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Hassan S, Bahar R, Johan MF, Mohamed Hashim EK, Abdullah WZ, Esa E, Abdul Hamid FS, Zulkafli Z. Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia. Diagnostics (Basel) 2023; 13:diagnostics13030373. [PMID: 36766477 PMCID: PMC9914462 DOI: 10.3390/diagnostics13030373] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis of thalassemia by conventional PCR-based DNA analysis is time- and resource-consuming owing to the phenotype variability, disease complexity, and molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up by an extensive diagnosis of the thalassemia-causing phenotype and the possible genetic modifiers. Data coming from advanced molecular techniques such as targeted sequencing by next-generation sequencing (NGS) and third-generation sequencing (TGS) are more appropriate and valuable for DNA analysis of thalassemia. While NGS is superior at variant calling to TGS thanks to its lower error rates, the longer reads nature of the TGS permits haplotype-phasing that is superior for variant discovery on the homologous genes and CNV calling. The emergence of many cutting-edge machine learning-based bioinformatics tools has improved the accuracy of variant and CNV calling. Constant improvement of these sequencing and bioinformatics will enable precise thalassemia detections, especially for the CNV and the homologous HBA and HBG genes. In conclusion, laboratory transiting from conventional DNA analysis to NGS or TGS and following the guidelines towards a single assay will contribute to a better diagnostics approach of thalassemia.
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Affiliation(s)
- Syahzuwan Hassan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | - Rosnah Bahar
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Muhammad Farid Johan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | | | - Wan Zaidah Abdullah
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ezalia Esa
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | | | - Zefarina Zulkafli
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
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2
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The genetic heterogeneity of β-globin gene defects in Sicily reflects the historic population migrations of the island. Blood Cells Mol Dis 2011; 46:282-7. [DOI: 10.1016/j.bcmd.2011.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 11/23/2022]
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3
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Colah R, Gorakshakar A, Nadkarni A. Global burden, distribution and prevention of β-thalassemias and hemoglobin E disorders. Expert Rev Hematol 2011; 3:103-17. [PMID: 21082937 DOI: 10.1586/ehm.09.74] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The β-thalassemias, including the hemoglobin E disorders, are not only common in the Mediterranean region, South-East Asia, the Indian subcontinent and the Middle East but have now become a global problem, spreading to much of Europe, the Americas and Australia owing to migration of people from these regions. Approximately 1.5% of the global population are heterozygotes or carriers of the β-thalassemias. While the overall frequencies of carriers of these disorders are known in most countries, there have been few attempts at micromapping and wherever this has been done, significant variations are seen even within small geographic regions. Thus, the figures for the estimated numbers of births each year of homozygous β-thalassemia and the severe compound states involving other hemoglobin disorders may be an underestimate. Screening strategies have varied from premarital to antenatal in different countries depending on socio-cultural and religious customs in different populations. Prenatal diagnosis programs are ongoing in many countries and the knowledge of the distribution of mutations has facilitated the establishment of successful control programs. Many of these were through North-South partnerships and networking. Yet, there are many countries in Asia where they are lacking, and South-South partnerships are now being developed in South-East Asia and the Indian subcontinent to link centers with expertise to centers where expertise needs to be developed. Although the carrier frequencies will remain unaltered, this will eventually help to bring down the burden of the birth of affected children with β-thalassemias and hemoglobin E disorders in Asia.
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Affiliation(s)
- Roshan Colah
- National Institute of Immunohaematology, Indian Council of Medical Research ,KEM Hospital Campus, Parel, Mumbai, India.
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4
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Incidence of haemoglobinopathies in various populations — The impact of immigration. Clin Biochem 2009; 42:1745-56. [DOI: 10.1016/j.clinbiochem.2009.05.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 05/22/2009] [Indexed: 11/19/2022]
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5
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Tan JAMA, Tan KL, Omar KZ, Chan LL, Wee YC, George E. Interaction of Hb South Florida (codon 1; GTG-->ATG) and HbE, with beta-thalassemia (IVS1-1; G-->A): expression of different clinical phenotypes. Eur J Pediatr 2009; 168:1049-54. [PMID: 19034506 DOI: 10.1007/s00431-008-0877-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/31/2008] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Interactions of different hemoglobin variants with thalassemia alleles can result in various clinical phenotypes. HbE-beta-thalassemia generally manifests with severe anemia where individuals exhibit beta-thalassemia major with regular blood transfusions or beta-thalassemia intermedia with periodic blood transfusions. This study presents a unique Malay family with three beta-globin gene defects-HbE, Hb South Florida, and IVS1-1 (G-->A). MATERIALS AND METHODS HbE activates a cryptic splice site that produces non-functional mRNAs. Hb South Florida is a rare beta-hemoglobin variant, and its interactions with other beta-thalassemia alleles have not been reported. IVS1-1 is a Mediterranean mutation that affects mRNA processing giving rise to beta(o)-thalassemia. RESULTS AND DISCUSSION Fifteen mutations along the beta-globin gene complex were analyzed using the amplification refractory mutation system. Hb South Florida was identified by direct sequencing using genomic DNA. CONCLUSION The affected child with HbE/IVS1-1 produced a beta-thalassemia major phenotype. Compound heterozygosity for Hb South Florida/IVS1-1 produced a beta-thalassemia carrier phenotype in the mother.
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Affiliation(s)
- Jin-Ai Mary Anne Tan
- Department of Molecular Medicine, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia.
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6
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Lemsaddek W, Picanço I, Seuanes F, Nogueira P, Mahmal L, Benchekroun S, Khattab M, Osório-Almeida L. The β‐Thalassemia Mutation/Haplotype Distribution in the Moroccan Population. Hemoglobin 2009; 28:25-37. [PMID: 15008262 DOI: 10.1081/hem-120028884] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The present study compiles the results of our own research and of a prior study on beta-thalassemia (thal) in Morocco, comprising a total of 187 beta-thalassemic chromosomes. Six major mutations: (beta0) codon 39 (C --> T), (beta+) IVS-I-6 (T --> C), (beta0) frameshift codon (FSC) 6 (-A), (beta0) FSC 8 (-AA), (beta0) IVS-I-1 (G --> A) and (beta+) -29 (A --> G) account for 75.7% of the independent chromosomes studied. A regional predominance was observed (Gharb and West regions) for the (beta+) IVS-I-6 (T --> C) mutation. Despite an observed heterogeneity of molecular anomalies, a direct method of diagnosis of the prevalent mutations is feasible in this population. The distributions of mutations and haplotypes are in conformity with the geographical location of Morocco and the historical links with both the Mediterranean communities that have successively interspersed with the Berbers, the Phoenicians, the Carthaginians, the Romans, the Arabs, the population of the Iberian Peninsula and, to a lesser degree, the Vandals and the Byzantines and permanently, with the Sub-Saharan Africans. In the adult population, the levels of fetal hemoglobin (Hb) in heterozygotes vary from trace quantities to 2.38 g/dL of total Hb. With the exception of the (beta0) codon 39 (C --> T) nonsense mutation, no statistically significant correlation was found, neither between mutation and Hb F levels, nor gender and Hb F levels in heterozygotes. The genetic markers for Hb F increase, located within cis active sites such as the XmnI site at -158 bp of the Ggamma-globin gene and the AT(X)T(Y) repeat region at -540 bp of the beta-globin gene, were assessed. The polymorphism XmnI shows linkage disequilibrium with haplotypes III, IV and IX, as previously observed in the Algerian, Sicilian and Portuguese beta-thal populations. Contrary to what has previously been reported for a population of beta-thal carriers of European descent, this sample does not show a statistically significant correlation between Hb F levels and the presence of the genetic markers XmnI restriction site at -158 bp of the Ggamma-globin gene and AT(X)T(Y) alleles at 5' of the beta-globin gene.
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Affiliation(s)
- Wafaâ Lemsaddek
- Laboratório de Genética Molecular, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Morales KR, Magaña MT, Ibarra B, Perea FJ. Diversity of the 5′ β-Globin Haplotype of Four β-Thalassemia Mutations in the Mexican Population. Hemoglobin 2009; 33:66-71. [DOI: 10.1080/03630260802625923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Dorit RL, Ohara O, Hwang CB, Kim JB, Blackshaw S. Direct DNA sequencing of PCR products. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2008; Chapter 15:Unit 15.2. [PMID: 18265116 DOI: 10.1002/0471142727.mb1502s56] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PCR products can be sequenced using either the dideoxy (Sanger) or chemical (Maxam-Gilbert) approaches. In the dideoxy methods presented here, the target sequence is amplified and an excess of one strand of the target sequence (relative to its complement) is then generated by "asymmetric PCR," where one primer is present in vast excess over the other. This single-stranded product serves as the template for conventional dideoxy sequencing methods. Another procedure prepares PCR products for use as templates fes for characterizing unlabeled product by genomic sequencing and chemical sequencing of end-labeled products are also presented.
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Affiliation(s)
- R L Dorit
- Yale University, New Haven, Connecticut, USA
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9
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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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10
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De Angioletti M, Lacerra G, Pagano L, Alessi M, D'Avino R, Manca L, Carestia C. β
-thalassaemia-87 C→G: relationship of the Hb F modulation and polymorphisms in compound heterozygous patients. Br J Haematol 2004; 126:743-9. [PMID: 15327529 DOI: 10.1111/j.1365-2141.2004.05089.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A clinical, haematological, biochemical and molecular study was carried out in 17 patients affected with thalassaemia intermedia, who were compound heterozygotes for the beta-thalassaemia mutation beta-87 C-->G to determine the genetic basis of their clinical heterogeneity. The beta-87 was found associated with haplotype VIII (beta-87/VIII) or V (beta-87/V). The 10 patients with the beta-87/VIII showed milder clinical conditions, with significantly higher levels of haemoglobin (Hb) (9.8 +/- 1.1 g/dl vs. 8.5 +/- 1.3 g/dl) and fetal haemoglobin (Hb F) (6.2 +/- 1.5 g/dl vs. 2.6 +/- 1.5 g/dl; P = 0.0034) and higher synthesis of (G)gamma ((G)gamma/(Total)gamma 69.4 +/- 2.6% vs. 42.8 +/- 16.2%; P = 0.0042) than the seven patients with the beta-87/V. The beta-87/VIII showed a configuration of rare polymorphisms in the 5' sub-haplotype, which have been reported to exert an increasing effect on Hb F. They were "T"-158 (G)gamma-globin gene, T-A-G in pre-(G)gamma framework, (TG)(11)(CG)(3) in the (G)gamma-IVS2, (AT)(9)N(12)(AT)(10) in LCR-HS2; in contrast, the haplotype V had, respectively, "C", T-G-A (TG)(19)(CG)(2)CACG in the (G)gamma-IVS2, and (AT)(10)N(12)(AT)(11). In all patients the beta-87 was associated with the (AT)(9)T(5) motif 5' beta-globin gene with increased affinity for the BP-1 protein, and with the (TG)(13) in the (A)gamma-IVS2. The high increase of the Hb F, mostly of the (G)gamma-type, strongly suggests the hypothesis that the 'T'-158 (G)gamma plays a principal role and that the other polymorphisms could exert a cooperative role in the modulation of Hb F in patients with erythropoietic stress.
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Affiliation(s)
- Maria De Angioletti
- Istituto di Genetica e Biofisica Adriano Buzzati Traverso, CNR, Via G. Marconi 10-12, 80125 Naples, Italy
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11
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Rigoli L, Meo A, Miceli MR, Alessio K, Caruso RA, La Rosa MA, Salpietro DC, Ricca M, Barberi I. Molecular analysis of beta-thalassaemia patients in a high incidence area of southern Italy. CLINICAL AND LABORATORY HAEMATOLOGY 2001; 23:373-8. [PMID: 11843884 DOI: 10.1046/j.1365-2257.2001.00367.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The prevalence of eight mutations in 84 patients with beta-thalassaemia major and in 16 subjects with thalassaemia intermedia was investigated. All of the patients were Italian, originating from Eastern Sicily (Messina area) and some Calabrian regions. Genomic DNA was amplified by polymerase chain reaction (PCR). DNA molecular investigations were performed by allele-specific oligonucleotide (ASO) hybridization, to identify the following beta-thalassaemia mutations: CD39 (C-T), IVS1-110 (G-A), IVS1-6 (T-C), IVS1-1 (G-A), IVS2-745 (C-G), IVS2-1 (G-A), -87 (C-G), CD6 A (-A). Our data underline that in thalassemia intermedia two mutations were statistically prevalent: IVS1-6 T-->C (P < 0.001) and CD 6-A (P < 0.05). CD 39 was statistically prevalent in beta-thalassaemia major patients (P < 0.01). The difference between the two groups was not statistically significant for all the other mutations. Five different genotypes were recorded among thalassaemia intermedia and 15 among beta-thalassaemia major patients. Twenty-five percent of the intermedia patients and 4.5% of the major patients had homozygosity for mild mutations (group I); 62.5% of the intermedia patients and 26.2% of the major patients had combinations of mild/severe mutations (group II). In addition, homozygosity or double heterozygosity for severe mutations (group III) was found in 12.5% of the intermedia patients and 69% of the major patients. Some genotypes were restricted to thalassaemia intermedia, including heterozygosity -87/IVS1-6 and IVS1-6/CD 6-A. It is essential to understand the distribution and frequency of the relevant mutations in each population where beta-thalassaemias exist. This is of particular importance for genotype-phenotype correlation and for carrier detection, genetic counselling and prenatal diagnosis.
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Affiliation(s)
- L Rigoli
- Department of Paediatrics, University of Messina, School of Medicine, Italy.
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12
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Flint J, Harding RM, Boyce AJ, Clegg JB. The population genetics of the haemoglobinopathies. BAILLIERE'S CLINICAL HAEMATOLOGY 1998; 11:1-51. [PMID: 10872472 DOI: 10.1016/s0950-3536(98)80069-3] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The haemoglobinopathies are the commonest single-gene disorders known, almost certainly because of the protection they provide against malaria, as attested by a number of observations. The geographical distributions of malaria and haemoglobinopathies largely overlap, and microepidemiological surveys confirm the close relationship between them. For two of the commonest disorders, haemoglobin S and alpha(+)-thalassaemia, there is also good clinical evidence for protection against malaria morbidity. However, not all the evidence appears to support this view. In some parts of the world malaria and haemoglobinopathies are not, and never have been, coexistent. It is also difficult to explain why the majority of haemoglobinopathies appear to be recent mutations and are regionally specific. Here we argue that these apparent inconsistencies in the malaria hypothesis are the result of processes such as genetic drift and migration and of demographic changes that have occurred during the past 10,000 years. When these factors are taken into account, selection by malaria remains the force responsible for the prevalence of the haemoglobinopathies.
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Affiliation(s)
- J Flint
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
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13
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Nişli G, Kavakli K, Aydinok Y, Oztop S, Cetingül N. Beta-thalassemia alleles in Aegean region of Turkey: effect on clinical severity of disease. Pediatr Hematol Oncol 1997; 14:59-65. [PMID: 9021814 DOI: 10.3109/08880019709030885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Beta (beta) globin gene analysis was performed in 54 homozygous beta-thalassemia patients followed up in the Pediatric Hematology Department of Medical School of Ege University. The spectrum of beta-thalassemia alleles and their effect on clinical severity of disease were investigated. Twelve different mutations were determined in our patients. The six most frequent alleles, IVSI-110 (G-A), IVSI-6 (T-C), IVSI-I (G-A), IVSII-745 (C-G), Cd39 (C-T), and FSC8, account for 80.6% of all the disease genes. Eleven percent of the chromosomes could not be identified with the probes used in this study. In 38 patients both of whose beta-thalassemia alleles were identified, the beta-thalassemia alleles were found to be the major determinant of the clinical severity of disease. The clinical progress of disease was also closely related to the degree of iron overload.
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Affiliation(s)
- G Nişli
- Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
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14
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Waye JS, Eng B, Patterson M, Wasi P, Chui DH, Francombe WH, Sher GD, Olivieri NF. Severity of beta-thalassemia due to genotypes involving the IVS-I-6 (T-->C) mutation. Am J Hematol 1995; 50:15-9. [PMID: 7668219 DOI: 10.1002/ajh.2830500104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Among individuals of Mediterranean or Middle Eastern descent, the IVS-I-6 (T-->C) mutation is one of the most common causes of beta-thalassemia. In this report, we describe the clinical phenotypes of a group of beta-thalassemia patients who are compound heterozygotes for the relatively mild IVS-I-6 (T-->C) beta-thalassemia mutation and more severe beta(+)- or beta (0)-thalassemia mutations. Although most of these patients are transfusion-dependent, the requirement for regular transfusions generally occurred late in childhood. A correlation between concomitant alpha-thalassemia and a mild transfusion-independent phenotype is not apparent, indicating the involvement of other ameliorating determinants.
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Affiliation(s)
- J S Waye
- Provincial Hemoglobinopathy DNA Diagnostic Laboratory, McMaster University Medical Centre, Hamilton, Ontario, Canada
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15
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Ratip S, Skuse D, Porter J, Wonke B, Yardumian A, Modell B. Psychosocial and clinical burden of thalassaemia intermedia and its implications for prenatal diagnosis. Arch Dis Child 1995; 72:408-12. [PMID: 7618906 PMCID: PMC1511109 DOI: 10.1136/adc.72.5.408] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Twenty eight patients with thalassaemia intermedia and their parents were interviewed using specifically designed questionnaires to evaluate psychosocial burden. Hospital notes were analysed for clinical burden. A wide variation was found for both patients and parents, ranging from virtually unaffected to severely affected. Normal sexual function and setting up a family were mentioned by patients and parents as being particularly important for quality of life. Over half (58%) of the patients had problems with sexual maturation and functioning, and continuous monitoring of all patients with thalassaemia intermedia by a paediatric endocrinologist is therefore strongly indicated. Most parents said, in light of their experiences, that they would opt for prenatal diagnosis and termination of affected pregnancies even if a genotype predicting the mild form of disorder were discovered.
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Affiliation(s)
- S Ratip
- Department of Haematology, University College London Medical School
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16
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Flint J, Harding RM, Boyce AJ, Clegg JB. The population genetics of the haemoglobinopathies. BAILLIERE'S CLINICAL HAEMATOLOGY 1993; 6:215-62. [PMID: 8353314 DOI: 10.1016/s0950-3536(05)80071-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The haemoglobinopathies are the commonest single gene disorders known, and are so common in some regions of the world that the majority of the population carries at least one genetic abnormality affecting the structure or synthesis of the haemoglobin molecule. The prevalence of the common haemoglobinopathies (the alpha- and beta-thalassaemias, HbS, HbC and HbE) is almost certainly a result of the protection they provide against malaria, as the epidemiological evidence reviewed in this chapter shows. World-wide, the distributions of malaria and the common haemoglobinopathies largely overlap, and micro-epidemiological surveys have confirmed the close relationship between the disorders. However, there are complications to this picture which appear to undermine the malaria hypothesis. First, in some areas, malaria and haemoglobinopathies are not coincident. Second, the malaria hypothesis does not easily explain why no two regions of the world have the same haemoglobinopathy or combination of haemoglobinopathies. The majority of mutations have arisen only once and are regionally specific. By using molecular characterization of mutations and the analysis of haplotypes on haemoglobinopathy-bearing chromosomes it is possible to show how a combination of selection by malaria, genetic drift and population movements can explain the first complication. In order to explain the second, we have argued that malaria selection has operated relatively recently on human populations (within the last 5000 years). The present distribution is then seen as the result of selection elevating sporadic mutations in local populations. In the absence of sufficient gene flow to spread all mutations to all populations, the consequence is a patchwork distribution of haemoglobinopathies. Given time, we would expect the mutations that protect and do not compromise the health of their carriers to become widely disseminated, but it is likely that human intervention will alter this process of natural selection.
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Affiliation(s)
- J Flint
- MRC Molecular Haematology Unit, John Radcliffe Hospital, Headington, Oxford, U.K
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17
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Affiliation(s)
- S L Thein
- MRC Molecular Haematology Unit, Radcliffe Hospital, Oxford, U.K
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18
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Flint J, Harding RM, Clegg JB, Boyce AJ. Why are some genetic diseases common? Distinguishing selection from other processes by molecular analysis of globin gene variants. Hum Genet 1993; 91:91-117. [PMID: 8462981 DOI: 10.1007/bf00222709] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Various processes (selection, mutation, migration and genetic drift) are known to determine the frequency of genetic disease in human populations, but so far it has proved almost impossible to decide to what extent each is responsible for the presence of a particular genetic disease. The techniques of gene and haplotype analysis offer new hope in addressing this issue, and we review relevant studies of three haemoglobinopathies: sickle cell anaemia, and alpha and beta thalassaemia. We show how for each disease it is possible to recognize a pattern of regionally specific mutations, found in association with one or a few haplotypes, that is best explained as the result of selection; other patterns are due to population migration and genetic drift. However, we caution that such conclusions can be drawn in special circumstances only. In the case of the haemoglobinopathies it is possible because a selective agent (malaria) was already suspected, and the investigations could be carried out in relatively genetically homogenous populations whose migratory histories are known. Moreover, some data reviewed here suggest that gene conversion and the haplotype composition of a population may affect the frequency of a mutation, making interpretation of gene frequencies difficult on the basis of standard population genetics theory. Hence attempts to use the same approaches with other genetic diseases are likely to be frustrated by a lack of suitably untrammelled populations and by difficulties accounting for poorly understood genetic processes. We conclude that although this combination of molecular and population genetics is successful when applied to the study of haemoglobinopathies, it may not be so easy to apply it to the study of other genetic diseases.
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Affiliation(s)
- J Flint
- MRC Molecular Haematology Unit, John Radcliffe Hospital, Oxford, UK
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Abstract
We have analysed the molecular basis of beta-thalassaemia in 22 Anglo-Saxon individuals, all of whom were heterozygous for beta-thalassaemia except for one, who was a compound heterozygote. Using a combination of allele-specific priming of the polymerase chain reaction (PCR) and direct sequencing of genomic DNA amplified by the PCR, 20/23 beta-thalassaemic genes were characterized. Nine different mutations were identified; four are commonly found in the Mediterranean, one in Asia, one has been described previously in both Europe and Asia, and three are rare mutations associated with a dominant beta-thalassaemia phenotype. In three individuals the mutation remains uncharacterized despite sequence analysis of the beta-globin gene and its immediate flanking regions. We report our findings and discuss the diversity of these mutations.
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Affiliation(s)
- G W Hall
- MRC Molecular Haematology Unit, John Radcliffe Hospital, Oxford
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20
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Renda M, Maggio A, Warren TC, Kazazian HH. Detection of an IVS-1 3' end (G-C) beta-thalassemia mutation in the AG invariant dinucleotide of the acceptor splice site in a Sicilian subject. Genomics 1992; 13:234-5. [PMID: 1577489 DOI: 10.1016/0888-7543(92)90232-h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M Renda
- Servizio Terapia e Prevenzione Talassemia, V. Cervello Hospital, Palermo, Italy
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21
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Affiliation(s)
- A E Kulozik
- Department of Paediatrics II, University of Ulm, Federal Republic of Germany
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22
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Affiliation(s)
- B Masala
- Institute of General Physiology and Biological Chemistry, University of Sassari, Italy
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23
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Trapani FD, Marino M, D'Alcamo E, Abate I, D'Agostino S, Lauricella S, Musicò M, Orlandi F, Sammarco P, Maggio A. Prenatal diagnosis of haemoglobin disorders by cordocentesis at 12 weeks' gestation. Prenat Diagn 1991; 11:899-904. [PMID: 1687161 DOI: 10.1002/pd.1970111204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Prenatal diagnosis of haemoglobin disorders is accepted to be a useful procedure to avoid births of infants with homozygous diseases. Advances in sampling and molecular techniques, such as polymerase chain reaction (PCR) and chorionic villus sampling (CVS), have made earlier and safer first-trimester prenatal diagnosis possible. However, these procedures need previous studies of at-risk couples, which can be very time-consuming when a number of different beta-thalassaemia mutations occur in the region. We describe the possibility of making a first-trimester prenatal diagnosis by cordocentesis and fetal blood analysis at the 12th week of gestation. We found no statistically significant difference (p greater than 0.05) between beta/gamma values in fetuses at the 12th and 18th weeks of gestation. In seven affected fetuses aborted at the 12th week of gestation, the diagnosis was confirmed in all cases by PCR analysis. These findings suggest that early cordocentesis could be an alternative procedure to CVS and PCR analysis.
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Affiliation(s)
- F D Trapani
- Department of Haematology, V. Cervello Hospital, Palermo, Italy
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24
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Varawalla NY, Old JM, Sarkar R, Venkatesan R, Weatherall DJ. The spectrum of beta-thalassaemia mutations on the Indian subcontinent: the basis for prenatal diagnosis. Br J Haematol 1991; 78:242-7. [PMID: 2064964 DOI: 10.1111/j.1365-2141.1991.tb04423.x] [Citation(s) in RCA: 165] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The beta-thalassaemia mutations in 702 unrelated carriers originating from seven different regions of the Indian subcontinent have been characterized using allele specific priming of the polymerase chain reaction (PCR). It was possible to identify the mutations in 688 (98%) of the individuals studied. Eleven different mutations were identified, of which five common ones accounted for 93.6%; namely the ones at IVS-1 position 5 (G-C), codons 8/9 (+G), IVS-1 position 1 (G-T), codons 41/42 (-CTTT) and the 619 bp deletion at the 3' end of the gene. The mutations at IVS-2 position 1 (G-A) and codon 30 (G-C), previously undescribed in Asian Indians, were found in two and six individuals respectively. Some regional variation in the distribution of beta-thalassaemia alleles was noted. These findings should prove useful for the development of a first trimester prenatal diagnosis programme based on direct detection of mutations.
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Affiliation(s)
- N Y Varawalla
- Institute of Molecular Medicine, John Radcliffe Hospital, Oxford
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25
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D'Alcamo E, Sammarco P, di Marzo R, Iapichino L, Pardo F, Maggio A, Balsamo V, Caronia F. Cystic fibrosis in the Sicilian population: linkage disequilibrium and prenatal diagnosis by polymerase chain reaction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 290:355-6. [PMID: 1950746 DOI: 10.1007/978-1-4684-5934-0_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- E D'Alcamo
- Centro Regionale FC, Ospedale dei Bambini, Palermo, Italy
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26
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LOMBARDO M, RAGUSA A, XIMENES B, LAPOUMÉROULIE C, LABIE D, ELION J, KRISHNAMOORTHY R, LOMBARDO T. Thalassemia in the Southeastern Part of Sicily. Ann N Y Acad Sci 1990. [DOI: 10.1111/j.1749-6632.1990.tb24343.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Maggio A, Di Marzo R, Giambona A, Renda M, Acuto S, Lo Gioco P, D'Alcamo E, Di Trapani F, Marino M, Abate I. Beta-thalassemia mutations in Sicily. Ann N Y Acad Sci 1990; 612:67-73. [PMID: 2291575 DOI: 10.1111/j.1749-6632.1990.tb24291.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- A Maggio
- Department of Hematology, V. Cervello Hospital, Palermo, Italy
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28
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Abstract
Care and life quality of thalassemic patients in Italy have greatly improved over the last years thanks to cooperation between many clinical centers. The achievement of the following points played an important role: 1. A national treatment protocol was adopted in 1980; it has been widely accepted and regularly updated. 2. A standardized format for recording clinical data and a computerized clinical record (Computhal) were adopted. 3. A national registry was set up in order to evaluate the patient age distribution and birth and death rates both at the regional and national level. 4. A quality assurance program (Cooley Care) was devised after key indicators for evaluating treatment were identified and a central data base was set up. 5. Cooperative clinical trials provided information on many pathological and therapeutical aspects of the disease (incidence of complications, causes of death). 6. Pilot studies were carried out on emerging problems (intensive chelation, desferrioxamine (DFO) pharmacokinetics and toxicity). 7. Attention was paid to psychological and social problems.
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Affiliation(s)
- V Gabutti
- Department of Pediatrics, University of Turin, Italy
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29
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Huisman TH. Frequencies of common beta-thalassaemia alleles among different populations: variability in clinical severity. Br J Haematol 1990; 75:454-7. [PMID: 2206995 DOI: 10.1111/j.1365-2141.1990.tb07781.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T H Huisman
- Department of Cell and Molecular Biology, Medical College of Georgia, Augusta 30912-2100
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30
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Kattamis C, Hu H, Cheng G, Reese AL, Gonzalez-Redondo JM, Kutlar A, Kutlar F, Huisman TH. Molecular characterization of beta-thalassaemia in 174 Greek patients with thalassaemia major. Br J Haematol 1990; 74:342-6. [PMID: 2334641 DOI: 10.1111/j.1365-2141.1990.tb02593.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mutations producing beta-thalassaemia in 174 Greek patients with thalassaemia major were investigated by dot-blot hybridization of oligonucleotide probes to genomic DNA amplified by the polymerase chain reaction procedure, by direct sequencing of amplified DNA, and by gene mapping. beta-thalassaemia in Greeks was found to be very heterogeneous at the molecular level as 17 different mutations were observed: 86.6% of the beta-thalassaemic genes, however, could be identified with five probes: IVS-I-110 (G----A) (42.5%), codon 39 (C----T) (17%), IVS-I-1 (G----A) (13.2%), IVS-I-6 (T----C) (7.2%) and IVS-II-745 (C----G) (6.9%). Several mutations which had not previously been reported in the Greek population and which occurred at an incidence of 2% or lower were observed in this study. The information obtained will facilitate the prenatal diagnosis of beta-thalassaemia in Greece.
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Affiliation(s)
- C Kattamis
- First Department of Pediatrics, University of Athens, Greece
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31
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Abstract
The clinical and hematological features of 202 Sicilian subjects with sickle cell disease are reported, 41 being homozygous for beta s (beta s beta s), 64 with beta zero thal beta s (beta zero beta s), and 97 beta+ thal beta s (beta+ beta s). Analysis of the findings showed that the disease observed in Sicilians is of intermediate severity and falls between the severe form observed in patients of African origin and the milder one seen in subjects of Arabian origin.
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Affiliation(s)
- G Schilirò
- Sicilian Cooperative Group for Hemoglobinopathy Studies
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32
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Deidda G, Novelletto A, Hafez M, al-Tonbary Y, Felicetti L, Terrenato L, Colombo B. A new beta-thalassemia mutation produced by a single nucleotide substitution in the conserved dinucleotide sequence of the IVS-I consensus acceptor site (AG----AA). Hemoglobin 1990; 14:431-40. [PMID: 2283297 DOI: 10.3109/03630269009032003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An Egyptian child with thalassemia major was found to carry two different haplotypes (I and VI) associated with two beta-thalassemic chromosomes. Analysis with several oligonucleotides and restriction enzymes, which identify the mutations most common in the Mediterranean area, allowed the identification of only one mutation, namely T----C at position 6 of the first intervening sequence (IVS-I). In order to characterize the other mutation the beta gene was amplified with polymerase chain reaction and sequenced. A G----A substitution was found at position 130 of the IVS-I which alters the conserved dinucleotide AG present in the consensus acceptor sequence, thus producing a beta (0)-thalassemia. This mutation was further confirmed by restriction analysis since it creates a new restriction site for the enzyme Afl II. It is concluded that this subject carries the IVS-I-6 mutation associated with haplotype VI, frequently observed in Mediterranean areas, and a new mutation at the acceptor site of the IVS-I, which has not been described before, associated with haplotype I. This thalassemic gene can be added to the list of mutations that can be identified by Southern analysis using Afl II.
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Affiliation(s)
- G Deidda
- Istituto di Biologia Cellulare, C.N.R., Roma, Italy
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33
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Ristaldi MS, Pirastu M, Rosatelli C, Monni G, Erlich H, Saiki R, Cao A. Prenatal diagnosis of beta-thalassaemia in Mediterranean populations by dot blot analysis with DNA amplification and allele specific oligonucleotide probes. Prenat Diagn 1989; 9:629-38. [PMID: 2798349 DOI: 10.1002/pd.1970090906] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this study, we describe a simple strategy to detect beta-thalassaemia mutations in prospective parents and to make prenatal diagnosis in pregnancies at risk in the Mediterranean population. Screening of prospective parents is carried out by dot blot analysis on enzymatically amplified DNA with a set of oligonucleotide probes complementary to the most common mutations in this population. Prenatal diagnosis is accomplished by the same procedure on enzymatically amplified amniocyte or trophoblast DNA. The main advantages of this procedure are the simplicity, sensitivity (0.05 micrograms of DNA), and rapidity (12-24 h). Further simplification is obtained by amplification of the DNA from crude amniotic cell lysate. The very low amount of fetal material necessary for this analysis eliminates the need to culture amniotic fluid cells and may decrease the fetal loss rate associated with trophoblast sampling. The number of specific DNA sequences obtained by the amplification procedure allowed us to use non-radioactive labelled oligonucleotide probes, which have several advantages compared to radioactive probes.
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Affiliation(s)
- M S Ristaldi
- Istituto di Ricerca sulle Talassemie e Anemie Mediterranee, CNR, Cagliari, Italy
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34
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Kollia P, Gonzalez-Redondo JM, Stoming TA, Loukopoulos D, Politis C, Huisman TH. Frameshift codon 5 [Fsc-5 (-CT)] thalassemia; a novel mutation detected in a Greek patient. Hemoglobin 1989; 13:597-604. [PMID: 2606727 DOI: 10.3109/03630268908993110] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sequence analysis and dot-blot hybridization of DNA from a Greek patient with a transfusion dependent thalassemia revealed the combination of a beta IVS-I-1 G----A mutation (beta(0) -thalassemia) and a hitherto undescribed frameshift mutation; the latter concerns the absence of a CT dinucleotide from codon 5 and results in a termination signal at the new codon 21 (also a beta (0)-thalassemia).
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Affiliation(s)
- P Kollia
- First Department of Medicine, University of Athens School of Medicine, Laikon Hospital, Greece
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35
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Di Marzo R, Maggio A, D'Agostino S, Dowling CE, Wong C, Kazazian HH. A rapid DNA method for first-trimester prenatal diagnosis. Br J Haematol 1988; 70:504-5. [PMID: 3219303 DOI: 10.1111/j.1365-2141.1988.tb02528.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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