic of G6PD A in Africa. Since the PvuII+ genotype seems to be rare in Europe, we conclude that all of these G6PD A-genes had their ancient origin in Africa, although in many of the Mexican patients with G6PD A –^202A/376G the gene may have been imported more recently from Spain, where this variant, formerly known as G6PD Betica, is also prevalent.     

Primate red cell enzymes: glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase

Glucose-6-phosphate dehydrogenase (E. C.: 1.1.1.49) phenotypes and 6-phosphogluconate dehydrogenase (E. C.: 1.1.1.44) phenotypes were determined by starch-gel electrophoresis of red cell hemolysates of Galago crassicaudatus subspp., Propithecus verreauxi, Lemur spp., Hapalemur griseus, and Macaca mulatta. A single glucose-6-phosphate dehydrogenase (G6PD) phenotype was found in each species. A single 6-phosphogluconate dehydrogenase (6PGD) phenotype was found in Lemur spp., Hapalemur griseus, and Galago crassicaudatus argentatus. In a group of six Propithecus verreauxi, three 6PGD phenotypes, PGD A, PGD AB, and PGD B, were found. Three phenotypes, PGD A, PGD AB, and PGD B, were found in 38 G. c. crassicaudatus. The three phenotypes in each species are apparently the products of two codominant autosomal alleles, PGD^A and PGD^B. The frequency of PGD^A in G. c. crassicaudatus is 0.263. A population of 260 free-ranging macaques displays a polymorphism at the 6PGD locus. Three phenotypes, PGD A, PGD AB, and PGD B, were found. These also appear to be controlled by two codominant autosomal alleles, PGD^A and PGD^B the frequency of PGD^A = 0.913. Additional analysis of three well-defined troops within the macaque population indicated that there are no significant differences between the troops or within the population at the 6PGD locus.     

Natural and synthetic alleles provide complementary insights into the nature of selection acting on the Men polymorphism of Drosophila melanogaster

Two malic enzyme alleles, Men^113A and Men^113G, occur at approximately equal frequency in North American populations of Drosophila melanogaster, while only Men^113A occurs in African populations. We investigated the population genetics, biochemical characteristics, and selective potential of these alleles. Comparable levels of nucleotide polymorphism in both alleles suggest that the Men^113G allele is not recently derived, but we find no evidence in the DNA sequence data for selection maintaining the polymorphism. Interestingly, the alleles differ in both V_max and K_m for the substrate malate. Triglyceride concentration and isocitrate dehydrogenase (IDH) and glucose-6-phosphate dehydrogenase (G6PD) activities are negatively correlated with the in vivo activities of the Men alleles. We examined the causality of the observed correlations using P-element excision-derived knockout alleles of the Men gene and found significant changes in the maximum activities of both IDH and G6PD, but not in triglyceride concentration, suggesting compensatory interactions between MEN, IDH, and G6PD. Additionally, we found significantly higher than expected levels of MEN activity in knockout heterozygotes, which we attribute to transvection effects. The distinct differences in biochemistry and physiology between the naturally occurring alleles and between the engineered alleles suggest the potential for selection on the Men locus.     

Distribution of Gd- alleles in some ethnic groups of the USSR

Summary A population study of Gd^- allele distribution was made in similar (age-sex) samples of schoolchildren and students from different ethnic groups: Russians, Ashkenazi Jews, and Azerbaijanians. Both the frequency and the spectrum of the Gd^- alleles were quite different. The Gd^- frequency in Russians (Kostroma region) was 0.36%; in Ashkenazim (Gomel region), 0.91%; in Azerbaijanians (Sheki region and Apsheron region), 3.6% and 10.5%, respectively. G6PD deficiency in Russians is represented by familial forms; in Ashkenazi Jews by class II alleles Kirovograd and Zhitomir; and in Azerbaijanians, by a wide spectrum of class II and III alleles. Genetic factors involved in the formation of Gd^- allele frequencies and the spectrum in these three ethnic groups are discussed.     

Genetic heterogeneity at the glucose-6-phosphate dehydrogenase locus in southern Italy: a study on a population from the Matera district

Summary Glucose-6-phosphate dehydrogenase (G6PD) has been analyzed by gel electrophoresis and by quantitative assay in an unselected sample of 1524 schoolboys from the province of Matera (Lucania) in southern Italy. We have identified 43 subjects with a G6PD variant. Of these, 31 had severe G6PD deficiency, nine had mild to moderate deficiency, and three had a non-deficient electrophoretic variant. The overall rate of G6PD deficiency was 2.6%. The frequency of G6PD deficiency, ranging from 7.2% on the Ionian Coast to zero on the eastern side of the Lucanian Apennines, appears to be inversely related to the distance of each town examined from the Ionian Coast, suggesting that this geographic distribution may reflect, at least in part, gene flow from Greek settlers. Biochemical characterization has shown that most of the G6PD deficiency in this population is accounted for by G6PD Mediterranean. In addition, we have found several examples of two other known polymorphic variants (G6PD Cagliari and G6PD A^–): three new polymorphic variants. G6PD Metaponto (class III), G6PD Montalbano (class III), and G6PD Pisticci (class IV); and two sporadic variants, G6PD Tursi (class III) and G6PD Ferrandina (class II). These data provide further evidence for the marked genetic heterogeneity of G6PD deficiency within a relatively narrow geographic-area and they prove the presence in the Italian peninsula of a sene (Gd ^A–) regarded as characteristically African.     

Linkage between a PvuII restriction fragment length polymorphism and G6PD A-202A/376G: evidence for a single origin of the common G6PD A — mutation

Summary DNA samples from 29 males with the G6PD A-phenotype and 14 males with a G6PD B phenotype were studied for the presence of each of four polymorphic restriction sites in the glucose-6-phosphate dehydrogenase locus. All G6PD A-subjects with the G6PD A-^202A/376G genotype, regardless of population origin, shared identical haplotypes. In view of the fact that at least one of the restriction sites, the PvuII site in the intron between exon 5 and 6, has thus far been uncommon in the populations studied, it seems likely that the G6PD A-mutation at nucleotide 202 arose relatively recently and in a single individual.     

Population genetic studies of the Aka Pygmies (Central Africa)

Summary Blood samples collected in a single Pygmy tribe, the Aka, living in Bokoka district (Central African Empire) were investigated with respect to the phenotype and gene frequencies of the following 12 enzyme systems: acid phosphatase, adenosine deaminase, adenylate kinase, carbonic anhydrase, esterase D, glucose-6-phosphate dehydrogenase, malate dehydrogenase, phosphoglucomutase 1, phosphoglucomutase 2, phosphogluconate dehydrogenase, superoxide dismutase and serum cholinesterase variants (locus E₁ and E₂). The data obtained in the study of genetic polymorphisms of this isolated and inbred population show a specific pattern with the following characteristics: the very low frequency of PGD^B and p^a alleles; the existence of two rare PGM variants at the PGM₂ locus, typical PGM ₂ ^6Pyg (4.2%) and PGM ₂ ⁹ (0.2%); the high frequency of the p^r allele (10.8%) and CA _II ² (8.22%) and ESD² genes (18.4%). Furthermore, at the G6PD locus four distinct alleles have been found: the negroid GDA-(4%) and GdA+(16%), the common GdB+(79.2%)-,and the rare Gd+^{Ibadan Austin} (0.7%). Cholinesterase typings disclosed the presence of the uncommon E ₁ ^f and E ₁ ^s genes distributed within a single breeding unit. The results are compared with other data previously reported on South African Khoisan and some Negroid populations; the particular genetic background of Pygmies is discussed.Otherwise known as Bi Aka     

G6PD Deficiency and Hemoglobinopathies: Molecular Epidemiological Characteristics and Healthy Effects on Malaria Endemic Bioko Island,Equatorial Guinea

Background

Glucose-6-phosphate dehydrogenase (G6PD) deficiency and hemoglobinopathies were the inherited conditions found mostly in African. However, few epidemiological data of these disorders was reported in Equatorial Guinea (EQG). This study aimed to assess the prevalence and healthy effects of G6PD deficiency and hemoglobinopathies among the people on malaria endemic Bioko Island, EQG.

Materials and Methods

Blood samples from 4,144 unrelated subjects were analyzed for G6PD deficieny by fluorescence spot test (FST), high-resolution melting assay and PCR-DNA sequencing. In addition, 1,186 samples were randomly selected from the 4,144 subjects for detection of hemoglobin S (HbS), HbC, and α-thalassemia deletion by complete blood count, PCR-DNA sequencing and reverse dot blot (RDB).

Results

The prevalence of malaria and anemia was 12.6% (522/4,144) and 32.8% (389/1,186), respectively. Overall, 8.7% subjects (359/4,144) were G6PD-deficient by FST, including 9.0% (249/2,758) males and 7.9% (110/1,386) females. Among the 359 G6PD-deficient individuals molecularly studied, the G6PD A^- (G202A/A376G) were detected in 356 cases (99.2%), G6PD Betica (T968C/A376G) in 3 cases. Among the 1,186 subjects, 201 cases were HbS heterozygotes, 35 cases were HbC heterozygotes, and 2 cases were HbCS double heterozygotes; 452 cases showed heterozygous α-thalassemia 3.7 kb deletion (-α^3.7 kb deletion) and 85 homozygous - α^3.7 kb deletion. The overall allele frequencies were HbS 17.1% (203/1186); HbC, 3.1% (37/1186); and –α^3.7 kb deletion 52.4% (622/1186), respectively.

Conclusions

High G6PD deficiency in this population indicate that diagnosis and management of G6PD deficiency is necessary on Bioko Island. Obligatory newborn screening, prenatal screening and counseling for these genetic disorders, especially HbS, are needed on the island.     

Apolipoprotein E polymorphism in Southern Iran: E4 allele in the lowest reported amounts

Background: Apolipoprotein E (apoE) with three major alleles E2, E3 and E4 is one of the critical genes in lipid metabolism. Common apoE alleles are in association with an increase in risk for central nervous and cardiovascular diseases such as Alzheimer’s disease, dementia, multiple sclerosis, atherosclerosis, coronary heart disease, hyperlipoproteinemia and stroke. ApoE3 is known as the most frequent allele in all populations, while association of apoE gene polymorphism with reported diseases have mostly been related to other two major alleles especially apoE4. Objective: To determine of apoE alleles frequencies in Southern Iran and comparison of those frequencies with other populations. Methods: DNA was extracted from the whole blood of 198 healthy unrelated candidates from population of Fars Province, Southern Iran, for apoE genotyping who were checked up by a physician. The frequencies of apoE alleles were compared with other populations by χ² test. Results: The frequencies of E2, E3 and E4 were 0.063, 0.886 and 0.051 respectively. These values were similar to those reported from populations of Kuwait, Oman, Lebanon, India, Turkey, Greece, Spain, Sardinia Islands of Italy and two Iranian populations but were different from South of Italy and Caucasians in other Europe regions, American, American-Indian, African, East Asian and Saudi populations (P < 0.05). Conclusion: The frequency of E4 allele as a genetic risk factor for some multifactorial diseases in the population of Southern Iran is in the lowest reported amounts in the world. Iranian population has Caucasoid origin but differs from some Caucasian populations in Europe and America. The results of present study are in agreement with the historical evidences which show admixture of Iranian population with other populations and some studies based on genetic polymorphisms in the population of Southern Iran.     

Genetic studies on free-ranging macaques of Cay Santiago. II. 6-phosphogluconate dehydrogenase and NADH-methemoglobin reductase (NADH-diaphorase).

For the population of 395 semi-free-ranging rhesus macaques (Macaca mulatta) that inhabited Cayo Santiago in 1976, 6-phosphogluconate dehydrogenase phenotypes of 378 animals were determined. Three phenotypes, controlled by two autosomal codominant alleles,PGD^A andPGD^B, were found by electrophoretic methods. The frequencies of the alleles are 0.898 and 0.102, respectively. The population, composed of five troops and peripheral males, is in Hardy-Weinberg equilibrium at this locus. The allele frequencies at the 6-phosphogluconate dehydrogenase locus in the population in 1976 were compared with frequencies in 1973; a statistically significant difference was found in one troop. The phenotypes of NADH-methemoglobin reductase (NADH-diaphorase) were determined electrophoretically for 372 animals. These phenotypes are probably the products of two autosomal codominant alleles,Dia¹ andDia², with frequencies of 0.786 and 0.214, respectively. The population is in equilibrium at this locus also. Tests of homogeneity at the dehydrogenase and reductase loci indicate that the allele frequencies are significantly different among the five troops in the population. Observed and expected phenotypic ratios in progeny were compared at the dehydrogenase and the reductase loci. The only significant deviation from expectation occurs among offspring of mothers heterozygous at the reductase locus. The observed distributions of alleles at the 6-phosphogluconate dehydrogenase locus and the NADH-methemoglobin reductase locus are probably the results of stochastic processes.     

Nucleotide variability at G6pd and the signature of malarial selection in humans

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy in humans. Deficiency alleles for this X-linked disorder are geographically correlated with historical patterns of malaria, and the most common deficiency allele in Africa (G6PD A-) has been shown to confer some resistance to malaria in both hemizygous males and heterozygous females. We studied DNA sequence variation in 5.1 kb of G6pd from 47 individuals representing a worldwide sample to examine the impact of selection on patterns of human nucleotide diversity and to infer the evolutionary history of the G6PD A- allele. We also sequenced 3.7 kb of a neighboring locus, L1cam, from the same set of individuals to study the effect of selection on patterns of linkage disequilibrium. Despite strong clinical evidence for malarial selection maintaining G6PD deficiency alleles in human populations, the overall level of nucleotide heterozygosity at G6pd is typical of other genes on the X chromosome. However, the signature of selection is evident in the absence of genetic variation among A- alleles from different parts of Africa and in the unusually high levels of linkage disequilibrium over a considerable distance of the X chromosome. In spite of a long-term association between Plasmodium falciparum and the ancestors of modern humans, patterns of nucleotide variability and linkage disequilibrium suggest that the A- allele arose in Africa only within the last 10,000 years and spread due to selection.     

The plasminogen polymorphism in South African Negro populations: genetics and anthropogenetics

Summary Genetic polymorphism of human plasminogen (PLG) was investigated in 1252 unrelated individuals from eight South African Bantu-speaking Negro tribes. PLG phenotypes were determined by isoelectric focusing (pH 3.5–9.5 and 5–8 gradients) of neuraminidase-treated samples and subsequent detection by caseinolytic overlay or immunoblotting with specific antibody. No significant difference in the distribution of PLG alleles among the eight ethnic groups was observed. The combined allele frequencies of the common alleles in South African Negroes were 0.6977 for PLG*A, 0.2736 for PLG*B. In addition, six rare alleles were seen: PLG*A3, *A1, *M2, *B1, *B2, *B3. The rare variant PLG*B2 was proven to segregate by autosomal Mendelian inheritance in a family. The combined frequency for the rare alleles was 0.0287. The distribution of phenotypes in the total population sample was found to be in Hardy-Weinberg equilibrium. A striking difference in PLG allele distribution between Negroes from South Africa and published Negroid frequencies from North America could be observed. This difference was also seen in comparison with Mongoloid populations; in contrast, PLG frequencies for South African Negroes were similar or almost identical to known Caucasoid distributions.     

Gammaglobulin groups (Gm and Inv) of various Southern African populations

Data are presented on the distribution of the Gm and Inv groups in approximately 3500 individuals belonging to a number of diverse Southern African populations. The indigenous peoples show the presence of the Gm alleles known to occur in Negroes (Gm^{1, 5, 13, 14}, Gm^{1, 5, 6, 14} and Gm^{1, 5, 6}) but the Bushmen possess some of them in very low frequencies and have, in addition and in appreciable frequencies the Gm¹ and Gm^{1, 13} alleles which have not been reported as occurring in West African populations. The distribution of the Gm^{1, 13} allele in various Bantu-speaking tribes of the sub-continent reveals a marked cline, increasing from north to south along the eastern seaboard. The correlation between the frequency of Gm^{1, 13} and the Khoisan morphological, features present in a number of the tribes, and with the linguistic evidence which has been used to group them is high. The Bushmen possess a Gm^{1, 5} allele and may also have a Gm^{1, 5, 13, 14, 17, 21} allele. A Gm^{1, 2, 5, 13, 14, 17} allele seems to be present in the Bantu. Its presence in Eastern New Guinea would also appear to be indicated by the population data presented here.     

African Glucose-6-Phosphate Dehydrogenase Alleles Associated with Protection from Severe Malaria in Heterozygous Females in Tanzania

X-linked Glucose-6-phosphate dehydrogenase (G6PD) A- deficiency is prevalent in sub-Saharan Africa populations, and has been associated with protection from severe malaria. Whether females and/or males are protected by G6PD deficiency is uncertain, due in part to G6PD and malaria phenotypic complexity and misclassification. Almost all large association studies have genotyped a limited number of G6PD SNPs (e.g. G6PD202 / G6PD376), and this approach has been too blunt to capture the complete epidemiological picture. Here we have identified 68 G6PD polymorphisms and analysed 29 of these (i.e. those with a minor allele frequency greater than 1%) in 983 severe malaria cases and controls in Tanzania. We establish, across a number of SNPs including G6PD376, that only female heterozygotes are protected from severe malaria. Haplotype analysis reveals the G6PD locus to be under balancing selection, suggesting a mechanism of protection relying on alleles at modest frequency and avoiding fixation, where protection provided by G6PD deficiency against severe malaria is offset by increased risk of life-threatening complications. Our study also demonstrates that the much-needed large-scale studies of severe malaria and G6PD enzymatic function across African populations require the identification and analysis of the full repertoire of G6PD genetic markers.