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Structural switching/polymorphism by sequential base substitution at quasi-palindromic SNP site (G → A) in LCR of human β-globin gene cluster. Int J Biol Macromol 2021; 201:216-225. [PMID: 34973267 DOI: 10.1016/j.ijbiomac.2021.12.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022]
Abstract
The human β-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression contains five tissue-specific DNase I-hypersensitive sites (HSs). A single nucleotide polymorphism (SNP) (A → G) present in HS4 region of locus control region (LCR), have shown a notable association between the G allele and the occurrence of β-thalassemia. This SNP site exhibiting a hairpin - duplex equilibrium manifested in A → B like DNA transition has previously been reported from this laboratory. Since, DNA is a dynamic and adaptable molecule, so any change of a single base within a primary DNA sequence can produce major biological consequences commonly manifested in genetic disorders such as sickle cell anemia and β-thalassemia. Herein, the differential behavior of sequential single base substitutions G → A on the quasi-palindromic sequence (d-TGGGGGCCCCA; HPG11) has been explored. A combination of native gel electrophoresis, circular dichroism (CD), and UV-thermal denaturation (Tm) techniques have been used to investigate the structural polymorphism associated with various variants of HPG11 i.e. HPG11A2 to HPG11A5. The CD spectra confirmed that all the HPG11 variants exhibit a hairpin - duplex equilibrium. Oligomer concentration dependence on CD spectra has been correlated with A → B DNA conformational transition. However, as revealed in gel electrophoresis, HPG11A2 → A5 exhibit the formation of a tetramolecular structure (four-way junction) at higher oligomer concentration. UV-melting studies also supported the melting of hairpin, duplex and four-way junction structure. This polymorphism pattern may possibly be significant for DNA-protein recognition, in the process of regulation of LCR in the β-globin gene.
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2
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Bhattacharyya KK, Chatterjee T, Mondal UB. A comprehensive screening program for β-thalassemia and other hemoglobinopathies in the Hooghly District of West Bengal, India, dealing with 21 137 cases. Hemoglobin 2017; 40:396-399. [PMID: 28276872 DOI: 10.1080/03630269.2016.1259169] [Citation(s) in RCA: 2] [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
We here present a report of population screening programs (January 2012-December 2015) conducted by the Thalassemia Control Unit, Imambara Sadar Hospital, Chinsurah, Hooghly in the Hooghly District of West Bengal, India for prevention of thalassemia. We screened β-thalassemia (β-thal) heterozygotes and homozygotes, and Hb E (HBB: c.79G > A)-β-thal compound heterozygotes. Among 21 137 cases, we found 1968 heterozygotes and 192 homozygotes or compound heterozygotes. Results were evaluated with standard hematological analyses including red cell indices, hemoglobin (Hb) typing and quantification. The participants of the screening program were divided into six groups (children, pre-marriage cases, post-marital cases, family members of affected individuals, family members of carriers and pregnant women). While considering the average frequency of carriers, many reports recorded both related individuals (family members of trait and affected individuals) as well as unrelated individuals such as school children and pregnant women. These would have to be considered separately and only the unrelated individuals taken to estimate carrier frequencies in this article that would give more realistic data on carrier frequency of unrelated individuals.
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Affiliation(s)
| | - Tridip Chatterjee
- b Institute of Genetic Medicine and Genomic Science , Kolkata , West Bengal , India
| | - Ujjalendu Bikash Mondal
- a Imambara Sadar Hospital , Thalassaemia Control Unit , Chinsurah, Hooghly , West Bengal , India
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3
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Panja A, Chowdhury P, Chakraborty S, Ghosh TK, Basu A. Cross-Sectional Study for the Detection of Mutations in the Beta-Globin Gene Among Patients with Hemoglobinopathies in the Bengali Population. Genet Test Mol Biomarkers 2017; 21:39-45. [DOI: 10.1089/gtmb.2016.0186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Amrita Panja
- Molecular Biology and Human Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, India
| | - Prosanto Chowdhury
- Peerless Hospital & B.K.Roy Research Centre, Burdwan Medical College and Hospital, Burdwan, India
| | | | - Tapan Kumar Ghosh
- Department of Pathology, Bankura Medical College and Hospital, Bankura, India
| | - Anupam Basu
- Molecular Biology and Human Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, India
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Dehghani H, Ghobakhloo S, Neishabury M. Electromobility Shift Assay Reveals Evidence in Favor of Allele-Specific Binding of RUNX1 to the 5' Hypersensitive Site 4-Locus Control Region. Hemoglobin 2016; 40:236-9. [PMID: 27492765 DOI: 10.1080/03630269.2016.1189931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In our previous studies on the Iranian β-thalassemia (β-thal) patients, we identified an association between the severity of the β-thal phenotype and the polymorphic palindromic site at the 5' hypersensitive site 4-locus control region (5'HS4-LCR) of the β-globin gene cluster. Furthermore, a linkage disequilibrium was observed between this region and XmnI-HBG2 in the patient population. Based on this data, it was suggested that the well-recognized phenotype-ameliorating role assigned to positive XmnI could be associated with its linked elements in the LCR. To investigate the functional significance of polymorphisms at the 5'HS4-LCR, we studied its influence on binding of transcription factors. Web-based predictions of transcription factor binding revealed a binding site for runt-related transcription factor 1 (RUNX1), when the allele at the center of the palindrome (TGGGG(A/G)CCCCA) was A but not when it was G. Furthermore, electromobility shift assay (EMSA) presented evidence in support of allele-specific binding of RUNX1 to 5'HS4. Considering that RUNX1 is a well-known regulator of hematopoiesis, these preliminary data suggest the importance of further studies to confirm this interaction and consequently investigate its functional and phenotypical relevance. These studies could help us to understand the molecular mechanism behind the phenotype modifying role of the 5'HS4-LCR polymorphic palindromic region (rs16912979), which has been observed in previous studies.
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Affiliation(s)
- Hossein Dehghani
- a Genetics Research Center, University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Sepideh Ghobakhloo
- a Genetics Research Center, University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Maryam Neishabury
- a Genetics Research Center, University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
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Chatterjee T, Chakravarty A, Chakravarty S. Population Screening and Prevention Strategies for Thalassemias and other Hemoglobinopathies of Eastern India: Experience of 18,166 cases. Hemoglobin 2015; 39:384-8. [DOI: 10.3109/03630269.2015.1068799] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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6
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Nagar R, Sinha S, Raman R. Genotype-phenotype correlation and report of novel mutations in β-globin gene in thalassemia patients. Blood Cells Mol Dis 2015; 55:10-4. [PMID: 25976460 DOI: 10.1016/j.bcmd.2015.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/27/2015] [Indexed: 11/30/2022]
Abstract
Heterogeneity in thalassemia is due to various modifying factors viz. coinheritance of α-gene defects, abnormal hemoglobin, XmnI polymorphism, variation in repeat sequences present in LCR, and silencer region of the gene. The present work on populations from eastern regions of India was undertaken to study the genetic profile of heterogeneity in thalassemia patients. Mutation analysis in 126 index families revealed the presence of 3 novel mutations: CD2 (-A) in the 1st exon, -42 (C-G), and -223 (T-C) in the promoter region of β-globin gene. The modifying effect of coexisting α-gene defects, and abnormal Hb (HbS) was clearly observed in our study, however ameliorating effect of T allele of XmnI polymorphism was not found. Analysis of the regulatory regions (LCR) exhibited new combinations (CA(15)TA(5) and CA(13)TA(8)) in HS1 region and one (AT)(10)T(3) in (AT)(x)T(y )silencer region. Thus disparate factors, when considered together, were able to explain several of the thalassemic phenotypes, otherwise not explained by the β globin mutations. However, there were still some cases in this group whose molecular origin could not be ascertained. Our findings confirm not only the extensive genotypic and clinical heterogeneity in β thalassemia but also the need to look for more modulators and modifiers to better understand the genotype-phenotype correlation in thalassemia.
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Affiliation(s)
- Rachana Nagar
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sujata Sinha
- Varanasi Regional Thalassemia Welfare Society, Varanasi, India
| | - Rajiva Raman
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
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Chatterjee T, Chakravarty A, Chakravarty S. Mutational spectrum of thalassemias and other hemoglobinopathies in West Bengal, Eastern India. Hemoglobin 2014; 38:405-8. [PMID: 25405918 DOI: 10.3109/03630269.2014.977448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Thalassemia, an autosomal recessive blood disease, shows a variety of clinical expression in terms of asymptomatic to severe blood transfusion dependence. More than 500 alleles have been characterized in or around the β-globin region. Most of the geographical regions have their own characteristic alleles that predominantly circulate within the communities present in that particular region. In this article, we try to throw some light to explore the spectrum of β-thalassemia (β-thal) alleles present in West Bengal, the eastern part of India. This study comprises thalassemia carriers and diseased persons from different districts of West Bengal. We not only explored the complete mutational spectrum of this state but we also tried to fix the critical range of the values of different hematological parameters [Hb A2, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH)] for the heterozygotes or carriers of β-thal with the same mutational background. At the same time, we also tried to evaluate the maximum weighted frequency of these parameters for the heterozygotes or carriers of β-thal with the same mutational background, so that by observing these cut-off values of standard hematological parameters, we were able to predict the carrier or diseased status for mass scale screening and also try to correlate the values of these parameters with different combinations of β-thal mutation-specific alleles that can be more informative in mass scale (carrier) screening.
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Affiliation(s)
- Tridip Chatterjee
- Department of Human Genetics, Institute of Genetic Medicine and Genomic Science , Kolkata, West Bengal , India
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Halder S, Chatterjee T, Chakravarty A, Chakravarty S, Chakrabarti A. Differential Regulation of Plasma Proteins between Members of a Family with Homozygous HbE and HbEβ-thalassemia. THALASSEMIA REPORTS 2014. [DOI: 10.4081/thal.2014.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this report we’ve compared the plasma protein profiles of 4 individuals in a family. Father and the younger son both are hemoglobin (Hb) Eβ-thalassemic {Cod 26 (G-A)/IVS 1- 5 (G-C)}, but the father never requires transfusion, whereas the younger son requires monthly blood transfusion. Mother and the elder son are HbEE {Cod 26 (G-A)/Cod 26 (GA)} without any history of transfusion. Proteomic study was done on the plasma fraction of the blood following ammonium sulphate precipitation. Proteins were separated by 2D-gel electrophoresis, expression of proteins compared by densitometry and proteins identified by tandem MALDI mass spectrometry. Proteins responsible in hemolysis, hypercoagulation and hemoglobin scavenging have shown differential regulation, establishing the relation between the differences in the levels of plasma proteins with the progression of the disease phenotype, manifested in the extent of transfusion dependence of the patient.
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Chatterjee T, Chakravarty A, Chakravarty S. Dilemmas in Considering β-Thalassemia Status in Subjects with Borderline HbA2 Values: A Pilot Study in Eastern India. THALASSEMIA REPORTS 2014. [DOI: 10.4081/thal.2014.2103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Interpreting hemoglobin disorders by high performance liquid chromatography can sometimes deceptive, especially with borderline HbA2 values. It is often problematic, especially in antenatal cases if the partner is a known thalassemia trait. We tested for underlying β-thalassemia mutations in 24 subjects with borderline HbA2 values (between 3.0%-4.0%). Amplification refractory mutation system-polymerase chain reaction was used to detect the five common Indian β-thalassemia mutations: [IVS-I-5 (G>C), Cod 15 (G-A), Cod 8/9 (+G), Fr. 41/42 (-TTCT) and Cod 26 (G-A)]. β-globin gene sequencing was performed if no mutation was detected. β-globin gene defect was not identified in any of the samples. There was no presence of any of the five common mutations in the small cohort. The average value of HbA2 in 24 normal samples was found to be 3.96. The average values for mean cell volume and mean cell hemoglobin (MCH) were found to be 82 and 28.8 pg respectively. Among these 24 normal samples, 13 had MCH below 27 pg and 11 had MCH above 27 pg. On the contrary, one thalassemic family was screened, in which the father of an HbE-β thalassemia patient was found to have HbA2 3.1, being a β-thalassemia carrier. Mutation analysis should be offered to all at-risk couples with borderline HbA2, especially those with values between 3.5% and 4.0% and microcytic hypochromic indices. As, cases with some specific mutational background or clinical condition shows abnormally low HbA2, so mutation screening should be performed in other partner if one partner found to be carrier or patient of thalassemia.
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10
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Endothelial progenitor cells as a possible component of stem cell niche to promote self-renewal of mesenchymal stem cells. Mol Cell Biochem 2014; 397:235-43. [PMID: 25239147 DOI: 10.1007/s11010-014-2191-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/13/2014] [Indexed: 01/19/2023]
Abstract
Stem cells dwell at the "stem cell niche" to accomplish a series of biological processes. The composition of the niche should be determined because the insufficient understanding of this feature limits the development in the study of stem cells. We showed in our study on mesenchymal stem cells (MSCs) that the MSCs first neighbored to CD31(+) cells, which proved to be endothelial progenitor cells (EPCs), and formed a group of cell colony before they exerted their biological functions. It was further proved that EPCs have close interactions with MSCs and promoted the self-renewal of the MSCs in vitro and in vivo. Together with these achievements, we hypothesized that EPCs may be a possible biological component of the MSC stem cell niche and affect the biological processes of MSCs.
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Bhattacharyya DM, Mukhopadhyay A, Basak J. Descriptive profile of β-thalassemia mutations in West Bengal population: a hospital-based study. Int J Hematol 2014; 99:345-53. [DOI: 10.1007/s12185-014-1511-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/08/2014] [Accepted: 01/15/2014] [Indexed: 11/30/2022]
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12
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Neishabury M, Zamani F, Keyhani E, Azarkeivan A, Abedini SS, Eslami MS, Kakroodi ST, Vesiehsari MJ, Najmabadi H. The influence of the BCL11A polymorphism on the phenotype of patients with beta thalassemia could be affected by the beta globin locus control region and/or the Xmn1-HBG2 genotypic background. Blood Cells Mol Dis 2013; 51:80-4. [DOI: 10.1016/j.bcmd.2013.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/20/2013] [Accepted: 02/23/2013] [Indexed: 10/27/2022]
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13
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Dabke P, Colah R, Ghosh K, Nadkarni A. Effect of Cis Acting Potential Regulators in the β Globin Gene Cluster on the Production of HbF in Thalassemia Patients. Mediterr J Hematol Infect Dis 2013; 5:e2013012. [PMID: 23505600 PMCID: PMC3591280 DOI: 10.4084/mjhid.2013.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/10/2013] [Indexed: 11/08/2022] Open
Abstract
The clinical presentation of β-thalassemia intermedia phenotypes are influenced by many factors. The persistence of fetal hemoglobin and several polymorphisms located in the promoters of γ- and β-globin genes are some of them. The aim of this study was to evaluate the combined effect of the -158 Gγ (C→T) polymorphism and of the (AT)x(T)y configuration, as well as their eventual association with elevated levels of HbF in β-thalassemia carriers, β-thalassemia intermedia, β-thalassemia major and normal controls of Indian origin. The -158 Gγ T allele was found to be associated with increased levels of HbF in β thalassemia carriers, and not in wild-type subjects. In the homozygous group, the -158 Gγ T allele was significantly higher in the thalassemia intermedia group (66%) as against the thalassemia major group (21%). The (AT)9(T)5 allele did not show any association with raised HbF levels. However 24% of milder cases showed presence of this allele. This study suggests that two regions of the β globin cluster, whether in cis or in trans to each other, can interact to enhance HbF expression when a β thalassemic determinant is present in heterozygosity and help in amelioration of the severity of the disease in homozygotes.
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Affiliation(s)
- Pooja Dabke
- National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai –4000 12
| | - Roshan Colah
- National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai –4000 12
| | - Kanjaksha Ghosh
- National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai –4000 12
| | - Anita Nadkarni
- National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai –4000 12
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Dabke P, Colah RB, Ghosh K, Nadkarni A. Effect of a group of genetic markers around the 5' regulatory regions of the β globin gene cluster linked to high HbF on the clinical severity of β thalassemia. Blood Cells Mol Dis 2012; 50:156-60. [PMID: 23211376 DOI: 10.1016/j.bcmd.2012.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/30/2012] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
The clinical and hematological course of β thalassemia intermedia is influenced by a number of genetic factors which play a role in increasing fetal haemoglobin levels. Several polymorphisms located in the promoters of β and γ globin gene are involved in influencing the disease severity. Our objective was to study the effect of cis-DNA haplotypes, motifs, or polymorphisms (Pre G γ globin gene haplotypes, Aγ-δ intergenic region haplotypes XmnI and (AT)(x)(T)(y) polymorphisms, β-LCR HS2 and HS3 site motifs) that may contribute to higher HbF levels and a milder clinical course. We found that a combination of T haplotype of the Aγ-δ intergenic region, TAG Pre-Gγ haplotype, presence of the XmnI polymorphism along with the (AT)(9)(T)(5) motif constitutes a topography that co-relates with raised HbF levels which may contribute in ameliorating the disease severity.
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Affiliation(s)
- Pooja Dabke
- National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai 4000 12, India
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Neishabury M, Zamani S, Azarkeivan A, Abedini SS, Darvish H, Zamani F, Najmabadi H. The modifying effect of Xmn1-HBG2 on thalassemic phenotype is associated with its linked elements in the beta globin locus control region, including the palindromic site at 5'HS4. Blood Cells Mol Dis 2011; 48:1-5. [PMID: 22036762 DOI: 10.1016/j.bcmd.2011.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 09/28/2011] [Indexed: 11/24/2022]
Abstract
The core sequence of 5'HS4-beta globin locus control region and Xmn1-HBG2 site were analyzed and compared among 86 thalassemia patients with homozygous or compound heterozygous beta globin gene mutations and 101 normal individuals. Frequency of the G allele in the polymorphic palindromic sequence of 5'HS4 (TGGGG A/G CCCCA) and positive Xmn1-HBG2 profile was significantly higher in thalassemia patients compared to the normal population. Linkage disequilibrium was observed between the G allele and positive Xmn1-HBG2 profile in patient population. Furthermore, dominance of IVSII-1 in the mutation spectrum of the patients enabled us to identify linkage disequilibrium relationships between IVSII-1, positive Xmn1-HBG2 and the G allele at 5'HS4. The frequency of milder clinical phenotype was significantly higher in patients with GG/++ than cases with AA/-- genotypic pattern in 5'HS4/Xmn1-HBG2 loci. These data together with biochemical evidence suggesting a role for the A/G polymorphism at 5'HS4 palindromic site on modifying chromatin structure and in the absence of any evidence from functional studies relating the Xmn1-HBG2 site to the increased gamma chain expression, suggest that the phenotype modifying role long time assigned to Xmn1-HBG2 is possibly played by more functionally potent elements linked to it in LCR.
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Affiliation(s)
- Maryam Neishabury
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Kulkarni GD, Kulkarni SS, Kadakol GS, Kulkarni BB, Kyamangoudar PH, Lakkakula BVKS, Thangaraj K, Shepur TA, Kulkarni ML, Gai PB. Molecular basis of β-thalassemia in Karnataka, India. Genet Test Mol Biomarkers 2011; 16:138-41. [PMID: 21978377 DOI: 10.1089/gtmb.2011.0035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In β-thalassemia, point mutations in the β-globin gene are largely responsible for either decreased or no β-globin synthesis. The β-globin gene has three exons and two introns. The molecular characterization of β-thalassemia is absolutely necessary for carrier screening, for genetic counseling, and to offer prenatal diagnosis. The objective of the present study was to identify the rare mutations in β-globin gene of β-thalassemia patients. We have sequenced the entire β-globin gene in 36 clinically identified thalassemia patients from the Karnataka region using polymerase chain reaction and sequencing. Our analysis revealed 11 β-thalassemia variants. The most common being IVSII-16 G>C, IVSI-5G>C, IVSII-74 T>G, codon 3 (T>C), and Poly A site (T>C). In addition, we have also documented a novel deletion at codon 6 (-CT) (HBB:c.16delCT). These data are useful in future molecular screening of the population for implementing a thalassemia prevention and control program. Further it is found that family studies and comprehensive hematological analyses would provide useful insights for accurate molecular diagnosis of thalassemia phenotype and offers an interesting subject for further investigations in the Indian populations.
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Affiliation(s)
- Gururaj D Kulkarni
- Research Center for DNA Diagnostics, Department of Applied Genetics, Karnatak University, Dharwad, Karnataka, India
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Fernandes AC, Shimmoto MMA, Furuzawa GK, Vicari P, Figueiredo MS. Molecular analysis of β-thalassemia patients: first identification of mutations HBB:c.93-2A>G and HBB:c.114G>A in Brazil. Hemoglobin 2011; 35:358-66. [PMID: 21797703 DOI: 10.3109/03630269.2011.588354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The various clinical phenotypes in β-thalassemias have stimulated the study of genetic factors that could modify the manifestations of these diseases. We examined 21 patients with β-thalassemia (β-thal) in order to identify some genetic modifying factors: β-thalassemia mutations, HBG2:g.-158C>T polymorphism, α-globin gene deletions and (AT)xNz(AT)y motif within the hypersensitive site 2-locus control region (HS2-LCR). In the 42 alleles analyzed, the most frequent mutations observed were HBB:c.92+6T>C (30.9%), HBB:c.118C>T (16.7%), HBB:c.93-21G>A (11.9%) and HBB:c.92+1G>A (4.8%); this finding is in accordance with previous data of the Brazilian population. The other genetic factors analyzed showed no relation with the severity of the disease. For the first time in Brazil, we report HBB:c.93-2A>G and HBB:c.114G>A mutations on the β-globin gene, both in a heterozygous state. This is also the first study to analyze the HS2-LCR in β-thalassemic individuals in the Brazilian population.
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Affiliation(s)
- Andrea Cristina Fernandes
- Disciplina de Hematologia e Hemoterapia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
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Analyzing 5′HS3 and 5′HS4 LCR core regions and NF-E2 in Iranian thalassemia intermedia patients with normal or carrier status for beta-globin mutations. Blood Cells Mol Dis 2011; 46:201-5. [DOI: 10.1016/j.bcmd.2010.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Accepted: 12/07/2010] [Indexed: 11/23/2022]
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Bilgen T, Arikan Y, Canatan D, Yeşilipek A, Keser I. The association between intragenic SNP haplotypes and mutations of the beta globin gene in a Turkish population. Blood Cells Mol Dis 2011; 46:226-9. [DOI: 10.1016/j.bcmd.2011.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/08/2011] [Accepted: 01/09/2011] [Indexed: 10/18/2022]
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20
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Arya V, Agarwal S, Pradhan M. Association of polymorphic pattern of the (AT) × (T)y motif of β-globin gene in North Indian thalassemia patients with variable clinical expression. Indian J Hematol Blood Transfus 2010; 26:21-3. [PMID: 23100997 DOI: 10.1007/s12288-010-0008-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 01/24/2009] [Indexed: 10/19/2022] Open
Abstract
Among the polymorphic genetic markers of the β-globin gene cluster, the (AT) × (T)y motif and a common C→T variation at -158 of the Gγ globin gene were investigate din 20 β-thalassemia IVSI-5 (G→C) homozygous patients with variable clinical manifestation and 10 normal subjects from north India to deduce any association with the co-inherited genetic polymorphism. We found (AT)(7)(T)(7) repeat motif in all the 20 chromosomes of normal subjects and two different sequence configuration(AT)(8)(T)(5), (AT)(9)(T)(5) in the patient group whereas the presence of -158(C→T) Gγ was quite polymorphic. We conclude that polymorphism -158(C→T) Gγ and (AT) × (T)y sequence variation other than (AT)(7)(T)(7) could influence the phenotype by increasing Hb F expression.
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Affiliation(s)
- Vandana Arya
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh India
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Sinha S, Black ML, Agarwal S, Colah R, Das R, Ryan K, Bellgard M, Bittles AH. Profiling β-thalassaemia mutations in India at state and regional levels: implications for genetic education, screening and counselling programmes. THE HUGO JOURNAL 2010; 3:51-62. [PMID: 21119755 DOI: 10.1007/s11568-010-9132-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 11/29/2009] [Accepted: 01/20/2010] [Indexed: 11/30/2022]
Abstract
UNLABELLED Thalassaemia and sickle cell disease have been recognized by the World Health Organization as important inherited disorders principally impacting on the populations of low income countries. To create a national and regional profile of β-thalassaemia mutations in the population of India, a meta-analysis was conducted on 17 selected studies comprising 8,505 alleles and offering near-national coverage for the disease. At the national level 52 mutations accounted for 97.5% of all β-thalassaemia alleles, with IVSI-5(G>C) the most common disease allele (54.7%). Population stratification was apparent in the mutation profiles at regional level with, for example, the prevalence of IVSI-5(G>C) varying from 44.8% in the North to 71.4% in the East. A number of major mutations, such as Poly A(T>C), were apparently restricted to a particular region of the country, although these findings may in part reflect the variant test protocols adopted by different centres. Given the size and genetic complexity of the Indian population, and with specific mutations for β-thalassaemia known to be strongly associated with individual communities, comprehensive disease registries need to be compiled at state, district and community levels to ensure the efficacy of genetic education, screening and counselling programmes. At the same, time appropriately designed community-based studies are required as a health priority to correct earlier sampling inequities which resulted in the under-representation of many communities, in particular rural and socioeconomically under-privileged groups. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11568-010-9132-3) contains supplementary material, which is available to authorized users.
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beta-Thalassaemia Major in a Spanish Patient due to a Compound Heterozygosity for CD39 C --> T/-28 A --> C. Adv Hematol 2009; 2009:476342. [PMID: 19960060 PMCID: PMC2778560 DOI: 10.1155/2009/476342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 02/01/2009] [Accepted: 06/23/2009] [Indexed: 11/26/2022] Open
Abstract
A Spanish male patient with β-thalassaemia major was studied. Compound heterozygosity was found for one of the most common β-globin gene mutations in the Spanish population (codon 39 C → T) and for a mutation in the TATA box element of the β-globin gene promoter (−28 A → C mutation). To our knowledge this is the first report of a CD39 C → T and −28 A → C change association and the first report of the −28 A → C substitution in a Spanish patient.
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Sen R, Chakrabarti S, Sengupta B, De M, Haldar A, Poddar S, Gajra B, Talukder G, Sengupta S. α-Thalassemia Among Tribal Populations of Eastern India. Hemoglobin 2009; 29:277-80. [PMID: 16370488 DOI: 10.1080/03630260500310711] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Five hundred and thirteen unrelated subjects belonging to various tribes of West Bengal, Arunachal Pradesh and Assam in Eastern India, were screened for the presence of alpha-thalassemia (thal) gene deletion(s) as a possible cause of unexplained anemia (Hb < 11 g/dL and/or MCH <28 pg, MCV < 78 fL). As reported earlier, beta-globin gene mutant alleles were found with a frequency of up to 20% in some tribes. In the present study, alpha-globin gene deletion alleles were found in 18% of subjects from West Bengal, 3.9% from Arunachal Pradesh and 3.84% from Assam tribesmen. Coexistence of alpha- and beta-globin gene abnormalities was observed in up to 18% of some tribal groups. The high inbreeding rate and lack of appropriate medical care make these populations particularly vulnerable.
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Affiliation(s)
- Rinini Sen
- Thalassaemia Counselling Unit, Vivekananda Institute of Medical Sciences, 99 Sarat Bose Road, Kolkata 700026, India.
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Eshghi P, Zadeh-Vakili A, Rashidi A, Miri-Moghadam E. An Unusually Frequent β-Thalassemia Mutation in an Iranian Province. Hemoglobin 2009; 32:387-92. [DOI: 10.1080/03630260701758932] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Papachatzopoulou A, Kourakli A, Makropoulou P, Kakagianne T, Sgourou A, Papadakis M, Athanassiadou A. Genotypic heterogeneity and correlation to intergenic haplotype within high HbF beta-thalassemia intermedia. Eur J Haematol 2006; 76:322-30. [PMID: 16519704 DOI: 10.1111/j.1600-0609.2005.00618.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES A molecular study was carried out of beta-thalassemia intermedia patients, compound heterozygotes for mutations usually found in beta-thalassemia major, with high levels of HbF in the absence of hereditary persistence of fetal hemoglobin (HPFH) syndrome. Our objective was to locate cis-DNA structures, DNA haplotypes, motifs, or polymorphisms that may correlate with the presence of high HbF. METHODS Allele-specific oligonucleotide (ASO) hybridization was used for the detection of mutations and restriction fragment length polymorphism (RFLP) analysis and automated sequencing for motifs, haplotypes, and polymorphisms. Southern blot was used for investigating alpha-thalassemia and/or alpha- or gamma-globin genes triplications. RNA extracted from burst forming unit-erythroid (BFU-e) colonies of peripheral blood mononuclear cell cultures was used in reverse transcriptase-polymerase chain reaction (RT-PCR) to investigate intergenic transcription. RESULTS We established that (i) the combination: T haplotype of the Agamma-delta-globin intergenic region, the motif (TA)9N10(TA)10 in the HS2 site of locus control region (LCR), and TAG pre-Ggamma haplotype is sufficient but not necessary for high HbF, (ii) the genetic determinant(s) for high HbF involves an element associated with this combination and must be present in the specific R haplotype occurring in beta-thalassemia intermedia and (iii) the genetic determinant(s) for high HbF does not involve the abolition of intergenic transcription in the Agamma-delta-globin intergenic region. CONCLUSIONS The genetic determinant(s) of high HbF in the absence of HPFH is linked to intergenic haplotype T and does not disrupt intergenic transcription.
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Zhang L, Dang F, Kaji N, Baba Y. Fast extraction, amplification and analysis of genes from human blood. J Chromatogr A 2005; 1106:175-80. [PMID: 16337635 DOI: 10.1016/j.chroma.2005.10.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 10/21/2005] [Accepted: 10/27/2005] [Indexed: 11/30/2022]
Abstract
In order to shorten the time spent on the sample preparation for gene analysis, a novel method was proposed through the combination of fast DNA extraction and purification by Generation capture disk, amplification by capillary polymerase chain reaction, and confirmation of amplification products by microchip electrophoresis. With this method, 3 microL blood was enough to obtain adequate target fragments in human genes. Under the optimal conditions in each step, the sample preparation for eight fragments in beta-globin gene and four fragments in ras gene could be finished within 20 min. Since all the experiments were performed on commercial instruments, this method showed a wide range of applicability. In addition, other advantages such as fast speed and low consumption of samples were demonstrated. All these merits proved that such a combination method was of great potential for the clinical diagnostics.
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Affiliation(s)
- Lihua Zhang
- Department of Molecular and Pharmaceutical Biotechnology, Graduate School of Pharmaceutical Sciences, The University of Tokushima, CREST, Japan Science and Technology Corporation (JST), Tokushima 770-8505, Japan
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Bandyopadhyay S, Mondal BC, Sarkar P, Chandra S, Das MK, Dasgupta UB. Two beta-globin cluster-linked polymorphic loci in thalassemia patients of variable levels of fetal hemoglobin. Eur J Haematol 2005; 75:47-53. [PMID: 15946310 DOI: 10.1111/j.1600-0609.2005.00416.x] [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: 11/30/2022]
Abstract
OBJECTIVE To correlate different polymorphisms of the beta-globin cluster with fetal hemoglobin (HbF) level in beta-thalassemia and E-beta thalassemia patients. METHODS Fifteen thalassemia patients, seven with high HbF and not requiring transfusion, eight with lower HbF and requiring transfusion were studied for beta-globin mutation, concurrent inheritance of alpha-thalassemia, RFLP haplotype, a C-->T polymorphism at -158 of Ggamma and configuration of an (AT)(x)T(y) motif at -540 of beta-globin gene. RESULTS Senegal 5'beta-haplotype and the polymorphism at -158 of G(gamma) was (P = 0.063) was linked to the high-HbF phenotype but the (AT)(9)T(5) configuration of the (AT)(x)T(y) motif was not (P = 0.6). Study of 30 chromosomes revealed 7 different configurations of the (AT)(x)T(y) motif. Association of these motifs with specific beta-globin mutations of this region has also been determined. CONCLUSION The senegal haplotype and the polymorphism at -158 of G(gamma) was linked to the high-HbF phenotype.
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Affiliation(s)
- Sanmay Bandyopadhyay
- Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, 92 APC Road, Kolkata 700009, India
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Dang F, Tabata O, Kurokawa M, Ewis AA, Zhang L, Yamaoka Y, Shinohara S, Shinohara Y, Ishikawa M, Baba Y. High-Performance Genetic Analysis on Microfabricated Capillary Array Electrophoresis Plastic Chips Fabricated by Injection Molding. Anal Chem 2005; 77:2140-6. [PMID: 15801748 DOI: 10.1021/ac0485031] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have developed a novel technique for mass production of microfabricated capillary array electrophoresis (mu-CAE) plastic chips for high-speed, high-throughput genetic analysis. The mu-CAE chips, containing 10 individual separation channels of 50-microm width, 50-microm depth, and a 100-microm lane-to-lane spacing at the detection region and a sacrificial channel network, were fabricated on a poly(methyl methacrylate) substrate by injection molding and then bonded manually using a pressure-sensitive sealing tape within several seconds at room temperature. The conditions for injection molding and bonding were carefully characterized to yield mu-CAE chips with well-defined channel and injection structures. A CCD camera equipped with an image intensifier was used to monitor simultaneously the separation in a 10-channel array with laser-induced fluorescence detection. High-performance electrophoretic separations of phiX174 HaeIII DNA restriction fragments and PCR products related to the human beta-globin gene and SP-B gene (the surfactant protein B) have been demonstrated on mu-CAE plastic chips using a methylcellulose sieving matrix in individual channels. The current work demonstrated greatly simplified the fabrication process as well as a detection scheme for mu-CAE chips and will bring the low-cost mass production and application of mu-CAE plastic chips for genetic analysis.
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Affiliation(s)
- Fuquan Dang
- Single-Molecule Bioanalysis Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Hayashi-cho 2217-14, Takamatsu 761-0395, Japan.
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Bashyam MD, Bashyam L, Savithri GR, Gopikrishna M, Sangal V, Devi ARR. Molecular genetic analyses of β-thalassemia in South India reveals rare mutations in the β-globin gene. J Hum Genet 2004; 49:408-413. [PMID: 15278762 DOI: 10.1007/s10038-004-0169-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 05/06/2004] [Indexed: 10/26/2022]
Abstract
beta-Thalassemia is the most prevalent single-gene disorder. Since no viable forms of treatment are available, the best course is prevention through prenatal diagnosis. In the present study, the prevalence of beta-thalassemia was extensively investigated in the South Indian population, especially from the state of Andhra Pradesh. Screening for causal mutations was carried out on genomic DNA isolated from patient blood samples by using the routine reverse dot blot (RDB) and amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) techniques. DNA sequencing was performed wherever necessary. Among the nine mutations identified, four, including IVS-1-5 (G-C) (IVS1+5G>T), codon 41/42 (-TTCT) (c.124_127delTTCT), codon 15 (G-A) (c.47G>A), and HbS (sickle mutation) (c.20A>T) mutations, accounted for about 98% of the total positive cases. Two mutations viz. codon 8/9 (+G) (c.27_28insG) and HbE (codon 26 G-A) (c.79G>A) exhibited a very low frequency of occurrence, whereas the IVS-1-1 (G-T) (IVS1+1G>T) and the 619 bp deletion (c.366_494del) mutations were absent. We also identified certain rare mutations during the diagnostic evaluation. Gene sequencing confirmed the codon 30 (G-C) (c.92G>C) mutation and the rare codon 5 (-CT) (c.17_18delCT) and IVS-II-837 (T-G) (IVSII-14T>G) mutations. This is the first report of the IVS II 837 mutation in the Indian population. We also report a novel diagnostic application during RDB-based screening for the detection of the (c.92G>C) mutations. Such a comprehensive mutation screening is essential for prenatal diagnosis of beta-thalassemia and control of this highly prevalent monogenic disorder in the Indian population.
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Affiliation(s)
- Murali Dharan Bashyam
- National Genomics and Transcriptomics Facility, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
- Department of Pathology, CCSR 3240, 269 Campus Drive, Stanford University School of Medicine, Stanford, CA, 94305-5176, USA
| | - Leena Bashyam
- Diagnostics division, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
- LSRA, Microbiology and Immunology, Fairchild D327, 299 Campus Drive, Stanford University School of Medicine, Stanford, CA, 94305-5124, USA
| | - Gorinabele R Savithri
- Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
| | - Munimanda Gopikrishna
- National Genomics and Transcriptomics Facility, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
| | - Vartul Sangal
- National Genomics and Transcriptomics Facility, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India
| | - Akela Radha Rama Devi
- Diagnostics division, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, 500076, India.
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Bandyopadhyay A, Bandyopadhyay S, Basak J, Mondal BC, Sarkar AA, Majumdar S, Das MK, Chandra S, Mukhopadhyay A, Sanghamita M, Ghosh K, Dasgupta UB. Profile of ?-thalassemia in eastern India and its prenatal diagnosis. Prenat Diagn 2004; 24:992-6. [PMID: 15614841 DOI: 10.1002/pd.1049] [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]
Abstract
OBJECTIVE To control the birth of thalassemic children in India. METHODS Mutations present in the population of eastern India and in carrier parents seeking prenatal diagnosis were detected by the PCR-based technique of ARMS (amplification refractory mutation system) or gap-PCR. To screen for maternal tissue contamination in CVS, haplotypes associated with the beta-globin gene clusters were constructed using six polymorphic restriction sites. Prenatal diagnosis was accomplished by checking presence of parental mutation in the DNA from chorionic villus sampling (CVS) collected at 8 to 10 weeks' gestation by appropriate technique. RESULTS Six hundred and fifty (650) unrelated beta-thalassemia chromosomes were screened for 11 common mutations to characterize the mutation distribution in this population. Starting from early 2000, 63 families from different parts of West Bengal and from surrounding areas have been offered prenatal counseling for beta-thalassemia. CONCLUSION The population of this region is conscious and willing to accept prenatal diagnosis as a means of control of thalassemia.
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Affiliation(s)
- Aditi Bandyopadhyay
- Department of Biophysics, Molecular Biology and Genetics, University of Calcutta, 92 A.P.C. Road, Kolkata-700 009, India
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Kaushik M, Kukreti R, Grover D, Brahmachari SK, Kukreti S. Hairpin-duplex equilibrium reflected in the A-->B transition in an undecamer quasi-palindrome present in the locus control region of the human beta-globin gene cluster. Nucleic Acids Res 2003; 31:6904-15. [PMID: 14627823 PMCID: PMC290256 DOI: 10.1093/nar/gkg887] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 09/24/2003] [Accepted: 10/09/2003] [Indexed: 11/12/2022] Open
Abstract
Our recent work on an A-->G single nucleotide polymorphism (SNP) at the quasi-palindromic sequence d(TGGGG[A/G]CCCCA) of HS4 of the human beta-globin locus control region in an Indian population showed a significant association between the G allele and the occurrence of beta-thalassemia. Using UV-thermal denaturation, gel assay, circular dichroism (CD) and nuclease digestion experiments we have demonstrated that the undecamer quasi- palindromic sequence d(TGGGGACCCCA) (HPA11) and its reported polymorphic (SNP) version d(TGG GGGCCCCA) (HPG11) exist in hairpin-duplex equilibria. The biphasic nature of the melting profiles for both the oligonucleotides persisted at low as well as high salt concentrations. The HPG11 hairpin showed a higher T(m) than HPA11. The presence of unimolecular and bimolecular species was also shown by non-denaturating gel electrophoresis experiments. The CD spectra of both oligonucleotides showed features of the A- as well as B-type conformations and, moreover, exhibited a concentration dependence. The disappearance of the 265 nm positive CD signal in an oligomer concentration-dependent manner is indicative of an A-->B transition. The results give unprecedented insight into the in vitro structure of the quasi-palindromic sequence and provide the first report in which a hairpin-duplex equilibrium has been correlated with an A-->B interconversion of DNA. The nuclease-dependent degradation suggests that HPG11 is more resistant to nuclease than HPA11. Multiple sequence alignment of the HS4 region of the beta-globin gene cluster from different organisms revealed that this quasi-palindromic stretch is unique to Homo sapiens. We propose that quasi-palindromic sequences may form stable mini- hairpins or cruciforms in the HS4 region and might play a role in regulating beta-globin gene expression by affecting the binding of transcription factors.
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Affiliation(s)
- Mahima Kaushik
- Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India
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