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Li S, He J, Chu L, Ren S, He W, Ma X, Wang Y, Zhang M, Kong L, Liang B, Li Q. F8 gene inversion and duplication cause no obvious hemophilia A phenotype. Front Genet 2023; 14:1098795. [PMID: 36845383 PMCID: PMC9947239 DOI: 10.3389/fgene.2023.1098795] [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: 11/15/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Hemophilia A (HA, OMIM#306700) is an X-linked recessive bleeding disorder caused by the defects in the F8 gene, which encodes coagulation factor VIII (FVIII). Intron 22 inversion (Inv22) is found in about 45% of patients with severe hemophilia A. Here, we reported a male without obvious hemophilia A phenotype but bearing an inherited segmental variant duplication encompassing F8 as well as Inv22. The duplication was approximately 0.16 Mb and involved from exon 1 to intron 22 of F8. This partial duplication and Inv22 in F8 was first found in the abortion tissue of his older sister with recurrent miscarriage. The genetic testing of his family revealed that his phenotypically normal older sister and mother also had this heterozygous Inv22 and a 0.16 Mb partial duplication of F8, while his father was genotypically normal. The integrity of the F8 gene transcript was verified by sequencing of the adjacent exons at the inversion breakpoint, which explained why this male had no phenotype for hemophilia A. Interestingly, although he had no significant hemophilia A phenotype, the expression of C1QA in his mother, sister, and the male subject was only about half of that in his father and normal population. Our report broadens the mutation spectrum of F8 inversion and duplication and its pathogenicity in hemophilia A.
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Affiliation(s)
- Shaoying Li
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Jianchun He
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Liming Chu
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Shuai Ren
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Wenzhi He
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Xiaoyan Ma
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Yanchao Wang
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Mincong Zhang
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | | | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Qing Li, ; Bo Liang,
| | - Qing Li
- Department of Obstetrics and Gynecology, Experimental Department of Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China,*Correspondence: Qing Li, ; Bo Liang,
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2
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Jourdy Y, Chatron N, Fretigny M, Dericquebourg A, Sanlaville D, Vinciguerra C. Comprehensive analysis of F8 large deletions: Characterization of full breakpoint junctions and description of a possible DNA breakage hotspot in intron 6. J Thromb Haemost 2022; 20:2293-2305. [PMID: 35894111 DOI: 10.1111/jth.15835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Large F8 deletions represent 3-5% of the variations found in severe hemophilia A patients, but only a few deletion breakpoints have been characterized precisely. OBJECTIVES Resolving at the nucleotide level 24 F8 large deletions to provide new data on the mechanisms involved in these rearrangements. METHODS Breakpoint junctions of 24 F8 large deletions were characterized using a combination of long-range polymerase chain reaction, whole F8 NGS sequencing, and Sanger sequencing. Repeat elements, non-B DNA, and secondary structures were analyzed around the breakpoints. RESULTS Deletions ranged from 1.667 kb to 0.5 Mb in size. Nine involved F8 neighboring genes. Simple blunt ends and 2-4 bp microhomologies were identified at the breakpoint junctions of 10 (42%) and 8 (33%) deletions, respectively. Five (21%) deletions resulted from homeologous recombination between two Alu elements. The remaining case corresponded to a more complex rearrangement with an insertion of a 19 bp-inverted sequence at the junction. Four different breakpoints were located in a 562-bp region in F8 intron 6. This finding suggested that this region, composed of two Alu elements, is a DNA breakage hotspot. Non-B DNA and secondary structures were identified in the junction regions and may contribute to DNA breakage. CONCLUSION Molecular characterization of deletion breakpoints revealed that non-homologous non-replicative DNA repair mechanisms and replication-based mechanisms seemed to be the main causative mechanisms of F8 large deletions. Moreover, we identified a possible F8 DNA breakage hotspot involved in non-recurrent rearrangements.
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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, UR 4609, Hémostase et thrombose, Lyon, France
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Mathilde Fretigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Amy Dericquebourg
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR 4609, Hémostase et thrombose, Lyon, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR 4609, Hémostase et thrombose, Lyon, France
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3
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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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Manderstedt E, Lind-Halldén C, Ljung R, Astermark J, Halldén C. Detection of F8 int22h inversions using digital droplet PCR and mile-post assays. J Thromb Haemost 2020; 18:1039-1049. [PMID: 32031725 DOI: 10.1111/jth.14760] [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: 12/16/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Inversions involving intron 22 (Inv22) of F8 are detected in approximately 45% of all severe hemophilia A patients. Diagnosis is complicated by the large size of the ~9.5 kb int22h repeated sequence, which generates the inversions. Methods such as long-range polymerase chain reaction (PCR) and inverse-shifting PCR are currently used diagnostically, but suffer from low PCR efficiencies and are difficult to standardize. OBJECTIVES To design and validate a sensitive and robust assay for the detection of F8 int22h inversions. METHODS Digital droplet PCR using mile-post assays was used to investigate archival DNA samples. RESULTS The detection of linkage as a function of physical distance between loci was investigated using an anchor locus and mile-post loci at 1, 6, 12 and 15 kb distances from the anchor locus. The proportion of linked molecules decreased with increasing distance between loci and showed 30% to 40% linked molecules for loci 12 to15 kb apart. Mile-post assays specific for wild type and Inv22 type 1 and 2 chromosomes were then designed and optimized. All three assays showed high specificities and sensitivities, with coefficients of variation <5% for all assays. Analysis of 106 patients and 20 carrier mothers showed complete concordance with previously known mutation status. The analysis demonstrated the robustness of the assays versus input DNA concentration (6 ng and higher) and level of fragmentation. CONCLUSIONS Digital droplet PCR and mile-post assays can be used to detect F8 int22h inversions. The assay systems are technically simple to perform, highly efficient, and robust.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Christina Lind-Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Rolf Ljung
- Department of Clinical Sciences, Pediatrics and Malmö Center for Thrombosis and Hemostasis, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Jan Astermark
- Department for Hematology Oncology and Radiation Physics, Center for Thrombosis and Hemostasis, Skåne University Hospital, Malmö, Sweden
| | - Christer Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
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5
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Xie X, Chen C, Liang Q, Wu X, Wang X, Wu W, Ding Q. Characterization of two large duplications of
F9
associated with mild and severe haemophilia B, respectively. Haemophilia 2019; 25:475-483. [PMID: 30866119 DOI: 10.1111/hae.13704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 01/23/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoling Xie
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
| | - Wenman Wu
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
- Faculty of Medical Laboratory Science, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
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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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Surin VL, Salomashkina VV, Pshenichnikova OS, Perina FG, Bobrova ON, Ershov VI, Budanova DA, Gadaev IY, Konyashina NI, Zozulya NI. New Missense Mutation His2026Arg in the Factor VIII Gene Was Revealed in Two Female Patients with Clinical Manifestation of Hemophilia A. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541806011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Pezeshkpoor B, Pavlova A, Oldenburg J, El-Maarri O. F8 genetic analysis strategies when standard approaches fail. Hamostaseologie 2017; 34:167-73. [DOI: 10.5482/hamo-13-08-0043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/25/2013] [Indexed: 11/05/2022] Open
Abstract
SummaryHaemophilia A is a common X-linked recessive disorder caused by mutations in F8 leading to deficiency or dysfunction of coagulant factor VIII (FVIII). Despite tremendous improvements in mutation screening methods, in a small group of patients with FVIII deficiency suffering from haemophilia A, no DNA change can be found. In these patients, analysis reveals no causal mutations even after sequencing the whole coding region of F8 including the flanking splice sites, as well as the promoter and the 3’ untranslated region (UTR). After excluding the mutations mimicking the haemophilia A phenotype in interacting partners of the FVIII protein affecting the half life and transport of the protein, mutations or rearrangements in non-coding regions of F8 have to be considered responsible for the haemophilia A phenotype.In this review, we present the experiences with molecular diagnosis of such cases and approaches to be applied for mutation negative patients.
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9
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Chen C, Xie X, Wu X, Lu Y, Wang X, Wu W, Hu Y, Ding Q. Complex recombination with deletion in the F8 and duplication in the TMLHE mediated by int22h copies during early embryogenesis. Thromb Haemost 2017; 117:1478-1485. [PMID: 28492696 DOI: 10.1160/th17-01-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/22/2017] [Indexed: 11/05/2022]
Abstract
Haemophilia A (HA) is a common X-linked recessive bleeding disorder and almost one half of patients with severe HA are caused by intron 22 inversion (Inv22) in the F8. Inv22 is considered to be almost exclusively of meiotic origin in germ cells during spermatogenesis and only one mosaic Inv22 female carrier with the mutation possibly occurring during mitosis of the embryo has been reported so far. Previously we have identified a novel complex recombination mediated by int22h copies in a sporadic severe HA pedigree and herein we have localised the sequences flanking the breakpoint region using genome walking technique, AccuCopy technique, gene chip and real-time PCR. The disease causing genetic variant registered an 18.1 kb deletion including part of int22h-1 through the intron 23 of F8 and a 113.3 kb duplication of part of int22h-2 through the intron 1 of TMLHE inserted in the religated region of the F8. Two intrinsically linked mechanisms of recombination-dependent DNA replication: microhomology-mediated break-induced replication (MMBIR) followed by break-induced replication (BIR) might be responsible for the incident of the complex recombination during early embryogenesis of the proband's mother.
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Affiliation(s)
| | | | | | | | | | | | | | - Qiulan Ding
- Qiulan Ding or Wenman Wu, Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin Second Road, Shanghai, 200025, China, Tel.: +86 21 54667770, Fax: +86 21 64333548, E-mail: , , or, Yiqun Hu, Faculty of Medical Laboratory Science, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin Second Road, Shanghai 200025, China, Tel.: +86 21 64669971, Fax: +86 21 63851293, E-mail:
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10
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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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11
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Lannoy N, Hermans C. Principles of genetic variations and molecular diseases: applications in hemophilia A. Crit Rev Oncol Hematol 2016; 104:1-8. [PMID: 27296059 DOI: 10.1016/j.critrevonc.2016.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 11/24/2022] Open
Abstract
DNA structure alterations are the ultimate source of genetic variations. Without them, evolution would be impossible. While they are essential for DNA diversity, defects in DNA synthesis can lead to numerous genetic diseases. Due to increasingly innovative technologies, our knowledge of the human genome and genetic diseases has grown considerably over the last few years, allowing us to detect another class of variants affecting the chromosomal structure. DNA sequence can be altered in multiple ways: DNA sequence changes by substitution, deletion, or duplication of some nucleotides; chromosomal structure alterations by deletion, duplication, translocation, and inversion, ranging in size from kilobases to mega bases; changes in the cell's genome size. If the alteration is located within a gene and sufficiently deleterious, it can cause genetic disorders. Due to the F8 gene's high rate of new small mutations and its location at the tip of X chromosome, containing high repetitive sequences, a wide variety of genetic variants has been described as the cause of hemophilia A (HA). In addition to the F8 intron 22 repeat inversion, HA can also result from point mutations, other inversions, complex rearrangements, such as duplications or deletions, and transposon insertions causing phenotypes of variable severity characterized by complete or partial deficiency of circulating FVIII. This review aims to present the origins, mechanisms, and consequences of F8 alterations. A sound understanding of the multiple genetic mechanisms responsible for HA is essential to determine the appropriate strategy for molecular diagnosis and detected each type of genetic variant.
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Affiliation(s)
- N Lannoy
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.
| | - C Hermans
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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12
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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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13
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Pezeshkpoor B, Oldenburg J. F8 gene: embedded in a region of genomic instability representing a hotspot of complex rearrangements. Haemophilia 2015; 21:513-5. [PMID: 25939373 DOI: 10.1111/hae.12687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 11/28/2022]
Affiliation(s)
- B Pezeshkpoor
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - J Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany
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14
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de Brasi C, El-Maarri O, Perry DJ, Oldenburg J, Pezeshkpoor B, Goodeve A. Genetic testing in bleeding disorders. Haemophilia 2014; 20 Suppl 4:54-8. [PMID: 24762276 DOI: 10.1111/hae.12409] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2014] [Indexed: 11/30/2022]
Abstract
The aim of molecular genetic analysis in families with haemophilia is to identify the causative mutation in an affected male as this provides valuable information for the patient and his relatives. For the patient, mutation identification may highlight inhibitor development risk or discrepancy between different factor VIII assays. For female relatives, knowledge of the familial mutation can facilitate carrier status determination and prenatal diagnosis. Recent advances in understanding mutations responsible for haemophilia and methods for their detection are presented. For reporting of such mutations, participation in external quality assessment ensures that essential patient and mutation details are routinely included and that pertinent information is incorporated in the interpretation.
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Affiliation(s)
- C de Brasi
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina; Instituto de Investigaciones Hematologicas Mariano R Castex, Academia Nacional de Medicina, Buenos Aires, Argentina
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15
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Seo JY, Lee KO, Kim SH, Oh D, Kim DK, Kim HJ. The genomic architecture of the PROS1 gene underlying large tandem duplication mutation that causes thrombophilia from hereditary protein S deficiency. Gene 2014; 547:295-9. [DOI: 10.1016/j.gene.2014.06.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/26/2014] [Accepted: 06/29/2014] [Indexed: 12/01/2022]
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16
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The role of microhomology in genomic structural variation. Trends Genet 2014; 30:85-94. [PMID: 24503142 DOI: 10.1016/j.tig.2014.01.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/03/2014] [Accepted: 01/05/2014] [Indexed: 02/06/2023]
Abstract
Genomic structural variation, which can be defined as differences in the copy number, orientation, or location of relatively large DNA segments, is not only crucial in evolution, but also gives rise to genomic disorders. Whereas the major mechanisms that generate structural variation have been well characterised, insights into additional mechanisms are emerging from the identification of short regions of DNA sequence homology, also known as microhomology, at chromosomal breakpoints. In addition, functional studies are elucidating the characteristics of microhomology-mediated pathways, which are mutagenic. Here, we describe the features and mechanistic models of microhomology-mediated events, discuss their physiological and pathological significance, and highlight recent advances in this rapidly evolving field of research.
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You GL, Ding QL, Lu YL, Dai J, Xi XD, Wang XF, Wang HL. Characterization of large deletions in the F8 gene using multiple competitive amplification and the genome walking technique. J Thromb Haemost 2013; 11:1103-10. [PMID: 23551875 DOI: 10.1111/jth.12205] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 03/15/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Large deletions in the F8 gene are responsible for approximately 3% of severe hemophilia A (HA) cases. However, only a few breakpoints in large deletions have been characterized. OBJECTIVES To identify large deletions in the F8 gene and to characterize the molecular mechanisms leading to these deletions. PATIENTS AND METHODS We used AccuCopy technology, a copy number variation (CNV) genotyping method based on multiplex competitive amplification, to confirm deletions in index patients and to screen potential female carriers in 10 HA families. Also, breakpoints of these large deletions were characterized by a primer walking strategy and genome walking technique. RESULTS Ten large deletions and four female carriers were identified by AccuCopy. The extents of deleted regions ranged from 1.3 to 68.5 kb. Exact breakpoints of these deletions were successfully characterized. Eight of them presented microhomologies at breakpoint junctions and several recombination-associated elements (repetitive elements, non-B conformation forming motifs and sequence motifs) were also observed in close proximity to the junctions. CONCLUSIONS AccuCopy technology is a reliable and efficient tool for detecting large deletions in the F8 gene and identifying HA female carriers. The genome walking technique is a highly specific, efficient and versatile method for characterizing the deletion breakpoints. Molecular characterization of deletion breakpoints revealed that non-homologous end joining and microhomology-mediated replication-dependent recombination were the major causative mechanisms of the 10 large deletions in the F8 gene.
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Affiliation(s)
- G L You
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Hampshire DJ, Abuzenadah AM, Cartwright A, Al-Shammari NS, Coyle RE, Eckert M, Al-Buhairan AM, Messenger SL, Budde U, Gürsel T, Ingerslev J, Peake IR, Goodeve AC. Identification and characterisation of mutations associated with von Willebrand disease in a Turkish patient cohort. Thromb Haemost 2013; 110:264-74. [PMID: 23702511 DOI: 10.1160/th13-02-0135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 05/04/2013] [Indexed: 11/05/2022]
Abstract
Several cohort studies have investigated the molecular basis of von Willebrand disease (VWD); however, these have mostly focused on European and North American populations. This study aimed to investigate mutation spectrum in 26 index cases (IC) from Turkey diagnosed with all three VWD types, the majority (73%) with parents who were knowingly related. IC were screened for mutations using multiplex ligation-dependent probe amplification and analysis of all von Willebrand factor gene (VWF) exons and exon/intron boundaries. Selected missense mutations were expressed in vitro. Candidate VWF mutations were identified in 25 of 26 IC and included propeptide missense mutations in four IC (two resulting in type 1 and two in recessive 2A), all influencing VWF expression in vitro. Four missense mutations, a nonsense mutation and a small in-frame insertion resulting in type 2A were also identified. Of 15 type 3 VWD IC, 13 were homozygous and two compound heterozygous for 14 candidate mutations predicted to result in lack of expression and two propeptide missense changes. Identification of intronic breakpoints of an exon 17-18 deletion suggested that the mutation resulted from non-homologous end joining. This study provides further insight into the pathogenesis of VWD in a population with a high degree of consanguineous partnerships.
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Affiliation(s)
- Daniel J Hampshire
- Haemostasis Research Group, Department of Cardiovascular Science, Faculty of Medicine, Dentistry and Health, University of Sheffield, Beech Hill Road, Sheffield, UK.
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Intron 22 homologous regions are implicated in exons 1-22 duplications of the F8 gene. Eur J Hum Genet 2013; 21:970-6. [PMID: 23299923 DOI: 10.1038/ejhg.2012.275] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 11/05/2012] [Accepted: 11/15/2012] [Indexed: 02/02/2023] Open
Abstract
The intron 22 inversion found in up to 50% of severe hemophilia A patients results from a recombination between three intron 22 homologous copies (int22h). This study evaluated the implication of these copies in the formation of extended duplications comprising exons 1-22 of the factor 8 (F8) gene and their association with hemophilia and mental retardation. Two hemophilic patients with moderate and severe phenotypes and a third nonhemophilic patient with developmental delay were studied. All exhibited a duplication of F8 gene exons 1-22 identified by multiplex ligation-dependent probe amplification along with abnormal patterns on Southern blotting and unexpected long-range PCR amplification. Breakpoint analysis using array comparative genomic hybridization was performed to delimit the extent of these rearrangements. These duplications were bounded on one side by the F8 intragenic int22h-1 repeat and on the other side by extragenic int22h-2 or int22h-3 copies. However, the simultaneous identification of a second duplication containing F8 gene exons 2-14 for the moderate patient and the classical intron 22 inversion for the severe patient are considered in this study as the genetic causal defects of hemophilia. This study shows that the well-known int22h copies are involved in extended duplications comprising F8 gene exons 1-22. These specific duplications are probably not responsible for hemophilia and intellectual disability, but should be carefully considered in genetic counseling, while continuing to investigate the causal mutation of hemophilia.
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Sanna V, Ceglia C, Tarsitano M, Lombardo B, Coppola A, Zarrilli F, Castaldo G, Di Minno G. Aberrant F8 gene intron 1 inversion with concomitant duplication and deletion in a severe hemophilia A patient from Southern Italy. J Thromb Haemost 2013; 11:195-7. [PMID: 23140572 DOI: 10.1111/jth.12061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V Sanna
- CEINGE-Biotecnologie Avanzate, Naples Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
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Pezeshkpoor B, Rost S, Oldenburg J, El-Maarri O. Identification of a third rearrangement at Xq28 that causes severe hemophilia A as a result of homologous recombination between inverted repeats. J Thromb Haemost 2012; 10:1600-8. [PMID: 22672522 DOI: 10.1111/j.1538-7836.2012.04809.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Intrachromosomal homologous recombination between inverted repeats on the X chromosome account for about half of severe hemophilia A cases. Repeats in F8 intron 1 and intron 22 can recombine with homologous inverted repeats located about 200 kb upstream and 500 kb downstream of F8, respectively, resulting in partial sequence inversion of the F8 open reading frame and, subsequently, no functional protein production. OBJECTIVES In the present study, we characterize a third novel homologous recombination at Xq28 consistent with absence of F8 transcription that we previously reported for the affected chromosome of the index patient as well as his mother and sister. RESULTS The rearrangement occurs between a repeat in F8 intron 1 (Int1R-1) and an inverted identical repeat (Int1R-2d) in intron 2 of a duplicated copy of IKBKG located about 386 kb upstream of F8. The rearrangement was confirmed by Southern blot and inverse PCR and results in failure of PCR amplification across Int1R-1. CONCLUSION We developed a PCR-based diagnostic method that can be used to screen for this genetic rearrangement in cases of severe hemophilia A for which mutations cannot be identified.
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Affiliation(s)
- B Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
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Kim HJ, Chung HS, Kim SK, Yoo K, Jung SY, Park IA, Lee KO, Kim SH, Kim HJ. Mutation spectrum and inhibitor risk in 100 Korean patients with severe haemophilia A. Haemophilia 2012; 18:1008-13. [PMID: 22741565 DOI: 10.1111/j.1365-2516.2012.02895.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2012] [Indexed: 12/01/2022]
Affiliation(s)
- H.-J. Kim
- Department of Laboratory Medicine & Genetics; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul; Korea
| | - H.-S. Chung
- Department of Laboratory Medicine & Genetics; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul; Korea
| | - S. K. Kim
- Department of Pediatrics; College of Medicine; Inha University Hospital; Incheon; Korea
| | - K.Y. Yoo
- Korea Hemophilia Foundation; Seoul; Korea
| | - S.-Y. Jung
- Korea Hemophilia Foundation; Seoul; Korea
| | - I.-A. Park
- Samsung Biomedical Research Institute; Samsung Medical Center; Seoul; Korea
| | - K.-O. Lee
- Samsung Biomedical Research Institute; Samsung Medical Center; Seoul; Korea
| | - S.-H. Kim
- Department of Laboratory Medicine & Genetics; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul; Korea
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Venceslá Á, Baena M, Garrido RP, Núñez R, Velasco F, Rosell J, Villar A, Jiménez-Yuste V, Baiget M, Tizzano EF. F8 gene dosage defects in atypical patients with severe haemophilia A. Haemophilia 2012; 18:708-13. [PMID: 22621702 DOI: 10.1111/j.1365-2516.2012.02818.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We performed molecular analysis of the factor 8 gene (F8) in 272 unrelated Spanish patients with haemophilia A (HA) and detected a mutation by routine analysis in 267 of them (98.1%). No mutation was detected in the remaining five patients despite clinical and laboratory confirmation of HA. The aim is to describe the molecular alterations in F8 discovered by gene dosage methodologies in three of these patients. For methodology, F8 sequencing, intragenic marker analysis, multiplex ligation-dependent probe amplification and quantitative real time-PCR were followed. One patient had Klinefelter syndrome (47,XXY) and a large deletion spanning exons 1-12 masked by the other F8 allele; the second patient showed a large duplication spanning exons 2-10 and the third patient revealed a non-contiguous double duplication of exons 14 and 23-25. The remaining two patients had mild HA and dosage results were normal. The application of gene dosage methods is useful to define haemophilic patients in whom mutations are not detected using other routine methods. Nevertheless, in a small percentage of patients (<1%), no molecular pathology can be identified after testing several genetic methodologies.
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Affiliation(s)
- Á Venceslá
- Department of Genetics, Hospital de Sant Pau, Barcelona and CIBERER U-705, Spain
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Hampshire DJ, Goodeve AC. The molecular basis of von Willebrand disease: the under investigated, the unexpected and the overlooked. Haematologica 2011; 96:798-800. [PMID: 21632843 DOI: 10.3324/haematol.2011.046623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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LANNOY N, ABINET I, BOSMANS A, LAMBERT C, VERMYLEN C, HERMANS C. Computational and molecular approaches for predicting unreported causal missense mutations in Belgian patients with haemophilia A. Haemophilia 2011; 18:e331-9. [DOI: 10.1111/j.1365-2516.2011.02640.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
von Willebrand disease is a common inherited bleeding disorder characterized by excessive mucocutaneous bleeding. Characteristic bleeding symptoms include epistaxis, easy bruising, oral cavity bleeding, menorrhagia, bleeding after dental extraction, surgery, and/or childbirth, and in severe cases, bleeding into joints and soft tissues. There are three subtypes: types 1 and 3 represent quantitative variants and type 2 is a group of four qualitative variants: (1) type 2A-characterized by defective von Willebrand factor-dependent platelet adhesion because of decreased high-molecular-weight von Willebrand factor multimers, (2) type 2B-caused by pathologically increased von Willebrand factor-platelet interactions, (3) type 2M-caused by decreased von Willebrand factor-platelet interactions not based on the loss of high-molecular-weight multimers, and (4) type 2N-characterized by reduced binding of von Willebrand factor to factor VIII. The diagnosis of von Willebrand disease requires specialized assays of von Willebrand factor and/or molecular genetic testing of von Willebrand factor. Severe bleeding episodes can be prevented or controlled with intravenous infusions of virally inactivated plasma-derived clotting factor concentrates containing both von Willebrand factor and factor VIII. Depending on the von Willebrand disease type, mild bleeding episodes usually respond to intravenous or subcutaneous treatment with desmopressin, a vasopressin analog. Other treatments that can reduce symptoms include fibrinolytic inhibitors and hormones for menorrhagia.
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Theophilus BDM, Baugh LM, Guilliatt AM, Motwani J, Williams MD. Deletions and duplications in the factor VIII gene identified using multiplex ligation-dependent probe amplification. J Thromb Haemost 2011; 9:605-7. [PMID: 21143378 DOI: 10.1111/j.1538-7836.2010.04165.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Goodeve AC. Another step towards understanding hemophilia A molecular pathogenesis. J Thromb Haemost 2010; 8:2693-5. [PMID: 21188793 DOI: 10.1111/j.1538-7836.2010.04071.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A C Goodeve
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK.
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