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Jourdy Y, Chatron N, Frétigny M, Zawadzki C, Lienhart A, Stieltjes N, Rohrlich PS, Thauvin-Robinet C, Volot F, Hamida YF, Hariti G, Leuci A, Dargaud Y, Sanlaville D, Vinciguerra C. Whole F8 gene sequencing identified pathogenic structural variants in the remaining unsolved patients with severe hemophilia A. J Thromb Haemost 2024; 22:1616-1626. [PMID: 38484912 DOI: 10.1016/j.jtha.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND No F8 genetic abnormality is detected in approximately 1% to 2% of patients with severe hemophilia A (HA) using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. OBJECTIVES The study aimed to identify the causal variation in families with a history of severe HA for whom genetic investigations failed. METHODS We performed whole F8 gene sequencing in 8 propositi. Genomic rearrangements were confirmed by Sanger sequencing of breakpoint junctions and/or quantitative polymerase chain reaction. RESULTS A structural variant disrupting F8 was found in each propositus, so that all the 815 families with a history of severe HA registered in our laboratory received a conclusive genetic diagnosis. These structural variants consisted of 3 balanced inversions, 3 large insertions of gained regions, and 1 retrotransposition of a mobile element. The 3 inversions were 105 Mb, 1.97 Mb, and 0.362 Mb in size. Among the insertions of gained regions, one corresponded to the insertion of a 34 kb gained region from chromosome 6q27 in F8 intron 6, another was the insertion of a 447 kb duplicated region from chromosome 9p22.1 in F8 intron 14, and the last one was the insertion of an Xq28 349 kb gained in F8 intron 5. CONCLUSION All the genetically unsolved cases of severe HA in this cohort were due to structural variants disrupting F8. This study highlights the effectiveness of whole F8 sequencing to improve the molecular diagnosis of HA when the conventional approach fails.
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Affiliation(s)
- Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France.
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Mathilde Frétigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Christophe Zawadzki
- Pôle de Biologie Pathologie Génétique, Institut d'Hématologie - Transfusion, CHU Lille, Lille, France
| | - Anne Lienhart
- Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | | | | | - Christel Thauvin-Robinet
- Centre de Génétique, Centre de Référence, Déficiences Intellectuelles de Causes Rares, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | | | | | - Ghania Hariti
- Laboratoire de recherche en hémostase, Université d'Alger 1, Alger, Algérie
| | - Alexandre Leuci
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Yesim Dargaud
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France; Hospices Civils de Lyon, Lyon Hemophilia Center and Clinical Haemostasis Unit, Bron, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Université Claude Bernard Lyon 1 - CNRS UMR 5261 -INSERM U1315, Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
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Chen Y, Xie T, Ma M, Yang J, Lv Y, Dong X. Case report: Identification of a novel triplication of alpha-globin gene by the third-generation sequencing: pedigree analysis and genetic diagnosis. Hematology 2023; 28:2277571. [PMID: 38059617 DOI: 10.1080/16078454.2023.2277571] [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: 08/06/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Thalassemia, a common autosomal hereditary blood disorder worldwide, mainly contains α- and β-thalassemia. The α-globin gene triplicates allele is harmless for carriers, but aggravates the phenotype of β-thalassemia. Therefore, it is particularly crucial to accurately detect the structural variants of α-globin gene clusters. CASE REPORT We reported a 28-year-old man, the proband, with microcytic hypochromic anemia. From pedigree analysis, his mother and sister had hypochromic microcytosis, and his father was normal. Genetic testing of thalassemia identified a novel α-globin gene triplicate named αααanti4.2del726bp (NC_000016.10:g.170769_174300dupinsAAAAAA) by third-generation sequencing (TGS) in the proband and his father, which was further validated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The genotypes of the proband's mother and sister were both -α3.7/αα compounded with heterozygous HBB:c.126_129delCTTT. They were categorized as silent α-thalassemia with co-inheritance of β-thalassemia trait. The proband's genotype additionally had the α-globin gene triplicates compared with his mother and sister, which increased the imbalance between α/β-globin, so the proband had more severe hematological parameters. The proband's wife was diagnosed as HBA2:c.427T > C heterozygosis, and his daughter had the novel α-globin gene triplicates compounded with HBA2:c.427T > C, therefore the girl might be asymptomatic. CONCLUSION The identification of the novel α-globin gene triplicates provides more insight for the research of thalassemia variants and indicates that TGS has significant advantages on genetic testing of thalassemia for the reliability, accuracy and comprehensiveness.
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Affiliation(s)
- Yujiao Chen
- Dehong Medical Group Hospital of Traditional Chinese Medicine, Dehong Dai and Jingpo Autonomous Prefecture, People's Republic of China
| | - Tiantian Xie
- Berry Genomics Corporation, Beijing, People's Republic of China
| | - Minhui Ma
- Berry Genomics Corporation, Beijing, People's Republic of China
| | - Juan Yang
- Kunming Kingmed Institute for Clinical Laboratory, Kunming, People's Republic of China
| | - Yihang Lv
- Department of Obstetrical, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Xudong Dong
- Department of Obstetrical, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, People's Republic of China
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Liu Y, Li D, Yu D, Liang Q, Chen G, Li F, Gao L, Li Z, Xie T, Wu L, Mao A, Wu L, Liang D. Comprehensive Analysis of Hemophilia A (CAHEA): Towards Full Characterization of the F8 Gene Variants by Long-Read Sequencing. Thromb Haemost 2023; 123:1151-1164. [PMID: 37285902 PMCID: PMC10686748 DOI: 10.1055/a-2107-0702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hemophilia A (HA) is the most frequently occurring X-linked bleeding disorder caused by heterogeneous variants in the F8 gene, one of the largest genes known. Conventional molecular analysis of F8 requires a combination of assays, usually including long-range polymerase chain reaction (LR-PCR) or inverse-PCR for inversions, Sanger sequencing or next-generation sequencing for single-nucleotide variants (SNVs) and indels, and multiplex ligation-dependent probe amplification for large deletions or duplications. MATERIALS AND METHODS This study aimed to develop a LR-PCR and long-read sequencing-based assay termed comprehensive analysis of hemophilia A (CAHEA) for full characterization of F8 variants. The performance of CAHEA was evaluated in 272 samples from 131 HA pedigrees with a wide spectrum of F8 variants by comparing to conventional molecular assays. RESULTS CAHEA identified F8 variants in all the 131 pedigrees, including 35 intron 22-related gene rearrangements, 3 intron 1 inversion (Inv1), 85 SNVs and indels, 1 large insertion, and 7 large deletions. The accuracy of CAHEA was also confirmed in another set of 14 HA pedigrees. Compared with the conventional methods combined altogether, CAHEA assay demonstrated 100% sensitivity and specificity for identifying various types of F8 variants and had the advantages of directly determining the break regions/points of large inversions, insertions, and deletions, which enabled analyzing the mechanisms of recombination at the junction sites and pathogenicity of the variants. CONCLUSION CAHEA represents a comprehensive assay toward full characterization of F8 variants including intron 22 and intron 1 inversions, SNVs/indels, and large insertions and deletions, greatly improving the genetic screening and diagnosis for HA.
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Affiliation(s)
- Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Guilan Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lu Gao
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Zhuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Le Wu
- Berry Genomics Corporation, Beijing, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Lingqian Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Desheng Liang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
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Spectrum of Causative Mutations in Patients with Hemophilia A in Russia. Genes (Basel) 2023; 14:genes14020260. [PMID: 36833187 PMCID: PMC9957479 DOI: 10.3390/genes14020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Hemophilia A (HA) is one of the most widespread, X-linked, inherited bleeding disorders, which results from defects in the F8 gene. Nowadays, more than 3500 different pathogenic variants leading to HA have been described. Mutation analysis in HA is essential for accurate genetic counseling of patients and their relatives. We analyzed patients from 273 unrelated families with different forms of HA. The analysis consisted of testing for intron inversion (inv22 and inv1), and then sequencing all functionally important F8 gene fragments. We identified 101 different pathogenic variants in 267 patients, among which 35 variants had never been previously reported in international databases. We found inv22 in 136 cases and inv1 in 12 patients. Large deletions (1-8 exons) were found in 5 patients, and we identified a large insertion in 1 patient. The remaining 113 patients carried point variants involving either single nucleotide or several consecutive nucleotides. We report herein the largest genetic analysis of HA patients issued in Russia.
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