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Zhou C, Du Y, Zhang H, Wei X, Li R, Wang J. Third-generation sequencing identified a novel complex variant in a patient with rare alpha-thalassemia. BMC Pediatr 2024; 24:330. [PMID: 38741052 DOI: 10.1186/s12887-024-04811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Thalassemias represent some of the most common monogenic diseases worldwide and are caused by variations in human hemoglobin genes which disrupt the balance of synthesis between the alpha and beta globin chains. Thalassemia gene detection technology is the gold standard to achieve accurate detection of thalassemia, but in clinical practice, most of the tests are only for common genotypes, which can easily lead to missing or misdiagnosis of rare thalassemia genotypes. CASE PRESENTATION We present the case of an 18-year-old Chinese female with abnormal values of routine hematological indices who was admitted for genetic screening for thalassemia. Genomic DNA was extracted and used for the genetic assays. Gap polymerase chain reaction and agarose gel electrophoresis were performed to detect HBA gene deletions, while PCR-reverse dot blot hybridization was used to detect point mutations in the HBA and HBB genes. Next-generation sequencing and third-generation sequencing (TGS) were used to identify known and potentially novel genotypes of thalassemia. We identified a novel complex variant αHb WestmeadαHb Westmeadαanti3.7/-α3.7 in a patient with rare alpha-thalassemia. CONCLUSIONS Our study identified a novel complex variant that expands the thalassemia gene variants spectrum. Meanwhile, the study suggests that TGS could effectively improve the specificity of thalassemia gene detection, and has promising potential for the discovery of novel thalassemia genotypes, which could also improve the accuracy of genetic counseling. Couples who are thalassemia carriers have the opportunity to reduce their risk of having a child with thalassemia.
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Affiliation(s)
- Cong Zhou
- Department of Medical Genetics/Prenatal Diagnostic Center, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yepei Du
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Haixia Zhang
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xing Wei
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Rui Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Jing Wang
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
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2
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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3
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Soler AM, Pedroso GA, Geraldo APM, Albuquerque DM, Costa FF, Santos MNN, Knijnenburg J, Harteveld CL, Sonati MF, da Luz JA. A novel α 0-thalassemia deletion in a Brazilian child with Hb H disease: -- Mococa. Int J Lab Hematol 2024. [PMID: 38566588 DOI: 10.1111/ijlh.14277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Affiliation(s)
- A M Soler
- Laboratorio de Genética Molecular Humana, Departamento de Ciencias Biológicas, Centro Universitario Regional (CENUR) Litoral Norte. Universidad de la República (UdelaR), Salto, Uruguay
| | - G A Pedroso
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - A P M Geraldo
- Integrated Center for Oncohematological Research in Childhood (CIPOI), UNICAMP, Campinas, SP, Brazil
| | - D M Albuquerque
- Center for Hematology and Hemotherapy, UNICAMP, Campinas, SP, Brazil
| | - F F Costa
- Center for Hematology and Hemotherapy, UNICAMP, Campinas, SP, Brazil
| | - M N N Santos
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - J Knijnenburg
- Department of Human and Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center-LUMC, Leiden, The Netherlands
| | - C L Harteveld
- Department of Human and Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center-LUMC, Leiden, The Netherlands
| | - M F Sonati
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - J A da Luz
- Laboratorio de Genética Molecular Humana, Departamento de Ciencias Biológicas, Centro Universitario Regional (CENUR) Litoral Norte. Universidad de la República (UdelaR), Salto, Uruguay
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4
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Liu S, Zuo D, Cheng H, He M, Wang Q, Lv L, Zhang Y, Ashraf J, Liu J, Song G. Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding. Genome Biol 2023; 24:282. [PMID: 38066616 PMCID: PMC10704732 DOI: 10.1186/s13059-023-03124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Many elite genes have been identified from the available cotton genomic data, providing various genetic resources for gene-driven breeding. However, backbone cultivar-driven breeding is the most widely applied strategy. Revealing the genetic basis of cultivar-driven strategy's restriction is crucial for transition of cotton breeding strategy. RESULT CRI12 is a backbone cultivar in cultivar-driven breeding. Here we sequence the pedigree of CRI12 using Nanopore long-read sequencing. We construct a graphical pedigree genome using the high-quality CRI12 genome and 13,138 structural variations within 20 different pedigree members. We find that low hereditary stability of elite segments in backbone cultivars is a drawback of cultivar-driven strategy. We also identify 623 functional segments in CRI12 for multiple agronomic traits in presence and absence variation-based genome-wide association study on three cohorts. We demonstrate that 25 deleterious segments are responsible for the geographical divergence of cotton in pathogen resistance. We also characterize an elite pathogen-resistant gene (GhKHCP) utilized in modern cotton breeding. In addition, we identify 386 pedigree fingerprint segments by comparing the segments of the CRI12 pedigree with those of a large cotton population. CONCLUSION We characterize the genetic patterns of functional segments in the pedigree of CRI12 using graphical genome method, revealing restrictions of cultivar-driven strategies in cotton breeding. These findings provide theoretical support for transitioning from cultivar-driven to gene-driven strategy in cotton breeding.
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Affiliation(s)
- Shang Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Dongyun Zuo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hailiang Cheng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Man He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qiaolian Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Limin Lv
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Youping Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Javaria Ashraf
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Ji Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Guoli Song
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Shimojima Yamamoto K, Tamura T, Okamoto N, Nishi E, Noguchi A, Takahashi I, Sawaishi Y, Shimizu M, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Identification of small-sized intrachromosomal segments at the ends of INV-DUP-DEL patterns. J Hum Genet 2023; 68:751-757. [PMID: 37423943 DOI: 10.1038/s10038-023-01181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
The mechanism of chromosomal rearrangement associated with inverted-duplication-deletion (INV-DUP-DEL) pattern formation has been investigated by many researchers, and several possible mechanisms have been proposed. Currently, fold-back and subsequent dicentric chromosome formation has been established as non-recurrent INV-DUP-DEL pattern formation mechanisms. In the present study, we analyzed the breakpoint junctions of INV-DUP-DEL patterns in five patients using long-read whole-genome sequencing and detected 2.2-6.1 kb copy-neutral regions in all five patients. At the end of the INV-DUP-DEL, two patients exhibited chromosomal translocations, which are recognized as telomere capture, and one patient showed direct telomere healing. The remaining two patients had additional small-sized intrachromosomal segments at the end of the derivative chromosomes. These findings have not been previously reported but they may only be explained by the presence of telomere capture breakage. Further investigations are required to better understand the mechanisms underlying this finding.
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Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Ikuko Takahashi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Yukio Sawaishi
- Department of Pediatrics, Akita Prefectural Center on Development and Disability, Akita, 010-0000, Japan
| | - Masaki Shimizu
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
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6
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Zulkeflee RH, Bahar R, Abdullah M, Mohd Radzi MAR, Md Fauzi A, Hassan R. Application of Targeted Next-Generation Sequencing for the Investigation of Thalassemia in a Developing Country: A Single Center Experience. Diagnostics (Basel) 2023; 13:diagnostics13081379. [PMID: 37189480 DOI: 10.3390/diagnostics13081379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Thalassemia is identified as a prevalent disease in Malaysia, known to be one of the developing countries. Fourteen patients with confirmed cases of thalassemia were recruited from the Hematology Laboratory. The molecular genotypes of these patients were tested using the multiplex-ARMS and GAP-PCR methods. The samples were repeatedly investigated using the Devyser Thalassemia kit (Devyser, Sweden), a targeted NGS panel targeting the coding regions of hemoglobin genes, namely the HBA1, HBA2, and HBB genes, which were used in this study. There were many different genetic variants found in 14 unrelated cases. Out of all fourteen cases, NGS was able to determine an additional -50 G>A (HBB:c.-100G>A) that were not identified by the multiplex-ARMS method, including HBA2 mutations, namely CD 79 (HBA2:c.239C>G). Other than that, CD 142 (HBA2:c.427T>C) and another non-deletional alpha thalassemia and alpha triplication were also not picked up by the GAP-PCR methods. We illustrated a broad, targeted NGS-based test that proposes benefits rather than using traditional screening or basic molecular methods. The results of this study should be heeded, as this is the first report on the practicality of targeted NGS concerning the biological and phenotypic features of thalassemia, especially in a developing population. Discovering rare pathogenic thalassemia variants and additional secondary modifiers may facilitate precise diagnosis and better disease prevention.
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Affiliation(s)
- Razan Hayati Zulkeflee
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Rosnah Bahar
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Marne Abdullah
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Muhammad Amiro Rasheeq Mohd Radzi
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Paediatrics, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Alina Md Fauzi
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Malaysia
| | - Rosline Hassan
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
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7
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Macedo R, Isidro J, Ferreira R, Pinto M, Borges V, Duarte S, Vieira L, Gomes JP. Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. Int J Mol Sci 2023; 24:ijms24032912. [PMID: 36769230 PMCID: PMC9918089 DOI: 10.3390/ijms24032912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
- Correspondence:
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8
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Uppuluri L, Wang Y, Young E, Wong JS, Abid HZ, Xiao M. Multiplex structural variant detection by whole-genome mapping and nanopore sequencing. Sci Rep 2022; 12:6512. [PMID: 35444207 PMCID: PMC9021263 DOI: 10.1038/s41598-022-10483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of structural variants (SVs) breakpoints is important in studying mutations, mutagenic causes, and functional impacts. Next-generation sequencing and whole-genome optical mapping are extensively used in SV discovery and characterization. However, multiple platforms and computational approaches are needed for comprehensive analysis, making it resource-intensive and expensive. Here, we propose a strategy combining optical mapping and cas9-assisted targeted nanopore sequencing to analyze SVs. Optical mapping can economically and quickly detect SVs across a whole genome but does not provide sequence-level information or precisely resolve breakpoints. Furthermore, since only a subset of all SVs is known to affect biology, we attempted to type a subset of all SVs using targeted nanopore sequencing. Using our approach, we resolved the breakpoints of five deletions, five insertions, and an inversion, in a single experiment.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.,Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jessica S Wong
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA.
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9
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Suhaimi SA, Zulkipli IN, Ghani H, Abdul-Hamid MRW. Applications of next generation sequencing in the screening and diagnosis of thalassemia: A mini-review. Front Pediatr 2022; 10:1015769. [PMID: 36245713 PMCID: PMC9557073 DOI: 10.3389/fped.2022.1015769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Thalassemias are a group of inherited blood disorders that affects 5-7% of the world population. Comprehensive screening strategies are essential for the management and prevention of this disorder. Today, many clinical and research laboratories have widely utilized next-generation sequencing (NGS) technologies to identify diseases, from germline and somatic disorders to infectious diseases. Yet, NGS application in thalassemia is limited and has just recently surfaced due to current demands in seeking alternative DNA screening tools that are more efficient, versatile, and cost-effective. This review aims to understand the several aspects of NGS technology, including its most current and expanding uses, advantages, and limitations, along with the issues and solutions related to its integration into routine screening and diagnosis of thalassemias. Hitherto, NGS has been a groundbreaking technology that offers tremendous improvements as a diagnostic tool for thalassemia in terms of its higher throughput, accuracy, and adaptability. The superiority of NGS in detecting rare variants, solving complex hematological problems, and providing non-invasive alternatives to neonatal diagnosis cannot be overlooked. However, several pitfalls still preclude its use as a stand-alone technique over conventional methods.
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Affiliation(s)
| | | | - Hazim Ghani
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei
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10
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Rangan A, Hein MS, Jenkinson WG, Koganti T, Aleff RA, Hilker CA, Blommel JH, Porter TR, Swanson KC, Lundquist P, Nguyen PL, Shi M, He R, Viswanatha DS, Jen J, Klee EW, Kipp BR, Hoyer JD, Wieben ED, Oliveira JL. Improved Characterization of Complex β-Globin Gene Cluster Structural Variants Using Long-Read Sequencing. J Mol Diagn 2021; 23:1732-1740. [PMID: 34839893 DOI: 10.1016/j.jmoldx.2021.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/30/2021] [Accepted: 08/18/2021] [Indexed: 10/19/2022] Open
Abstract
Complex insertion-deletion (indel) events in the globin genes manifest in widely variable clinical phenotypes. Many are incompletely characterized because of a historic lack of efficient methods. A more complete assessment enables improved prediction of clinical impact, which guides emerging therapeutic choices. Current methods have limited capacity for breakpoint assignment and accurate assessment of mutation extent, especially in cases containing duplications or multiple deletions and insertions. Technology, such as long-read sequencing, holds promise for significant impact in the characterization of indel events because of read lengths that span large regions, resulting in improved resolution. Four known complex β-globin gene cluster indel types were assessed using single-molecule, real-time sequencing technology and showed high correlation with previous reports, including the Caribbean locus control deletion (g.5,305,478_5,310,336del), a large β-gene duplication containing the Hb S mutation (g.4,640,335_5,290,171dup with g.5,248,232T>A, c.20A>T; variant allele fraction, 64%), and two nested variants (double deletions with intervening inversion): the Indian Gγ(Aγδβ)0-thalassemia (g.5,246,804-5,254,275del, g.5,254,276_5,269,600inv, and g.5,269,601_5,270,442del) and the Turkish/Macedonian (δβ)0 thalassemia (g.5,235,064_5,236,652del, g.5,236,653_5,244,280inv, and g.5,244,281_5,255,766del). Our data confirm long-read sequencing as an efficient and accurate method to identify these clinically significant complex events. Limitations include high-complexity sample preparation requirements, which hinder routine use in clinical laboratories. Continued improvements in sample and data workflow processes are needed to accommodate volumes in a tertiary clinical laboratory.
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Affiliation(s)
- Aruna Rangan
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Molly S Hein
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Tejaswi Koganti
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ross A Aleff
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | | | - Joseph H Blommel
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Tavanna R Porter
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kenneth C Swanson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patrick Lundquist
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Phuong L Nguyen
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rong He
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - David S Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - James D Hoyer
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric D Wieben
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jennifer L Oliveira
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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11
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Jiang F, Lyu GZ, Zhang VW, Li DZ. Identification of thalassemia gene cluster deletion by long-read whole-genome sequencing (LR-WGS). Int J Lab Hematol 2021; 43:859-865. [PMID: 33400392 DOI: 10.1111/ijlh.13452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION At present, a variety of molecular detection methods are obtained to diagnose thalassemia accurately. Although exome sequencing or specific panels have been widely used in clinical diagnosis of genetic diseases, the positive rate is about 25%-30%. Because the detection range is limited to exons and splice sites, and the read length is usually 100-150 bp, there are limitations in the detection of globin gene clusters with pseudogenes. METHODS In this study, seven thalassemia patients were selected to perform whole-genome sequencing (WGS) with long read at 400 bp to make accurate detection for thalassemia deletions. And we used PCR and Sanger sequencing to confirm the gene deletions in the patients. RESULTS WGS analysis detected a rare 172 kb deletion on the α-globin gene cluster at chr16: 57 009-330 001, 19 kb deletion at chr16: 215 396-234 699, 11 kb deletion at chr16:220 861-231 981; and 27 kb deletion on the β-globin gene deletion at chr11: 5 222 878-5 250 288, 21.4 kb deletion at chr11: 5 236 361-5 257 771, 78.9 kb deletion at chr11: 5 191 121-5 270 050. All the seven patients carried heterozygous deletions, including three in α-gene cluster, three in β-gene cluster, and one in both globin clusters. CONCLUSION Our results indicate that long-read WGS will be beneficial to the diagnosis of genetic diseases with pseudogenes or highly duplicated sequences and will enable clinical geneticists to inform high-risk couples and provide prenatal diagnosis.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | | | | | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
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12
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Yanagishita T, Imaizumi T, Yamamoto-Shimojima K, Yano T, Okamoto N, Nagata S, Yamamoto T. Breakpoint junction analysis for complex genomic rearrangements with the caldera volcano-like pattern. Hum Mutat 2020; 41:2119-2127. [PMID: 32906213 DOI: 10.1002/humu.24108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022]
Abstract
Chromosomal triplications can be classified into recurrent and nonrecurrent triplications. Most of the nonrecurrent triplications are embedded in duplicated segments, and duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) has been established as one of the mechanisms of triplication. This study aimed to reveal the underlying mechanism of the TRP-DUP-TRP pattern of chromosomal aberrations, in which the appearance of moving averages obtained through array-based comparative genomic hybridization analysis is similar to the shadows of the caldera volcano-like pattern, which were first identified in two patients with neurodevelopmental disabilities. For this purpose, whole-genome sequencing using long-read Nanopore sequencing was carried out to confirm breakpoint junctions. Custom array analysis and Sanger sequencing were also used to detect all breakpoint junctions. As a result, the TRP-DUP-TRP pattern consisted of only two patterns of breakpoint junctions in both patients. In patient 1, microhomologies were identified in breakpoint junctions. In patient 2, more complex architectures with insertional segments were identified. Thus, replication-based mechanisms were considered as a mechanism of the TRP-DUP-TRP pattern.
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Affiliation(s)
- Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | - Tamami Yano
- Department of Pediatrics, Akita University, Akita, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan.,Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
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13
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Imaizumi T, Yamamoto-Shimojima K, Yanagishita T, Ondo Y, Nishi E, Okamoto N, Yamamoto T. Complex chromosomal rearrangements of human chromosome 21 in a patient manifesting clinical features partially overlapped with that of Down syndrome. Hum Genet 2020; 139:1555-1563. [PMID: 32535809 DOI: 10.1007/s00439-020-02196-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/06/2020] [Indexed: 01/16/2023]
Abstract
The chromosomal region critical in Down syndrome has long been analyzed through genotype-phenotype correlation studies using data from many patients with partial trisomy 21. Owing to that, a relatively small region of human chromosome 21 (35.9 ~ 38.0 Mb) has been considered as Down syndrome critical region (DSCR). In this study, microarray-based comparative genomic hybridization analysis identified complex rearrangements of chromosome 21 in a patient manifesting clinical features partially overlapped with that of Down syndrome. Although the patient did not show up-slanting palpebral fissures and single transverse palmar creases, other symptoms were consistent with Down syndrome. Rearrangements were analyzed by whole-genome sequencing using Nanopore long-read sequencing. The analysis revealed that chromosome 21 was fragmented into seven segments and reassembled by six connected points. Among 12 breakpoints, 5 are located within the short region and overlapped with repeated segments. The rearrangement resulted in a maximum gain of five copies, but no region showed loss of genomic copy numbers. Breakpoint-junctions showed no homologous region. Based on these findings, chromoanasynthesis was considered as the mechanism. Although the distal 21q22.13 region was not included in the aberrant regions, some of the genes located on the duplicated regions, SOD1, SON, ITSN1, RCAN1, and RUNX1, were considered as possible candidate genes for clinical features of the patient. We discussed the critical region for Down syndrome, with the literature review.
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Affiliation(s)
- Taichi Imaizumi
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Japan Society for the Promotion of Science (RPD), Tokyo, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yumiko Ondo
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ward, Tokyo, 162-8666, Japan.
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan.
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan.
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.
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14
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Chen DM, Ma S, Tang XL, Yang JY, Yang ZL. Diagnosis of the accurate genotype of HKαα carriers in patients with thalassemia using multiplex ligation-dependent probe amplification combined with nested polymerase chain reaction. Chin Med J (Engl) 2020; 133:1175-1181. [PMID: 32433049 PMCID: PMC7249720 DOI: 10.1097/cm9.0000000000000768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Patients carrying the HongKongαα (HKαα) allele and -α/ααα could be misdiagnosed as -α/αα by the current conventional thalassemia detection methods, leading to inaccurate genetic counseling and an incorrect prenatal diagnosis. This study was aimed to accurately analyze the genotypes of HKαα carriers and -α/ααα. METHODS Samples were collected in our hospital from July 2017 to October 2019. Twenty-four common types of Chinese thalassemia were screened by gap-polymerase chain reaction (Gap-PCR) and reverse dot blot (RDB). Anti-4.2 multiplex-PCR was used to confirm carriers of the ααα duplication with -α deletion. Two-round nested PCR and multiplex ligation-dependent probe amplification (MLPA) were applied to accurately identify and confirm their genotypes. For data analysis, we used descriptive statistics and Fisher's exact tests. RESULTS Two thousand five hundred and forty-four cases were identified as thalassemia in 5488 peripheral blood samples. The results showed that α, β, and αβ compound thalassemia were identified in 1190 (46.78%), 1286 (50.55%), and 68 (2.67%) cases, respectively. A total of 227 samples from thalassemia patients were identified as -α/αα by Gap-PCR, and the genotypes of two samples were uncertain. There was a difference between Gap-PCR and combined groups (Gap-PCR combined with nested PCR and MLPA) in detecting HKαα (P < 0.05). Among the 229 patients, 20 patients were identified as HKαα carriers and one was identified as -α/ααα by two-round nested PCR and MLPA, including 15 patients with HKαα/αα, three with HKαα/αα and β-thalassemia coinheritance, one with HKαα/--, one with HKαα/-α and β-thalassemia coinheritance, and one with -α/ααα and β-thalassemia coinheritance. CONCLUSIONS ααα and HKαα genotypes of patients carrying -α need to be detected to reduce the misdiagnosis rate of patients carrying HKαα and -α3.7/ααα alleles. More accurate genetic counseling can be provided in the clinic using nested PCR combined with MLPA.
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Affiliation(s)
- Dong-Mei Chen
- Clinical Medical School, Southwest Medical University, Luzhou, Sichuan 646000, China
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Shi Ma
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Xiang-Lan Tang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Ji-Yun Yang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Zheng-Lin Yang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, Sichuan 610072, China
- Natural Products Research Center, Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, Sichuan 610072, China
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15
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Visual genotyping of thalassemia by using pyrrolidinyl peptide nucleic acid probes immobilized on carboxymethylcellulose-modified paper and enzyme-induced pigmentation. Mikrochim Acta 2020; 187:238. [PMID: 32189135 DOI: 10.1007/s00604-020-4197-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
A simple probe pair was designed for the detection of hemoglobin E (HbE) genotype, a single-point mutation that leads to abnormal red blood cells commonly found in South East Asia. The key to differentiation is the use of a conformationally constrained peptide nucleic acid (PNA) that was immobilized on carboxymethylcellulose-modified paper. This was then used for target DNA binding and visualization by an enzyme-catalyzed pigmentation. The biotinylated target DNA bound to the immobilized probe was visually detected via alkaline phosphatase-linked streptavidin. This enzyme conjugate catalyzed the dephosphorylation of the substrate 5-bromo-4-chloro-3-indolyl phosphate, leading to a series of reactions that generate an intense, dark blue pigment. The test was validated with 100 DNA samples, which shows good discrimination among different genotypes (normal, HbE, and heterozygous) with 100% accuracy when optimal conditions of analysis were applied. The method does not require temperature control and can be performed at ambient temperature. This is an attractive feature for diagnosis in primary care, which accounts for a large part of affected population. Graphical abstract Schematic representation of a paper-based sensor for the detection of the gene Hemoglobin E. The interaction between an immobilized peptide nucleic acid and a DNA target leads to enzymatic pigmentation, allowing simple visual readout with up to 100% accuracy.
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16
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Pang D, Shang X, Cai D, Zhu F, Cheng Y, Zhong J, Yi S, Zhang Q, Xu X. Thalassaemia intermedia caused by coinheritance of a β‐thalassaemia mutation and a
de novo
duplication of α‐globin genes in the paternal allele. Br J Haematol 2019; 186:620-624. [DOI: 10.1111/bjh.15958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Dejian Pang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Xuan Shang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
- Guangdong Genetics Testing Engineering Research CentreGuangzhou Guangdong China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application Guangzhou GuangdongChina
| | - Decheng Cai
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Fei Zhu
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Yi Cheng
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Jianmei Zhong
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Sheng Yi
- Prenatal Diagnostic Centre Guangxi Zhuang Autonomous Region Women and Children Care Hospital Nanning Guangxi China
| | - Qianqian Zhang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Xiangmin Xu
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
- Guangdong Genetics Testing Engineering Research CentreGuangzhou Guangdong China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application Guangzhou GuangdongChina
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17
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Ferreira RD, Mota NO, Pedroso GA, Kimura EM, Geraldo APM, Santos MNN, Costa FF, Sonati MF. First report of εγδβ 0 -thalassemia in a Brazilian family. Int J Lab Hematol 2018; 40:e96-e98. [PMID: 29851275 DOI: 10.1111/ijlh.12863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- R D Ferreira
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - N O Mota
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - G A Pedroso
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - E M Kimura
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - A P M Geraldo
- Integrated Center for Pediatric Hematology/Oncology Research (CIPOI), School of Medical Sciences, State University of Campinas- UNICAMP, Campinas, SP, Brazil
| | - M N N Santos
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - F F Costa
- Hematology and Hemotherapy Center, UNICAMP, Campinas, SP, Brazil
| | - M F Sonati
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas - UNICAMP, Campinas, SP, Brazil
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18
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Harteveld CL. Diagnosis of Haemoglobinopathies: New Scientific Advances. THALASSEMIA REPORTS 2018. [DOI: 10.4081/thal.2018.7473] [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
The molecular defects underlying haemoglobinopathies are both deletions and point mutations in the alpha- or beta-globin genes or gene-clusters. To detect point mutations causing alpha- or beta-thalassaemia, direct sequencing is the method of choice to detect the widest spectrum of molecular defects. The most established approach in DNA diagnostics to screen for the most common deletion defects causing alpha-thalassaemia or beta-thalassaemia is gap- PCR, Multiplex Ligation-dependent Probe Amplification (MLPA) and Sanger Sequencing technology to detect breakpoint sequences of previously uncharacterized deletions/duplications. We demonstrate the recent advances in the determination of duplications and deletions causing alpha- or beta-thalassemia, using Next Generation Sequencing, array Comparative Genome Hybridization and Target Locus Amplification. We present three cases in which the use of advanced technologies allow the diagnosis of unexpected disease genotypes.
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Farashi S, Harteveld CL. Molecular basis of α-thalassemia. Blood Cells Mol Dis 2017; 70:43-53. [PMID: 29032940 DOI: 10.1016/j.bcmd.2017.09.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 02/05/2023]
Abstract
α-Thalassemia is an inherited, autosomal recessive, disorder characterized by a microcytic hypochromic anemia. It is one of the most common monogenic gene disorders in the world population. The clinical severity varies from almost asymptomatic, to mild microcytic hypochromic, and to a lethal hemolytic condition, called Hb Bart's Hydrops Foetalis Syndrome. The molecular basis are usually deletions and less frequently, point mutations affecting the expression of one or more of the duplicated α-genes. The clinical variation and increase in disease severity is directly related to the decreased expression of one, two, three or four copies of the α-globin genes. Deletions and point mutations in the α-globin genes and their regulatory elements have been studied extensively in carriers and patients and these studies have given insight into the α-globin genes are regulated. By looking at naturally occurring deletions and point mutations, our knowledge of globin-gene regulation and expression will continue to increase and will lead to new targets of therapy.
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Affiliation(s)
- Samaneh Farashi
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelis L Harteveld
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands.
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