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Pena R, Lopes P, Gaspar G, Miranda A, Faustino P. Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7 kb α-thalassemia deletion. Mol Biol Rep 2024; 51:612. [PMID: 38704770 PMCID: PMC11070386 DOI: 10.1007/s11033-024-09530-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The α-Major Regulatory Element (α-MRE), also known as HS-40, is located upstream of the α-globin gene cluster and has a crucial role in the long-range regulation of the α-globin gene expression. This enhancer is polymorphic and several haplotypes were identified in different populations, with haplotype D almost exclusively found in African populations. The purpose of this research was to identify the HS-40 haplotype associated with the 3.7 kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and determine its ancestry and influence on patients' hematological phenotype. METHODS AND RESULTS We selected 111 Portuguese individuals previously analyzed by Gap-PCR to detect the presence of the -α3.7del: 50 without the -α3.7del, 34 heterozygous and 27 homozygous for the -α3.7del. The HS-40 region was amplified by PCR followed by Sanger sequencing. Four HS-40 haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between individuals with and without the -α3.7del, being haplotype D and genotype AD the most prevalent in patients with this deletion in homozygosity. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are separated from these and found more closely related to the African population. CONCLUSION This study revealed for the first time an association of the HS-40 haplotype D with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have clinical importance as in vitro analysis of haplotype D showed a decrease in its enhancer activity on α-globin gene.
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Affiliation(s)
- Rita Pena
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Pedro Lopes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Gisela Gaspar
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Armandina Miranda
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Paula Faustino
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal.
- Grupo Ecogenética e Saúde Humana, Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal.
- Laboratório Associado TERRA, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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Galactéros F. Le globule rouge drépanocytaire. Données génétiques et structurelles. Rev Med Interne 2023; 44:4S2-4S6. [PMID: 38049243 DOI: 10.1016/s0248-8663(23)01302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Sickle cell disease is syndromic, associating a hemolytic anemia, a vaso-obstructive vascular disease, and an infectious risk linked to the precocity of the splenic function loss. The willingly hyperacute and potentially fatal character of the two last elements of the pathophysiologic syndrome, has, quite rightly, focused the therapeutic researches on them. Great success in those two domains have allowed a very important gain in life expectancy. However, chronic progressive organ dysfunction began to appear in older than 25 years-old patients. It concerns mainly renal, hepatic, cardiac functions and pulmonary arterial pressure and may lead to organ failure and premature death. Since some 25 years, the clinical research demonstrated an association between such complications and intravascular hemolytic rate, and it turned to a causative relationship. This present paper try to summarize the actual knowledge on the structural and genetic aspects of sickle cell anemia hemolysis. © 2023 Société nationale française de médecine interne (SNFMI). Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- F Galactéros
- Unité des maladies génétiques du globule rouge (UMGGR), médecine interne, GHU Henri-Mondor AP-HP et U-PEC, France.
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3
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Luo S, Chen X, Zeng D, Tang N, Yuan D, Liu B, Chen L, Zhong Q, Li J, Liu Y, Chen J, Wang X, Yan T. Detection of four rare thalassemia variants using Single-molecule realtime sequencing. Front Genet 2022; 13:974999. [PMID: 36159974 PMCID: PMC9493964 DOI: 10.3389/fgene.2022.974999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --27.3/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α3.7α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination.
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Affiliation(s)
- Shiqiang Luo
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Xingyuan Chen
- Department of Laboratory Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Academy of Medical Sciences, Nanning, China
| | - Dingyuan Zeng
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Ning Tang
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Dejian Yuan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Bailing Liu
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Lizhu Chen
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Qingyan Zhong
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Jianping Chen
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Xiaoyuan Wang
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
| | - Tizhen Yan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
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4
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Alimohammadi-Bidhendi S, Azadmehr S, Razipour M, Zeinali S, Eslami M, Davoudi-Dehaghani E. Regulatory Mutation Study in Cases with Unsolved Hypochromic Microcytic Anemia and α-Major Regulatory Element Haplotype Analysis in Iran. Hemoglobin 2021; 45:37-40. [PMID: 33775199 DOI: 10.1080/03630269.2021.1882482] [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
α-Thalassemia (α-thal) is an inherited blood disorder with different clinical manifestations. Although genetic causes of anemia are identified routinely in the majority of α-thal cases, a pathogenic variant in a few cases remains undiagnosed. In this study, some reported regulatory mutations have been investigated in five unsolved α-thal carriers. α-Major regulatory element (α-MRE) haplotype analysis has also been performed in Iran for the first time. Four regions, including the HBA2 core promoter, the highly conserved sequence of hypersensitive-40 (HS-40), a region containing regulatory single nucleotide polymorphism (SNP) CR062116, and a region containing rs7203560, were screened for changes by Sanger sequencing in a total of five unsolved suspected α-thal carriers. The frequencies of α-MRE haplotypes B and C were also determined in control samples with normal hematological indices. No pathogenic variant was found in the investigated regions. Haplotype frequencies observed for B and C haplotypes fell into the range of frequencies observed in previous studies. The investigated genotypes in the control group were in the Hardy-Weinberg equilibrium. This study can provide evidence that there is no association between the B haplotype and microcytic hypochromic anemia. The cause of anemia remains a mystery in our unsolved cases, which demonstrates the need for further studies on the causes of hypochromic microcytic anemia in individuals with intact α- and β-globin genes without iron deficiency.
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Affiliation(s)
- Sara Alimohammadi-Bidhendi
- Department of Genetics, Faculty of Advanced Technologies in Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sarah Azadmehr
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Genetics, Faculty of Basic Sciences, Shahr-e Rey, Payame Noor University, Tehran, Iran
| | - Masoumeh Razipour
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Medical Genetics Laboratory of Dr. Zeinali, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Maryam Eslami
- Departments of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran.,Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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5
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Soler AM, Piellusch BF, da Silveira L, Pedroso GA, López P, Savio E, Sonati MDF, da Luz J. Alpha thalassemia and alpha-MRE haplotypes in Uruguayan patients with microcytosis and hypochromia without anemia. Genet Mol Biol 2021; 44:e20200399. [PMID: 33769430 PMCID: PMC7995682 DOI: 10.1590/1678-4685-gmb-2020-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Alpha thalassemia is the most common genetic disorder across the world, being the α-3.7 deletion the most frequent mutation. In order to analyze the spectrum and origin of alpha thalassemia mutations in Uruguay, we obtained a sample of 168 unrelated outpatients with normal hemoglobin levels with microcytosis and hypochromia from two cities: Montevideo and Salto. The presence of α-thalassemia mutations was investigated by gap-PCR, restriction endonucleases analysis and HBA2 and HBA1 genes sequencing, whereas the alpha-MRE haplotypes were investigated by sequencing. We found 55 individuals (32.7%) with α-thalassemia mutations, 51(30.4%) carrying the -α3.7 deletion, one with the -α4.2 deletion and three having the rare punctual mutation HBA2:c.-59C>T. Regarding alpha-MRE analysis, we observed a significant higher frequency of haplotype D, characteristic of African populations, in the sample with the -α3.7 deletion. These results show that α-thalassemia mutations are an important determinant of microcytosis and hypochromia in Uruguayan patients with microcytosis and hypochromia without anemia, mainly due to the -α3.7 deletion. The alpha-MRE haplotypes and the α-thalassemia mutations spectrum suggest a predominant, but not exclusive, African origin of these mutations in Uruguay.
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Affiliation(s)
- Ana María Soler
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Bruna Facanali Piellusch
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Lorena da Silveira
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
| | - Gisele Audrei Pedroso
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Pablo López
- Universidad de la República (UdelaR), Facultad de Medicina, Hospital de Clínicas Manuel Quintela, Departamento de Laboratorio de Patología Clínica, Montevideo, Uruguay
| | - Enrique Savio
- Administración de los Servicios de Salud del Estado (ASSE), Hospital Departamental de Salto, Servicio de Laboratorio Clínico, Salto, Uruguay
| | - María de Fatima Sonati
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patología Clínica, Campinas, SP, Brazil
| | - Julio da Luz
- Universidad de la República (UdelaR), Centro Universitario Regional (CENUR) Litoral Norte, Departamento de Ciencias Biológicas, Laboratorio de Genética Molecular Humana, Salto, Uruguay
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Milton JN, Rooks H, Drasar E, McCabe EL, Baldwin CT, Melista E, Gordeuk VR, Nouraie M, Kato GR, Minniti C, Taylor J, Campbell A, Luchtman-Jones L, Rana S, Castro O, Zhang Y, Thein SL, Sebastiani P, Gladwin MT, Steinberg MH. Genetic determinants of haemolysis in sickle cell anaemia. Br J Haematol 2013; 161:270-8. [PMID: 23406172 PMCID: PMC4129543 DOI: 10.1111/bjh.12245] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/29/2012] [Indexed: 12/31/2022]
Abstract
Haemolytic anaemia is variable among patients with sickle cell anaemia and can be estimated by reticulocyte count, lactate dehydrogenase, aspartate aminotransferase and bilirubin levels. Using principal component analysis of these measurements we computed a haemolytic score that we used as a subphenotype in a genome-wide association study. We identified in one cohort and replicated in two additional cohorts the association of a single nucleotide polymorphism in NPRL3 (rs7203560; chr16p13·3) (P = 6·04 × 10(-07) ). This association was validated by targeted genotyping in a fourth independent cohort. The HBA1/HBA2 regulatory elements, hypersensitive sites (HS)-33, HS-40 and HS-48 are located in introns of NPRL3. Rs7203560 was in perfect linkage disequilibrium (LD) with rs9926112 (r(2) = 1) and in strong LD with rs7197554 (r(2) = 0·75) and rs13336641 (r(2) = 0·77); the latter is located between HS-33 and HS-40 sites and next to a CTCF binding site. The minor allele for rs7203560 was associated with the -∝(3·7) thalassaemia gene deletion. When adjusting for HbF and ∝ thalassaemia, the association of NPRL3 with the haemolytic score was significant (P = 0·00375) and remained significant when examining only cases without gene deletion∝ thalassaemia (P = 0·02463). Perhaps by independently down-regulating expression of the HBA1/HBA2 genes, variants of the HBA1/HBA2 gene regulatory loci, tagged by rs7203560, reduce haemolysis in sickle cell anaemia.
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Affiliation(s)
| | - Helen Rooks
- King’s College School of Medicine, King’s College London, London, UK
| | - Emma Drasar
- King’s College School of Medicine, King’s College London, London, UK
- Molecular Haematology, King’s College London, London, UK
| | | | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA
| | - Efi Melista
- Center for Human Genetics, Boston University, Boston, MA
| | | | - Mehdi Nouraie
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Gregory R. Kato
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Caterina Minniti
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - James Taylor
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Andrew Campbell
- Pediatric Hematology Oncology, University of Michigan, Ann Arbor, MI
| | - Lori Luchtman-Jones
- Hematology, Children’s National Medical Center, Howard University, Washington, DC
| | - Sohail Rana
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Oswaldo Castro
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
- Center For Sickle Cell Disease, Howard University, Washington, DC
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Swee Lay Thein
- King’s College School of Medicine, King’s College London, London, UK
- Molecular Haematology, King’s College London, London, UK
| | | | - Mark T. Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Martin H. Steinberg
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA
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Suemasu C, Kimura E, Oliveira D, Bezerra M, Araújo A, Costa F, Sonati M. Characterization of alpha thalassemic genotypes by multiplex ligation-dependent probe amplification in the Brazilian population. Braz J Med Biol Res 2011; 44:16-22. [DOI: 10.1590/s0100-879x2010007500144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/03/2010] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | - A.S. Araújo
- Fundação de Hematologia e Hemoterapia de Pernambuco, Brasil
| | - F.F. Costa
- Universidade Estadual de Campinas, Brasil
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Ribeiro D, Zaccariotto T, Santos M, Costa F, Sonati M. Influence of the polymorphisms of the α-major regulatory element HS-40 on in vitro gene expression. Braz J Med Biol Res 2009; 42:783-6. [DOI: 10.1590/s0100-879x2009005000014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 05/07/2009] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | - F.F. Costa
- Universidade Estadual de Campinas, Brasil
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9
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Higgs DR, Wood WG. Long-range regulation of ?? globin gene expression during erythropoiesis. Curr Opin Hematol 2008; 15:176-83. [DOI: 10.1097/moh.0b013e3282f734c4] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Chen L, Lu S, Ram J. Compressed pattern matching in DNA sequences. PROCEEDINGS. IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE 2006:62-8. [PMID: 16448000 DOI: 10.1109/csb.2004.1332418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose derivative Boyer-Moore (d-BM), a new compressed pattern matching algorithm in DNA sequences. This algorithm is based on the Boyer-Moore method, which is one of the most popular string matching algorithms. In this approach, we compress both DNA sequences and patterns by using two bits to represent each A, T, C, G character. Experiments indicate that this compressed pattern matching algorithm searches long DNA patterns (length > 50) more than 10 times faster than the exact match routine of the software package Agrep, which is known as the fastest pattern matching tool. Moreover, compression of DNA sequences by this method gives a guaranteed space saving of 75%. In part the enhanced speed of the algorithm is due to the increased efficiency of the Boyer-Moore method resulting from an increase in alphabet size from 4 to 256.
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Harteveld CL, Voskamp A, Phylipsen M, Akkermans N, den Dunnen JT, White SJ, Giordano PC. Nine unknown rearrangements in 16p13.3 and 11p15.4 causing alpha- and beta-thalassaemia characterised by high resolution multiplex ligation-dependent probe amplification. J Med Genet 2005; 42:922-31. [PMID: 15894596 PMCID: PMC1735959 DOI: 10.1136/jmg.2005.033597] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Approximately 80% of the alpha- and 10% of the beta-thalassaemias are caused by genomic deletions involving the alpha- and beta-globin gene clusters on chromosomes 16p13.3 and 11p15.5, respectively. Gap-PCR, Southern blot analysis, and fluorescent in situ hybridisation are commonly used to identify these deletions; however, many deletions go undetected using conventional techniques. METHODS Patient samples for which no abnormalities had been found using conventional DNA techniques were analysed by a three colour multiplex ligation-dependent probe amplification assay. Two sets of 35 and 50 probes, covering a region of 700 kb of the alpha- and 500 kb of the beta-globin gene cluster, respectively, were designed to detect rearrangements in the alpha- and beta-globin gene clusters. RESULTS In 19 out of 38 patient samples, we found 11 different alpha-thalassaemia deletions, six of which were not previously described. Two novel deletions leaving the alpha-globin gene cluster intact were found to cause a complete downregulation of the downstream alpha-genes. Similarly, 31 out of 51 patient samples were found to carry 10 different deletions involving the beta-globin gene cluster, three of which were not previously described. One involves the deletion of the locus control region leaving the beta-globin gene cluster intact. CONCLUSIONS These deletions, which are not easily detected by conventional techniques, may have clinical implications during pregnancy ranging from mild to life threatening microcytic haemolytic anaemia in neonates. The approach as described here is a rapid and sensitive method for high resolution analysis of the globin gene clusters and for any region of the genome.
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Affiliation(s)
- C L Harteveld
- Center of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands.
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