1
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Jourdy Y, Bardel C, Fretigny M, Diguet F, Rollat-Farnier PA, Mathieu ML, Labalme A, Sanlaville D, Edery P, Vinciguerra C, Schluth-Bolard C. Complete characterisation of two new large Xq28 duplications involving F8 using whole genome sequencing in patients without haemophilia A. Haemophilia 2021; 28:117-124. [PMID: 34480810 DOI: 10.1111/hae.14402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/28/2021] [Accepted: 08/21/2021] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Depending on the location of insertion of the gained region, F8 duplications can have variable clinical impacts from benign impact to severe haemophilia A phenotype. AIM To characterize two large Xq28 duplications involving F8 incidentally detected by chromosome microarray analysis (CMA) in two patients presenting severe intellectual disability but no history of bleeding disorder. METHODS Whole genome sequencing (WGS) was performed in order to characterize the two large Xq28 duplications at nucleotide level. RESULTS In patient 1, a 60-73 kb gained region encompassing the exons 23-26 of F8 and SMIM9 was inserted at the int22h-2 locus following a non-homologous recombination between int22h-1 and int22h-2. We hypothesized that two independent events, micro-homology-mediated break-induced replication (MMBIR) and break-induced replication (BIR), could be involved in this rearrangement. In patient 2, the CMA found duplication from 101 to 116-kb long encompassing the exons 16-26 of F8 and SMIM9. The WGS analysis identified a more complex rearrangement with the presence of three genomic junctions. Due to the multiple micro-homologies observed at breakpoints, a replication-based mechanism such as fork stalling and template switching (FoSTeS) was greatly suspected. In both cases, these complex rearrangements preserved an intact copy of the F8. CONCLUSION This study highlights the value of WGS to characterize the genomic junction at the nucleotide level and ultimately better describe the molecular mechanisms involved in Xq28 structural variations. It also emphasizes the importance of specifying the structure of the genomic gain in order to improve genotype-phenotype correlation and genetic counselling.
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Affiliation(s)
- Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie Biologique, Bron, France.,UR 4609 Hémostase et thrombose, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Bardel
- Hospices Civils de Lyon, Groupement Hospitalier Est, Cellule bioinformatique de la plateforme de séquençage NGS, Lyon, France.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France.,Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
| | - Mathilde Fretigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie Biologique, Bron, France
| | - Flavie Diguet
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
| | - Pierre-Antoine Rollat-Farnier
- Hospices Civils de Lyon, Groupement Hospitalier Est, Cellule bioinformatique de la plateforme de séquençage NGS, Lyon, France.,Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
| | - Marie-Laure Mathieu
- Hospices Civils de Lyon, Groupe Hospitalier Est Service de Neuropédiatrie, Bron, France
| | - Audrey Labalme
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France.,Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Patrick Edery
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France.,CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie Biologique, Bron, France.,UR 4609 Hémostase et thrombose, Université Claude Bernard Lyon 1, Lyon, France
| | - Caroline Schluth-Bolard
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France.,Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
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2
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Fahiminiya S, Rivard GE, Scott P, Montpetit A, Bacot F, St-Louis J, Mitchell GA, Foulkes WD, Soucy JF, Gauthier J. A full molecular picture of F8 intron 1 inversion created with optical genome mapping. Haemophilia 2021; 27:e638-e640. [PMID: 34232555 DOI: 10.1111/hae.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/17/2021] [Accepted: 06/26/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Somayyeh Fahiminiya
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Georges-Etienne Rivard
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Hematology-Oncology, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Patrick Scott
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada
| | | | - François Bacot
- Centre d'expertise et de services Génome Québec, Montreal, Québec, Canada
| | - Jean St-Louis
- Division of Hematology-Oncology, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Grant A Mitchell
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Jean-Francois Soucy
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Julie Gauthier
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
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3
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Wang X, Wang H, Tan H, Liu XP, Li H. An aberrant F8 intron 1 inversion with concomitant large duplication and deletion in a Chinese severe hemophilia A patient. ACTA ACUST UNITED AC 2021; 26:53-57. [PMID: 33382022 DOI: 10.1080/16078454.2020.1867793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Hemophilia A (HA, OMIM: 306700) is an X-linked recessive bleeding disorder, caused by defects of the F8 gene which encodes the coagulation factor VIII (FVIII). F8 intron 22 and intron 1 inversion (Inv22 and Inv1) account for ∼45% and 1-5% of severe HA cases, respectively. We herein described an aberrant Inv1 with concomitant large duplication and deletion in a Chinese severe HA patient. METHODS Long distance PCR and multiplex PCR were used to detect Inv22 and Inv1. Multiplex ligation-dependent probe amplification (MLPA) was applied to examine exonic duplication and deletion of the F8 gene. Coverage analysis of read depth data from whole-genome sequencing (WGS) was used to analyze the intronic duplication and deletion of the F8 gene. RESULTS We have identified an aberrant F8 Inv1 in a 1-year-old Chinese severe HA patient showing inversed int1h-1 and normal int1h-2. Coverage analysis of WGS data further illustrated the aberrant Inv1 with concomitant a duplication of 117 kb and a deletion of 1.8 kb. CONCLUSION In conclusion, we reported an aberrant Inv1 with concomitant large duplication and deletion in a severe Chinese HA patient. Moreover, WGS provides rapid genetic diagnosis of hereditary disorders with point mutations, deletions, insertions and CNVs.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hongmei Wang
- Department of Clinical Laboratory, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, People's Republic of China
| | - Haowen Tan
- Aegicare Biotech, Shenzhen, People's Republic of China
| | - Xiu-Ping Liu
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, People's Republic of China
| | - Huijun Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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4
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Partial F8 gene duplication (factor VIII Padua) associated with high factor VIII levels and familial thrombophilia. Blood 2021; 137:2383-2393. [PMID: 33275657 DOI: 10.1182/blood.2020008168] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
High coagulation factor VIII (FVIII) levels comprise a common risk factor for venous thromboembolism (VTE), but the underlying genetic determinants are largely unknown. We investigated the molecular bases of high FVIII levels in 2 Italian families with severe thrombophilia. The proband of the first family had a history of recurrent VTE before age 50 years, with extremely and persistently elevated FVIII antigen and activity levels (>400%) as the only thrombophilic defects. Genetic analysis revealed a 23.4-kb tandem duplication of the proximal portion of the F8 gene (promoter, exon 1, and a large part of intron 1), which cosegregated with high FVIII levels in the family and was absent in 103 normal controls. Targeted screening of 50 unrelated VTE patients with FVIII levels ≥250% identified a second thrombophilic family with the same F8 rearrangement on the same genetic background, suggesting a founder effect. Carriers of the duplication from both families showed a twofold or greater upregulation of F8 messenger RNA, consistent with the presence of open chromatin signatures and enhancer elements within the duplicated region. Testing of these sequences in a luciferase reporter assay pinpointed a 927-bp region of F8 intron 1 associated with >45-fold increased reporter activity in endothelial cells, potentially mediating the F8 transcriptional enhancement observed in carriers of the duplication. In summary, we report the first thrombophilic defect in the F8 gene (designated FVIII Padua) associated with markedly elevated FVIII levels and severe thrombophilia in 2 Italian families.
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Tokoro M, Tamura S, Suzuki N, Kakihara M, Hattori Y, Odaira K, Suzuki S, Takagi A, Katsumi A, Hayakawa F, Okamoto S, Suzuki A, Kanematsu T, Matsushita T, Kojima T. Aberrant X chromosomal rearrangement through multi-step template switching during sister chromatid formation in a patient with severe hemophilia A. Mol Genet Genomic Med 2020; 8:e1390. [PMID: 32627361 PMCID: PMC7507428 DOI: 10.1002/mgg3.1390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/17/2020] [Accepted: 06/01/2020] [Indexed: 11/16/2022] Open
Abstract
Background Hemophilia A (HA) is an X‐linked recessive bleeding disorder caused by pathogenic variants of the coagulation factor VIII gene (F8). Half of the patients with severe HA have a recurrent inversion in the X chromosome, that is, F8 intron 22 or intron 1 inversion. Here, we characterized an abnormal F8 due to atypical complex X chromosome rearrangements in a Japanese patient with severe HA. Methods Recurrent F8 inversions were tested with inverse shifting‐PCR. The genomic structure was investigated using PCR‐based direct sequencing or quantitative PCR. Results The proband's X chromosome had a 119.5 kb insertion, a reverse duplex of an extragenic sequence on the F8 telomere region into the F8 intron 1 with two breakpoints. The telomeric breakpoint was a joining from the F8 intron 1 to the inverted FUNDC2 via a two‐base microhomology, and the centromeric breakpoint was a recombination between F8 intron 1 homologous sequences. The rearrangement mechanism was suggested as a multi‐step rearrangement with template switching such as fork stalling and template switching (FoSTeS)/microhomology‐mediated break‐induced replication (MMBIR) and/or homologous sequence‐associated recombination during a sister chromatid formation. Conclusion We identified the aberrant X chromosome with a split F8 due to a multi‐step rearrangement in a patient with severe HA.
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Affiliation(s)
- Mahiru Tokoro
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shogo Tamura
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuaki Suzuki
- Department of Transfusion Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Misaki Kakihara
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuna Hattori
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koya Odaira
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sachiko Suzuki
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Takagi
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Shubun University, Ichinomiya, Japan
| | - Akira Katsumi
- Department of Transfusion Medicine, National Center for Geriatrics and Gerontology, Obu City, Japan
| | - Fumihiko Hayakawa
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuichi Okamoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsuo Suzuki
- Department of Clinical Laboratory, Nagoya University Hospital, Nagoya, Japan
| | - Takeshi Kanematsu
- Department of Clinical Laboratory, Nagoya University Hospital, Nagoya, Japan
| | - Tadashi Matsushita
- Department of Transfusion Medicine, Nagoya University Hospital, Nagoya, Japan.,Department of Clinical Laboratory, Nagoya University Hospital, Nagoya, Japan
| | - Tetsuhito Kojima
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
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6
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Lannoy N, Hermans C. Review of molecular mechanisms at distal Xq28 leading to balanced or unbalanced genomic rearrangements and their phenotypic impacts on hemophilia. Haemophilia 2018; 24:711-719. [DOI: 10.1111/hae.13569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2018] [Indexed: 01/18/2023]
Affiliation(s)
- N. Lannoy
- Hemostasis and Thrombosis Unit; Hemophilia Clinic; Division of Hematology; Cliniques Universitaires Saint-Luc; Brussels Belgium
| | - C. Hermans
- Hemostasis and Thrombosis Unit; Hemophilia Clinic; Division of Hematology; Cliniques Universitaires Saint-Luc; Brussels Belgium
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7
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Xin Y, Zhou J, Ding Q, Chen C, Wu X, Wang X, Wang H, Jiang X. A pericentric inversion of chromosome X disruptingF8and resulting in haemophilia A. J Clin Pathol 2017; 70:656-661. [DOI: 10.1136/jclinpath-2016-204050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/04/2022]
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8
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Lannoy N, Bandelier C, Grisart B, Reginster M, Ronge-Collard E, Vikkula M, Hermans C. Tandem inversion duplication withinF8Intron 1 associated with mild haemophilia A. Haemophilia 2015; 21:516-22. [DOI: 10.1111/hae.12675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/16/2022]
Affiliation(s)
- N. Lannoy
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
| | - C. Bandelier
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
| | - B. Grisart
- Center of Human Genetics; Institut de Pathologie et de Génétique (IPG); Charleroi (Gosselies) Belgium
| | - M. Reginster
- Department of Hemato-oncology; Centre Hospitalier Regional de Huy; Huy Belgium
| | - E. Ronge-Collard
- Hemostasis Laboratory; Department of Biological Chemistry; Centre Hospitalier Regional de Liège; Liege Belgium
| | - M. Vikkula
- Laboratory of Human Molecular Genetics de Duve Institute; Université Catholique de Louvain; Bruxelles Belgium
| | - C. Hermans
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
- Haemostasis and Thrombosis Unit; Haemophilia Clinic; Division of Haematology; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
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