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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hamasaki-Katagiri N, Lin BC, Simon J, Hunt RC, Schiller T, Russek-Cohen E, Komar AA, Bar H, Kimchi-Sarfaty C. The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia. Haemophilia 2017; 23:e8-e17. [PMID: 27933712 PMCID: PMC5226872 DOI: 10.1111/hae.13107] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2016] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated. AIM To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia. METHODS Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin). RESULTS In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101-151 nucleotide fragment length appears to be a feasible range for structuring future studies. CONCLUSION mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications.
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Affiliation(s)
- Nobuko Hamasaki-Katagiri
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Brian C. Lin
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jonathan Simon
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ryan C. Hunt
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Tal Schiller
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Estelle Russek-Cohen
- Division of Biostatistics, Center for Biologics Evaluation & Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Haim Bar
- Department of Statistics, College of Liberal Arts and Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Chava Kimchi-Sarfaty
- Laboratory of Hemostasis, Division of Hematology Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
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