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Sen A, Seenappa V, Chakrabarti P, Dolai TK. First Report of the 3'-Untranslated Region +1506 (A>C) [NM_000518.5: c.*32A>C] mutation on the β-Globin Gene in the Indian Population. Hemoglobin 2021; 45:325-328. [PMID: 34886762 DOI: 10.1080/03630269.2021.2011314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The 3'-untranslated region (3'-UTR) is well known to be associated with the post-transcriptional regulation, because of the presence of important sequences that influence the fate of mRNA, and thus, in protein synthesis. The present study describes a point mutation on the β-globin 3'-UTR, +1506 (A>C) (HBB: c.*32A>C) in an Indian family during prenatal diagnosis (PND) screening of an at-risk couple. The members of the family heterozygous for this mutation presented with a typical β-thalassemia (β-thal) phenotype. The haplotype analysis of the β-globin gene cluster was determined for this mutation and observed to be linked with haplotype [- + - + + + +]. Common α-globin gene deletions, triplication, and the Xmnl polymorphism, were also looked for and found to be absent in the family. The identified HBB: c.*32A>C mutation is located in the first adenylate uridylate (AU) motif of the four AU motifs situated in the 3'-UTR region of the β-globin gene. Bioinformatics analysis revealed binding of two miRNAs, hsa-miR-451a and hsa-miR-3914, at the mutation position, possibly influencing the mRNA stability by recruiting RNA binding proteins. This is the third publication reporting the 3'-UTR +1506 (A>C) mutation worldwide and the first report of the existence of this mutation in the Indian population, emphasizing the high heterogeneity of this population.
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Affiliation(s)
- Aditi Sen
- Department of Haematology, Nil Ratan Sircar Medical College and Hospital, Kolkata, West Bengal, India
| | - Venu Seenappa
- Department of Molecular Genetics, Lifecell International Pvt. Ltd, Chennai, Tamil Nadu, India
| | - Prantar Chakrabarti
- Department of Haematology, Vivekananda Institute of Medical Sciences, Kolkata, West Bengal, India
| | - Tuphan Kanti Dolai
- Department of Haematology, Nil Ratan Sircar Medical College and Hospital, Kolkata, West Bengal, India
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Soler AM, Piellusch BF, da Silveira L, Pedroso GA, López P, Savio E, Sonati MDF, da Luz J. Alpha thalassemia and alpha-MRE haplotypes in Uruguayan patients with microcytosis and hypochromia without anemia. Genet Mol Biol 2021; 44:e20200399. [PMID: 33769430 PMCID: PMC7995682 DOI: 10.1590/1678-4685-gmb-2020-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Alpha thalassemia is the most common genetic disorder across the world, being the α-3.7 deletion the most frequent mutation. In order to analyze the spectrum and origin of alpha thalassemia mutations in Uruguay, we obtained a sample of 168 unrelated outpatients with normal hemoglobin levels with microcytosis and hypochromia from two cities: Montevideo and Salto. The presence of α-thalassemia mutations was investigated by gap-PCR, restriction endonucleases analysis and HBA2 and HBA1 genes sequencing, whereas the alpha-MRE haplotypes were investigated by sequencing. We found 55 individuals (32.7%) with α-thalassemia mutations, 51(30.4%) carrying the -α3.7 deletion, one with the -α4.2 deletion and three having the rare punctual mutation HBA2:c.-59C>T. Regarding alpha-MRE analysis, we observed a significant higher frequency of haplotype D, characteristic of African populations, in the sample with the -α3.7 deletion. These results show that α-thalassemia mutations are an important determinant of microcytosis and hypochromia in Uruguayan patients with microcytosis and hypochromia without anemia, mainly due to the -α3.7 deletion. The alpha-MRE haplotypes and the α-thalassemia mutations spectrum suggest a predominant, but not exclusive, African origin of these mutations in Uruguay.
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Affiliation(s)
- Ana María Soler
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Bruna Facanali Piellusch
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Lorena da Silveira
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Gisele Audrei Pedroso
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Pablo López
- Universidad de la República (UdelaR), Facultad de Medicina, Hospital de Clínicas Manuel Quintela, Departamento de Laboratorio de Patología Clínica, Montevideo, Uruguay
| | - Enrique Savio
- Administración de los Servicios de Salud del Estado (ASSE), Hospital Departamental de Salto, Servicio de Laboratorio Clínico, Salto, Uruguay
| | - María de Fatima Sonati
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Julio da Luz
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
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Tepakhan W, Srewaradachpisal K, Kanjanaopas S, Jomoui W. Genetics background of β-thalassemia (3.5 kb deletion) in Southern Thailand: Haplotype analysis using novel reverse dot blot hybridization. Ann Hum Genet 2021; 85:115-124. [PMID: 33559179 DOI: 10.1111/ahg.12416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/30/2022]
Abstract
β-thalassemia (β-thal) (3.5 kb deletion or NC_000011.10:g.5224302-5227791del3490bp) is a common mutation in southern Thailand. This study aimed to determine genetic diversity in subjects with β-thal (3.5 kb deletion) alleles and to ascertain the origin of this mutation using haplotype and phylogenetic analysis. The study was carried out on members of the southern Thai population, including 45 normal individuals, 116 heterozygous β-thal (3.5 kb deletion) and one homozygous β-thal (3.5 kb deletion). The 5'-haplotype in β-globin gene cluster was examined using newly developed reverse dot blot hybridization (RDB) and compared with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed 100% concordance between the haplotype patterns of these two methods. From a total of 324 chromosomes, nine haplotypes were segregated. Haplotype H2 (+ - - - -) was the predominant haplotype observed in all 118 β-thal (3.5 kb deletion) chromosomes, which revealed a single origin. The phylogenetic tree demonstrated that β-thal (3.5 kb deletion) has an older genetic defect in this region. Moreover, the developed RDB is simple, less time-consuming, inexpensive, and does not restriction enzyme digestion.
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Affiliation(s)
- Wanicha Tepakhan
- Faculty of Medicine, Department of Pathology, Prince of Songkla University, Songkhla, Thailand
| | | | - Sataron Kanjanaopas
- Faculty of Medicine, Department of Pathology, Prince of Songkla University, Songkhla, Thailand
| | - Wittaya Jomoui
- Faculty of Medicine, Department of Pathology, Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Nakhon Nayok, Thailand
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Huang K, Ge S, Yi W, Bi H, Lin K, Sun H, Huang X, Chu J, Ma S, Yang Z. Interactions of unstable hemoglobin Rush with thalassemia and hemoglobin E result in thalassemia intermedia. Hematology 2019; 24:459-466. [DOI: 10.1080/16078454.2019.1621020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kai Huang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Shijun Ge
- Clinical laboratory, People’s hospital of Dehong Dai and Jingpo Minorities Autonomous Prefecture, Mangshi, People’s Republic of China
| | - Wei Yi
- Clinical laboratory, People’s hospital of Dehong Dai and Jingpo Minorities Autonomous Prefecture, Mangshi, People’s Republic of China
| | - Hui Bi
- Department of Hematology, The Second Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Keqin Lin
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Xiaoqin Huang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Shaohui Ma
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
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Ozturk O, Arikan S, Atalay A, Atalay EO. Time estimations by network of beta globin gene cluster haplotypes linked with Hb D-Los Angeles [β121 (GH4) Glu → Gln GAA → CAA] mutation in the world populations. Mol Genet Genomic Med 2018; 6:1181-1187. [PMID: 30417580 PMCID: PMC6305635 DOI: 10.1002/mgg3.499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/22/2022] Open
Abstract
Background β‐Globin gene cluster haplotypes associated with the Hb D‐Los Angeles mutation have been reported in many different locations in different populations including Italy, Iran, Thailand, Belgium, Mexico, Holland, and Turkey. In this study, we have identified genetic relationships and formation periods between the haplotypes reported in the world regarding the Hb D‐Los Angeles. Methods We comparatively analyzed the RFLP (restriction fragment length polymorphism) data in Denizli region and world populations using Arlequin 3.5 statistical software program. The data obtained from the Arlequin software were then entered into the Phylogenetic Network software to calculate the age estimates and to discover possible links between the haplotypes. Results We observed the frequencies of the β‐globin gene haplotypes for the seven polymorphic restriction sites around the world and calculated the estimated time of haplotypes using Network software on the basis of ancestral haplotypes. We performed the phylogenetic network analysis of the haplotypes linked with Hb D‐Los Angeles mutation by processing the data of frequency and age estimations with Network software. Conclusion Our period of time results suggests that HAP1 was formed before modern human migration to Asia and/or independent origin of the Hb D‐Los Angeles mutation from other populations. Considering that the population in Denizli region started the Hb D‐Los Angeles mutation past about 40,000 years ago, it can be said that HAP1, HAP15, and HAP21 belong to the gene pool with an external effect. Our period of time results of HAP6 is compatible with published dating results.
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Affiliation(s)
- Onur Ozturk
- Department of Biophysics, Inonu University School of Medicine, Malatya, Turkey
| | - Sanem Arikan
- Department of Biophysics, Pamukkale University School of Medicine, Denizli, Turkey
| | - Ayfer Atalay
- Department of Biophysics, Pamukkale University School of Medicine, Denizli, Turkey
| | - Erol O Atalay
- Department of Biophysics, Pamukkale University School of Medicine, Denizli, Turkey
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Fong C, Barreto G. Presencia de haplotipos no africanos incrementa la diversidad genética en pacientes con anemia falciforme en Colombia. ACTA BIOLÓGICA COLOMBIANA 2018. [DOI: 10.15446/abc.v23n3.69218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El objetivo de este estudio fue identificar la frecuencia de haplotipos dentro del cluster de Beta globina presente en pacientes con anemia falciforme en Colombia, establecer la presencia de haplotipos no africanos en esta población, así como verificar variaciones en el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina. Se analizaron 83 individuos con anemia falciforme, los haplotipos se formaron utilizando cinco sitios de restricción dentro del cluster de Beta globina, se estableció la frecuencia de haplotipos, se calculó el grado de desequilibrio de ligamiento entre los sitios de restricción, así como la similitud genética de esta población con otra de afectados en América. Los haplotipos más frecuentes en la población fueron Benín ( 35,1 %) y Bantú (26, 5 %), ambos africanos. Sin embargo, haplotipos presentes en poblaciones indígenas americanas y europeas alcanzaron frecuencias entre el 2 – 10 %, así como haplotipos que no han sido reportados en otras poblaciones. Los sitios de restricción presentaron bajo o nulo desequilibrio de ligamiento entre ellos. Al compararse con otras poblaciones, la población colombiana presentó mayor similitud con la población de Venezuela en donde Benin y Bantú son también predominantes. Nuestros resultados muestran que el mestizaje ha facilitado el paso de la mutación para la anemia falciforme a un contexto genético no africano (amerindio y europeo). Además, el mestizaje también ha alterado el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina generando modificaciones que pueden tener influencia en estudios de asociación dentro de esta población de afectados.
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β-globin gene cluster haplotypes in ethnic minority populations of southwest China. Sci Rep 2017; 7:42909. [PMID: 28205625 PMCID: PMC5311981 DOI: 10.1038/srep42909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China.
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Abstract
The functional theory of psychogenic illness proposes that the human capacity for psychological states to cause physical illness evolved during the Paleolithic as an adaptive mechanism for ensuring mutually interdependent behaviour under conditions when mutual interdependence was essential for survival. This integrative theory is consistent with existing data from several disciplines, including archaeology, anthropology, ecology and health psychology, and leads to two sorts of empirical consequence for health psychology. First, the theory acts as a heuristic for suggesting the most predictive psychological units for use in health psychology: the current weak or inconsistent results may be the consequence of using an inappropriate psychological unit, namely behavioural aggregation. Secondly, the theory provides predictions about how psychological variables should interact with type of disease, age and sex.
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Wagner SC, Lindenau JD, Castro SMD, Santin AP, Zaleski CF, Azevedo LA, Ribeiro Dos Santos ÂKC, Dos Santos SEB, Hutz MH. High Frequency of Hb E-Saskatoon (HBB: c.67G > A) in Brazilians: A New Genetic Origin? Hemoglobin 2016; 40:228-30. [PMID: 27250692 DOI: 10.1080/03630269.2016.1189433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hb E-Saskatoon [β22(B4)Glu→Lys, HBB: c.67G > A] is a rare, nonpathological β-globin variant that was first described in a Canadian woman of Scottish and Dutch ancestry and has since then been detected in several populations. The aim of the present study was to identify the origin of Hb E-Saskatoon in Brazil using β-globin haplotypes and genetic ancestry in carriers of this hemoglobin (Hb) variant. Blood samples were investigated by isoelectric focusing (IEF) and high performance liquid chromatography (HPLC) using commercial kits. Hb E-Saskatoon was confirmed by amplification of the HBB gene, followed by sequence analysis. Haplotypes of the β-globin gene were determined by polymerase chain reaction (PCR), followed by digestion with specific restriction enzymes. Individual ancestry was estimated with 48 biallelic insertion/deletions using three 16-plex PCR amplifications. The IEF pattern was similar to Hbs C (HBB: c.19G > A) and Hb E (HBB: c.79G > A) [isoelectric point (pI): 7.59-7.65], and HPLC results showed an elution in the Hb S (HBB: c.20A > T) window [retention time (RT): 4.26-4.38]. DNA sequencing of the amplified β-globin gene showed a mutation at codon 22 (GAA>AAA) corresponding to Hb E-Saskatoon. A total of 11 cases of this variant were identified. In nine unrelated individuals, Hb E-Saskatoon was in linkage disequilibrium with haplotype 2 [+ - - - -]. All subjects showed a high degree of European contribution (mean = 0.85). Hb E-Saskatoon occurred on the β-globin gene of haplotype 2 in all Brazilian carriers. These findings suggest a different genetic origin for this Hb variant from that previously described.
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Affiliation(s)
- Sandrine C Wagner
- a Universidade Federal de Ciencias da Saude , Porto Alegre , Brazil.,b Departamento de Genética , Instituto de Biociências, Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil
| | - Juliana D Lindenau
- b Departamento de Genética , Instituto de Biociências, Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil
| | - Simone M de Castro
- c Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil and
| | - Ana Paula Santin
- c Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil and
| | - Carina F Zaleski
- c Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil and
| | - Laura A Azevedo
- c Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil and
| | | | - Sidney E B Dos Santos
- d Laboratório de Genética Humana e Médica , Universidade Federal do Pará , Belém , Brazil
| | - Mara H Hutz
- b Departamento de Genética , Instituto de Biociências, Universidade Federal do Rio Grande do Sul , Porto Alegre , Brazil
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Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV, Magalhaes JV. Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS One 2014; 9:e87438. [PMID: 24498106 PMCID: PMC3907521 DOI: 10.1371/journal.pone.0087438] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/24/2013] [Indexed: 11/18/2022] Open
Abstract
Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ∼6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.
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Affiliation(s)
| | - Martha T. Hamblin
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | | | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | | | - Leon V. Kochian
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture – Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
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Luz JD, Ávila A, Icasuriaga S, Gongóra M, Castillo L, Serrón A, Kimura EM, Costa FF, Sans M, Sonati MDF. Frequency and spectrum of hemoglobinopathy mutations in a Uruguayan pediatric population. Genet Mol Biol 2013; 36:316-22. [PMID: 24130436 PMCID: PMC3795163 DOI: 10.1590/s1415-47572013005000027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 04/12/2013] [Indexed: 11/22/2022] Open
Abstract
Hemoglobinopathies are the most common recessive diseases worldwide but their prevalence in Uruguay has not been investigated. In this study, 397 unrelated outpatient children from the Pereira Rosell Hospital Center (CHPR), as well as 31 selected patients with microcytic anemia and 28 β-thalassemia carriers were analyzed for hemoglobinopathies by using biochemical and molecular biology methods. Parametric and non-parametric methods were used to compare the hematological indices between groups of genotypes. Of the 397 patients in the first group, approximately 1% (0.76% HbS and 0.25% β-thalassemia) had a mutation in the HBB gene and 3.3% had β-thalassemia. These mutations had a heterogeneous distribution that varied according to individual ancestry. HbS was found exclusively in individuals with declared African ancestry and had a carrier frequency of 2.2%. The frequency of α-thalassemia carriers in outpatients of European and African ancestry was 1.2% and 6.5%, respectively. In contrast, the frequency of α-thalassemia carriers in patients with microcytic anemia was 25.8%, significantly higher (p < 0.01) than that observed in the sample as a whole and in Afro-descendants and Euro-descendants. Significant differences were observed in the hematological parameters between individuals with thalassemia genotypes and those with a normal genotype. These results indicate that hemoglobinopathies are a relevant health problem in Uruguay.
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Affiliation(s)
- Julio Da Luz
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo,
Uruguay
| | - Amalia Ávila
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo,
Uruguay
| | - Sandra Icasuriaga
- Departamento de Laboratorio Clínico, Centro Hospitalario Pereira Rosell, Montevideo,
Uruguay
| | - María Gongóra
- Servicio de Hemato-Oncología Pediátrica, Centro Hospitalario Pereira Rosell, Montevideo,
Uruguay
| | - Luis Castillo
- Servicio de Hemato-Oncología Pediátrica, Centro Hospitalario Pereira Rosell, Montevideo,
Uruguay
| | - Alejandra Serrón
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo,
Uruguay
| | - Elza Miyuki Kimura
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP,
Brazil
| | - Fernando Ferreira Costa
- Hemocentro, Faculdade de Ciências Médicas, Universidad Estadual de Campinas, Campinas, SP,
Brazil
| | - Mónica Sans
- Departmento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo,
Uruguay
| | - Maria de Fátima Sonati
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP,
Brazil
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Distribution of beta-globin haplotypes among the tribes of southern Gujarat, India. Gene 2013; 521:287-92. [DOI: 10.1016/j.gene.2013.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/13/2012] [Accepted: 02/27/2013] [Indexed: 11/17/2022]
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Saslis-Lagoudakis CH, Williamson EM, Savolainen V, Hawkins JA. Cross-cultural comparison of three medicinal floras and implications for bioprospecting strategies. JOURNAL OF ETHNOPHARMACOLOGY 2011; 135:476-87. [PMID: 21457769 DOI: 10.1016/j.jep.2011.03.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 02/18/2011] [Accepted: 03/22/2011] [Indexed: 05/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE One of the major drawbacks of using ethnomedicinal data to direct testing of plants which may find pharmaceutical use is that certain plants without bioactivity might be traditionally used. An accepted way of highlighting bioactive plants is to compare usage in different cultures. This approach infers that presumed independent discovery by different cultures provides evidence for bioactivity. Although several studies have made cross-cultural comparisons, they focussed on closely related cultures, where common patterns might be the result of common cultural traditions. The aim of this study was to compare three independent ethnomedicinal floras for which similarities can be more robustly interpreted as independent discoveries, and therefore likely to be indication for efficacy. MATERIALS AND METHODS Data from the literature were compiled about the ethnomedicinal floras for three groups of cultures (Nepal, New Zealand and the Cape of South Africa), selected to minimise historical cultural exchange. Ethnomedicinal applications were divided in 13 categories of use. Regression and binomial analyses were performed at the family level to highlight ethnomedicinal "hot" families. General and condition-specific analyses were carried out. Results from the three regions were compared. RESULTS Several "hot" families (Anacardiaceae, Asteraceae, Convolvulaceae, Clusiaceae, Cucurbitaceae, Euphorbiaceae, Geraniaceae, Lamiaceae, Malvaceae, Rubiaceae, Sapindaceae, Sapotaceae and Solanaceae) were recovered in common in the general analyses. Several families were also found in common under different categories of use. CONCLUSIONS Although profound differences are found in the three ethnomedicinal floras, common patterns in ethnomedicinal usage are observed in widely disparate areas of the world with substantially different cultural traditions. As these similarities are likely to stem from independent discoveries, they strongly suggest that underlying bioactivity might be the reason for this convergent usage. The global distribution of prominent usage of families used in common obtained by this study and the wider literature is strong evidence that these families display exceptional potential for discovery of previously overlooked or new medicinal plants and should be placed in high priority in bioscreening studies and conservation schemes.
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Affiliation(s)
- C Haris Saslis-Lagoudakis
- School of Biological Sciences, Plant Science Laboratories, University of Reading, Whiteknights, Reading RG6 6BX, UK.
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Dos Santos Silva W, de Nazaré Klautau-Guimarães M, Grisolia CK. β-globin haplotypes in normal and hemoglobinopathic individuals from Reconcavo Baiano, State of Bahia, Brazil. Genet Mol Biol 2010; 33:411-7. [PMID: 21637405 PMCID: PMC3036130 DOI: 10.1590/s1415-47572010005000042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 01/15/2010] [Indexed: 11/22/2022] Open
Abstract
Five restriction site polymorphisms in the β-globin gene cluster (HincII-5‘ ε, HindIII-G γ, HindIII-A γ, HincII- ψβ1 and HincII-3‘ ψβ1) were analyzed in three populations (n = 114) from Reconcavo Baiano, State of Bahia, Brazil. The groups included two urban populations from the towns of Cachoeira and Maragojipe and one rural Afro-descendant population, known as the “quilombo community”, from Cachoeira municipality. The number of haplotypes found in the populations ranged from 10 to 13, which indicated higher diversity than in the parental populations. The haplotypes 2 (+ - - - -), 3 (- - - - +), 4 (- + - - +) and 6 (- + + - +) on the βA chromosomes were the most common, and two haplotypes, 9 (- + + + +) and 14 (+ + - - +), were found exclusively in the Maragojipe population. The other haplotypes (1, 5, 9, 11, 12, 13, 14 and 16) had lower frequencies. Restriction site analysis and the derived haplotypes indicated homogeneity among the populations. Thirty-two individuals with hemoglobinopathies (17 sickle cell disease, 12 HbSC disease and 3 HbCC disease) were also analyzed. The haplotype frequencies of these patients differed significantly from those of the general population. In the sickle cell disease subgroup, the predominant haplotypes were BEN (Benin) and CAR (Central African Republic), with frequencies of 52.9% and 32.4%, respectively. The high frequency of the BEN haplotype agreed with the historical origin of the afro-descendant population in the state of Bahia. However, this frequency differed from that of Salvador, the state capital, where the CAR and BEN haplotypes have similar frequencies, probably as a consequence of domestic slave trade and subsequent internal migrations to other regions of Brazil.
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Da Luz J, Kimura EM, Costa FF, Sonati MDF, Sans M. Beta-globin gene cluster haplotypes in Afro-Uruguayans from two geographical regions (South and North). Am J Hum Biol 2010; 22:124-8. [PMID: 19533614 DOI: 10.1002/ajhb.20961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The beta-globin gene cluster haplotypes were identified in 52 and 40 chromosomes from two Afro-Uruguayan populations located in the South and North of the country, respectively. In both regions, the 5' haplotype 2 (+ - - - -), characteristic of non-African populations, was the most frequent, reflecting a strong process of admixture in Afro-Uruguayans (0.355 and 0.262, respectively). The haplotypes 3 (- - - - +) and 4 (- + - - +), characteristics of African sub-Saharan populations, present inverse frequencies in North and South: whereas in the South haplotype 3 is the second most frequent (0.232), and haplotype 4 presents a low frequency (0.019), in the North haplotype 4 is the third most frequent (0.140), and haplotype 3 only reaches an intermediate frequency (0.088). The pairwise F(ST) and the exact test of differentiation show genetic heterogeneity between both regions. Nei's genetic distance show that South and North present affinities with Bantu groups, although the North present the smallest genetic distance with the Mandenka, a Senegalese population. With respect to 3' haplotypes, haplotype I was the most frequent in both populations, followed by haplotype II, characteristic of sub-Saharan Africans. The high frequencies of haplotype III-Asian could indicate admixture with Native American populations. The differences observed between both Uruguayan regions could be explained by microevolutionary events as genetic drift, founder effects, differential admixture, and/or distinct origin of the African slaves introduced in those regions.
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Affiliation(s)
- Julio Da Luz
- Departamento de Genética, Universidad de la República, Montevideo, Uruguay
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Arends A, Chacín M, Bravo-Urquiola M, De O TA, Álvarez M, Castillo O, Guevara JM. Hemoglobin variants, hematological parameters andβ-globin gene cluster haplotypes in an isolated Amerindian group from the Orinoco River Delta. Ann Hum Biol 2009; 35:250-5. [DOI: 10.1080/03014460701877999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Anabel Arends
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
- Instituto Anatómico ‘José Izquierdo’, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Marycarmen Chacín
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
- Instituto Anatómico ‘José Izquierdo’, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Martha Bravo-Urquiola
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
- Instituto Anatómico ‘José Izquierdo’, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Tibisay Arends De O
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
- Instituto Anatómico ‘José Izquierdo’, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Maritza Álvarez
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
| | - Omar Castillo
- Universidad de Carabobo, Maracay, Estado Aragua, Venezuela
| | - Jose M. Guevara
- Laboratorio de Investigación de Hemoglobinas Anormales, Servicio de Hematología ‘Dr Tulio Arends’ Hospital Universitario de Caracas, Caracas, Venezuela
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Shimizu K, Nagaoka E, Okada Y, Takeuchi Y, Harihara S, Omoto K, Imanishi T, Kim W, Shin DJ, Hao L, Jin F. Characteristics of the β-Globin Gene Cluster Haplotypes of Three Han Chinese Populations at Beijing, Xi’an, and Kunming as Compared with Those of Other Asian Populations. Biochem Genet 2008; 46:566-82. [DOI: 10.1007/s10528-008-9171-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 03/28/2008] [Indexed: 10/21/2022]
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18
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Callegari-Jacques SM, Crossetti SG, Kohlrausch FB, Salzano FM, Tsuneto LT, Petzl-Erler ML, Hill K, Hurtado AM, Hutz MH. The β-globin gene cluster distribution revisited—Patterns in Native American populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 134:190-7. [PMID: 17596858 DOI: 10.1002/ajpa.20653] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New frequencies for the beta-globin gene cluster haplotypes are presented for the Aché (N = 82 individuals), Guarani (N = 76), and Kaingang (N = 54), three Native South American populations that live in an area between parallels 20 degrees S and 30 degrees S not covered by previous studies at this locus. The haplotype frequencies obtained for the three populations are within the interval observed for 28 other Native American populations. The Aché show much less haplotypes (five) than the other two populations (9-10), the haplotype prevalences being more similar to those of the Guarani than to the Kaingang. The Native American total heterozygosity was about half (0.41) that obtained for the African populations (0.71), but was not much different from those obtained for other continents. A geographical pattern was disclosed in South America by mapping the frequencies of the most common haplotype (haplotype 2), and by means of spatial correlation analysis. The analysis of molecular variance (AMOVA) and pairwise F(ST) data suggest three distinct sectors for the genetic landscape of Native South America: the Andes, the Center/Southeast region, and the Amazon.
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Affiliation(s)
- Sidia M Callegari-Jacques
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil.
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19
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Luz JAD, Sans M, Kimura EM, Albuquerque DM, Sonati MDF, Costa FF. alpha-thalassemia, HbS, and beta-globin gene cluster haplotypes in two Afro-Uruguayan sub-populations from northern and southern Uruguay. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000400002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Piras I, Vona G, Falchi A, Latini V, Ristaldi S, Vacca L, Varesi L, Calò CM. β-globin cluster haplotypes in normal individuals and β039-thalassemia carriers from Sardinia, Italy. Am J Hum Biol 2005; 17:765-72. [PMID: 16254903 DOI: 10.1002/ajhb.20442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Seven polymorphic sites in the beta-globin cluster in association with specific thalassemia mutations were analyzed in a sample from Sardinia, Italy. In order to verify previous works carried out on normal samples (beta(A)/beta(A)) and family studies on beta-thalassemia homozygotes individuals, the haplotype frequencies in both normal individuals (beta(A)/beta(A)) and beta(0)39-thalassemia carriers (beta(A)/beta0) were studied. In our work chromosomes carrying beta(0)39 mutation are characterized by a prevalence of haplotype II (- + + - + + +) (52%) relative to haplotype I (+- - - - + +) (29%), in contrast, among chromosomes with beta(A) the frequency of haplotype I is much greater than that of haplotype II. These data confirm what was found by other authors. Nevertheless, our results disagree with those of previous studies of Sardinians, both in frequencies values and in the numbers of haplotypes identified. Population analysis performed with samples carrying the beta-thalassemic mutation highlighted the peculiarity of Sardinians with respect to other Mediterranean populations. The Corsican population is most similar to the Sardinian population, confirming previous analyses performed with both classical markers and mitochondrial and genomic DNA.
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Affiliation(s)
- I Piras
- Department of Experimental Biology, Section of Anthropological Sciences, University of Cagliari, Monserrato, Italy
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22
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SHIMIZU KOJI, HARIHARA SHINJI. Re-evaluation of the .BETA.-globin gene cluster haplotypes in Japanese, Koreans, and three Colombian Amerinds (Wayuu, Kamsa, and Inga tribes). ANTHROPOL SCI 2004. [DOI: 10.1537/ase.00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KOJI SHIMIZU
- Laboratory of Biology, Naruto University of Education
| | - SHINJI HARIHARA
- Division of Anthropology, Department of Biological Science, Graduate School of Science, The University of Tokyo
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23
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Vívenes De Lugo M, Rodríguez-Larralde A, Castro De Guerra D. Beta-globin gene cluster haplotypes as evidence of African gene flow to the northeastern coast of Venezuela. Am J Hum Biol 2003; 15:29-37. [PMID: 12552576 DOI: 10.1002/ajhb.10120] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In order to study the origin of mutation HBB*S in Sucre and Anzoátegui states and the genetic affinities of these Venezuelan populations with other human groups, the beta-globin gene cluster haplotypes were determined for 28 sickle cell and/or S-beta thalassemia patients and for 37 individuals with normal hematological parameters. Bantu, Benin, Senegal, and atypical haplotypes were identified in 50%, 36%, 2%, and 12% of the HBB*S chromosomes, respectively. Similar results have been published for Venezuelan patients from the central states, but a different trend is shown in a publication based on a group of patients from different regions of the country. For HBB*A, haplotype 2 (+ - - - -), characteristic of non-African groups, was the most common (39%), followed by haplotype 3 (- - - - +) of African origin, and haplotype 6 (- + + - +), also typical of non-Africans. The results reveal a high level of admixture of the Sucre-Anzoátegui population. The importance of specific conditions which have acted differently in the Venezuelan populations, such as founder effect, genetic drift, isolation, and endogamy are discussed. Genetic distances between the Sucre-Anzoátegui sample and several other human populations calculated on the basis of the HBB*S and HBB*A haplotypes revealed similar results, the closest genetic relationships being observed in relation to Bantu-speaking groups. These results confirm the utility of the beta-globin haplotypes for population studies and contribute to knowledge of the Venezuelan gene pool.
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Affiliation(s)
- Merlyn Vívenes De Lugo
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Medicina Experimental, Laboratorio de Genética Humana, Caracas 1020 A, Venezuela
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Mousinho-Ribeiro RDC, Pante-de-Sousa G, Santos EJMD, Guerreiro JF. Genetic relationships among native americans based on beta-globin gene cluster haplotype frequencies. Genet Mol Biol 2003. [DOI: 10.1590/s1415-47572003000300002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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25
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Crawford DC, Caggana M, Harris KB, Lorey F, Nash C, Pass KA, Tempelis C, Olney RS. Characterization of beta-globin haplotypes using blood spots from a population-based cohort of newborns with homozygous HbS. Genet Med 2002; 4:328-35. [PMID: 12394345 DOI: 10.1097/00125817-200209000-00003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE A population-based cohort from three state newborn screening programs was used to describe beta-globin gene cluster variation. METHODS Blood spots from newborns homozygous for HbS were genotyped for five restriction fragment length polymorphisms (RFLPs) to construct beta-globin haplotypes. Haplotype distributions were compared by race/ethnicity and sex. Expected heterozygosities were calculated and compared with observed heterozygosities. RESULTS Haplotype distributions did not differ between sexes for either blacks or Hispanics. Neither racial/ethnic group deviated from Hardy-Weinberg equilibrium; however, Hispanics had higher heterozygosity at two RFLPs compared with blacks. CONCLUSION The differences between populations probably reflect recent migration and admixture rather than selection.
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Affiliation(s)
- Dana C Crawford
- National Center on Birth Defects and Developmental Disabilities, Division of Applied Public Health Training, Epidemiology Program Office, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
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26
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Affiliation(s)
- PETER E. SMOUSE
- Center for Theoretical and Applied Genetics, and Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08903–0231, USA
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Currat M, Trabuchet G, Rees D, Perrin P, Harding RM, Clegg JB, Langaney A, Excoffier L. Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation. Am J Hum Genet 2002; 70:207-23. [PMID: 11741197 PMCID: PMC384889 DOI: 10.1086/338304] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2001] [Accepted: 10/22/2001] [Indexed: 11/03/2022] Open
Abstract
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.
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Affiliation(s)
- Mathias Currat
- Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva, Geneva, Switzerland.
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28
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Mesa NR, Mondragón MC, Soto ID, Parra MV, Duque C, Ortíz-Barrientos D, García LF, Velez ID, Bravo ML, Múnera JG, Bedoya G, Bortolini MC, Ruiz-Linares A. Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: pre- and post-Columbian patterns of gene flow in South America. Am J Hum Genet 2000; 67:1277-86. [PMID: 11032789 PMCID: PMC1288567 DOI: 10.1016/s0002-9297(07)62955-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2000] [Accepted: 09/06/2000] [Indexed: 11/29/2022] Open
Abstract
To evaluate sex-specific differences in gene flow between Native American populations from South America and between those populations and recent immigrants to the New World, we examined the genetic diversity at uni- and biparental genetic markers of five Native American populations from Colombia and in published surveys from native South Americans. The Colombian populations were typed for five polymorphisms in mtDNA, five restriction sites in the beta-globin gene cluster, the DQA1 gene, and nine autosomal microsatellites. Elsewhere, we published results for seven Y-chromosome microsatellites in the same populations. Autosomal polymorphisms showed a mean G(ST) of 6.8%, in agreement with extensive classical marker studies of South American populations. MtDNA and Y-chromosome markers resulted in G(ST) values of 0.18 and 0.165, respectively. When only Y chromosomes of confirmed Amerind origin were used in the calculations (as defined by the presence of allele T at locus DYS199), G(ST) increased to 0.22. G(ST) values calculated from published data for other South American natives were 0.3 and 0.29 for mtDNA and Amerind Y chromosomes, respectively. The concordance of these estimates does not support an important difference in migration rates between the sexes throughout the history of South Amerinds. Admixture analysis of the Colombian populations suggests an asymmetric pattern of mating involving mostly immigrant men and native women.
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Affiliation(s)
- N R Mesa
- Laboratorio de Genética Molecular, Departamento de Fisiología y Bioquímica, Medellín, Colombia
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29
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Mesa NR, Mondragon MC, Soto ID, Parra MV, Duque C, Ortiz‐Barrientos D, Garcia LF, Velez ID, Bravo ML, Munera JG, Bedoya G, Bortolini M, Ruiz‐Linares A. Autosomal, mtDNA, and Y‐Chromosome Diversity in Amerinds: Pre‐ and Post‐Columbian Patterns of Gene Flow in South America. Am J Hum Genet 2000. [DOI: 10.1086/321214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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30
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Mattevi VS, Fiegenbaum M, Salzano FM, Weiss KM, Moore J, Monsalve MV, Devine DV, Hutz MH. Beta-globin gene cluster haplotypes in two North American indigenous populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2000; 112:311-7. [PMID: 10861349 DOI: 10.1002/1096-8644(200007)112:3<311::aid-ajpa3>3.0.co;2-q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Haplotypes derived from five polymorphic restriction sites were determined in 50 Carrier-Sekani and 70 Mvskoke chromosomes, and the results were integrated with those previously obtained for 11 South American Indian populations. Eleven haplotypes were identified in the Mvskokes, while five were observed in the Carrier-Sekani. As in South American natives, haplotype 2 (+----) and 6 (-++ -+) were the most prevalent among the Mvskoke (46% and 30%, respectively). In the Carrier-Sekani, haplotype 2 was also the most common, but haplotype 5 (-+ -++) was somewhat more frequent (18%) than 6 (12%). High heterozygosities, as well as genetic differentiation, were observed among these two North American and two other South American groups (Mapuche and Xavante). They could be due to non-Indian admixture in the Mvskoke and Mapuche, but the findings in the other two populations require some other type of explanation.
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Affiliation(s)
- V S Mattevi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
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Peterson RJ, Goldman D, Long JC. Effects of worldwide population subdivision on ALDH2 linkage disequilibrium. Genome Res 1999; 9:844-52. [PMID: 10508843 PMCID: PMC310807 DOI: 10.1101/gr.9.9.844] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/1999] [Accepted: 06/29/1999] [Indexed: 11/25/2022]
Abstract
The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations across five continents were estimated by maximum-likelihood from genotypes at six closely linked ALDH2 nucleotide substitutions. Linkage disequilibrium was partitioned into three components: within populations, among populations within continents, and among continents. It was found that population subdivision among continents had a larger and more disparate effect on linkage disequilibrium than subdivision among local populations. Further, linkage disequilibrium did not increase with population divergence as predicted by a simple model. Rather, the patterns of linkage disequilibrium were complicated because of the interplay of a near absence of recombination, the linkage disequilibrium that existed prior to the divergence of modern humans, subsequent mutation, population subdivision, random genetic drift, and perhaps natural selection. These results suggest that simple models may not well predict patterns of linkage disequilibrium in human populations.
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Affiliation(s)
- R J Peterson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892-8110 USA.
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32
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Pante-De-Sousa G, Mousinho-Ribeiro RC, Dos Santos EJ, Guerreiro JF. Beta-globin haplotypes analysis in Afro-Brazilians from the Amazon region: evidence for a significant gene flow from Atlantic West Africa. Ann Hum Biol 1999; 26:365-73. [PMID: 10462156 DOI: 10.1080/030144699282679] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Beta-globin gene cluster haplotypes were analysed in betaA-, betaS- and betaC-globin gene-bearing chromosomes in black people from Curiau, Pacoval and Trombetas, three communities made up of descendants of African slaves, located in the Northern region of Brazil. The betaA haplotype distribution is consistent with the African origin of the populations, with some degree of local differentiation and admixture with people of Caucasian ancestry and/or Amerindians. In addition, the betaS haplotype distribution (60% Bantu; 30% Senegal and 10% Benin) suggests that although African slaves brought to Northern region have been predominantly from regions where the Bantu haplotype predominates, there is also evidence of the presence of slaves from West Africa, particularly from the Atlantic West.
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Affiliation(s)
- G Pante-De-Sousa
- Laboratory of Human and Medical Genetics, Federal University of Pará, Brazil
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Kaufman L, Carnese FR, Goicoechea A, Dejean C, Salzano FM, Hutz MH. Beta-globin gene cluster haplotypes in the Mapuche Indians of Argentina. Genet Mol Biol 1998. [DOI: 10.1590/s1415-47571998000400003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Haplotypes derived from five polymorphic restriction sites in the beta-globin gene cluster were investigated in 86 chromosomes from the Argentinian Mapuche. These results were integrated with those previously obtained for ten Brazilian Indian tribes. Eight haplotypes were identified, the most frequent being 2 (57%) and 6 (27%). The presence of haplotype 3 in 2% of the Mapuche chromosomes is probably an evidence of admixture with individuals of African ancestry. Due to the high number of haplotypes observed, heterozygosity as measured by the Gini-Simpson index was higher in the Mapuche than in Brazilian Indians. The haplotypic distribution in the Mapuche was also significantly different from those of all Brazilian tribes investigated. This heterogeneity could be at least partially explained by admixture with non-Indian populations.
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Abstract
Molecular genetic-data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection.
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Affiliation(s)
- L B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City 84112, USA
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de Guerra DC, Hutz MH, Bortolini MC, Salzano FM. Beta-globin gene cluster haplotypes in an admixed Venezuelan population. Am J Hum Biol 1997; 9:323-327. [PMID: 28561294 DOI: 10.1002/(sici)1520-6300(1997)9:3<323::aid-ajhb5>3.0.co;2-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/1995] [Accepted: 05/25/1996] [Indexed: 11/12/2022] Open
Abstract
Haplotype frequencies for the beta-globin gene cluster were determined in 96 chromosomes from a Venezuelan mixed population. Twelve haplotypes were observed, the most frequent of which were 2, 3, and 4; all others showed prevalences below 10%. When the results were compared with those of 13 other groups using a phylogenetic tree, they clustered in an intermediate position somewhat nearer to those of four sub-Saharan African populations. This is in accordance with historical and other genetic data which indicate an important contribution of people of African ancestry to this population. The high heterozygosity (80%) and the intermediate position in the tree, on the other hand, possibly reflect past intermixture of these African-derived individuals with Europeans and Amerindians. Am. J. Hum. Biol. 9:323-327, 1997. © 1997 Wiley-Liss, Inc.
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Affiliation(s)
- Dinorah Castro de Guerra
- Laboratorio de Genética Humana, Instituto Venezolano de Investigaciones Científicas, Caracas 1020A, Venezuela
| | - Mara Helena Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
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Abstract
Distance analysis and factor analysis, based on Q-mode correlation coefficients, were applied to 23 craniofacial measurements in 1,802 recent and prehistoric crania from major geographical areas of the Old World. The major findings are as follows: 1) Australians show closer similarities to African populations than to Melanesians. 2) Recent Europeans align with East Asians, and early West Asians resemble Africans. 3) The Asian population complex with regional difference between northern and southern members is manifest. 4) Clinal variations of craniofacial features can be detected in the Afro-European region on the one hand, and Australasian and East Asian region on the other hand. 5) The craniofacial variations of major geographical groups are not necessarily consistent with their geographical distribution pattern. This may be a sign that the evolutionary divergence in craniofacial shape among recent populations of different geographical areas is of a highly limited degree. Taking all of these into account, a single origin for anatomically modern humans is the most parsimonious interpretation of the craniofacial variations presented in this study.
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Affiliation(s)
- T Hanihara
- Department of Anatomy, Tohoku University School of Medicine, Sendai, Japan
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Bevilaqua LR, Mattevi VS, Ewald GM, Salzano FM, Santos RV, Hutz MH. Beta-globin gene cluster haplotype distribution in five Brazilian Indian tribes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1995; 98:395-401. [PMID: 8599376 DOI: 10.1002/ajpa.1330980402] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Haplotypes derived from five polymorphic restriction sites in the beta-globin gene cluster were investigated in 139 individuals from five different Brazilian Indian tribes by the polymerase chain reaction (PCR). Eight haplotypes were identified. Haplotypes 2 ((+)----) and 6 (-)++(-)+) were the most frequent and were common to all tribes. Their prevalences ranged from 60% to 93% and from 3% to 18%, respectively. Average heterozygosity measured by the Gini-Simpson index is markedly reduced among these Brazilian Indians when compared with Europeans (56%), but much less (8%) in relation to Asiatics, suggesting the absence of an important bottleneck effect in the early colonization of South America. The coefficient of gene differentiation (GST') was estimated as 0.082 among six Brazilian Indian tribes, but when only three Tupi-Mondé-speaking tribes were considered, this estimate was reduced to 0.030.
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Affiliation(s)
- L R Bevilaqua
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Vincek V, Bontrop R, O'Huigin C, Figueroa F. Polymorphism of the beta-globin region in apes: implications for the origin of human haplotypes. Mamm Genome 1994; 5:376-9. [PMID: 8043954 DOI: 10.1007/bf00356558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- V Vincek
- Department of Microbiology and Immunology, University of Miami School of Medicine, Florida 33101
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Pollitzer WS. Ethnicity and human biology. Am J Hum Biol 1994; 6:3-11. [DOI: 10.1002/ajhb.1310060103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/1992] [Accepted: 11/14/1992] [Indexed: 11/12/2022] Open
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Chakraborty R, Weiss KM. Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1991; 86:497-506. [PMID: 1776656 DOI: 10.1002/ajpa.1330860405] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several surveys have found evidence for founder effects in Amerindian mitochondrial DNA because of the existence of rare Asian morphs in high frequencies in some Amerindian populations and the occurrence of several new morphs not seen elsewhere in the world. These reports, however, do not address whether or not the present genetic variation in the mtDNA genome in Amerindians has reached the steady-state distribution predicted by the mutation-drift theory of population genetics. The present work suggests that in three Amerindian populations (Pima, Maya, and Ticuna) a steady state has apparently been reached, and hence the initial founder effect has probably dissipated during the evolution of Amerindians in the New World. This result is consistent with the genetic variation in nuclear genes in similar populations, shown through surveys of protein variation in earlier work and, more recently, in studies of restriction fragment length polymorphisms.
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Affiliation(s)
- R Chakraborty
- Center for Demographic and Population Genetics, University of Texas Graduate School of Biomedical Sciences, Houston 77225
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Chamberlain AT. A chronological framework for human origins. WORLD ARCHAEOLOGY 1991; 23:137-46. [PMID: 16471008 DOI: 10.1080/00438243.1991.9980166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC. African populations and the evolution of human mitochondrial DNA. Science 1991; 253:1503-7. [PMID: 1840702 DOI: 10.1126/science.1840702] [Citation(s) in RCA: 898] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.
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Affiliation(s)
- L Vigilant
- Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720
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Livingstone FB. Phylogenies and the forces of evolution. Am J Hum Biol 1991; 3:83-89. [DOI: 10.1002/ajhb.1310030202] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/1990] [Revised: 11/14/1990] [Accepted: 11/19/1990] [Indexed: 11/06/2022] Open
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