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Nomura S. Current Status and Challenges in Delivering Comprehensive Care for Patients with Hemophilia. J Blood Med 2023; 14:629-637. [PMID: 38125786 PMCID: PMC10730945 DOI: 10.2147/jbm.s446204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
The importance of comprehensive care as a treatment strategy for patients with hemophilia is recognized worldwide. Comprehensive care entails addressing full spectrum of medical and psychological aspects impacting both patients and their families. The primary objective of comprehensive care for individuals with hemophilia is to enable them to lead their daily lives just as anyone else would. To achieve this goal, it is necessary to have a positive and collaborative approach across various healthcare disciplines. This extends beyond clinical specialists, encompassing pediatricians, hematologists, orthopedic surgeons, dental and oral surgeons, gynecologists, nurses, physical therapists, clinical psychologists, and other professionals from diverse fields. This review article discusses the current status and challenges associated with comprehensive care for patients with hemophilia. We categorize these challenges as follows: hemophilic arthritis, rehabilitation, oral care, transitioning from pediatric to adult care, addressing carrier issues, and providing psychological care. There is still substantial work to be undertaken in addressing these hurdles and advancing the quality of comprehensive care for hemophilia patients.
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Affiliation(s)
- Shosaku Nomura
- Center of Thrombosis and Hemostasis, Kansai Medical University Medical Center, Moriguchi, Osaka, Japan
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2
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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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3
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Hiramoto T, Inaba H, Baatartsogt N, Kashiwakura Y, Hayakawa M, Kamoshita N, Nishimasu H, Nureki O, Kinai E, Ohmori T. Genome editing of patient-derived iPSCs identifies a deep intronic variant causing aberrant splicing in hemophilia A. Blood Adv 2023; 7:7017-7027. [PMID: 37792826 PMCID: PMC10690555 DOI: 10.1182/bloodadvances.2023010838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
The importance of genetic diagnosis for patients with hemophilia has been recently demonstrated. However, the pathological variant cannot be identified in some patients. Here, we aimed to identify the pathogenic intronic variant causing hemophilia A using induced pluripotent stem cells (iPSCs) from patients and genome editing. We analyzed siblings with moderate hemophilia A and without abnormalities in the F8 exon. Next-generation sequencing of the entire F8 revealed 23 common intron variants. Variant effect predictor software indicated that the deep intronic variant at c.5220-8563A>G (intron 14) might act as a splicing acceptor. We developed iPSCs from patients and used genome editing to insert the elongation factor 1α promoter to express F8 messenger RNA (mRNA). Then, we confirmed the existence of abnormal F8 mRNA derived from aberrant splicing, resulting in a premature terminal codon as well as a significant reduction in F8 mRNA in iPSCs due to nonsense-mediated RNA decay. Gene repair by genome editing recovered whole F8 mRNA expression. Introduction of the intron variant into human B-domain-deleted F8 complementary DNA suppressed factor VIII (FVIII) activity and produced abnormal FVIII lacking the light chain in HEK293 cells. Furthermore, genome editing of the intron variant restored FVIII production. In summary, we have directly proven that the deep intronic variant in F8 results in aberrant splicing, leading to abnormal mRNA and nonsense-mediated RNA decay. Additionally, genome editing targeting the variant restored F8 mRNA and FVIII production. Our approach could be useful not only for identifying causal variants but also for verifying the therapeutic effect of personalized genome editing.
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Affiliation(s)
- Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Hiroshi Inaba
- Department of Laboratory Medicine, Tokyo Medical University, Tokyo, Japan
| | - Nemekhbayar Baatartsogt
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Yuji Kashiwakura
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Morisada Hayakawa
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Nobuhiko Kamoshita
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ei Kinai
- Department of Laboratory Medicine, Tokyo Medical University, Tokyo, Japan
| | - Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
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4
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Dericquebourg A, Fretigny M, Leuci A, Zawadzki C, Huguenin Y, Castet SM, Dargaud Y, Vinciguerra C, Jourdy Y. Whole F8 gene sequencing combined with splicing functional analyses led to a substantial increase of the molecular diagnosis yield for non-severe haemophilia A. Haemophilia 2023; 29:1320-1333. [PMID: 37410802 DOI: 10.1111/hae.14824] [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: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
INTRODUCTION Conventional genetic investigation fails to identify the F8 causal variant in 2.5%-10% of haemophilia A (HA) patients with non-severe phenotypes. In these cases, F8 deep intronic variants could be causal. AIM To identify pathogenic F8 deep intronic variants in genetically unresolved families with non-severe HA analysed in the haematology laboratory of the Hospices Civils de Lyon. METHODS The whole F8 was analysed by next generation sequencing. The pathogenic impact of candidate variants identified was assessed using both in silico analysis (MaxEntScan and spliceAI) and functional analysis (RNA or minigene assay). RESULTS Sequencing was performed in 49/55 families included for which a DNA sample from a male propositus was available. In total, 33 candidate variants from 43 propositi were identified. These variants corresponded to 31 single nucleotide substitutions, one 173-bp deletion, and an 869-bp tandem triplication. No candidate variant was found in six propositi. The most frequent variants found were the association of [c.2113+1154G>C and c.5374-304C>T], identified in five propositi, and the c.2114-6529C>G identified in nine propositi. Four variants had been previously described as HA-causing. Splicing functional assay found a deleterious impact for 11 substitutions (c.671-94G>A, c.788-312A>G, c.2113+1154G>C, c.2114-6529C>G, c.5999-820A>T, c.5999-786C>A, c.5999-669G>T, c.5999-669G>A, c.5999-669G>C, c.6900+4104A>C, and c.6901-2992A>G). The HA-causing variant was identified in 33/49 (67%) cases. In total, F8 deep intronic variants caused 8.8% of the non-severe HA among the 1643 families analysed in our laboratory. CONCLUSION The results emphasise the value of whole F8 gene sequencing combined with splicing functional analyses to improve the diagnosis yield for non-severe HA.
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Affiliation(s)
- Amy Dericquebourg
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Mathilde Fretigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Alexandre Leuci
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Christophe Zawadzki
- Pôle de Biologie Pathologie Génétique, Institut d'Hématologie - Transfusion, CHU Lille, Lille, France
| | - Yoann Huguenin
- Centre de Ressources et de Compétence des Maladies Hémorragiques Constitutionnelles, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Sabine-Marie Castet
- Centre de Ressources et de Compétence des Maladies Hémorragiques Constitutionnelles, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Yesim Dargaud
- Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
- Unité d'Hémostase Clinique, Centre National de Reference de l'Hémophilie, Hôpital Cardiologique Louis Pradel, Université Lyon, 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
| | - 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
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Dardik R, Janczar S, Lalezari S, Avishai E, Levy-Mendelovich S, Barg AA, Martinowitz U, Babol-Pokora K, Mlynarski W, Kenet G. Four Decades of Carrier Detection and Prenatal Diagnosis in Hemophilia A: Historical Overview, State of the Art and Future Directions. Int J Mol Sci 2023; 24:11846. [PMID: 37511607 PMCID: PMC10380558 DOI: 10.3390/ijms241411846] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Hemophilia A (HA), a rare recessive X-linked bleeding disorder, is caused by either deficiency or dysfunction of coagulation factor VIII (FVIII) resulting from deleterious mutations in the F8 gene encoding FVIII. Over the last 4 decades, the methods aimed at determining the HA carrier status in female relatives of HA patients have evolved from phenotypic studies based on coagulation tests providing merely probabilistic results, via genetic linkage studies based on polymorphic markers providing more accurate results, to next generation sequencing studies enabling highly precise identification of the causative F8 mutation. In parallel, the options for prenatal diagnosis of HA have progressed from examination of FVIII levels in fetal blood samples at weeks 20-22 of pregnancy to genetic analysis of fetal DNA extracted from chorionic villus tissue at weeks 11-14 of pregnancy. In some countries, in vitro fertilization (IVF) combined with preimplantation genetic diagnosis (PGD) has gradually become the procedure of choice for HA carriers who wish to prevent further transmission of HA without the need to undergo termination of pregnancies diagnosed with affected fetuses. In rare cases, genetic analysis of a HA carrier might be complicated by skewed X chromosome inactivation (XCI) of her non-hemophilic X chromosome, thus leading to the phenotypic manifestation of moderate to severe HA. Such skewed XCI may be associated with deleterious mutations in X-linked genes located on the non-hemophilic X chromosome, which should be considered in the process of genetic counseling and PGD planning for the symptomatic HA carrier. Therefore, whole exome sequencing, combined with X-chromosome targeted bioinformatic analysis, is highly recommended for symptomatic HA carriers diagnosed with skewed XCI in order to identify additional deleterious mutations potentially involved in XCI skewing. Identification of such mutations, which may profoundly impact the reproductive choices of HA carriers with skewed XCI, is extremely important.
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Affiliation(s)
- Rima Dardik
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Szymon Janczar
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Shadan Lalezari
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Einat Avishai
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Sarina Levy-Mendelovich
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Assaf Arie Barg
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Uri Martinowitz
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Katarzyna Babol-Pokora
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Gili Kenet
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
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6
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Borràs N, Castillo-González D, Comes N, Martin-Fernandez L, Rivero-Jiménez RA, Chang-Monteagudo A, Ruiz-Moleón V, Garrote-Santana H, Vidal F, Macías-Abraham C. Molecular study of a large cohort of 109 haemophilia patients from Cuba using a gene panel with next generation sequencing-based technology. Haemophilia 2021; 28:125-137. [PMID: 34708896 DOI: 10.1111/hae.14438] [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: 07/07/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION In several countries, molecular diagnosis of haemophilia A (HA) and B (HB) is hampered by a lack of resources for DNA analysis. The advent of next-generation sequencing (NGS) has enabled gene analysis at a reasonable cost. AIM Describe a collaboration between Cuban and Spanish researchers to identify candidate variants and investigate the molecular epidemiology of 106 Cuban haemophilia patients using NGS. PATIENTS/METHODS The molecular analysis protocol included well-established LR-PCR procedures to detect F8 inversions, NGS with a 30-gene panel to sequence F8 and F9, and multiplex ligation-dependent probe amplification to identify large structural variants. RESULTS One-hundred and thirty-one candidate variants were identified along F8, F9, and VWF; 72 were unique and 28 (39%) had not been previously recorded. Putative variants were identified in 105/106 patients. Molecular characterization enabled confirmation and reclassification of: 90 HA (85%), 15 HB (14%), and one type 2N VWD (1%). Null variants leading to non-production of FVIII or FIX were common in severe HA (64%), moderate HA (74%), and severe HB (60%), whereas missense variants were frequent in mild HA (57%) and moderate or mild HB (83%). Additional variants in VWF were identified in 16 patients. CONCLUSION This is the first description of the molecular epidemiology of HA and HB in Cuba. Variants identified in index cases will be of value for local implementation of familial studies and prenatal diagnosis using the molecular approaches available in Cuba. The results of this protocolled genetic study improved the accuracy of the clinical diagnosis and will facilitate management of these patients.
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Affiliation(s)
- Nina Borràs
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Natalia Comes
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | - Laura Martin-Fernandez
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | | | | | | | | | - Francisco Vidal
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto Carlos III (ISCIII), Madrid, Spain
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7
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Chen J, Li Q, Lin S, Li F, Huang L, Jin W, Yang X, Li Y, Li K, Xiong Y, Fan D, Zheng L, Luo D, Li L, Yang X. The spectrum of FVIII gene variants detected by next generation sequencing in 236 Chinese non-inversion hemophilia A pedigrees. Thromb Res 2021; 202:8-13. [PMID: 33706050 DOI: 10.1016/j.thromres.2021.02.027] [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: 09/20/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The reported variants of hemophilia A are mainly from European subjects and American subjects of European descent, and limited data are available from more diverse ethnic backgrounds. This study was performed to identify the causative variants in a large HA cohort from Chinese population. MATERIALS AND METHODS A total of 236 HA pedigrees were included. Molecular analysis of F8 gene was performed using next-generation sequencing (NGS) and then validated by Sanger sequencing and multiplex ligation probe amplification (MLPA) results. Variants were classified as pathogenic, likely pathogenic, variant of unknown significance, likely benign, and benign according to the American College of Medical Genetics and Genomics guidelines. RESULTS A total of 186 F8 variants were identified, with 139 (139/186, 74.73%) point mutations, 44 (44/186, 23.66%) small insertions/deletions (InDels), and 3 (3/186, 1.61%) large deletions, they included 80 pathogenic and 84 likely pathogenic variants. Of these variants, 119 had been reported previously, and 67 were novel. No potentially causative mutations were found in the targeted F8 region in seventeen HA pedigrees. CONCLUSIONS The spectrum of F8 variants identified in this study provides additional information about HA and enriches our knowledge of the variant spectrum in a wider range of ethnic backgrounds.
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Affiliation(s)
- Juanjuan Chen
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Qiang Li
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Sheng Lin
- Lab of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, China
| | - Fenxia Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Limin Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Wangjie Jin
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yihong Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yufeng Xiong
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Dongmei Fan
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Lei Zheng
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Dixian Luo
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Chenzhou Center for Clinical Pathological Laboratory, National and Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Affiliated The First People's Hospital of Chenzhou, Chenzhou 432000, China.
| | - Liyan Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
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8
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Mosaad RM, Amr KS, Rabie EA, Mostafa NO, Habib SA, El-Kamah GY. Genomic alterations in the F8 gene correlating with severe hemophilia A in Egyptian patients. Mol Genet Genomic Med 2020; 9:e1575. [PMID: 33342086 PMCID: PMC8077131 DOI: 10.1002/mgg3.1575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/02/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
Background Hemophilia A (HA) is an inherited X‐linked recessive coagulation disorder caused by factor VIII (F8) deficiency. F8 rearrangements involving intron 22 (int22) and intron 1 (int1) account for almost half of severe HA phenotype also a hotspot exon 14 provides numerous mutational patterns. This study aims to identify F8 gene mutations among Egyptian HA patients. Methods DNA samples from 60 HA patients were screened for int22 and int1 rearrangements using simplified inverse shifting PCR (IS‐PCR) followed by exon 14 sequencing. Also, four uncharacterized patients were studied by targeted exome sequencing. Results In 33.3% of the studied patients, we identified three int22 rearrangements, three exon 14 mutations (two frameshift; one novel (NM_000132.3:c.2734_2735delAA, p.(N912Ffs*6)), a second reported mutation (NM_000132.3:c.3091_3094delAGAA, p.(K1031Lfs*9)), and one nonsense mutation (NM_000132.3:c.2440C>T, p.(R814*)). All identified mutations were detected in patients with severe HA phenotype. Targeted exome sequencing could not detect any known pathogenic variants. Conclusion Intron 22 rearrangement and exon 14 mutations correlate with most severe hemophilia A Egyptian patients.
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Affiliation(s)
- Rehab M Mosaad
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Division (HGGR), National Research Centre (NRC), Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics, HGGR, NRC, Cairo, Egypt
| | - Eman A Rabie
- Medical Molecular Genetics, HGGR, NRC, Cairo, Egypt.,Biotechnology Program, School of Sciences and Engineering, The American University in Cairo (AUC), Cairo, Egypt
| | - Naglaa O Mostafa
- Department of Hematology, Pediatric Hospital, Cairo University, Cairo, Egypt
| | - Sonia A Habib
- Department of Pediatrics, Medical Division, NRC, Cairo, Egypt
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9
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Lassalle F, Jourdy Y, Jouan L, Swystun L, Gauthier J, Zawadzki C, Goudemand J, Susen S, Rivard GE, Lillicrap D. The challenge of genetically unresolved haemophilia A patients: Interest of the combination of whole F8 gene sequencing and functional assays. Haemophilia 2020; 26:1056-1063. [PMID: 33094873 DOI: 10.1111/hae.14179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The causative variant remains unidentified in 2%-5% of haemophilia A (HA) patients despite an exhaustive sequencing of the full F8 coding sequence, splice consensus sequences, 5'/3' untranslated regions and copy number variant (CNV) analysis. Next-generation sequencing (NGS) has provided significant improvements for a complete F8 analysis. AIM The aim of this study was to identify and characterize pathogenic non-coding variants in F8 of 15 French and Canadian HA patients genetically unresolved, through the use of NGS, mRNA sequencing and functional confirmation of aberrant splicing. METHODS We sequenced the entire F8 gene using an NGS capture method. We analysed F8 mRNA in order to detect aberrant transcripts. The pathogenic effect of candidate intronic variants was further confirmed using a minigene assay. RESULTS After bioinformatic analysis, 11 deep intronic variants were identified in 13 patients (8 new variants and 3 previously reported). Three variants were confirmed to be likely pathogenic with the presence of an aberrant transcript during mRNA analysis and minigene assay. We also found a small intronic deletion in 6 patients, recently described as causing mild HA. CONCLUSION With this comprehensive work combining NGS and functional assays, we report new deep intronic variants that cause HA through splicing alteration mechanism. Functional analyses are critical to confirm the pathogenic effect of these variants and will be invaluable in the future to study the large number of variants of uncertain significance that may affect splicing that will be found in the human genome.
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Affiliation(s)
- Fanny Lassalle
- CHU Lille, Institut d'Hématologie - Transfusion, Pôle de Biologie Pathologie Génétique, Lille, France.,Univ Lille, Inserm, U1011 - EGID, Institut Pasteur de Lille, Lille, France
| | - Yohann Jourdy
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, France.,EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - Loubna Jouan
- Integrated Centre for Pediatric Clinical Genomics, CHU Sainte Justine, Montreal, Canada
| | - Laura Swystun
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Julie Gauthier
- Molecular Diagnostic Laboratory and Division of Medical Genetics, Department of Pediatrics, CHU Sainte Justine, Montreal, Canada
| | - Christophe Zawadzki
- CHU Lille, Institut d'Hématologie - Transfusion, Pôle de Biologie Pathologie Génétique, Lille, France
| | - Jenny Goudemand
- CHU Lille, Institut d'Hématologie - Transfusion, Pôle de Biologie Pathologie Génétique, Lille, France
| | - Sophie Susen
- CHU Lille, Institut d'Hématologie - Transfusion, Pôle de Biologie Pathologie Génétique, Lille, France.,Univ Lille, Inserm, U1011 - EGID, Institut Pasteur de Lille, Lille, France
| | | | - David Lillicrap
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
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10
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Haddad-Mashadrizeh A, Hemmat J, Aslamkhan M. Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements. Heliyon 2020; 6:e04727. [PMID: 32944665 PMCID: PMC7481535 DOI: 10.1016/j.heliyon.2020.e04727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/03/2019] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Increasing data show that intronic derived regulatory elements, such as transcription factor binding sites (TFBs), play key roles in gene regulation, and malfunction. Accordingly, characterizing the sequence context of the intronic regions of the human coagulation factor VIII (hFVIII) gene can be important. In this study, the intronic regions of the hFVIII gene were scrutinized based on in-silico methods. The results disclosed that these regions harbor a rich array of functional elements such as repetitive elements (REs), splicing sites, and transcription factor binding sites (TFBs). Among these elements, TFBs and REs showed a significant distribution and correlation to each other. This survey indicated that 31% of TFBs are localized in the intronic regions of the gene. Moreover, TFBs indicate a strong bias in the regions far from splice sites of introns with mapping to different REs. Accordingly, TFBs showed highly bias toward Short Interspersed Elements (SINEs), which in turn they covering about 12% of the total of REs. However, the distribution pattern of TFBs-REs showed different bias in the intronic regions, spatially into the Introns 13 and 25. The rich array of SINE-TFBs and CR1-TFBs were situated within 5′UTR of the gene that may be an important driving force for regulatory innovation of the hFVIII gene. Taken together, these data may lead to revealing intronic regions with the capacity to renewing gene regulatory networks of the hFVIII gene. On the other hand, these correlations might provide the novel idea for a new hypothesis of molecular evolution of the FVIII gene, and treatment of Hemophilia A which should be considered in future studies.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Recombinant Proteins Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jafar Hemmat
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Muhammad Aslamkhan
- Human Genetics & Molecular Biology Dept., University of Health Sciences, Lahore, Pakistan.,Honorary Senior Lecturer in the School of the Medicine University of Liverpool, Liverpool, UK
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11
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Huang L, Li L, Lin S, Chen J, Li K, Fan D, Jin W, Li Y, Yang X, Xiong Y, Li F, Yang X, Li M, Li Q. Molecular analysis of 76 Chinese hemophilia B pedigrees and the identification of 10 novel mutations. Mol Genet Genomic Med 2020; 8:e1482. [PMID: 32875744 PMCID: PMC7667291 DOI: 10.1002/mgg3.1482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Hemophilia B (HB) is an X-linked recessive inherited bleeding disorder caused by mutations in the F9 gene that lead to plasma factor IX deficiency. To identify the causative mutations in HB, a molecular analysis of HB pedigrees in China was performed. METHODS Using next-generation sequencing (NGS) and an in-house bioinformatics pipeline, 76 unrelated HB pedigrees were analyzed. The mutations identified were validated by comparison with the results of Sanger sequencing or Multiplex Ligation-dependent Probe Amplification assays. The pathogenicity of the causative mutations was classified following the American College of Medical Genetics and Genomics guidelines. RESULTS The mutation detection rate was 94.74% (72/76) using NGS. Of the 76 HB pedigrees analyzed, 59 causative variants were found in 72 pedigrees, with 38 (64.41%) missense mutations, 9 (15.25%) nonsense mutations, 2 (3.39%) splicing mutations, 5 (8.47%) small deletions, 4 (6.78%) large deletions, and 1 intronic mutation (1.69%). Of the 59 different F9 mutations, 10 were novel: c.190T>G, c.199G>T, c.290G>C, c.322T>A, c.350_351insACAATAATTCCTA, c.391+5delG, c.416G>T, c.618_627delAGCTGAAACC, c.863delA, and c.1024_1027delACGA. Of these 10 novel mutations, a mosaic mutation, c.199G>T(p.Glu67Ter), was identified in a sporadic HB pedigree. Using in-silico analysis, these novel variants were predicted to be disease-causing. However, no potentially causative mutations were found in the F9 coding sequences of the four remaining HB pedigrees. In addition, two HB pedigrees carrying additional F8/F9 mutations were discovered. CONCLUSION The identification of these mutations enriches the spectrum of F9 mutations and provides further insights into the pathogenesis of HB in the Chinese population.
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Affiliation(s)
- Limin Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Liyan Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sheng Lin
- Laboratory of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, China
| | - Juanjuan Chen
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Dongmei Fan
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wangjie Jin
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yihong Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Clinical Innovation & Research Center (CIRC), Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Yufeng Xiong
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Fenxia Li
- Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Ming Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Qiang Li
- The Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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12
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Dericquebourg A, Jourdy Y, Fretigny M, Lienhart A, Claeyssens S, Ternisien C, Boisseau P, Rohrlich P, Négrier C, Vinciguerra C. Identification of new
F8
deep intronic variations in patients with haemophilia A. Haemophilia 2020; 26:847-854. [DOI: 10.1111/hae.14134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Amy Dericquebourg
- Service d’Hématologie BiologiqueCentre de Biologie et Pathologie Est Hospices Civils de Lyon France
- EA 4609 Hémostase et cancerUniversité Claude Bernard Lyon 1Univ. Lyon France
| | - Yohann Jourdy
- Service d’Hématologie BiologiqueCentre de Biologie et Pathologie Est Hospices Civils de Lyon France
- EA 4609 Hémostase et cancerUniversité Claude Bernard Lyon 1Univ. Lyon France
| | - Mathilde Fretigny
- Service d’Hématologie BiologiqueCentre de Biologie et Pathologie Est Hospices Civils de Lyon France
| | - Anne Lienhart
- Unité d'Hémostase CliniqueHôpital Cardiologique Louis Pradel Lyon, Hospices Civils de Lyon France
| | - Ségolène Claeyssens
- Centre de Ressources et de Compétences Maladies Hémorragiques Constitutionnelles Centre Hospitalier Universitaire de Toulouse‐Purpan Toulouse France
| | | | | | | | - Claude Négrier
- Service d’Hématologie BiologiqueCentre de Biologie et Pathologie Est Hospices Civils de Lyon France
- EA 4609 Hémostase et cancerUniversité Claude Bernard Lyon 1Univ. Lyon France
- Unité d'Hémostase CliniqueHôpital Cardiologique Louis Pradel Lyon, Hospices Civils de Lyon France
| | - Christine Vinciguerra
- Service d’Hématologie BiologiqueCentre de Biologie et Pathologie Est Hospices Civils de Lyon France
- EA 4609 Hémostase et cancerUniversité Claude Bernard Lyon 1Univ. Lyon France
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13
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Jourdy Y, Frétigny M, Lassalle F, Lillicrap D, Négrier C, Vinciguerra C. The highly prevalent deletions in F8 intron 13 found in French mild hemophilia A patients result from both founder effect and recurrent de novo events. J Thromb Haemost 2020; 18:1087-1093. [PMID: 32073743 DOI: 10.1111/jth.14771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Recently, our group has reported a 13-bp deletion in a poly(T)-track in the F8 intron 13 as the causative variant in approximately 6% of all cases of mild haemophilia A (HA) in France. The systematic screening of mild HA patients for this deletion identified individuals carrying deletions from 9 to 14-bp in the same region. AIMS To demonstrate that these highly prevalent deletions could result from a recurrent molecular mechanism and to determine the clinical significance of deletions other than 13-bp in size. METHODS Haplotype analysis using five polymorphic markers was performed in 71 unrelated French mild hemophilia A patients. Minigene analysis was performed to study the splicing impact of deletions from 1 to 14-bp. RESULTS A peculiar haplotype (H1) was identified in 22.5% of patients carrying the 13-bp deletion. Haplotypes differing from H1 only for the two most distal markers were found in more than the half of patients. These results confirmed the founder effect origin for the 13-bp deletion. However, the 9 patients carrying other sizes of deletion had a different haplotype suggesting that these deletions arose independently. Supporting the recurrent mechanism hypothesis, similar deletions were also found in 3/19 genetically unresolved mild Canadian patients. In vitro splicing analysis confirmed that deletions larger than 9-bp had a deleterious impact on splicing of F8 transcript. CONCLUSION We demonstrated that the poly(T)-track in F8 intron 13 is a deletion hotspot. We recommend that deletions in this region should be specifically investigated in all genetically unresolved mild HA patients.
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Affiliation(s)
- Yohann Jourdy
- Centre de Biologie et Pathologie Est, Service d'hématologie Biologique, Hospices Civils de Lyon, Bron, France
- Equipe d'accueil EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - Mathilde Frétigny
- Centre de Biologie et Pathologie Est, Service d'hématologie Biologique, Hospices Civils de Lyon, Bron, France
| | - Fanny Lassalle
- Inserm U1011 - EGID, Institut Pasteur de Lille, Université de Lille, CHU Lille, Lille, France
- Hematology and Transfusion, CHU Lille, Lille, France
| | - David Lillicrap
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Claude Négrier
- Centre de Biologie et Pathologie Est, Service d'hématologie Biologique, Hospices Civils de Lyon, Bron, France
- Equipe d'accueil EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - Christine Vinciguerra
- Centre de Biologie et Pathologie Est, Service d'hématologie Biologique, Hospices Civils de Lyon, Bron, France
- Equipe d'accueil EA 4609 Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
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14
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Villarreal-Martínez L, Ibarra-Ramirez M, Calvo-Anguiano G, Lugo-Trampe JDJ, Luna-Záizar H, Martínez-de-Villarreal LE, Meléndez-Aranda L, Jaloma-Cruz AR. Molecular genetic diagnosis by next-generation sequencing in a cohort of Mexican patients with haemophilia and report of novel variants. Blood Cells Mol Dis 2020; 83:102423. [PMID: 32224444 DOI: 10.1016/j.bcmd.2020.102423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Molecular analysis in haemophilia is currently used in the diagnosis, treatment and prognosis of this disease. Hispanic populations in Latin America have been of interest to researchers due to the reportedly high prevalence of inhibitors in these patients. AIM To perform next-generation sequencing (NGS) in a cohort of Mexican patients with HA and HB and correlate with clinical phenotypes. METHODS Patients with Haemophilia A (HA) or haemophilia B (HB), were evaluated using NGS with an Ion AmpliSeq Custom Panel. Odds ratios (ORs) for associations between F8 variants and inhibitors were obtained. RESULTS A total of 85 patients (60 with HA and 25 with HB) were included. Pathogenic variants in F8 were found in 93.3% of HA patients and in F9 in 96% of HB patients. Twelve novel potentially pathogenic variants were found. Inhibitors were observed in 20% of patients with severe HA. Four patients clinically diagnosed with HA were negative for F8 variants. CONCLUSION Overall detection rate of pathogenic variants in F8 and F9 genes was 94.6%. We identified 12 non previously reported variants and pathogenic variants in other coagulation related genes. Molecular diagnosis of HA and HB permits better options for management, assessment and genetic counseling.
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Affiliation(s)
- Laura Villarreal-Martínez
- Hematology Service, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, Mexico
| | - Marisol Ibarra-Ramirez
- Department of Genetics, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, Mexico
| | - Geovana Calvo-Anguiano
- Department of Genetics, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, Mexico
| | - José de Jesús Lugo-Trampe
- Department of Genetics, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, Mexico
| | - Hilda Luna-Záizar
- Departamento de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara. Guadalajara, Jalisco, Mexico
| | - Laura Elia Martínez-de-Villarreal
- Department of Genetics, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, Mexico
| | - Lennon Meléndez-Aranda
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico; Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara Guadalajara, Jalisco, Mexico
| | - Ana-Rebeca Jaloma-Cruz
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico.
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15
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Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. Blood 2020; 134:2082-2091. [PMID: 31064749 DOI: 10.1182/blood.2018891192] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/22/2019] [Indexed: 12/17/2022] Open
Abstract
A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multidisciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2396 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbor variants associated with rare bleeding, thrombotic, or platelet disorders (BTPDs). The molecular diagnostic rate was determined by the clinical phenotype, with an overall rate of 49.2% for all thrombotic, coagulation, platelet count, and function disorder patients and a rate of 3.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 745 unique variants, including copy number variants (CNVs) and intronic variants, as pathogenic, likely pathogenic, or variants of uncertain significance. Half of these variants (50.9%) are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BTPDs. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 894 index patients providing evidence that introducing an HTS genetic test is a valuable addition to laboratory diagnostics in patients with a high likelihood of having an inherited BTPD.
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16
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Jankowska KI, McGill J, Pezeshkpoor B, Oldenburg J, Atreya CD, Sauna ZE. Clinical manifestation of hemophilia A in the absence of mutations in the F8 gene that encodes FVIII: role of microRNAs. Transfusion 2019; 60:401-413. [PMID: 31785023 DOI: 10.1111/trf.15605] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hemophilia A (HA) is associated with mutations in the F8 gene that expresses factor VIII (FVIII). Unexpectedly, HA also manifests in a small subset of individuals with no mutations (exonic or intronic) in their F8 gene. MicroRNAs (miRNAs) cause translational interference, affecting protein quality and stoichiometry. Here, by analyzing miRNAs of two patients from this subset, we evaluated miRNA-based FVIII suppression as a testable hypothesis to explain FVIII deficiency in patients with HA with no F8 gene mutations. STUDY DESIGN AND METHODS To test the hypothesis, miRNA sequencing from two patients with mild and moderate HA with no mutations in their F8 gene, followed by experimental verification, was used to identify a group of upregulated miRNAs in patients with HA compared to normal controls; with binding sites in the 3' untranslated region (UTR) of F8 messenger RNA (mRNA), a prerequisite for miRNA-based gene regulation. From this pool, miR-374b-5p and miR-30c-5p, known to be expressed in human liver, where FVIII is expressed, were subjected to extensive characterization. RESULTS In two cell lines that constitutively express FVIII, we demonstrated that overexpression of miR-374b or miR-30c decreased FVIII expression, while an miR-30c inhibitor partially restored FVIII expression. CONCLUSION These data support a role for microRNAs in fine-tuning F8 gene regulation. Based on our findings, our current model suggests that in HA cases where the F8 gene is normal and is predicted to express normal levels of FVIII, F8 mRNA 3' UTR targeting miRNAs may be responsible for a FVIII-deficiency phenotype clinically manifesting as HA.
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Affiliation(s)
| | - Joseph McGill
- OTAT/DPPT/HB in the Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | | | - Zuben E Sauna
- OTAT/DPPT/HB in the Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
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17
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Beskorovainaya TS, Milovidova TB, Schagina OA, Ryzhkova OP, Polyakov AV. Complex Molecular Diagnostics of Hemophilia A in Russian Patients. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419080027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Chatron N, Schluth-Bolard C, Frétigny M, Labalme A, Vilchez G, Castet SM, Négrier C, Sanlaville D, Vinciguerra C, Jourdy Y. Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing. J Thromb Haemost 2019; 17:1097-1103. [PMID: 31021037 DOI: 10.1111/jth.14460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/18/2019] [Indexed: 01/23/2023]
Abstract
Essentials No F8 genetic abnormality is detected in about 2% of severe hemophilia A patients. Detection of F8 structural variants remains a challenge. We identified a new F8 rearrangement in a severe hemophilia A patient using nanopore sequencing. We highlight the value of single-molecule long-read sequencing technologies in a genomics laboratory. BACKGROUND No F8 genetic abnormality is detected in about 2% of severe hemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. OBJECTIVE To characterize, in a genetically unresolved severe hemophilia A patient, a new Xq28 rearrangement disrupting F8 using comprehensive molecular techniques including nanopore sequencing. RESULTS Long-range polymerase chain reaction (PCR) performed throughout F8 identified a nonamplifiable region in intron 25 indicating the presence of a genomic rearrangement. F8 messanger ribonucleic acid (mRNA) analysis including 3'rapid amplification of complementary deoxyribonucleic acid (cDNA) ends and nanopore sequencing found the presence of a F8 fusion transcript in which F8 exon 26 was replaced by a 742-bp pseudoexon corresponding to a noncoding region located at the beginning of the long arm of chromosome X (Xq12; chrX: 66 310 352-66 311 093, GRCh37/hg19). Cytogenetic microarray analysis found the presence of a Xq11.1q12 gain of 3.8 Mb. The PCR amplification of junction fragments and fluorescent in situ hybridization (FISH) analysis found that the Xq11q12 duplicated region was inserted in the F8 intron 25 genomic region. CONCLUSION We characterized a novel genomic rearrangement in which a 3.8-Mb Xq11.1q12 gain inserted in the F8 intron 25 led to an aberrant fusion transcript in a patient with severe hemophilia A (HA), using comprehensive molecular techniques. This study highlights the value of single-molecule long-read sequencing technologies for molecular diagnosis of HA especially when conventional genetic approaches have failed.
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Affiliation(s)
- Nicolas Chatron
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | - Caroline Schluth-Bolard
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | | | - Audrey Labalme
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Gaëlle Vilchez
- Groupe Hospitalier Est, Cellule bioinformatique de la plateforme de séquençage NGS du CHU de Lyon, Bron, France
| | - Sabine-Marie Castet
- Centre de ressources et compétences-maladies hémorragiques constitutionnelles, Hôpital Universitaire de Bordeaux, Bordeaux, France
| | - Claude Négrier
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
| | - Damien Sanlaville
- Service de génétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard, Lyon, France
| | - Christine Vinciguerra
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
| | - Yohann Jourdy
- Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
- EA 4609 Hémostase et cancer, Université Claude Bernard, Lyon, France
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