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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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2
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Rendtorff ND, Karstensen HG, Lodahl M, Tolmie J, McWilliam C, Bak M, Tommerup N, Nazaryan-Petersen L, Kunst H, Wong M, Joss S, Carelli V, Tranebjærg L. Identification and analysis of deletion breakpoints in four Mohr-Tranebjærg syndrome (MTS) patients. Sci Rep 2022; 12:14959. [PMID: 36056138 PMCID: PMC9440042 DOI: 10.1038/s41598-022-18040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
Mohr-Tranebjærg syndrome is an X-linked syndrome characterized by sensorineural hearing impairment in childhood, followed by progressive neurodegeneration leading to a broad phenotypic spectrum. Genetically MTS is caused by pathogenic variants in the TIMM8A gene, including gene deletions and larger contiguous gene deletions. Some of the latter involve the neighboring gene BTK, resulting in agammaglobulinemia. By next-generation mate-pair sequencing we have mapped the chromosomal deletion breakpoints of one MTS case and three XLA-MTS cases and used breakpoint-spanning PCR to fine map the breakpoints by Sanger sequencing. Two of the XLA-MTS cases presented with large deletions (63.5 and 27.2 kb), and the junctional regions were characterized by long stretches of microhomology, indicating that the events have emerged through homologous recombination. Conversely, the MTS case exhibited a small 2 bp region of microhomology, and the regions were not characterized by extensive microhomology. The third XLA-MTS case had a more complex breakpoint, including a 59 bp inverted insertion, thus at least four breakpoints were involved in this event. In conclusion, mate-pair library generation combined with next-generation sequencing is an efficient method for breakpoint identification, also in regions characterized by repetitive elements.
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Affiliation(s)
- Nanna Dahl Rendtorff
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Helena Gásdal Karstensen
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Lodahl
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - John Tolmie
- Clinical Genetics Service, Laboratory Medicine Building, Southern General Hospital, Glasgow, Scotland
| | - Catherine McWilliam
- Clinical Genetics, Human Genetics Unit, Ninewells Hospital, Dundee, Scotland
| | - Mads Bak
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henricus Kunst
- Department of Otorhinolaryngology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Melanie Wong
- Department of Allergy and Immunology, The Children's Hospital at Westmead, Sydney, Australia
| | - Shelagh Joss
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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3
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Córdova-Fletes C, Rivera H, Aguayo-Orozco TA, Martínez-Jacobo LA, Garza-González E, Robles-Espinoza CD, Basurto-Lozada P, Avalos-Gómez HG, Esparza-García E, Domínguez-Quezada MG. A chromoanagenesis-driven ultra-complex t(5;7;21)dn truncates neurodevelopmental genes in a disabled boy as revealed by whole-genome sequencing. Eur J Med Genet 2022; 65:104579. [PMID: 35933106 DOI: 10.1016/j.ejmg.2022.104579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 05/30/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022]
Abstract
Germline or constitutional chromoanagenesis-related complex chromosomal rearrangements (CCRs) are rare, apparently "all-at-once", catastrophic events that occur in a single cell cycle, exhibit an unexpected complexity, and sometimes correlate with a severe abnormal phenotype. The term chromoanagenesis encompasses three distinct phenomena, namely chromothripsis, chromoanasynthesis, and chromoplexy. Herein, we found hallmarks of chromothripsis and chromoplexy in an ultra-complex t(5; 7;21)dn involving several disordered breakpoint junctions (BPJs) accompanied by some microdeletions and the disruption of neurodevelopmental genes in a patient with a phenotype resembling autosomal dominant MRD44 (OMIM 617061). G-banded chromosomes and FISH showed that the CCR implied the translocation of the 5p15.2→pter segment onto 7q11.23; in turn, the fragment 7q11.23→qter of der(7) separated into two pieces: the segment q11.23→q32 translocated onto 5p15.2 and fused to 21q22.1→ter in the der(5) while the distal 7q32→qter segment translocated onto der(21) at q22.1. Subsequent whole-genome sequencing unveiled that CCT5, CMBL, RETREG1, MYO10, and TRIO from der(5), IMMP2L, TES, VPS37D, DUS4L, TYW1B, and FEZF1-AS1 from der(7), and TIAM1 and SOD1 from der(21), were disrupted by BPJs, whereas some other genes (predicted to be haplosufficient or inconsequential) were completely deleted. Although remarkably CCT5, TRIO, TES, MYO10, and TIAM1 (and even VPS37D) cooperate in key biological processes for normal neuronal development such as cell adhesion, migration, growth, and/or cytoskeleton formation, the disruption of TRIO most likely caused the patient's MRD44-like phenotype, including intellectual disability, microcephaly, finger anomalies, and facial dysmorphia. Our observation represents the first truncation of TRIO related to a chromoanagenesis event and therefore expands the mutational spectrum of this crucial gene. Moreover, our findings indicate that more than one mechanism is involved in modeling the architecture of ultra-complex rearrangements.
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Affiliation(s)
- Carlos Córdova-Fletes
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico.
| | - Horacio Rivera
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Thania Alejandra Aguayo-Orozco
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico; División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Lizeth Alejandra Martínez-Jacobo
- Departamento de Ciencias Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Mexico
| | - Elvira Garza-González
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico; Wellcome Sanger Institute, Hinxton, UK
| | - Patricia Basurto-Lozada
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico
| | | | - Eduardo Esparza-García
- Hospital de Pediatría, UMAE-CMNO, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Ma Guadalupe Domínguez-Quezada
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.
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Pellestor F, Gaillard JB, Schneider A, Puechberty J, Gatinois V. Chromoanagenesis, the mechanisms of a genomic chaos. Semin Cell Dev Biol 2021; 123:90-99. [PMID: 33608210 DOI: 10.1016/j.semcdb.2021.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Designated under the name of chromoanagenesis, the phenomena of chromothripsis, chromanasynthesis and chromoplexy constitute new types of complex rearrangements, including many genomic alterations localized on a few chromosomal regions, and whose discovery over the last decade has changed our perception about the formation of chromosomal abnormalities and their etiology. Although exhibiting specific features, these new catastrophic mechanisms generally occur within a single cell cycle and their emergence is closely linked to genomic instability. Various non-exclusive exogenous or cellular mechanisms capable of generating chromoanagenesis have been evoked. However, recent experimental data shed light on 2 major processes, which following a defect in the mitotic segregation of chromosomes, can generate a cascade of cellular events leading to chromoanagenesis. These mechanisms are the formation of micronuclei integrating isolated chromosomal material, and the occurrence of chromatin bridges around chromosomal material resulting from telomeric fusions. In both cases, the cellular and molecular mechanisms of fragmentation, repair and transmission of damaged chromosomal material are consistent with the features of chromoanagenesis-related complex chromosomal rearrangements. In this review, we introduce each type of chromoanagenesis, and describe the experimental models that have allowed to validate the existence of chromoanagenesis events and to better understand their cellular mechanisms of formation and transmission, as well as their impact on the stability and the plasticity of the genome.
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Affiliation(s)
- F Pellestor
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France.
| | - J B Gaillard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - A Schneider
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - J Puechberty
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - V Gatinois
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France
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5
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Poot M. Chromothripsis and Duplications as Underappreciated Genomic Gremlins. Mol Syndromol 2021; 11:239-242. [PMID: 33510597 DOI: 10.1159/000512565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
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Eisfeldt J, Pettersson M, Petri A, Nilsson D, Feuk L, Lindstrand A. Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. Hum Genet 2020; 140:775-790. [PMID: 33315133 PMCID: PMC8052244 DOI: 10.1007/s00439-020-02242-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy—a catastrophic event caused by erroneous transcription factor binding.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Petri
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Lars Feuk
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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Brás A, Rodrigues AS, Rueff J. Copy number variations and constitutional chromothripsis (Review). Biomed Rep 2020; 13:11. [PMID: 32765850 PMCID: PMC7391299 DOI: 10.3892/br.2020.1318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Both copy number variations (CNVs) and chromothripsis are phenomena that involve complex genomic rearrangements. Chromothripsis results in CNVs and other structural changes. CNVs are frequently observed in the human genome. Studies on CNVs have been increasing exponentially; the Database of Genomic Variants shows an increase in the number of data published on structural variations added to the database in the last 15 years. CNVs may be a result of replicative and non-replicative mechanisms, and are hypothesized to serve important roles in human health and disease. Chromothripsis is a phenomena of chromosomal rearrangement following chromosomal breaks at multiple locations and involves impaired DNA repair. In 2011, Stephens et al coined the term chromothripsis for this type of fragmenting event. Several proposed mechanisms have been suggested to underlie chromothripsis, such as p53 inactivation, micronuclei formation, abortive apoptosis and telomere fusions in telomere crisis. Chromothripsis gives rise to normal or abnormal phenotypes. In this review, constitutional chromothripsis, which may coexist with multiple de novo CNVs are described and discussed. This reviews aims to summarize recent advances in our understanding of CNVs and chromothripsis, and describe the effects of these phenomena on human health and birth defects.
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Affiliation(s)
- Aldina Brás
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
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Hattori A, Fukami M. Established and Novel Mechanisms Leading to de novo Genomic Rearrangements in the Human Germline. Cytogenet Genome Res 2020; 160:167-176. [DOI: 10.1159/000507837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 01/05/2023] Open
Abstract
During gametogenesis, the human genome can acquire various de novo rearrangements. Most constitutional genomic rearrangements are created through 1 of the 4 well-known mechanisms, i.e., nonallelic homologous recombination, erroneous repair after double-strand DNA breaks, replication errors, and retrotransposition. However, recent studies have identified 2 types of extremely complex rearrangements that cannot be simply explained by these mechanisms. The first type consists of chaotic structural changes in 1 or a few chromosomes that result from “chromoanagenesis (an umbrella term that covers chromothripsis, chromoanasynthesis, and chromoplexy).” The other type is large independent rearrangements in multiple chromosomes indicative of “transient multifocal genomic crisis.” Germline chromoanagenesis (chromothripsis) likely occurs predominantly during spermatogenesis or postzygotic embryogenesis, while multifocal genomic crisis appears to be limited to a specific time window during oogenesis and early embryogenesis or during spermatogenesis. This review article introduces the current understanding of the molecular basis of de novo rearrangements in the germline.
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Cleal K, Baird DM. Catastrophic Endgames: Emerging Mechanisms of Telomere-Driven Genomic Instability. Trends Genet 2020; 36:347-359. [PMID: 32294415 DOI: 10.1016/j.tig.2020.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022]
Abstract
When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, hyperactivation of autophagy, and cell death. Recently, it has become apparent that that the resolution of dicentric chromosomes, which arise from telomere fusions during crisis, can initiate a sequence of events that leads to chromothripsis, a form of extreme genomic catastrophe. Chromothripsis is characterized by localized genomic regions containing tens to thousands of rearrangements and it is becoming increasingly apparent that chromothripsis occurs widely across tumor types and has a clinical impact. Here we discuss how telomere dysfunction can initiate genomic complexity and the emerging mechanisms of chromothripsis.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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Plesser Duvdevani M, Pettersson M, Eisfeldt J, Avraham O, Dagan J, Frumkin A, Lupski JR, Lindstrand A, Harel T. Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome. Am J Med Genet A 2020; 182:1143-1151. [PMID: 32125084 DOI: 10.1002/ajmg.a.61539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023]
Abstract
Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6)(q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.
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Affiliation(s)
- Morasha Plesser Duvdevani
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Ortal Avraham
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Judith Dagan
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Nazaryan-Petersen L, Bjerregaard VA, Nielsen FC, Tommerup N, Tümer Z. Chromothripsis and DNA Repair Disorders. J Clin Med 2020; 9:jcm9030613. [PMID: 32106411 PMCID: PMC7141117 DOI: 10.3390/jcm9030613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements, resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells, resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underlie chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei, followed by the incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome, and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in sonic hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA repair genes, resulting in chromosome instability and chromothripsis-like rearrangements.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Victoria Alexandra Bjerregaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
| | | | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-292-048-55
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12
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Poot M. Genomic Earthquakes in the Human Germline and Their Ramifications. Mol Syndromol 2020; 10:291-293. [PMID: 32021602 DOI: 10.1159/000503366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 02/05/2023] Open
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13
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Uguen K, Jubin C, Duffourd Y, Bardel C, Malan V, Dupont JM, El Khattabi L, Chatron N, Vitobello A, Rollat-Farnier PA, Baulard C, Lelorch M, Leduc A, Tisserant E, Tran Mau-Them F, Danjean V, Delepine M, Till M, Meyer V, Lyonnet S, Mosca-Boidron AL, Thevenon J, Faivre L, Thauvin-Robinet C, Schluth-Bolard C, Boland A, Olaso R, Callier P, Romana S, Deleuze JF, Sanlaville D. Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization. Mol Genet Genomic Med 2020; 8:e1114. [PMID: 31985172 PMCID: PMC7057128 DOI: 10.1002/mgg3.1114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base-pair resolution, but the use of short-read sequencing is limited by repetitive sequences, and long-read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked-reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short-read to linked-read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short-read WGS. METHODS We included 13 patients carrying various SVs. Whole genome analyses were performed using paired-end HiSeq X sequencing with (linked-read strategy) or without (short-read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short-read strategy and LongRanger for long-read strategy. Variant interpretations were first blinded. RESULTS The short-read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked-read strategy identified 10/13 SVs, including one (patient 7) missed by the short-read strategy. CONCLUSION In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV.
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Affiliation(s)
- Kévin Uguen
- Service de Génétique Médicale, CHRU de Brest, Brest, France.,HCL, Service de Génétique, BRON Cedex, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Claire Bardel
- HCL, Cellule bioinformatique de la plateforme NGS du CHU Lyon, BRON Cedex, France.,Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Villeurbanne, France
| | - Valérie Malan
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Jean-Michel Dupont
- Institut Cochin, INSERM U1016, Université Paris Descartes, Faculté de Médecine, APHP, HUPC, site Cochin, Laboratoire de Cytogénétique, Paris, France
| | - Laila El Khattabi
- Institut Cochin, INSERM U1016, Université Paris Descartes, Faculté de Médecine, APHP, HUPC, site Cochin, Laboratoire de Cytogénétique, Paris, France
| | | | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Céline Baulard
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Marc Lelorch
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Aurélie Leduc
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Emilie Tisserant
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Vincent Danjean
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LIG, Grenoble, France
| | - Marc Delepine
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | | | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Stanislas Lyonnet
- Fédération de Génétique et Institut Imagine, UMR-1163, Université de Paris, Hôpital Necker-Enfants Malades, APHP Paris, France
| | - Anne-Laure Mosca-Boidron
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire de génétique chromosomique et moléculaire, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- Centre de génétique, Hôpital Couple-Enfant, CHU Grenoble Alpes, La Tronche, Grenoble, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire de génétique chromosomique et moléculaire, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Serge Romana
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
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14
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Nazaryan-Petersen L, Oliveira IR, Mehrjouy MM, Mendez JMM, Bak M, Bugge M, Kalscheuer VM, Bache I, Hancks DC, Tommerup N. Multigenic truncation of the semaphorin-plexin pathway by a germline chromothriptic rearrangement associated with Moebius syndrome. Hum Mutat 2019; 40:1057-1062. [PMID: 31033088 DOI: 10.1002/humu.23775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 11/07/2022]
Abstract
Moebius syndrome (MBS) is a congenital disorder caused by paralysis of the facial and abducens nerves. Although a number of candidate genes have been suspected, so far only mutations in PLXND1 and REV3L are confirmed to cause MBS. Here, we fine mapped the breakpoints of a complex chromosomal rearrangement (CCR) 46,XY,t(7;8;11;13) in a patient with MBS, which revealed 41 clustered breakpoints with typical hallmarks of chromothripsis. Among 12 truncated protein-coding genes, SEMA3A is known to bind to the MBS-associated PLXND1. Intriguingly, the CCR also truncated PIK3CG, which in silico interacts with REVL3 encoded by the other known MBS-gene REV3L, and with the SEMA3A/PLXND1 complex via FLT1. Additional studies of other complex rearrangements may reveal whether the multiple breakpoints in germline chromothripsis may predispose to complex multigenic disorders.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Inês R Oliveira
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Regulation and Evaluation of Medicines and Health products, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Mana M Mehrjouy
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Juan M M Mendez
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Merete Bugge
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Iben Bache
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dustin C Hancks
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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15
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Koltsova AS, Pendina AA, Efimova OA, Chiryaeva OG, Kuznetzova TV, Baranov VS. On the Complexity of Mechanisms and Consequences of Chromothripsis: An Update. Front Genet 2019; 10:393. [PMID: 31114609 PMCID: PMC6503150 DOI: 10.3389/fgene.2019.00393] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
In the present review, we focus on the phenomenon of chromothripsis, a new type of complex chromosomal rearrangements. We discuss the challenges of chromothripsis detection and its distinction from other chromoanagenesis events. Along with already known causes and mechanisms, we introduce aberrant epigenetic regulation as a possible pathway to chromothripsis. We address the issue of chromothripsis characteristics in cancers and benign tumours, as well as chromothripsis inheritance in cases of its occurrence in germ cells, zygotes and early embryos. Summarising the presented data on different phenotypic effect of chromothripsis, we assume that its consequences are most likely determined not by the chromosome shattering and reassembly themselves, but by the genome regions involved in the rearrangement.
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Affiliation(s)
- Alla S Koltsova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna A Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga A Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Olga G Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Tatyana V Kuznetzova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia
| | - Vladislav S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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16
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Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements. PLoS Genet 2019; 15:e1007858. [PMID: 30735495 PMCID: PMC6368290 DOI: 10.1371/journal.pgen.1007858] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/28/2018] [Indexed: 11/19/2022] Open
Abstract
Complex chromosomal rearrangements (CCRs) are rearrangements involving more than two chromosomes or more than two breakpoints. Whole genome sequencing (WGS) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements, but problems remain for mapping breakpoints in repetitive regions of the genome, which are known to be prone to rearrangements. Hence, multiple complementary WGS experiments are sometimes needed to solve the structures of CCRs. We have studied three individuals with CCRs: Case 1 and Case 2 presented with de novo karyotypically balanced, complex interchromosomal rearrangements (46,XX,t(2;8;15)(q35;q24.1;q22) and 46,XY,t(1;10;5)(q32;p12;q31)), and Case 3 presented with a de novo, extremely complex intrachromosomal rearrangement on chromosome 1. Molecular cytogenetic investigation revealed cryptic deletions in the breakpoints of chromosome 2 and 8 in Case 1, and on chromosome 10 in Case 2, explaining their clinical symptoms. In Case 3, 26 breakpoints were identified using WGS, disrupting five known disease genes. All rearrangements were subsequently analyzed using optical maps, linked-read WGS, and short-read WGS. In conclusion, we present a case series of three unique de novo CCRs where we by combining the results from the different technologies fully solved the structure of each rearrangement. The power in combining short-read WGS with long-molecule sequencing or optical mapping in these unique de novo CCRs in a clinical setting is demonstrated.
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17
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Kurtas NE, Xumerle L, Giussani U, Pansa A, Cardarelli L, Bertini V, Valetto A, Liehr T, Clara Bonaglia M, Errichiello E, Delledonne M, Zuffardi O. Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception? Mol Genet Genomic Med 2018; 7:e00496. [PMID: 30565424 PMCID: PMC6393660 DOI: 10.1002/mgg3.496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/02/2018] [Indexed: 01/17/2023] Open
Abstract
Background Chromothripsis, which is the local massive shattering of one or more chromosomes and their reassembly in a disordered array with frequent loss of some fragments, has been mainly reported in association with abnormal phenotypes. We report three unrelated healthy persons, two of which parenting a child with some degree of intellectual disability, carrying a chromothripsis involving respectively one, two, and three chromosomes, which was detected only after whole‐genome sequencing. Unexpectedly, in all three cases a fragment from one of the chromothripsed chromosomes resulted to be inserted within a nonchromothripsed one. Methods Conventional cytogenetic techniques, paired‐end whole‐genome sequencing, polymerase chain reaction, and Sanger sequencing were used to characterize complex rearrangements, copy‐number variations, and breakpoint sequences in all three families. Results In two families, one parent was carrier of a balanced chromothripsis causing in the index case a deletion and a noncontiguous duplication at 3q in case 1, and a t(6;14) translocation associated with interstitial 14q deletion in case 2. In the third family, an unbalanced chromothripsis involving chromosomes 6, 7, and 15 was inherited to the proband by the mosaic parent. In all three parents, the chromothripsis was concurrent with an insertional translocation of a portion of one of the chromothriptic chromosomes within a further chromosome that was not involved in the chromothripsis event. Conclusion Our findings show that (a) both simple and complex unbalanced rearrangements may result by the recombination of a cryptic parental balanced chromothripsis and that (b) insertional translocations are the spy of more complex rearrangements and not simply a three‐breakpoint event.
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Affiliation(s)
| | - Luciano Xumerle
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | | | | | | | | | | | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Lecco, Italy
| | | | - Massimo Delledonne
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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18
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Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLoS Genet 2018; 14:e1007780. [PMID: 30419018 PMCID: PMC6258378 DOI: 10.1371/journal.pgen.1007780] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 01/25/2023] Open
Abstract
Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both “simple” and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements. Clustered copy number variants (CNVs) as detected by chromosomal microarray are often reported as germline chromoanagenesis. However, such cases might need further investigation by whole genome sequencing (WGS) to accurately resolve the complexity of the structural rearrangement and predict underlying mutational mechanisms. Here, we used WGS to characterize 83 breakpoint-junctions (BPJs) from 21 clustered CNVs, and outlined the rearrangement connectivity pictures. Cases with only deletions often had additional structural rearrangements, such as insertions and inversions, which could be a result of multiple double-strand DNA breaks followed by non-homologous repair, typical to chromothripsis. In contrast, cases with only duplications or combinations of deletions and duplications, demonstrated mostly interspersed duplications and BPJs enriched with microhomology, consistent with serial template switching during DNA replication (chromoanasynthesis). Only two rearrangements were repeat mediated. In aggregate, our results suggest that multiple CNVs clustered on a single chromosome may arise through either chromothripsis or chromoanasynthesis.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agne Lieden
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jesper Ottosson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jelena Gacic
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Tina Duelund Hjortshøj
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Cathrine Jespersgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Rayan Houssari
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Laura Pignata
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- * E-mail: (AL); (ZT)
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (AL); (ZT)
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