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Sinha S, Dutta AK, Bhattacharya P, Bhattacharya S, Das MK. Spectrum of Rare and Novel Indel Mutations Responsible for β Thalassemia in Eastern India. Indian J Clin Biochem 2024; 39:207-213. [PMID: 38577149 PMCID: PMC10987419 DOI: 10.1007/s12291-022-01098-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 01/04/2023]
Abstract
There is limited data available regarding the clinical utility of routine molecular diagnosis of β Thalassaemia in addition to HPLC-based screening in low resource settings. The current study highlights the caveats of an HPLC-based screening compared to the inclusion of genetic confirmation as a second-tier test and its implications in terms of genotype-phenotype correlation. A prospective, institution-based, observational study was conducted at the Department of Paediatric Medicine, including 103 children aged up to 12 years. Five common mutations for β Thalassemia and the HbE mutation in the HBB gene were tested by a two-tiered approach using multiplex ARMS PCR and PCR RFLP methods respectively. Sanger sequencing of all three exons of the HBB gene was performed in all negative cases. Sequencing revealed many rare pathogenic mutations like c.316-106 C > G (dbSNP: 34,690,599); Hb Kairouan (c.92G > C); c.33 C > A (dbSNP rs35799536); c.47G > A (dbSNP rs63750783); c.51delC (HbVar ID 799); c.[93-2 A > C] and c.118 C > T (HbVar ID 845). We detected a novel Pathogenic M_000518.5(HBB):c.164_168delinsGGCATCA (p.Val55fs) mutation in a heterozygous state which was reported in the ClinVar database with accession ID VCV000590977.2. We also encountered several cases of silent carrier on HPLC and de novo occurrence of mutation. We conclude that the multiplex touchdown ARMS PCR methodology employed in the present study provides a low-cost solution for molecular diagnostics of Β Thalassaemia. The problem of silent carriers in HPLC is significant enough to rethink if we need supplemental genetic testing in the couple when one of the partners is a carrier. Supplementary Information The online version contains supplementary material available at 10.1007/s12291-022-01098-w.
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Affiliation(s)
- Sajan Sinha
- Department of Paediatrics, IPGME&R and SSKM Hospital, Kolkata, India
| | - Atanu Kumar Dutta
- Department of Biochemistry, All India Institute of Medical Sciences, Second Floor, Medical College Block, NH - 34 Connector Basantapur, Saguna, 741245 Kalyani, West Bengal India
| | | | | | - Mrinal Kanti Das
- Department of Paediatrics, IPGME&R and SSKM Hospital, Kolkata, India
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Kabir T, Anwar S, Mourosi JT, Akter S, Hosen MJ. α- and β-Globin Gene Mutations in Individuals with Hemoglobinopathies in the Chattogram and Sylhet Regions of Bangladesh. Hemoglobin 2023; 47:3-10. [PMID: 36890736 DOI: 10.1080/03630269.2023.2166526] [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: 03/10/2023]
Abstract
Hemoglobinopathies, including α- and β-thalassemias and sickle cell disease, are among the most widely disseminated hereditary blood disorders worldwide. Bangladesh is considered a hotspot for hemoglobinopathies, and these diseases cause a significant health concern in the country. However, the country has a dearth of knowledge on the molecular etiology and carrier frequency of thalassemias, primarily due to a lack of diagnostic facilities, limited access to information, and the absence of efficient screening programs. This study sought to investigate the spectrum of mutations underlying hemoglobinopathies in Bangladesh. We developed a set of polymerase chain reaction (PCR)-based techniques to detect mutations in α- and β-globin genes. We recruited 63 index subjects with previously diagnosed thalassemia. Along with age- and sex-matched control subjects, we assessed several hematological and serum indices and genotyped them using our PCR-based methods. We identified that parental consanguinity was associated with the occurrence of these hemoglobinopathies. Our PCR-based genotyping assays identified 23 HBB genotypes, with the codons 41/42 (-TTCT) (HBB: c.126_129delCTTT) mutation leading the spectrum. We also observed the presence of cooccurring HBA conditions, of which the participants were not aware. All index participants in this study were on iron chelation therapies, yet we found they had very high serum ferritin (SF) levels, indicating inefficient management of the individuals undergoing such treatments. Overall, this study provides essential information on the hemoglobinopathy mutation spectrum in Bangladesh and highlights the need for nationwide screening programs and an integrated policy for diagnosing and managing individuals with hemoglobinopathies.
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Affiliation(s)
- Tamanna Kabir
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Saeed Anwar
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Jarin Taslem Mourosi
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Shanjida Akter
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mohammad Jakir Hosen
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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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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Vuong VVH, Tran TH, Nguyen PD, Thi NN, Le Thi P, Minh Nguyet DT, Nguyen MH, Bui TH, Ta TV, Tran VK. Feasibility of combining short tandem repeats (STRs) haplotyping with preimplantation genetic diagnosis (PGD) in screening for beta thalassemia. PLoS One 2022; 17:e0278539. [PMID: 36476827 PMCID: PMC9728894 DOI: 10.1371/journal.pone.0278539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
β-thalassemia is an autosomal recessive disease with the reduction or absence in the production of β-globin chain in the hemoglobin, which is caused by mutations in the Hemoglobin subunit beta (HBB) gene. In Vietnam, the number of β-thalassemia carriers range from 1.5 to 25.0%, depending on ethnic and geographical areas, which is much higher than WHO's data worldwide (1.5%). Hence, preimplantation genetic diagnosis (PGD) plays a crucial role in reducing the rate of β-thalassemia affected patients/carriers. In this research, we report the feasibility and reliability of conducting PGD in combination with the use of short tandem repeat (STR) markers in facilitating the birth of healthy children. Six STRs, which were reported to closely linked with the HBB gene, were used on 15 couples of β-thalassemia carriers. With 231 embryos, 168 blastocysts were formed (formation rate of 72.73%), and 88 were biopsied and examined with STRs haplotyping and pedigree analysis. Thus, the results were verified by Sanger sequencing, as a definitive diagnosis. Consequently, 11 over 15 couples have achieved pregnancy of healthy or at least asymptomatic offspring. Only three couples failed to detect any signs of pregnancy such as increased Human Chorionic Gonadotropin (HCG) level, foetal sac, or heart; and one couple has not reached embryo transfer as they were proposed to continue with HLA-matching to screen for a potential umbilical cord blood donor sibling. Thus, these results have indicated that the combination of PGD with STRs analysis confirmed by Sanger sequencing has demonstrated to be a well-grounded and practical clinical strategy to improve the detection of β-thalassemia in the pregnancies of couples at-risk before embryo transfer, thus reducing β-thalassemia rate in the population.
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Affiliation(s)
- Vu Viet Ha Vuong
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Hospital of Post and Telecommunications, Hanoi, Vietnam
| | - Thinh Huy Tran
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Biochemistry Department, Hanoi Medical University, Hanoi, Vietnam
- Hanoi Medical University Hospital, Hanoi Medical University, Hanoi, Vietnam
| | - Phuoc-Dung Nguyen
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | | | - Phuong Le Thi
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | | | - Manh-Ha Nguyen
- Hanoi Medical University Hospital, Hanoi Medical University, Hanoi, Vietnam
| | - The-Hung Bui
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Center for Molecular Medicine, Clinical Genetics Unit, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Thanh Van Ta
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Biochemistry Department, Hanoi Medical University, Hanoi, Vietnam
- Hanoi Medical University Hospital, Hanoi Medical University, Hanoi, Vietnam
| | - Van-Khanh Tran
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- * E-mail:
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Kopparthy P, Kelkar AH, Aggarwal K, De Filippis S, Fletcher B. Red Blood Cell Exchange in a Patient With Extramedullary Hematopoiesis and Cor Pulmonale Secondary to Beta Thalassemia. Cureus 2021; 13:e13638. [PMID: 33824791 PMCID: PMC8011980 DOI: 10.7759/cureus.13638] [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] [Indexed: 01/19/2023] Open
Abstract
Rationale: Beta thalassemia is a congenital defect in the production of the beta globin chain. Patients with beta thalassemia major will have higher levels of hemoglobin F (HbF), which is suboptimal in releasing oxygen to tissue. Herein, we describe the use of red blood cell (RBC) exchange transfusion, a therapy typically used in sickle cell patients, in the management of a patient with beta thalassemia with extensive extramedullary hematopoiesis and elevated levels of HbF. Patient concerns: A 34-year-old male of mixed African American and Southeast Asian descent with a known history of beta thalassemia major presented with progressive dyspnea on exertion with marked fatigue. Diagnoses: The patient was transferred to our facility for management of acute hypoxemic, hypercapnic respiratory failure associated with cor pulmonale. Interventions: The patient was initially managed with non-invasive positive pressure support ventilation (NIPPV) and intravenous diuresis. Hydroxyurea and epoprostenol nebulization were added to his treatment regimen; however, he progressively became more unstable, necessitating inotropic support. With extramedullary hematopoiesis leading to mass-like effect on critical organs and very high HbF (96%) thought to contribute to his presentation, red blood cell exchange transfusion was initiated once the blood pressure stabilized. Outcomes: The patient clinically improved, and was discharged home within a week on supplemental oxygen by nasal cannula and long-term red blood cell exchange. Lessons: We postulated that significantly elevated HbF contributed to the patient’s chronic hypoxia and subsequent respiratory complications. Based on the patient's clinical improvement following the intervention, we believe that RBC exchange transfusion could be considered in the management of beta thalassemia patients with significantly elevated levels of HbF.
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Affiliation(s)
- Pallavi Kopparthy
- Division of Hematology & Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
| | - Amar H Kelkar
- Division of Hematology & Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
| | - Kunal Aggarwal
- Medical Education, Saint George's University School of Medicine, True Blue, GRD
| | | | - Brad Fletcher
- Division of Hematology & Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
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Tariq A, Khurshid S, Sajjad M. Evaluation of the High Resolution Melting Approach for Detection of β-Thalassemia Gene Mutations. Hemoglobin 2021; 45:20-24. [PMID: 33602051 DOI: 10.1080/03630269.2020.1867566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
β-Thalassemia (β-thal), an autosomal recessive hemoglobinopathy, is one of the most common genetic disorders in Pakistan. Awareness of this disease, genetic counseling, extended family carrier screening and prenatal diagnosis (PND) are helpful in prevention and control. Currently, direct DNA sequencing and multiple amplification refractory mutation system-polymerase chain reaction (MARMS-PCR) are the methods used to detect β-thal mutations, the latter being the most widely used. This study aimed to evaluate PCR-high resolution melting (PCR-HRM) analysis for the detection of most common β-thal mutations that are found in Pakistan. This study was designed to identify the β-thal mutations using PCR-HRM analysis in a total of 90 samples [blood and chorionic villus sampling (CVS)]. These samples were first screened for routine mutations by MARMS-PCR and then evaluated by PCR-HRM analysis. The results of PCR-HRM analyses were further confirmed by direct DNA sequencing and all analyses interpreted the same results in all 90 samples. Eleven cases (36.6%) were detected to carry IVS-I-5 (G>C) (HBB: c0.92 + 5G>C), six cases (20.0%) with frameshift codons (FSC) 41/42 (-TTCT) (HBB: c.126_129delCTTT), five cases (16.0%) were diagnosed with codon 15 (G>A) (HBB: c.47G>A), three cases (10.0%) were found with codon 30 (G>C) (HBB: c.93G>C), one case was diagnosed with FSC 16 (-C) (HBB: c.51delC), one with IVS-I-1 (G>T) (HBB: c0.92 + 1G>T) and one with codon 5 (-CT) (HBB: c.17_18delCT). The PCR-HRM analysis represents a less tedious and more useful method for the detection of β-globin gene mutations.
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Affiliation(s)
- Amna Tariq
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.,Punjab Thalassaemia Prevention Programme, Sir Ganga Ram Hospital, Lahore, Pakistan
| | - Sana Khurshid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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Auda FM, Saleh AA, Ali DS. The frequency of 6 beta-thalassemia mutations in the Iraqi patients from Najaf province. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Nezhad FH, Nezhad KH, Choghakabodi PM, Keikhaei B. Prevalence and Genetic Analysis of α- and β-Thalassemia and Sickle Cell Anemia in Southwest Iran. J Epidemiol Glob Health 2019; 8:189-195. [PMID: 30864762 PMCID: PMC7377559 DOI: 10.2991/j.jegh.2018.04.103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/25/2018] [Indexed: 11/01/2022] Open
Abstract
This prospective study assessed the prevalence and genetic analysis of α- and β-thalassemia and sickle cell anemia (SCA) in Southwest Iran. Hematological indices were measured in 17,581 couples living in Khuzestan Province, Southwest Iran. Individuals with mean corpuscular volume <80, mean corpuscular hemoglobin <27, hemoglobin A2 ≥3/5 were considered as β-thalassemia traits. Prevalence of minor β-thalassemia, α-thalassemia, SCA, iron deficiency anemia, and silent thalassemia were respectively identified in 995 (5.6%), 1169 (6.65%), 1240 (7.05%), 911 (5.18%), and 1134 (6.45%) individuals using a multiplex amplification refractory mutation system, and direct DNA sequencing of globin genes. Three codons IVS-II-1 (G → A; 26%; n = 13), IVS-I-1 (G → T; 16%; n = 8), and IVS-I-110 (G → A; 14%; n = 7) were the most frequent mutants and IVS-II-1 was the most common β-thalassemia mutation. Also, based on a gap-polymerase chain reaction assay, genotype frequencies of α-globin mutations were -α3.7 kb (50%; n = 25), Med/ααthal (12%; n = 6), and -α4.2/αα (10%; n = 5), which were the most frequent deletion mutants (72% in total). The most common deletion (50%) was -α3.7 kb. Our data suggest that the population of Southwest Iran is at high risk of α- and β-thalassemia caused by these deletion mutants and SCA. Our findings will be useful for developing an efficient control program and genetic counseling.
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Affiliation(s)
- Forozan H Nezhad
- Research Center of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Khojasteh H Nezhad
- Research Center of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parastoo M Choghakabodi
- Research Center of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bijan Keikhaei
- Research Center of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Deng Z, Li Q, Yi H, Zhang Y, Yang F, Li H, Luo L, Ma L, Yang Z, He Y, Cui L. Hemoglobin E protects against acute Plasmodium vivax infections in a Kachin population at the China-Myanmar border. J Infect 2018; 77:435-439. [PMID: 29964138 DOI: 10.1016/j.jinf.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Hemoglobin E (HbE, β26 Glu-Lys) is the most prevalent hemoglobinopathy in Southeast Asia. This study aimed to determine whether HbE protects against clinical Plasmodium vivax malaria in Southeast Asia. METHODS In a case-control study performed in villages along the China-Myanmar border, we determined the prevalence of HbE in 257 villagers who had acute P. vivax infections and in 157 control healthy villagers. RESULTS HbE in P. vivax patients (17.4%) was significantly less prevalent than in the healthy villager population (36.3%). Moreover, there was a complete lack of HbEE homozygotes in the vivax patients as compared to 9.5% prevalence in the healthy villagers. Using the HbAA group as the reference, both the HbEA heterozygotes and HbEE homozygotes had significantly lower odds of presenting with acute P. vivax infections. Furthermore, HbEA heterozygotes also had significantly lower P. vivax asexual parasite densities. HbEA did not affect the proportion of P. vivax patients with gametocytemia nor the gametocyte densities. CONCLUSIONS HbE offers significant protection against the occurrence and parasite density of acute P. vivax infections and provides a renewed perspective on P. vivax malaria as a potentially strong driving force behind the high frequencies of HbE in the Kachin population.
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Affiliation(s)
- Zeshuai Deng
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Qing Li
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Haoan Yi
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Yanjie Zhang
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Fang Yang
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Hong Li
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Lan Luo
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China
| | - Limei Ma
- Department of Histology and Embryology, Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, China
| | - Yongshu He
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, Yunnan Province, China.
| | - Liwang Cui
- Department of Entomology, The Pennsylvania State University, Pennsylvania, United States of America.
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Traivaree C, Monsereenusorn C, Rujkijyanont P, Prasertsin W, Boonyawat B. Genotype-phenotype correlation among beta-thalassemia and beta-thalassemia/HbE disease in Thai children: predictable clinical spectrum using genotypic analysis. J Blood Med 2018; 9:35-41. [PMID: 29695942 PMCID: PMC5905821 DOI: 10.2147/jbm.s159295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Introduction Beta-thalassemia is a group of inherited hemolytic anemias and one of the most common genetic disorders in Thailand. The clinical spectrum of beta-thalassemia disease ranges from mild to severe clinical symptoms including mild beta-thalassemia intermedia (TI) and severe beta-thalassemia major (TM). Objective This study aimed to determine the correlation between beta-globin gene (HBB) mutations and their phenotypic manifestations by evaluating patients' clinical characteristics, transfusion requirements, growth and hematologic parameters, and hemoglobin typing among pediatric patients treated at Phramongkutklao Hospital. Materials and methods Seventy beta-thalassemia patients, including 63 with beta-thalassemia/hemoglobin E (HbE) and 7 with either homozygous or compound heterozygous beta-thalassemia, were enrolled in this study. Their clinical presentation, growth parameters and laboratory findings were reviewed and analyzed. The mean follow-up time was 10.52±5.62 years. Mutation analysis in each individual was performed using multiplex amplification refractory mutation system (M-ARMS), direct DNA sequencing of beta-globin gene and gap PCR for 3.4 kb deletion detection. Results All 7 homozygous and compound heterozygous beta-thalassemia patients were classified in TM. Among 63 patients with beta-thalassemia/HbE, 58 were classified in TM and 4 were classified in TI. Mean age at diagnosis was 0.8±0.49 years for homozygous or compound heterozygous beta-thalassemia and 3.43±3.5 years for beta-thalassemia/HbE. The most common HBB mutation was HBB:c.126_129delCTTT [codon 41/42 (-TCTT)] found in 34 alleles (48.6%). The height for age was also lower in homozygous beta-thalassemia patients (<3rd percentile) compared to compound heterozygous beta-thalassemia patients (25-50th percentile). Conclusion This study revealed a genotype-phenotype correlation of the most prevalent beta-thalassemia in Thai children using diagnostic capacity in genotypic analysis of HBB mutation. Our findings can provide a better prediction of clinical manifestation and severity by early identification of the type of the HBB mutations.
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Affiliation(s)
- Chanchai Traivaree
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Chalinee Monsereenusorn
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Piya Rujkijyanont
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Warakorn Prasertsin
- Department of Pediatrics, Queen Savang Vadhana Memorial Hospital, Chonburi, Thailand
| | - Boonchai Boonyawat
- Division of Genetics, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
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Samarah F, Srour MA. Factor V Leiden G1691A and prothrombin G20210A mutations among Palestinian patients with sickle cell disease. BMC HEMATOLOGY 2018; 18:1. [PMID: 29372059 PMCID: PMC5771009 DOI: 10.1186/s12878-018-0097-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/04/2018] [Indexed: 11/11/2022]
Abstract
Background Vascular thrombosis is an important pathophysiological aspect of sickle cell disease (SCD). This study aimed to investigate the prevalence and clinical impact of factor V Leiden G1691A (FVL) and prothrombin G20210A mutations among Palestinian sickle cell disease (SCD) patients. Methods A total of 117 SCD patients, including 59 patients with sickle cell anemia (SS), 33 patients with sickle β-thalassemia and 25 individuals with sickle cell trait (AS) were studied. The control group consisted of 118 healthy individuals. FVL and prothrombin G20210A mutations were determined by RFLP PCR. Results Analysis of the clinical history of SCD patients revealed that seven patients have had vascular complications such as ischemic stroke or deep vein thrombosis. In SCD patients, the inheritance of the FVL mutation showed a significantly higher incidence of pain in joints, chest and abdomen as well as regular dependence on blood transfusion compared to SCD with the wild type. Age- and sex-adjusted logistic regression analysis revealed a significant association between FVL and sickle cell anemia with an odds ratio (OR) of 5.6 (95% confidence intervals [CI] of 1.91–39.4, P = 0.039) in SS patients. However, increased prevalence of the FVL in AS subjects and sickle β-thalassemia patients was not statistically significant compared to controls (OR 3.97, 95% CI 0.51–28.6, P = 0.17 and OR 3.59, 95% CI 0.35–41.6, P = 0.26, respectively). The distribution of prothrombin G20210A mutation among SCD patients compared to controls was not significantly different, thus our findings do not support an association of this mutation with SCD. Conclusions FVL was more prevalent among SS patients compared to controls and it was associated with higher incidence of disease complications among SCD patients.
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Affiliation(s)
- Fekri Samarah
- 1Department of Medical Technology, Faculty of Allied Health Sciences, Arab American University in Jenin, Jenin, Palestine
| | - Mahmoud A Srour
- 2Department of Medical Laboratory Sciences, Faculty of Health professions, Al-Quds University, Jerusalem, Palestine.,3Present address: Department of Biology & Biochemistry, Faculty of Science, Birzeit University, Birzeit, Palestine
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Berg JS, Powell CM. Potential Uses and Inherent Challenges of Using Genome-Scale Sequencing to Augment Current Newborn Screening. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023150. [PMID: 26438605 DOI: 10.1101/cshperspect.a023150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since newborn screening (NBS) began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders. Recent developments now make it possible to sequence an infant's genome relatively quickly and economically. Clinical application of whole-exome and whole-genome sequencing is expanding at a rapid pace but presents many challenges. Its utility in NBS has yet to be demonstrated and its application in the pediatric population requires examination, not only for potential clinical benefits, but also for the unique ethical challenges it presents.
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Affiliation(s)
- Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264
| | - Cynthia M Powell
- Departments of Pediatrics and Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264
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Boonyawat B, Monsereenusorn C, Traivaree C. Molecular analysis of beta-globin gene mutations among Thai beta-thalassemia children: results from a single center study. APPLICATION OF CLINICAL GENETICS 2014; 7:253-8. [PMID: 25525381 PMCID: PMC4266330 DOI: 10.2147/tacg.s73058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Background Beta-thalassemia is one of the most common genetic disorders in Thailand. Clinical phenotype ranges from silent carrier to clinically manifested conditions including severe beta-thalassemia major and mild beta-thalassemia intermedia. Objective This study aimed to characterize the spectrum of beta-globin gene mutations in pediatric patients who were followed-up in Phramongkutklao Hospital. Patients and methods Eighty unrelated beta-thalassemia patients were enrolled in this study including 57 with beta-thalassemia/hemoglobin E, eight with homozygous beta-thalassemia, and 15 with heterozygous beta-thalassemia. Mutation analysis was performed by multiplex amplification refractory mutation system (M-ARMS), direct DNA sequencing of beta-globin gene, and gap polymerase chain reaction for 3.4 kb deletion detection, respectively. Results A total of 13 different beta-thalassemia mutations were identified among 88 alleles. The most common mutation was codon 41/42 (-TCTT) (37.5%), followed by codon 17 (A>T) (26.1%), IVS-I-5 (G>C) (8%), IVS-II-654 (C>T) (6.8%), IVS-I-1 (G>T) (4.5%), and codon 71/72 (+A) (2.3%), and all these six common mutations (85.2%) were detected by M-ARMS. Six uncommon mutations (10.2%) were identified by DNA sequencing including 4.5% for codon 35 (C>A) and 1.1% initiation codon mutation (ATG>AGG), codon 15 (G>A), codon 19 (A>G), codon 27/28 (+C), and codon 123/124/125 (-ACCCCACC), respectively. The 3.4 kb deletion was detected at 4.5%. The most common genotype of beta-thalassemia major patients was codon 41/42 (-TCTT)/codon 26 (G>A) or betaE accounting for 40%. Conclusion All of the beta-thalassemia alleles have been characterized by a combination of techniques including M-ARMS, DNA sequencing, and gap polymerase chain reaction for 3.4 kb deletion detection. Thirteen mutations account for 100% of the beta-thalassemia genes among the pediatric patients in our study.
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Affiliation(s)
- Boonchai Boonyawat
- Division of Genetics, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Chalinee Monsereenusorn
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Chanchai Traivaree
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
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Teh LK, Lee TY, Tan JAMA, Lai MI, George E. The use of Taqman genotyping assays for rapid confirmation of β-thalassaemia mutations in the Malays: accurate diagnosis with low DNA concentrations. Int J Lab Hematol 2014; 37:79-89. [PMID: 24725998 DOI: 10.1111/ijlh.12240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/12/2014] [Indexed: 11/30/2022]
Abstract
INTRODUCTION In Malaysia, β-thalassaemia is a common inherited blood disorder in haemoglobin synthesis with a carrier rate of 4.5%. Currently, PCR-incorporating techniques such as amplification refractory mutation system (ARMS) or reverse dot blot hybridization (RDBH) are used in β-thalassaemia mutation detection. ARMS allows single-mutation identification using two reactions, one for wild type and another for mutant alleles. RDBH requires probe immobilization and optimization of hybridization and washing temperatures which is time consuming. The aim of our study was to investigate whether β-thalassaemia mutations can be identified in samples with low DNA concentrations. METHODS Genotype identification of common β-thalassaemia mutations in Malays was carried out using Taqman genotyping assays. RESULTS Results show that the Taqman assays allow mutation detection with DNA template concentrations as low as 2-100 ng. In addition, consistent reproducibility was observed in the Taqman assays when repeated eight times and at different time intervals. CONCLUSION The developed sensitive Taqman assays allow molecular characterization of β-thalassaemia mutations in samples with low DNA concentrations. The Taqman genotyping assays have potential as a diagnostic tool for foetal blood, chorionic villi or pre-implantation genetic diagnosis where DNA is limited and precious.
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Affiliation(s)
- L-K Teh
- Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Malaysia
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15
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Birth prevalence of disorders detectable through newborn screening by race/ethnicity. Genet Med 2012; 14:937-45. [PMID: 22766612 DOI: 10.1038/gim.2012.76] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
PURPOSE The purpose of this study was to describe the birth prevalence of genetic disorders among different racial/ethnic groups through population-based newborn screening data. METHODS Between 7 July 2005 and 6 July 2010 newborns in California were screened for selected metabolic, endocrine, hemoglobin, and cystic fibrosis disorders using a blood sample collected via heel stick. The race and ethnicity of each newborn was self-reported by the mother at the time of specimen collection. RESULTS Of 2,282,138 newborns screened, the overall disorder detection rate was 1 in 500 births. The disorder with the highest prevalence among all groups was primary congenital hypothyroidism (1 in 1,706 births). Birth prevalence for specific disorders varied widely among different racial/ethnic groups. CONCLUSION The California newborn screening data offer a unique opportunity to explore the birth prevalence of many genetic disorders across a wide spectrum of racial/ethnicity classifications. The data demonstrate that racial/ethnic subgroups of the California newborn population have very different patterns of heritable disease expression. Determining the birth prevalence of these disorders in California is a first step to understanding the short- and long-term medical and treatment needs faced by affected communities, especially those groups that are impacted by more severe disorders.
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Bravo-Urquiola M, Arends A, Gómez G, Montilla S, Gerard N, Chacin M, Berbar T, García O, García G, Velasquez D, Castillo O, Krishnamoorthy R. Molecular Spectrum of β-Thalassemia Mutations in the admixed Venezuelan population, and their linkage to β-Globin Gene Haplotypes. Hemoglobin 2012; 36:209-18. [DOI: 10.3109/03630269.2012.674997] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Affiliation(s)
- Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College and Department of Pediatrics, AIIMS, New Delhi, India
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Hung CC, Chen SU, Lin SY, Fang MY, Chang LJ, Tsai YY, Lin LT, Yang YS, Lee CN, Su YN. Preimplantation genetic diagnosis of β-thalassemia using real-time polymerase chain reaction with fluorescence resonance energy transfer hybridization probes. Anal Biochem 2010; 400:69-77. [DOI: 10.1016/j.ab.2009.12.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/13/2009] [Accepted: 12/15/2009] [Indexed: 02/07/2023]
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Shih HC, Er TK, Chang TJ, Chang YS, Liu TC, Chang JG. Rapid identification of HBB gene mutations by high-resolution melting analysis. Clin Biochem 2009; 42:1667-76. [PMID: 19631632 DOI: 10.1016/j.clinbiochem.2009.07.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/03/2009] [Accepted: 07/14/2009] [Indexed: 11/18/2022]
Abstract
OBJECTIVE This study was undertaken to identify HBB gene mutation. DESIGN AND METHODS Herein we evaluated high-resolution melting analysis in the identification of HBB mutations. RESULTS We have successfully established a diagnostic strategy for identifying HBB gene mutations including c.-78A>G, c.-79A>G, c.2T>G, c.79_80insT, c.84_85insC, c.123_124insT, c.125_128delTCTT, c.130 G>T, c.170G>A, c.216_217ins A and c.316-197 C>T from wild-type DNA using HRM analysis. The results of HRM analysis were confirmed by direct DNA sequencing. CONCLUSIONS In summary, we report that HRM analysis is an appealing technique for the identification of HBB mutations. We also believe that HRM can be used as a method for prenatal diagnosis of beta-thalassemia.
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Affiliation(s)
- Hung-Chang Shih
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Mirasena S, Shimbhu D, Sanguansermsri M, Sanguansermsri T. Detection of beta-thalassemia mutations using a multiplex amplification refractory mutation system assay. Hemoglobin 2008; 32:403-9. [PMID: 18654891 DOI: 10.1080/03630260701798391] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We developed two sets of a multiplex amplification refractory mutation system (M-ARMS) assay to identify specific beta-thalassemia (beta-thal) mutations that are common in Thailand. The first one was for the detection of mutants with codon 17 (A>T), IV S-I-1 (G >T)), codons 41/42 (-TCT T) and codons 71/72 (+A), while the second one was for the -87 (C>A), -28 (A>G) and IVS-II-654 (C>T). Application of the proposed assay to 282 persons with beta-thal trait revealed a positive result in 276 cases (97.8%). There were 258 cases (91.5%) positive for the set 1 M-ARMS assay and 18 cases (6.4%) were positive for set 2. Six cases (2.2%) were negative for both sets 1 and 2, and were further characterized by DNA sequencing. The mutations detected by the set 1 M-ARMS assay were 113 cases (40.1%) of codons 41/42, 95 (33.7%) of codon 17, 41 (14.5%) of IVS-I-1 and nine cases (3.2%) of codons 71/72, while by set 2 there were 12 cases (4.2%) of -28, four cases(1.4%) of -87 and two cases (0.7%) of IVS-II-654. Mutations undetectable by M-ARMS assay were two cases of codons 27/28 (+C), one case of codon 35 (C>A), one of codon 43 (G>T), one of -31 (A>G) and one of IVS-I-5 (C>G). The M-ARMS assay proved to be a valuable tool for the analysis of beta-thal mutations. The method is robust, accurate, simple, speedy and cost-effective. The application of this assay will facilitate genetic counseling and prenatal diagnosis for severe thalassemia in high-risk pregnancies.
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Affiliation(s)
- Saisiri Mirasena
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Hung CC, Su YN, Lin CY, Chang YF, Chang CH, Cheng WF, Chen CA, Lee CN, Lin WL. Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations. BMC Biotechnol 2008; 8:62. [PMID: 18694524 PMCID: PMC2525636 DOI: 10.1186/1472-6750-8-62] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 08/12/2008] [Indexed: 11/24/2022] Open
Abstract
Background Beta-thalassemia is a common autosomal recessive hereditary disease in the Meditertanean, Asia and African areas. Over 600 mutations have been described in the beta-globin (HBB), of which more than 200 are associated with a beta-thalassemia phenotype. Results We used two highly-specific mutation screening methods, mismatch-specific endonuclease and denaturing high-performance liquid chromatography, to identify mutations in the HBB gene. The sensitivity and specificity of these two methods were compared. We successfully distinguished mutations in the HBB gene by the mismatch-specific endonuclease method without need for further assay. This technique had 100% sensitivity and specificity for the study sample. Conclusion Compared to the DHPLC approach, the mismatch-specific endonuclease method allows mutational screening of a large number of samples because of its speed, sensitivity and adaptability to semi-automated systems. These findings demonstrate the feasibility of using the mismatch-specific endonuclease method as a tool for mutation screening.
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Affiliation(s)
- Chia-Cheng Hung
- 1Institute of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan.
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Affiliation(s)
- Linda L. McCabe
- Departments of Human Genetics and Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles
- UCLA Center for Society and Genetics
| | - Edward R.B. McCabe
- Departments of Human Genetics and Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles
- UCLA Center for Society and Genetics
- California Nanosystems Institute
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, Los Angeles, California 90095; ,
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WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics 2007; 8:275. [PMID: 17697334 PMCID: PMC1976135 DOI: 10.1186/1471-2164-8-275] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Accepted: 08/14/2007] [Indexed: 11/29/2022] Open
Abstract
Background Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at .
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Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A 2007; 104:10110-5. [PMID: 17551006 PMCID: PMC1891248 DOI: 10.1073/pnas.0703834104] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Copy-number variants (CNVs) are an abundant form of genetic variation in humans. However, approaches for determining exact CNV breakpoint sequences (physical deletion or duplication boundaries) across individuals, crucial for associating genotype to phenotype, have been lacking so far, and the vast majority of CNVs have been reported with approximate genomic coordinates only. Here, we report an approach, called BreakPtr, for fine-mapping CNVs (available from http://breakptr.gersteinlab.org). We statistically integrate both sequence characteristics and data from high-resolution comparative genome hybridization experiments in a discrete-valued, bivariate hidden Markov model. Incorporation of nucleotide-sequence information allows us to take into account the fact that recently duplicated sequences (e.g., segmental duplications) often coincide with breakpoints. In anticipation of an upcoming increase in CNV data, we developed an iterative, "active" approach to initially scoring with a preliminary model, performing targeted validations, retraining the model, and then rescoring, and a flexible parameterization system that intuitively collapses from a full model of 2,503 parameters to a core one of only 10. Using our approach, we accurately mapped >400 breakpoints on chromosome 22 and a region of chromosome 11, refining the boundaries of many previously approximately mapped CNVs. Four predicted breakpoints flanked known disease-associated deletions. We validated an additional four predicted CNV breakpoints by sequencing. Overall, our results suggest a predictive resolution of approximately 300 bp. This level of resolution enables more precise correlations between CNVs and across individuals than previously possible, allowing the study of CNV population frequencies. Further, it enabled us to demonstrate a clear Mendelian pattern of inheritance for one of the CNVs.
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Affiliation(s)
- Jan O. Korbel
- Departments of *Molecular Biophysics and Biochemistry and
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- To whom correspondence may be addressed. E-mail: , , or
| | - Alexander Eckehart Urban
- Genetics, Yale University School of Medicine, New Haven, CT 06520
- Departments of Molecular, Cellular, and Developmental Biology and
| | - Fabian Grubert
- Genetics, Yale University School of Medicine, New Haven, CT 06520
| | - Jiang Du
- Computer Science, Yale University, New Haven, CT 06520; and
| | | | - Peter Starr
- Departments of *Molecular Biophysics and Biochemistry and
| | - Guoneng Zhong
- Departments of *Molecular Biophysics and Biochemistry and
| | - Beverly S. Emanuel
- **Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | | | - Michael Snyder
- Departments of Molecular, Cellular, and Developmental Biology and
- To whom correspondence may be addressed. E-mail: , , or
| | - Mark B. Gerstein
- Departments of *Molecular Biophysics and Biochemistry and
- Computer Science, Yale University, New Haven, CT 06520; and
- To whom correspondence may be addressed. E-mail: , , or
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Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A 2006; 103:4534-9. [PMID: 16537408 PMCID: PMC1450206 DOI: 10.1073/pnas.0511340103] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Deletions and amplifications of the human genomic sequence (copy number polymorphisms) are the cause of numerous diseases and a potential cause of phenotypic variation in the normal population. Comparative genomic hybridization (CGH) has been developed as a useful tool for detecting alterations in DNA copy number that involve blocks of DNA several kilobases or larger in size. We have developed high-resolution CGH (HR-CGH) to detect accurately and with relatively little bias the presence and extent of chromosomal aberrations in human DNA. Maskless array synthesis was used to construct arrays containing 385,000 oligonucleotides with isothermal probes of 45-85 bp in length; arrays tiling the beta-globin locus and chromosome 22q were prepared. Arrays with a 9-bp tiling path were used to map a 622-bp heterozygous deletion in the beta-globin locus. Arrays with an 85-bp tiling path were used to analyze DNA from patients with copy number changes in the pericentromeric region of chromosome 22q. Heterozygous deletions and duplications as well as partial triploidies and partial tetraploidies of portions of chromosome 22q were mapped with high resolution (typically up to 200 bp) in each patient, and the precise breakpoints of two deletions were confirmed by DNA sequencing. Additional peaks potentially corresponding to known and novel additional CNPs were also observed. Our results demonstrate that HR-CGH allows the detection of copy number changes in the human genome at an unprecedented level of resolution.
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Affiliation(s)
- Alexander Eckehart Urban
- *Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
- Department of Genetics and
| | - Jan O. Korbel
- Molecular Biophysics and Biochemistry Department, Yale University School of Medicine, New Haven, CT 06520
| | - Rebecca Selzer
- NimbleGen Systems, Inc., 1 Science Court, Madison, WI 53711
| | - Todd Richmond
- NimbleGen Systems, Inc., 1 Science Court, Madison, WI 53711
| | - April Hacker
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - George V. Popescu
- *Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
- Department of Genetics and
| | - Joseph F. Cubells
- **Departments of Human Genetics, and Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Roland Green
- NimbleGen Systems, Inc., 1 Science Court, Madison, WI 53711
| | - Beverly S. Emanuel
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; and
| | - Mark B. Gerstein
- Molecular Biophysics and Biochemistry Department, Yale University School of Medicine, New Haven, CT 06520
| | - Sherman M. Weissman
- Department of Genetics and
- To whom correspondence may be addressed. E-mail:
or
| | - Michael Snyder
- *Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
- To whom correspondence may be addressed. E-mail:
or
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