DNA haplotypes and frameworks associated with the beta-globin gene in the Kachari population of Assam (India)

DNA haplotypes and frameworks associated with the beta-globin gene were determined in a Tibeto-Burman group, the Kachari, from Upper Assam, India, using restriction analysis at eight restriction sites. Of the total of 59 subjects, 26 were homozygous for HBB*A and 33 homozygous for HBB*E. Complete haplotype determination in 33 subjects revealed a conspicuous difference in haplotype distribution between HBB*A- and HBB*E-bearing chromosomes. The Southeast Asian HBB*E-associated haplotype -+- +- (27-2 in the present terminology) predominated on HBB*E chromosomes. The previously established beta-globin-associated frameworks 1, 2 and 3 were evenly distributed among the HBB*A chromosomes, whereas all HBB*E chromosomes had framework 2. These findings favor a common origin of the HBB*E gene in Southeast Asia and Assam.     

Major gene mutations associated with obesity and diabetes mellitus

Obesity and diabetes mellitus are associated with low or elevated serum leptin and insulin levels (U-like relation). Mutations in LEP and INS are linked to decreases in leptin and insulin while mutations in LEPR and INSR are linked to their increase. Homozygous LEP mutations are associated with the early onset of severe obesity and the diverse impairment of physiological functions. The recessive LEPR mutations are associated with similar pathology in homozygous state. Missense mutations of INS are dominant and induce the synthesis of chimeric proinsulin, which may interfere with the folding and processing of active insulin molecules. In the heterozygous state, they cause insulin deficiency and PND. Recessive INS mutations do not induce the synthesis of anomalous proinsulin, and they are only associated with PND in the homozygous state. Mutations of INSR induce insulin resistance, lipodystrophy, other pathologies, and suggest the important role of insulin in glucose level regulation and in the stimulation of fat accumulation.     

Analysis of cystic fibrosis gene mutations and associated haplotypes in the Croatian population

The aim of this study was to reveal the CFTR gene mutation status in the Croatian population as well as to establish the haplotypes associated with cystic fibrosis (CF) and those associated with specific gene mutations. A total of 48 unrelated CF patients from Croatia were examined. Among 96 tested alleles, we found nine different mutations: DeltaF508, 58.33%; G542X, 3.12%; N1303K, 2.08%; R1162X; 621 + 1G --> T; G85E; Y569C; E585X; and S466X, 1.04%. Analysis of three polymorphic loci revealed 15 different haplotypes. Two of them (21-23-13 and 21-17-13) occurred with a higher frequency (40% and 24%). Both of these haplotypes also carried a CFTR gene mutation (DeltaF508 or G542X) on 27 out of 32 chromosomes. Among 12 (of all together 29) CF alleles on which no mutations were found, we detected 10 different haplotypes. Because there are still no published data on the distribution of polymorphic loci in Croatia, nor haplotypes associated with mutations in the CFTR gene, our results greatly contribute to knowledge regarding the genetic background of CF in this region.     

Beta-thalassemia mutations in Indonesia and their linkage to beta haplotypes.

A total of 72 chromosomes from 36 Indonesian patients, 23 with beta-thalassemia major and 13 with Hb E-beta-thalassemia, were analyzed by specific oligonucleotide hybridization after DNA amplification. Thirteen had the beta E mutation (codon 26 GAG----AAG). Of the 59-beta-thalassemic chromosomes, 32 were of the variant IVS-1 nt5 (G----C). Seven had the mutation IVS-2 nt654 (C----T), one had the mutation codon 41/42 (deletion CTTT), and one had the mutation codon 17 (AAG----TAG). Another six with the mutation IVS-1 nt1 (G----T), one with the mutation IVS-1 nt1 (G----A), four with the mutation codon 15 (TGG----TAG), one with a mutation codon 30 (AGG----ACG), and one with a mutation codon 35 (deletion C) were first identified by direct sequencing of a patient's genomic DNA followed by further hybridizing other patients' DNA with the appropriate oligonucleotide probes. Five did not carry the common mutations previously described in Asian populations. The four most prevalent mutations encountered made up 83% of the total number of beta-thalassemic chromosomes studied. The most common mutation, IVS-1 nt5 (G----C), was mostly associated with two different haplotypes.     

Distribution of beta-globin haplotypes among the tribes of southern Gujarat,India

The present study was carried out in Indo-European speaking tribal population groups of southern Gujarat (India) to elucidate the allelic and haplotypic content of β-globin system in individuals with HbAA genotypes. 6 neutral restriction sites of the β-globin system were analysed and various statistical parameters were estimated to draw meaningful interpretations. All the 6 sites were found to be polymorphic and most were in Hardy–Weinberg Equilibrium in the studied group. Haplotypes were constructed using two different combinations of the 6 restriction sites analysed. Analysis of the 5 sites revealed a set of three predominant haplotypes, ‘+−−−−’, ‘−++−+’ and ‘−+−++’; and haplotypes ‘+−−’, ‘++−’ and ‘+++’ were found to be the most frequent when the 3 sites were used to construct the haplotypes. Haplotypic heterozygosity levels (> 83%) observed in the present study group were comparable to those observed in African and Afro-American populations and greater than other world populations. All the ancestral haplotypes, +−−−−−, −++−+, −+−++ and −−−−+ were found in the study group. The distribution pattern of various haplotypes was consistent with the global pattern. The paucity of comparable data from other Indian populations restricted one from making interpretations about the study group's relationships with other Indian populations but the results were indicative of older population histories or experience of gene flow by the study group and their affinities with populations of southern India.     

Characteristic beta-globin gene cluster haplotypes of Evenkis and Oroqens in north China

Haplotype frequencies of the beta-globin gene cluster were estimated for 114 Evenkis and 81 Oroqens from northeast China, and their characteristics were compared with those in Japanese, Koreans, and three Colombian Amerindian groups of South America (Wayuu, Kamsa, and Inga tribes). A major 5' subhaplotype (5' to the delta-globin gene) was + - - - - in Evenkis, whereas + - - - -, - + + - +, and - + - + + were the major subhaplotypes in Oroqens. One possible candidate for an ancestral 5' subhaplotype, - - - - -, was found in one Evenki (0.5%) and three Oroqen chromosomes (2.0%). They were observed as heterozygous forms for + ---- and -----. Major haplotypes were +-----+, + -----+-, and + - - - - + + in Evenkis, whereas they were +-----+,-++-+-+, +----+-, and -+-++-+ in Oroqens. The lowest Nei's genetic distance values of Evenkis or Oroqens based on the 5' subhaplotype frequency distributions were observed in relation to the Wayuu or Koreans, respectively, but those of Evenkis and Oroqens based on the haplotype frequency distributions were found in relation to Koreans.     

Missense mutations associated with RFLP haplotypes 1 and 4 of the human phenylalanine hydroxylase gene.

We report missense mutations associated with haplotype 1 and haplotype 4 alleles of the human phenylalanine hydroxylase (PAH) gene. Individual exon-containing regions were amplified by polymerase chain reaction from genomic DNA of a PKU patient who was a haplotype 1/4 compound heterozygote. The amplified DNA fragments were subcloned into M13 for sequence analysis. Missense mutations were observed in exons 5 and 7, resulting in the substitution of Arg by Gln at residues 158 and 261 of the enzyme, respectively. Expression analysis in heterozygous mammalian cells after site-directed mutagenesis demonstrated that the Arg158-to-Gln158 mutation is a PKU mutation, whereas the Arg261-to-Gln261 mutation is apparently silent in the assay system. Hybridization analysis using allele-specific oligonucleotide probes demonstrated that the Arg158-to-Gln158 mutation is present in two of six mutant haplotype 4 alleles among the Swiss and constitutes about 40% of all mutant haplotype 4 alleles in the European population. The mutation is not present in normal alleles or in any mutant alleles of other haplotypes. The results provide conclusive evidence that there is linkage disequilibrium between mutation and haplotype in the PAH gene and that multiple mutations have occurred in the PAH gene of a prevalent haplotype among Caucasians.     

Detection of beta-globin gene mutations by polymerase chain reaction.

The polymerase chain reaction and oligonucleotide probe hybridization technique were applied to the detection of two common mutations of the beta-globin gene found in Chinese, namely the 4-base pair deletion at the 41-42 codons and the C to T substitution at nucleotide 654 of IVS-2. The accuracy of the method was established using beta-thalassemia cases with known mutations or haplotypes of the restriction fragment length polymorphism (RFLP). A further 11 cases of thalassemia intermediate and thalassemia minor were then analysed with the same approach. Our results showed that 5 of the 11 cases carried the TCTT-deletion at codons 41-42. Our method is economical both in terms of materials and time needed and in an alternative to the use of the molecular RFLP approach in the prenatal diagnosis of beta-thalassemia.     

Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients.

Identification of mutations causing cystic fibrosis (CF) in the Turkish population is essential for assessment of the molecular basis of CF in Turkey and the development of strategies for prenatal diagnosis and genetic counseling. Here, we present an updated report of mutations found in the Turkish CF population from an extensive screening study of the entire coding region, including exon-intron boundaries and the promoter region. Cases for which mutations could not be identified were also screened for previously defined large alterations and (TG)mTn-M470V loci. This study revealed a total of 27 different mutations accounting for almost 60% of disease genes in the Turkish population. In this study, we also identified the haplotypes associated with 17 mutations and those associated with unknown mutations. The mutation spectrum of CF in Turkey and its associated haplotypes indicated the presence of a major Mediterranean component in the contemporary Turkish population.     

Distribution of beta-thalassemia mutations in south China and their association with haplotypes.

DNA from 93 Chinese beta-thalassemia chromosomes were hybridized to eight different mutant oligomers to determine their specific mutation. Four mutations accounted for 87% of the chromosomes; in descending frequencies, these mutations were codon 41/42, IVS-2 nt654, codon 17, and -28. Since codon 41/42 mutation can be associated with multiple beta-thalassemia haplotypes, codon 41/42 is probably a hot spot for the 4-bp deletion. The distributions of these mutations were mapped to various regions in south China. These data are useful for the planning of prenatal diagnosis programs in other Chinese communities worldwide.     

Evolution of beta-globin haplotypes in human populations

The beta-globin haplotypes of 852 chromosomes from 12 populations in the Asia-Pacific region are described. These data are combined with those from other populations in an investigation of the affinities of regional human populations. Both partial maximum-likelihood and distance Wagner methods indicate that Africans are the most divergent group, with the remaining populations branching in the following order: Australian Aborigines, Highland Melanesians, Lowland Melanesians, Indonesians and Micronesians, Polynesians, east Asians, Indians, and Europeans. This pattern of relationship is consistent with that indicated by other data. Analysis of the evolution and distribution of haplotype occurrence provides some limited support for an origin of modern humans in Africa. Otherwise, however, it was not useful in further elucidating the evolutionary history of human populations.     

Wilson disease mutations associated with uncommon haplotypes in mediterranean patients

This study reports 12 novel mutations of the Wilson disease (WD) gene which have been detected by the molecular analysis of 29 patients of Mediterranean descent carrying uncommon chromosomal haplotypes at the WD locus. These mutations include two nonsense, one splice site and nine missense. The missense mutations lie in regions of the WD gene critical for its function, such as the transmembrane region, the transduction domain and the ATP loop and ATP-binding domain, indicating that they are disease-causing mutations. These new findings improve our knowledge for the role played by functional domains on the ATP7B function. Received: 20 March 1996     

Alpha-globin gene haplotypes in Polynesians: their relationships to population groups and gene rearrangements.

Five hundred two alpha-globin gene haplotypes were established in three Polynesian populations, Samoans, Maoris, and Niueans. Limited diversity of haplotypes was found in Polynesians, in whom six common haplotypes (Ia, IIa, IId, IIe, IIIa, and IVa) predominate. Haplotypes Ia and IIa enable Polynesians to be distinguished from Melanesians. Differences in haplotype profiles between the above Polynesian populations support their separate clustering on the basis of previous globin gene analyses and proposed theories of migration. The -alpha/, alpha alpha alpha/, -zeta/, and zeta zeta zeta/rearrangements are each associated exclusively with a particular haplotype, providing evidence of a single evolutionary origin for each. Therefore, a minimum of four DNA crossover events account for the separate origins of these rearrangements in the Polynesians.     

Red cell genetic abnormalities, beta-globin gene haplotypes, and APOB polymorphism in the Great Andamanese, a primitive Negrito tribe of Andaman and Nicobar Islands, India.

The Great Andamanese are a primitive Negrito tribe of the Andaman and Nicobar Islands, India, with a total population of 37. We studied 29 individuals from eight families from this population for abnormal hemoglobins, G6PD deficiency, DNA haplotypes, and apolipoprotein B (APOB, gene) polymorphism. Hb E was detected in five individuals, the prevalence of Hb E heterozygotes being 14.3%. One individual had beta-thalassemia trait. One female was G6PD deficient and showed the G6PD Orissa mutation. Haplotype analysis of the beta-globin gene cluster showed that the betaE chromosomes were linked to two haplotypes (- - - - - + + and + + - + + + +) representing the framework 1 gene, whereas the betaA chromosomes showed eight different haplotypic patterns corresponding to framework 1 and 3 genes. APOB polymorphism analysis showed that the 631-base-pair (bp) allele was the predominant one with a high homozygosity rate, which could be due to the higher rate of inbreeding in this isolated group. The presence of Hb E and our findings on haplotype analysis supports the hypothesis that the Great Andamanese are reasonably believed to be the surviving representatives of the Negrito race that once flourished in the entire Southeast Asian region in ancient times.     

Some atypical and rare sickle cell gene haplotypes in populations of Andhra Pradesh, India.

We have investigated the clinical, hematological, and molecular genetic characteristics of sickle cell anemia patients from 6 populations of Andhra Pradesh, South India. Of 72 sickle cell chromosomes (HBB*S) 60 belong to characteristic Arab-Indian haplotypes, 6 to variant Arab-Indian haplotypes, 1 to a Bantu haplotype, 2 to a Cameroon haplotype, and 3 to rare haplotypes. This is the first report of a Bantu haplotype in an Indian population. Some information on haplotype characteristics of normal chromosomes (HBB*A) is also presented. The average hemoglobin level was 7.3 g% and mean fetal hemoglobin (HbF) level was 12.6%. The higher HbF levels corroborate earlier observations in sickle cell homozygotes from India. Clinical investigations have revealed splenomegaly and painful crises as the most common features in these patients.     

Origin of rat beta-globin haplotypes containing three and five genes

We have reported in rat three adult beta-gene haplotypes containing either five or three genes. Detailed sequence analysis reveals that the leftmost gene is the major gene and that at the opposite end downstream lies the minor gene. All of the genes lying between them are minor-major hybrids indicating their origin by unequal crossing-over. In two haplotypes beta-globin genes were found with an L1(1) element inserted directly into IVS2. The described results allow the formulation of a pathway of mutational events leading from the ancient two-beta-gene rodent ancestor through a three-gene haplotype to five-gene haplotypes, one of which is postulated to have arisen in common laboratory strains since their capture in the wild.     

The detection of beta-globin gene mutations in beta-thalassemia using oligonucleotide probes and amplified DNA

DNA amplification combined with the use of synthetic oligonucleotide probes has become an important tool in the identification of base substitutions. We report the use of this DNA amplification technique for the detection of mutations in beta-thalassemia. A series of oligonucleotide primers are synthesized which span the beta-globin gene; one primer is complementary to the coding strand and the other to the non-coding strand. The primers are chosen so that there is little homology with other DNA segments, especially the delta gene. Each set of primers spans an area of the gene between 100 and 300 bp, while the suspected mutation point is located between these two primers. With the use of such a primer set, the beta-globin gene region is amplified by denaturation, annealing and DNA synthesis. The amplification cycle is repeated 25-30 times, using the Klenow fragment of DNA polymerase I. The resulting amplified DNA is hybridized with normal and synthetic deoxynucleotide probes using a standard dot-blot method. We have designed a set of primers and experimental conditions which should prove useful to diagnostic centers for detection of numerous beta-thalassemia mutations.     

Character of two mutations of the beta-globin gene in beta 0-thalassemia in Azerbaijan

Molecular nature of two beta 0-thalassaemia-causing mutations in beta-globin gene in Azerbaijanian population has been elucidated, viz., C-T transition in 39 codon (nonsense mutation) and previously unknown G deletion in 82/83 codons.     

Frequency and origin of haplotypes associated with the beta-globin gene cluster in individuals with trait and sickle cell anemia in the Atlantic and Pacific coastal regions of Colombia

Sickle cell anemia is a genetic disease with high prevalence in people of African descent. There are five typical haplotypes associated with this disease and the haplotypes associated with the beta-globin gene cluster have been used to establish the origin of African-descendant people in America. In this work, we determined the frequency and the origin of haplotypes associated with hemoglobin S in a sample of individuals with sickle cell anemia (HbSS) and sickle cell hemoglobin trait (HbAS) in coastal regions of Colombia. Blood samples from 71 HbAS and 79 HbSS individuals were obtained. Haplotypes were determined based on the presence of variable restriction sites within the β-globin gene cluster. On the Pacific coast of Colombia the most frequent haplotype was Benin, while on the Atlantic coast Bantu was marginally higher than Benin. Eight atypical haplotypes were observed on both coasts, being more diverse in the Atlantic than in the Pacific region. These results suggest a differential settlement of the coasts, dependent on where slaves were brought from, either from the Gulf of Guinea or from Angola, where the haplotype distributions are similar. Atypical haplotypes probably originated from point mutations that lost or gained a restriction site and/or by recombination events.     

Relationships between %Hb F or %G gamma and the haplotypes in the beta-globin gene cluster in the normal adult Japanese and Korean populations.

Haplotypes or subhaplotypes in the beta-globin gene cluster were examined in 31 normal Japanese and 21 Korean families. Major haplotypes were VII, V, and I, which shared a common subhaplotype [+----], and occurred in 70% of the Japanese and 68% of the Koreans. Three haploypes which shared a common subhaplotype [-+-++], bearing the XmnI site 5' to the G gamma-globin gene, occurred in 13% of the Japanese and 7.3% of the Koreans. One subhaplotype [-++-+], which is closely linked to the A gamma T-globin gene, had an incidence of 6.6% in the Japanese and 20% in the Koreans. Rare subhaplotypes [---++], and [- +] which has been observed mainly in Melanesians and Polynesians, and a very rare subhaplotype [-----] were observed. The present study suggests that high or low G gamma-globin chain production is closely related to subhaplotypes [-+-++] and [+----], respectively, among the normal adult population.