ß-Globin polymorphisms in Amerindian populations from the Brazilian Amazon.

OBJECTIVES: This investigation was performed to examine genetic variation at the ß-globin locus in a sample of 30 healthy individuals from native populations in South America. The patterns of haplotypic variation were compared with those of previous studies including samples for various worldwide populations in an attempt to make inferences about the occupation of the Americas from a deeper temporal perspective than is typically available with haploid markers. METHODS: A 2.67-kb segment containing the ß-globin gene and its flanking regions was examined for genetic variation in a sample of 60 chromosomes from native populations in South America. The fragment was PCR-amplified and directly sequenced. To determine linkage relationships in compound heterozygotes, we used the amplification refractory mutation system. In addition, we assessed genetic variability and differentiation among populations, and we performed tests of selective neutrality. These analyses were performed for Brazilian Amerindian group and other worldwide populations previously studied. RESULTS: Eleven polymorphic sites were found in the studied fragment, which distinguished eight different haplotypes, three recombinants haplotypes (present as single copies) and five previously described haplotypes, including some of those most highly differentiated. Genetic variation found in the pooled sample is substantial. CONCLUSIONS: Although only five known haplotypes are observed in Amazonia, some of these are highly divergent, resulting in patterns of molecular polymorphism equal to or higher than those from other world regions.

Southeast Asian ovalocytosis and pregnancy in a malaria-endemic region of Papua New Guinea.

The band 3 deletion for southeast Asian ovalocytosis (SAO) occurs commonly in southeast Asia and the western Pacific. Southeast Asian ovalocytosis is associated with protection against cerebral malaria in children and therefore could reduce sequestration of erythrocytes parasitized by Plasmodium falciparum in the brain microvasculature. Sequestration of parasitized erythrocytes in the placenta accounts for much of the pathology of malaria during pregnancy. Therefore, we investigated the effect of SAO on malaria during pregnancy in the malaria-hyperendemic north coastal region of Papua New Guinea. The frequency of SAO in 927 women attending hospital for delivery was 8.7% (95% confidence interval = 6.9-10.5). Markers of fertility, the frequency of miscarriages and stillbirths, maternal anemia, placental and peripheral malaria at delivery, and birth weight were similar in women with and without SAO. In summary, although we can not exclude an interaction between SAO and malaria during pregnancy, we found no evidence that it provided a clinical benefit in this population.

Common 5' beta-globin RFLP haplotypes harbour a surprising level of ancestral sequence mosaicism.

Blocks of linkage disequilibrium (LD) in the human genome represent segments of ancestral chromosomes. To investigate the relationship between LD and genealogy, we analysed diversity associated with restriction fragment length polymorphism (RFLP) haplotypes of the 5' beta-globin gene complex. Genealogical analyses were based on sequence alleles that spanned a 12.2-kb interval, covering 3.1 kb around the psibeta gene and 6.2 kb of the delta-globin gene and its 5' flanking sequence known as the R/T region. Diversity was sampled from a Kenyan Luo population where recent malarial selection has contributed to substantial LD. A single common sequence allele spanning the 12.2-kb interval exclusively identified the ancestral chromosome bearing the "Bantu" beta(s) (sickle-cell) RFLP haplotype. Other common 5' RFLP haplotypes comprised interspersed segments from multiple ancestral chromosomes. Nucleotide diversity was similar between psibeta and R/T-delta-globin but was non-uniformly distributed within the R/T-delta-globin region. High diversity associated with the 5' R/T identified two ancestral lineages that probably date back more than 2 million years. Within this genealogy, variation has been introduced into the 3' R/T by gene conversion from other ancestral chromosomes. Diversity in delta-globin was found to lead through parts of the main genealogy but to coalesce in a more recent ancestor. The well-known recombination hotspot is clearly restricted to the region 3' of delta-globin. Our analyses show that, whereas one common haplotype in a block of high LD represents a long segment from a single ancestral chromosome, others are mosaics of short segments from multiple ancestors related in genealogies of unsuspected complexity.

Analysis of variation in the human beta-globin gene cluster using a novel DHPLC technique.

We have implemented a technique combining allele-specific PCR (AS-PCR) and denaturing high-performance liquid chromatography (DHPLC) to identify new polymorphic variants within an intergenic region in the beta-globin cluster. This technique is applicable to the detection of new variants in genomic regions where variation is apportioned into distinct classes of haplotype. Duplexes for DHPLC analysis were created by denaturation and re-annealing of a mixture of two AS-PCR products of known and unknown sequence from the same haplotypic class, permitting detection of new haplotypes in each class. A 454bp fragment 3.5kb 5' to the human delta-globin gene, which may have a gene regulatory function, was analysed in 840 chromosomes from a global sampling of human populations using this method. Two divergent haplotypes were found to predominate in all populations studied, possibly as a result of balancing selection.

Direct measurement of the male recombination fraction in the human beta-globin hot spot.

Recombination was measured across nine intervals in the human beta-globin gene cluster by single-sperm analysis. A recombination fraction of approximately 0.9% was calculated across an approximately 11 kb region using a new method to estimate recombination fractions from single-sperm typing data. No recombination was detected in an adjacent approximately 90 kb region that extends upstream of the beta-globin cluster. These data are consistent with previous estimates based on population genetic analysis, and suggest a recombination rate of nearly two orders of magnitude greater than the genome average of approximately 1 cM/Mb. Because recombination hot spots will destroy linkage disequilibrium across small physical regions, knowledge about the location and strength of such hot spots could be extremely valuable for genetic association studies.

Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation.

A large and ethnically well-defined Mandenka sample from eastern Senegal was analyzed for the polymorphism of the beta-globin gene cluster on chromosome 11. Five RFLP sites of the 5' region were investigated in 193 individuals revealing the presence of 10 different haplotypes. The frequency of the sickle-cell anemia causing mutation (beta(S)) in the Mandenka estimated from this sample is 11.7%. This mutation was found strictly associated with the single Senegal haplotype. Approximately 600 bp of the upstream region of the beta-globin gene were sequenced for a subset of 94 chromosomes, showing the presence of four transversions, five transitions, and a composite microsatellite polymorphism. The sequence of 22 beta(S) chromosomes was also identical to the previously defined Senegal haplotype, suggesting that this mutation is very recent. Monte Carlo simulations (allowing for a specific balancing selection model, a logistic growth of the population, and variable initial frequencies of the Senegal haplotype) were used to estimate the age of the beta(S) mutation. Resulting maximum-likelihood estimates are 45-70 generations (1,350-2,100 years) for very different demographic scenarios. Smallest confidence intervals (25-690 generations) are obtained under the hypothesis that the Mandenka population is large (N(e) >5,000) and stationary or that it has undergone a rapid demographic expansion to a current size of >5,000 reproducing individuals, which is quite likely in view of the great diversity found on beta(A) chromosomes.

Interaction of the OOO globin gene haplotype and sickle haemoglobin

We have studied the interaction of the OOO/OO gene arrangements with various á globin genotypes (AA, AS, AC, SS and SC). Whereas this interaction has no detectable clinical or haematological effects in subjects with AA, SS or SC genotypes it is associated with a significantly increased level of Hb S or Hb C in heterozygotes for these variants. These findings indicate that the additional O globin gene in the OOO gene arrangement is functional (Summary)

The interaction of alpha-thalassemia and homozygous sickle-cell disease

Patients with homozygous sickle-cell disease may be homozygous for alpha-thalassemia 2 (O-/O-), may be heterozygous for alpha-thalessemia 2 (O-/OO), or may have a normal alpha-globin-gene complement (OO/OO). We compared the clinical and hematologic features of 44 patients who had sickle-cell disease and homozygous alpha-thalassemia 2 with those of controls with the two hematologic conditions. The patients with homozygous alpha-thalassemia 2 had significantly higher red-cell counts and levels of hemoglobin and hemoglobin Aý, as well as significantly lower hemoglobin F, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, mean corpuscular volume, reticulocyte counts, irreversibly-sickled-cell counts, and serum total billirubin levels, than those with a normal alpha-globin-gene complement. Heterozygotes (O-/OO) had intermediate values. In the group with homozygous alpha-thalassemia 2, fewer patients had episodes of acute chest syndrome and chronic leg ulceration and more patients had splenomegaly, as compared with patients in the other two subgroups. These data confirmed previous suggestions that alpha-thalassemia inhibits in vivo sickling in homozygous sickle-cell disease and may be an important genetic determinant of its hematologic severity.

The genetics and molecular basis of alpha thalassaemia in association with Hb S in Jamaican Negroes

We have studied seven Jamaican Negro families in whom the genes for O thalassaemia and the sickle cell mutation (ás) were independently segretated. Using a combination of techniques we identified two O thalassaemia phenotypes which resemble the reserve (O thalassaemia 1) and mild (O thalassaemia 2) determinants previously described in Orientals. This study has enabled us to clearly correlate the phenotype of O thalassaemia with the genotype in this population. Furthermore, since in each family O thalassaemia was present in association with the gene for the sickle cell mutation we have determined the proportion of Hb S in the peripheral blood of individuals with the OO/OO, -O/-O genotype who are also heterozygous for the ás mutation. Genetic analysis in these families shows that in each case subjects with the O thalassaemia 1 phenotype are homozygous for the O thalassaemia 2 defect (-O/-O). We have found no instances of the genotype --/OO in this population which may explain the rarity of the severe O thalassaemia 2 homozygotes from this population shows that the (-O/) haplotype results from a deletion of one of the linked pair of O globin and that this had probably arisen by an unequal crossover between non-homologous O genes (AU)

Detection of alpha thalassaemia in Negro infants

A prospective study of 2191 Negro infants in Jamaica showed that approximately 7 percent of them had detectable levels of Hb Bart's (Y4) in the neonatal period. The red cell indices, globin chain biosynthesis and restriction endonuclease mapping of DNA from these infants were used to determine the significance of Hb Bart's at birth. The results indicate that the genotypes OO/OO, - O/OO and - O/-O are associated with 0 percent, 0.1-2 percent, and greater than 2 percent Hb Bart's respectively. Although trace amounts of Hb Bart's may be associated with the genotype - O/OO this is not always the case and therefore haemoglobin analysis in the neonatal period cannot be used to diagnose this genotype with any certainty (AU)

Linkage relationships between beta- and delta-structural loci and African forms of beta thalassaemia

Five families are described in which there have been matings between individuals doubly heterozygous for beta thalassaemia and the delta-chain variant haemoglobin A2' to normal persons. In all there were 24 informative offspring. There were no crossovers between the beta-thalassaemia and delta-chain loci; in three of the families the genes were linked in cis and in two families the genes were found in trans.Together with previously reported families there have now been 58 opportunities for crossing over between the beta-thalassaemia and delta-chain loci and there have been two possible and one highly probable crossovers. Of the total of 9 families reported to date 4 have had the genes for beta thalassaemia and Hb A2' in cis and 5 in trans. These findings are contrasted with the findings in families where a beta-chain structural variant and Hb A2' have been observed together and these genes have always been found in trans and never in cis. The reasons for linkage disequilibrium of this type are discussed. It is concluded tentatively that the distance between the delta-structural and beta-thalassaemia loci is greater than that between the delta-structural and beta-structural loci. To date this conclusion can only be applied to the beta+ -thalassaemia and beta-thalassaemia genes as found in the African population, since this is the only population with a high incidence of delta-chain mutants which allow linkage analysis of this type to be carried out. (AU)

Benign sickle-cell an‘mia

Clinical, h‘matological, genetic, chemical, and oxygen-affinity studies have been carried out on a group of 18 Shiite Saudi Arabians with sickle-cell an‘mia. Apart from occasional attacks of mild musculo-skeletal pain they are well and have few of the complications which are usual in the sickling disorders. The unusually mild course of the illness is attributable, at least in part, to a genetically determined ability to produce large amounts of fetal h‘moglobin (Summary)

Haemoglobin H disease caused by alpha-thalassaemia and a new abnormal haemoglobin with an elongated alpha-chain (Hb constant spring) - abstract

Of the 120 or so variants of human haemoglobin polypeptide chains so far described, nearly all are the result of the substitution of a single amino acid residue for another, or a deletion of one or more residues in the chain, caused by a point mutation in the codens of the chromosomal DNA. Hb H disease is also a genetically determined haemolytic anaemia, common in Orientals, but is caused by a reduced rate of synthesis of the O-chain of normal haemoglobin, resulting in an excess of á-chains (Hb H). A study of a Chinese family in Jamaica has revealed a slow moving haemoglobin in three children who have clinical haemoglobin H disease and in their fathers and siblings who have no haematological abnormality. The mothers have classical O-thalassaemia trait, as do some of the other siblings. Detailed biochemical analysis of this variant has shown that the O-chain is abnormal and is elongated by the addition of 31 residues to the 141 of the normal OA-chain. The extra residues are continuous with the normal C-terminal (O-141 Arg.) Biosynthetic studies, incorporating H(to 3rd power) leucine have indicated a low rate of synthesis for this abnormal chain. Interest lies in the nature of the genetic defect which could produce this abnormalty. While considering several hypotheses, the authors favour the theory that the genetic codon for 'end of chain' is the site of a mutation. This hypothesis is strengthened by finding Glutamine to be the next residue after the C-terminal Arginine. This extra piece of chain bears no resemblance to any known human globin chain sequence, so that it is unlikely that it has resulted from an unequal crossing over in a similar way to the Lepore haemoglobins. It may be that the messenge RNA for the normal OA-chain is longer than is required to direct synthesis of the chain. Further studies are in progress to try and define the nature of this genetic defect (AU)

Haemoglobin-H disease due to a unique haemoglobin variant with an elongated O-chain

The clinical and genetic properties of an unusual O-chain variant of human haemoglobin are described. It constitutes less than 1 percent of the total haemoglobin in heterozygotes and, when inherited together with an O-thalassaemia gene, produces the clinical picture of haemoglobin-H disease. Preliminary structural studies indicatge that, in addition to the 141 aminoacid residues which constitute the normal O-chain, this variant has about 31 extra residues attached to the C-terminal end.(SUMMARY)