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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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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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Deng X, Fang H, Pathak A, Zou AM, Neufeld-Kaiser W, Malouf EA, Failor RA, Hisama FM, Liu YJ. Deletion of FUNDC2 and CMC4 on Chromosome Xq28 Is Sufficient to Cause Hypergonadotropic Hypogonadism in Men. Front Genet 2020; 11:557341. [PMID: 33193636 PMCID: PMC7537572 DOI: 10.3389/fgene.2020.557341] [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: 04/30/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
Background Hypergonadotropic hypogonadism (HH) is characterized by low sex steroid levels and secondarily elevated gonadotropin levels with either congenital or acquired etiology. Genetic factors leading to HH have yet to be fully elucidated. Methods Here, we report on genome and transcriptome data analyses from a male patient with HH and history of growth delay who has an inherited deletion of chromosome Xq28. Expression analyses were done for this patient and his unaffected family members and compared to normal controls to identify dysregulated genes due to this deletion. Results Our patient’s Xq28 deletion is 44,806 bp and contains only two genes, FUNDC2 and CMC4. Expression of both FUNDC2 and CMC4 are completely abolished in the patient. Gene ontology analyses of differentially expressed genes (DEGs) in the patient in comparison to controls show that significantly up-regulated genes in the patient are enriched in Sertoli cell barrier (SCB) regulation, apoptosis, inflammatory response, and gonadotropin-releasing regulation. Indeed, our patient has an elevated follicle stimulating hormone (FSH) level, which regulates Sertoli cell proliferation and spermatogenesis. In his mother and sister, who are heterozygous for this deletion, X-chromosome inactivation (XCI) is skewed toward the deleted X, suggesting a mechanism to avoid FSH dysregulation. Conclusion Compared to the previously reported men with variable sized Xq28 deletions, our study suggests that loss of function of FUNDC2 and CMC4 results in dysregulation of apoptosis, inflammation, and FSH, and is sufficient to cause Xq28-associated HH.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - He Fang
- Department of Pathology, University of Washington, Seattle, WA, United States
| | | | - Angela M Zou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Emily A Malouf
- Division of Medical Genetics, University of Washington, Seattle, WA, United States
| | - Richard A Failor
- Division of Metabolism, Endocrinology, and Nutrition, University of Washington, Seattle, WA, United States
| | - Fuki M Hisama
- Division of Medical Genetics, University of Washington, Seattle, WA, United States
| | - Yajuan J Liu
- Department of Pathology, University of Washington, Seattle, WA, United States
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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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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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Mousavi SH, Mesbah-Namin SA, Zeinali S, Jazebi M, Dabbagh A, Hosseini SMR, Zafarghandi Motlagh F, Shiravand Y, Dorgalaleh A. A large deletion, spanning exons 1 to 25 of F8 gene, and a high-titer factor VIII inhibitor, in severe hemophilia A. Int J Lab Hematol 2020; 42:e138-e140. [PMID: 32125779 DOI: 10.1111/ijlh.13174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Sayed Hamid Mousavi
- Department of the Clinical Biochemistry, Faculty of Medical Sciences, Kateb University, Kabul, Afghanistan.,Afghanistan National Charity Organization for Special Diseases (ANCOSD), Kabul, Afghanistan
| | - Seyed Alireza Mesbah-Namin
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sirous Zeinali
- Iranian Molecular Medicine Network, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Jazebi
- Iranian Comprehensive Hemophilia Care Center (ICHCC), Tehran, Iran
| | - Ali Dabbagh
- Anesthesiology Department, Anesthesiology Research Center, Shahid Beheshti University of Medicine, Tehran, Iran
| | | | | | - Yavar Shiravand
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Akbar Dorgalaleh
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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8
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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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9
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Ma S, Chen C, Liang Q, Wu X, Wang X, Wu W, Liu Y, Ding Q. Phenotype and genotype of FXIII deficiency in two unrelated probands: identification of a novel F13A1 large deletion mediated by complex rearrangement. Orphanet J Rare Dis 2019; 14:182. [PMID: 31340840 PMCID: PMC6657060 DOI: 10.1186/s13023-019-1144-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/25/2019] [Indexed: 01/27/2023] Open
Abstract
Background Inherited Factor XIII deficiency (FXIIID) is one of the most severe and under-diagnosed rare bleeding disorders. Only 5 large deletions involving one or more exons in F13A1 have been reported, and lacking of multiplex ligation-dependent probe amplification (MLPA) assay might underestimate the copy number variations (CNVs) in F13A1 and F13B. We had characterized the clinical presentation of two unrelated severe FXIIID probands and explored the pathogenic mechanisms. Results Both probands experienced several episodes of fatal bleeding and delayed wound healings prior to diagnosis. FXIII activity was measured by the ammonia release assay, and FXIII-A and FXIII-B antigens were determined by ELISA. All the exons including exon-intron boundaries and promoter regions of F13A1 and F13B were amplified and directly sequenced. Copy number variations (CNVs) of F13A1 and F13B were detected by the CNVplex® method. Breakpoints of the F13A1 large deletion were identified by quantitative primer walking combined long-range PCR (LR-PCR) strategies. Proband 1 was found to have compound heterozygous mutations of a novel small deletion (c.1147del) and a missense mutation p.Arg383Ser. Proband 2 was compound heterozygous for a novel large deletion (g.[77815_112815del;112837_116628del]) and a missense mutation p.Arg716Gly in F13A1. Bioinformatics analysis of the large deletion breakpoints predicted that two fork stalling and template switching and/or microhomology-mediated break-induced replication (FoSTeS/MMBIR) events with two homologies of TCT and C might be responsible for the complex rearrangement. Prophylactic replacement therapy was immediately administered for the two probands upon establishment of the diagnosis. Conclusions We detected two type I FXIIID pedigrees and adopted CNVplex® method to detect CNVs of F13A1 and F13B for the first time. A large heterozygous deletion of g.[77815_112815del;112837_116628del] in F13A1, mediated by two FoSTeS/MMBIR events, was identified. Electronic supplementary material The online version of this article (10.1186/s13023-019-1144-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siyu Ma
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China.,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Faculty of Medical Laboratory Science, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Yan Liu
- Department of Burns and Plastic Surgery, Ruijin Hospital Affiliated to Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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10
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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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11
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Johnsen JM, Fletcher SN, Huston H, Roberge S, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska S, Koerper MA, Morales J, Pierce GF, Aschman DJ, Konkle BA. Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative. Blood Adv 2017; 1:824-834. [PMID: 29296726 PMCID: PMC5727804 DOI: 10.1182/bloodadvances.2016002923] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/22/2017] [Indexed: 01/05/2023] Open
Abstract
Hemophilia A and B are rare, X-linked bleeding disorders. My Life, Our Future (MLOF) is a collaborative project established to genotype and study hemophilia. Patients were enrolled at US hemophilia treatment centers (HTCs). Genotyping was performed centrally using next-generation sequencing (NGS) with an approach that detected common F8 gene inversions simultaneously with F8 and F9 gene sequencing followed by confirmation using standard genotyping methods. Sixty-nine HTCs enrolled the first 3000 patients in under 3 years. Clinically reportable DNA variants were detected in 98.1% (2357/2401) of hemophilia A and 99.3% (595/599) of hemophilia B patients. Of the 924 unique variants found, 285 were novel. Predicted gene-disrupting variants were common in severe disease; missense variants predominated in mild-moderate disease. Novel DNA variants accounted for ∼30% of variants found and were detected continuously throughout the project, indicating that additional variation likely remains undiscovered. The NGS approach detected >1 reportable variants in 36 patients (10 females), a finding with potential clinical implications. NGS also detected incidental variants unlikely to cause disease, including 11 variants previously reported in hemophilia. Although these genes are thought to be conserved, our findings support caution in interpretation of new variants. In summary, MLOF has contributed significantly toward variant annotation in the F8 and F9 genes. In the near future, investigators will be able to access MLOF data and repository samples for research to advance our understanding of hemophilia.
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Affiliation(s)
- Jill M Johnsen
- Bloodworks Northwest, Seattle, WA
- Department of Medicine and
| | | | | | | | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Chevy Chase, MD
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12
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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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13
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Jourdy Y, Chatron N, Fretigny M, Carage ML, Chambost H, Claeyssens-Donadel S, Roussel-Robert V, Negrier C, Sanlaville D, Vinciguerra C. Molecular cytogenetic characterization of five F8 complex rearrangements: utility for haemophilia A genetic counselling. Haemophilia 2017; 23:e316-e323. [PMID: 28475226 DOI: 10.1111/hae.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Genomic inversions are usually balanced, but unusual patterns have been described in haemophilia A (HA) patients for intron 22 (Inv22) and intron 1 (Inv1) inversions leading to the hypothesis of more complex rearrangements involving deletions or duplications. AIM To characterize five abnormal patterns either in Southern blot and long-range PCR for Inv22 or in PCR for Inv1. MATERIALS AND METHODS All patients were studied using cytogenetic microarray analysis (CMA). RESULTS In all cases, CMA analysis found that each inversion was associated with complex Xq28 rearrangement. In three patients, CMA analysis showed large duplication ranging from 230 to 1302 kb and encompassing a various number of contiguous genes among which RAB39B. RAB39B duplication is a strong candidate gene for X-linked intellectual disability (XLID). Surprisingly, none of the severe HA patients with RAB39B duplication reported in this study or in the literature exhibited XLID. We hypothesise that F8 complex rearrangement down regulated RAB39B expression. In the two remaining patients, CMA analysis found Xq28 large deletion (from 285 to 522 kb). Moyamoya syndrome was strongly suspected in one of them who carried BRCC3 deletion. CONCLUSION Because several F8 neighbouring genes are associated with other pathologies such as XLID and cardiovascular disease, all HA patients where complex Xq28 rearrangement was suspected should be referred to a geneticist for possible utility of a pangenomic study. Such investigation should be carefully considered in genetic counselling in female carriers to assess the risk of transmitting severe HA with a "contiguous gene syndrome".
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Affiliation(s)
- Y Jourdy
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d'hématologie Biologique, Lyon, France.,Univ Lyon, EA 4609 Hémostase et cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - N Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Laboratoire de Cytogénétique Constitutionnelle, Bron, France.,Univ Lyon, CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - M Fretigny
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d'hématologie Biologique, Lyon, France
| | - M L Carage
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d'hématologie Biologique, Lyon, France
| | - H Chambost
- Centre de traitement de l'hémophilie, CHU La Timone, Marseille, France
| | | | - V Roussel-Robert
- Centre de traitement de l'hémophilie, Hôpital Cochin, Paris, France
| | - C Negrier
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d'hématologie Biologique, Lyon, France.,Univ Lyon, EA 4609 Hémostase et cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - D Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Laboratoire de Cytogénétique Constitutionnelle, Bron, France.,Univ Lyon, CRNL, équipe GENDEV INSERM U1028, CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - C Vinciguerra
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d'hématologie Biologique, Lyon, France.,Univ Lyon, EA 4609 Hémostase et cancer, Université Claude Bernard Lyon 1, Lyon, France
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14
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AccuCopy quantification combined with pre-amplification of long-distance PCR for fast analysis of intron 22 inversion in haemophilia A. Clin Chim Acta 2016; 458:78-83. [DOI: 10.1016/j.cca.2016.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/30/2016] [Accepted: 04/13/2016] [Indexed: 12/15/2022]
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15
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Nakamura Y, Ando Y, Takagi Y, Murata M, Kozuka T, Nakata Y, Hasebe R, Takagi A, Matsushita T, Shima M, Kojima T. Distinct X chromosomal rearrangements in four haemophilia B patients with entire F9 deletion. Haemophilia 2015; 22:433-9. [PMID: 26686734 DOI: 10.1111/hae.12849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/09/2015] [Accepted: 09/14/2015] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Haemophilia B is an X-linked bleeding disorder caused by a coagulation factor IX gene (F9) abnormality. Numerous F9 defects have been identified to date; however, only a few with an entire F9 deletion have been reported in detail. AIM To elucidate the cause of severe haemophilia B, we investigated the precise X chromosome abnormalities in four Japanese patients who did not show all amplifications in F9-specific PCR. METHODS We analysed the patient's genomic DNA using Multiplex ligation-dependent probe amplification (MLPA). To assess the extent of any deletions, we further performed mapping PCRs, inverse PCRs or long-range PCRs and direct sequencing analyses of the X chromosome. RESULTS We detected entire F9 deletions in four haemophilia B patients and identified the precise deleted regions of the X chromosome including F9. Patient 1 had a 149-kb deletion with breakpoints 90-kb upstream and 30-kb downstream from F9. Patients 2 and 3 showed 273-kb and 1.19-Mb deletions respectively. Patient 4 had two deleted regions: a 1663-bp deletion 1.34-Mb upstream from F9 and a 7.2-Mb deletion including F9. These distinct breakpoints found in four different patients suggest that the mechanism of X chromosome deletion may be different between individuals. Non-allelic homologous recombination (NAHR), microhomology-mediated break-induced replication (MMBIR) or fork stalling and template switching (FoSTeS) may occur in respective X chromosomes of the four haemophilia B patients analysed. CONCLUSIONS We identified diverse X chromosomal rearrangements in four haemophilia B patients, which might be caused by distinct mechanisms of genomic rearrangement.
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Affiliation(s)
- Y Nakamura
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Ando
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takagi
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Murata
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - T Kozuka
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakata
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - R Hasebe
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Takagi
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Matsushita
- Department of Transfusion Medicine, Nagoya University Hospital, Nagoya, Japan
| | - M Shima
- Department of Paediatric, Nara Medical University, Nara, Japan
| | - T Kojima
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
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16
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Novel severe hemophilia A and moyamoya (SHAM) syndrome caused by Xq28 deletions encompassing F8 and BRCC3 genes. Blood 2014; 123:4002-4. [DOI: 10.1182/blood-2014-02-553685] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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17
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Aguado C, Gayà-Vidal M, Villatoro S, Oliva M, Izquierdo D, Giner-Delgado C, Montalvo V, García-González J, Martínez-Fundichely A, Capilla L, Ruiz-Herrera A, Estivill X, Puig M, Cáceres M. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence. PLoS Genet 2014; 10:e1004208. [PMID: 24651690 PMCID: PMC3961182 DOI: 10.1371/journal.pgen.1004208] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/14/2014] [Indexed: 01/17/2023] Open
Abstract
In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies.
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Affiliation(s)
- Cristina Aguado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sergi Villatoro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Meritxell Oliva
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Víctor Montalvo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Judit García-González
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | | | - Laia Capilla
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Biologia Celular, Fisiologia i Immunologia. Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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