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Liu D, Nong X, Lai F, Nong C, Wang T, Tang Y. Noninvasive Prenatal Diagnosis of SEA-Thalassemia by Combining 1000 Genomes Database and Relative Haplotype Dosage. Hemoglobin 2024:1-8. [PMID: 38632980 DOI: 10.1080/03630269.2024.2327830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024]
Abstract
To explore a noninvasive method for diagnosis of SEA-thalassemia and to investigate whether the regional factors affect the accuracy of this method. The method involved using a public database and bioinformatics software to construct parental haplotypes for proband and predicting fetal genotypes using relative haplotype dosage. We screened and downloaded sequencing data of couples who were both SEA-thalassemia carriers from the China National Genebank public data platform, and matched the sequencing data format with that of the reference panel using Ubuntu system tools. We then used Beagle software to construct parental haplotypes, predicted fetal haplotypes by relative haplotype dosage. Finally, we used Hidden Markov Model and Viterbi algorithm to determine fetal pathogenic haplotypes. All noninvasive fetal genotype diagnosis results were compared with gold standard gap-PCR electrophoresis results. Our method was successful in diagnosing 13 families with SEA-thalassemia carriers. The best diagnostic results were obtained when Southern Chinese Han was used as the reference panel, and 10 families showed full agreement between our noninvasive diagnostic results and the gap-PCR electrophoresis results. The accuracy of our method was higher when using a Chinese Han as the reference panel for haplotype construction in the Southern Chinese Han region as opposed to Beijing Chinese region. The combined use of public databases and relative haplotype dosage for diagnosing SEA-thalassemia is a feasible approach. Our method produces the best noninvasive diagnostic results when the test samples and population reference panel are closely matched in both ethnicity and geography. When constructing parental haplotypes with our method, it is important to consider the effect of region in addition to population background alone.
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Affiliation(s)
- Dewen Liu
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xuejuan Nong
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Fengming Lai
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chen Nong
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Taizhong Wang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yulian Tang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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Chaemsaithong P, Luewan S, Taweevisit M, Chiangjong W, Pongchaikul P, Thorner PS, Tongsong T, Chutipongtanate S. Placenta-Derived Extracellular Vesicles in Pregnancy Complications and Prospects on a Liquid Biopsy for Hemoglobin Bart's Disease. Int J Mol Sci 2023; 24:5658. [PMID: 36982732 PMCID: PMC10055877 DOI: 10.3390/ijms24065658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Extracellular vesicles (EVs) are nano-scaled vesicles released from all cell types into extracellular fluids and specifically contain signature molecules of the original cells and tissues, including the placenta. Placenta-derived EVs can be detected in maternal circulation at as early as six weeks of gestation, and their release can be triggered by the oxygen level and glucose concentration. Placental-associated complications such as preeclampsia, fetal growth restriction, and gestational diabetes have alterations in placenta-derived EVs in maternal plasma, and this can be used as a liquid biopsy for the diagnosis, prediction, and monitoring of such pregnancy complications. Alpha-thalassemia major ("homozygous alpha-thalassemia-1") or hemoglobin Bart's disease is the most severe form of thalassemia disease, and this condition is lethal for the fetus. Women with Bart's hydrops fetalis demonstrate signs of placental hypoxia and placentomegaly, thereby placenta-derived EVs provide an opportunity for a non-invasive liquid biopsy of this lethal condition. In this article, we introduced clinical features and current diagnostic markers of Bart's hydrops fetalis, extensively summarize the characteristics and biology of placenta-derived EVs, and discuss the challenges and opportunities of placenta-derived EVs as part of diagnostic tests for placental complications focusing on Bart's hydrop fetalis.
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Affiliation(s)
- Piya Chaemsaithong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Suchaya Luewan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiangmai University, Chiangmai 50200, Thailand
| | - Mana Taweevisit
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok 10330, Thailand
| | - Wararat Chiangjong
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
- Integrative Computational BioScience Center, Mahidol University, Nakhon Pathom 73170, Thailand
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
| | - Paul Scott Thorner
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Theera Tongsong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiangmai University, Chiangmai 50200, Thailand
| | - Somchai Chutipongtanate
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Long J, Sun L, Gong F, Zhang C, Mao A, Lu Y, Li J, Liu E. Third-generation sequencing: A novel tool detects complex variants in the α-thalassemia gene. Gene 2022; 822:146332. [PMID: 35181504 DOI: 10.1016/j.gene.2022.146332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Thalassemia is a monogenic disorder with a high carrier rate in the southern region of China. Most laboratories currently follow the protocol of testing hematologic indicators in individuals with positive hematologic indicators and then using the hot-spot mutation test kit. A novel thalassemia gene test is performed if there is a mismatch between the hematology and hot-spot mutation test results. However, due to the large population in southern China, some individuals carry complex α-globin gene cluster (CAGC) variants in NG_000006.1, which are difficult to detect using conventional thalassemia genetic analysis protocols, leading to missed or false genetic test results for individuals carrying these complex α-globin gene cluster variants. When an individual carries a complex α-thalassemia gene variant, and an individual carries a β- thalassemia gene variant, there may be clinical symptoms that might complicate clinical consultation and prenatal diagnosis if not accurately detected. Third-generation sequencing (TGS) enables long-read single-molecule sequencing with high detection accuracy, and long-length DNA chain reads in high-fidelity reads mode. TGS can be used to analyze high homology and rich GC DNA sequences. RESULTS Four samples that showed abnormalities in the thalassemia genetic test were studied using TGS, revealing that they carried genotypes with complex α-globin gene cluster variants, one of which was a complex variant αα anti3.7 α anti3.7 α 17.2. CONCLUSIONS TGS detects complex α-globin gene cluster variants. This study may provide a reference protocol for the use of TGS for the detection of complex α-globin gene cluster variants. TGS can reveal individuals with complex α-thalassemia genotypes in the population and improve the accuracy of genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Ju Long
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China.
| | - Lei Sun
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Feifei Gong
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Chenghong Zhang
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Aiping Mao
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Yulin Lu
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Jiaqi Li
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Enqi Liu
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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