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Xia C, Kumar D, You B, Streck DL, Osborne L, Dermody J, Jiang JG, Pletcher BA. Wolf-Hirschhorn Syndrome with Hyperparathyroidism: A Case Report and a Narrative Review of the Literature. J Pediatr Genet 2023; 12:312-317. [PMID: 38162156 PMCID: PMC10756731 DOI: 10.1055/s-0041-1729751] [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: 11/26/2020] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Wolf-Hirschhorn syndrome (WHS) is a contiguous gene deletion condition. The WHS core phenotype includes developmental delays, intellectual disabilities, seizures, and distinctive facial features. Various other comorbidities have also been reported, such as hearing loss, heart defects, as well as eye problems and kidney problems. In this report, we present a case of WHS accompanied by hyperparathyroidism and hypercalcemia, which has not been previously reported. A girl was born at 37 weeks of gestation by vaginal delivery. She was small for the gestational age (2,045 g) and admitted to neonatal intensive care unit. She had typical WHS facial features and was found to have bilateral small kidneys associated with transient metabolic acidosis and renal insufficiency. She had right-sided sensorineural hearing loss, a small atrial septal defect, and colpocephaly and hypoplasia of corpus callosum. She had a single seizure which was well controlled with an oral antiepileptic medication. Cytogenetic studies demonstrated a large terminal chromosome 4p deletion (21.4 Mb) and 4p duplication (2.1 Mb) adjacent to the deletion. A unique finding in this patient is her consistently elevated levels of parathyroid hormone and serum calcium, suggesting hyperparathyroidism. We present this rare case along with a review of the literature and hope to draw an attention to a potential relationship between WHS and hyperparathyroidism.
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Affiliation(s)
- Changqing Xia
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Dibyendu Kumar
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Bei You
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Deanna L. Streck
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Lisa Osborne
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - James Dermody
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Jie-Gen Jiang
- Institute of Medical Genetics and Genomics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
| | - Beth A. Pletcher
- Department of Pediatrics, Rutgers New Jersey Medical School, Newark, New Jersey, United States
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2
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Shimojima Yamamoto K, Tamura T, Okamoto N, Nishi E, Noguchi A, Takahashi I, Sawaishi Y, Shimizu M, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Identification of small-sized intrachromosomal segments at the ends of INV-DUP-DEL patterns. J Hum Genet 2023; 68:751-757. [PMID: 37423943 DOI: 10.1038/s10038-023-01181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
The mechanism of chromosomal rearrangement associated with inverted-duplication-deletion (INV-DUP-DEL) pattern formation has been investigated by many researchers, and several possible mechanisms have been proposed. Currently, fold-back and subsequent dicentric chromosome formation has been established as non-recurrent INV-DUP-DEL pattern formation mechanisms. In the present study, we analyzed the breakpoint junctions of INV-DUP-DEL patterns in five patients using long-read whole-genome sequencing and detected 2.2-6.1 kb copy-neutral regions in all five patients. At the end of the INV-DUP-DEL, two patients exhibited chromosomal translocations, which are recognized as telomere capture, and one patient showed direct telomere healing. The remaining two patients had additional small-sized intrachromosomal segments at the end of the derivative chromosomes. These findings have not been previously reported but they may only be explained by the presence of telomere capture breakage. Further investigations are required to better understand the mechanisms underlying this finding.
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Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, 594-1101, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Ikuko Takahashi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, 010-8543, Japan
| | - Yukio Sawaishi
- Department of Pediatrics, Akita Prefectural Center on Development and Disability, Akita, 010-0000, Japan
| | - Masaki Shimizu
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-0801, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
- Division of Gene Medicine, Graduate Scholl of Medical Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
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3
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Ait Saada A, Guo W, Costa AB, Yang J, Wang J, Lobachev K. Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. Nucleic Acids Res 2023; 51:3722-3734. [PMID: 36919609 PMCID: PMC10164571 DOI: 10.1093/nar/gkad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby >73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.
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Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Burssed B, Zamariolli M, Favilla BP, Meloni VA, Goloni-Bertollo EM, Bellucco FT, Melaragno MI. Fold-back mechanism originating inv-dup-del rearrangements in chromosomes 13 and 15. Chromosome Res 2023; 31:10. [PMID: 36826604 DOI: 10.1007/s10577-023-09720-0] [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: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023]
Abstract
Intrachromosomal rearrangements involve a single chromosome and can be formed by several proposed mechanisms. We reported two patients with intrachromosomal duplications and deletions, whose rearrangements and breakpoints were characterized through karyotyping, chromosomal microarray, fluorescence in situ hybridization, whole-genome sequencing, and Sanger sequencing. Inverted duplications associated with terminal deletions, known as inv-dup-del rearrangements, were found in 13q and 15q in these patients. The presence of microhomology at the junction points led to the proposal of the Fold-back mechanism for their formation. The use of different high-resolution techniques allowed for a better characterization of the rearrangements, with Sanger sequencing of the junction points being essential to infer the mechanisms of formation as it revealed microhomologies that were missed by the previous techniques. A karyotype-phenotype correlation was also performed for the characterized rearrangements.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bianca Pereira Favilla
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Eny Maria Goloni-Bertollo
- Genetics and Molecular Biology Research Unit, Department of Molecular Biology, São José Do Rio Preto Medical School, São José Do Rio Preto, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.
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5
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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Redaelli S, Conconi D, Sala E, Villa N, Crosti F, Roversi G, Catusi I, Valtorta C, Recalcati MP, Dalprà L, Lavitrano M, Bentivegna A. Characterization of Chromosomal Breakpoints in 12 Cases with 8p Rearrangements Defines a Continuum of Fragility of the Region. Int J Mol Sci 2022; 23:ijms23063347. [PMID: 35328767 PMCID: PMC8954119 DOI: 10.3390/ijms23063347] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/29/2022] Open
Abstract
Improvements in microarray-based comparative genomic hybridization technology have allowed for high-resolution detection of genome wide copy number alterations, leading to a better definition of rearrangements and supporting the study of pathogenesis mechanisms. In this study, we focused our attention on chromosome 8p. We report 12 cases of 8p rearrangements, analyzed by molecular karyotype, evidencing a continuum of fragility that involves the entire short arm. The breakpoints seem more concentrated in three intervals: one at the telomeric end, the others at 8p23.1, close to the beta-defensin gene cluster and olfactory receptor low-copy repeats. Hypothetical mechanisms for all cases are described. Our data extend the cohort of published patients with 8p aberrations and highlight the need to pay special attention to these sequences due to the risk of formation of new chromosomal aberrations with pathological effects.
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Affiliation(s)
- Serena Redaelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
- Correspondence: (D.C.); (A.B.)
| | - Elena Sala
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, 20900 Monza, Italy; (E.S.); (N.V.); (F.C.)
| | - Nicoletta Villa
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, 20900 Monza, Italy; (E.S.); (N.V.); (F.C.)
| | - Francesca Crosti
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, 20900 Monza, Italy; (E.S.); (N.V.); (F.C.)
| | - Gaia Roversi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, 20900 Monza, Italy; (E.S.); (N.V.); (F.C.)
| | - Ilaria Catusi
- Medical Cytogenetics Laboratory, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy; (I.C.); (C.V.); (M.P.R.)
| | - Chiara Valtorta
- Medical Cytogenetics Laboratory, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy; (I.C.); (C.V.); (M.P.R.)
| | - Maria Paola Recalcati
- Medical Cytogenetics Laboratory, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy; (I.C.); (C.V.); (M.P.R.)
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, 20900 Monza, Italy; (E.S.); (N.V.); (F.C.)
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (G.R.); (L.D.); (M.L.)
- Correspondence: (D.C.); (A.B.)
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7
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MacKinnon RN, Peverall J, Campbell LJ, Wall M. Detailed molecular cytogenetic characterisation of the myeloid cell line U937 reveals the fate of homologous chromosomes and shows that centromere capture is a feature of genome instability. Mol Cytogenet 2020; 13:50. [PMID: 33317567 PMCID: PMC7737353 DOI: 10.1186/s13039-020-00517-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The U937 cell line is widely employed as a research tool. It has a complex karyotype. A PICALM-MLLT10 fusion gene formed by the recurrent t(10;11) translocation is present, and the myeloid common deleted region at 20q12 has been lost from its near-triploid karyotype. We carried out a detailed investigation of U937 genome reorganisation including the chromosome 20 rearrangements and other complex rearrangements. RESULTS SNP array, G-banding and Multicolour FISH identified chromosome segments resulting from unbalanced and balanced rearrangements. The organisation of the abnormal chromosomes containing these segments was then reconstructed with the strategic use of targeted metaphase FISH. This provided more accurate karyotype information for the evolving karyotype. Rearrangements involving the homologues of a chromosome pair could be differentiated in most instances. Centromere capture was demonstrated in an abnormal chromosome containing parts of chromosomes 16 and 20 which were stabilised by joining to a short section of chromosome containing an 11 centromere. This adds to the growing number of examples of centromere capture, which to date have a high incidence in complex karyotypes where the centromeres of the rearranged chromosomes are identified. There were two normal copies of one chromosome 20 homologue, and complex rearrangement of the other homologue including loss of the 20q12 common deleted region. This confirmed the previously reported loss of heterozygosity of this region in U937, and defined the rearrangements giving rise to this loss. CONCLUSIONS Centromere capture, stabilising chromosomes pieced together from multiple segments, may be a common feature of complex karyotypes. However, it has only recently been recognised, as this requires deliberate identification of the centromeres of abnormal chromosomes. The approach presented here is invaluable for studying complex reorganised genomes such as those produced by chromothripsis, and provides a more complete picture than can be obtained by microarray, karyotyping or FISH studies alone. One major advantage of SNP arrays for this process is that the two homologues can usually be distinguished when there is more than one rearrangement of a chromosome pair. Tracking the fate of each homologue and of highly repetitive DNA regions such as centromeres helps build a picture of genome evolution. Centromere- and telomere-containing elements are important to deducing chromosome structure. This study confirms and highlights ongoing evolution in cultured cell lines.
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Affiliation(s)
- Ruth N. MacKinnon
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital, PO Box 2900, Fitzroy, Melbourne, 3065 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Joanne Peverall
- PathWest Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Australia
| | - Lynda J. Campbell
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital, PO Box 2900, Fitzroy, Melbourne, 3065 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Services, Parkville, Melbourne, Australia
- Murdoch Children’s Research Institute, Parkville, Melbourne, Australia
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Caldwell S, Sagaser K, Nelson Z, Frey J, Wardrop J, Boomer T, McCullough R, Schwartz S. Deletion rescue resulting in segmental homozygosity: A mechanism underlying discordant NIPT results. Am J Med Genet A 2020; 182:2666-2670. [PMID: 32798301 DOI: 10.1002/ajmg.a.61801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/04/2020] [Indexed: 11/07/2022]
Abstract
With the increasing capabilities of non-invasive prenatal testing (NIPT), detection of sub-chromosomal deletions and duplications are possible. This case series of deletion rescues resulting in segmental homozygosity helps provide a biological explanation for NIPT discrepancies and adds to the dearth of existing literature surrounding segmental UPD cases and their underlying mechanisms. In the three cases presented here, NIPT reported a sub-chromosomal deletion (in isolation or as part of a complex finding). Diagnostic testing, however, revealed segmental homozygosity or UPD for the region reported deleted on NIPT. Postnatal placental testing was pursued in two cases and confirmed the NIPT findings. This discordance between the screening and diagnostic testing is suggestive of a corrective post-zygotic event, such as telomere capture and/or deletion rescue, ultimately resulting in segmental homozygosity and fetoplacental mosaicism. Imprinted chromosomes and autosomal recessive disease genes make homozygosity an important clinical consideration. Amniocentesis with SNP microarray is particularly useful in determining both copy number and UPD issues alike.
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Affiliation(s)
| | - Katelynn Sagaser
- Division of Maternal Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zoe Nelson
- Mount Sinai West Medical Center, New York, New York, USA
| | - Jennifer Frey
- Division of Medical Genetics, Henry Ford Health System, Detroit, Michigan, USA
| | | | | | | | - Stuart Schwartz
- Cytogenetics Laboratory, Laboratory Corporation of America® Holdings, Research Triangle Park, North Carolina, USA
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9
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Li BZ, Putnam CD, Kolodner RD. Mechanisms underlying genome instability mediated by formation of foldback inversions in Saccharomyces cerevisiae. eLife 2020; 9:58223. [PMID: 32762846 PMCID: PMC7467729 DOI: 10.7554/elife.58223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023] Open
Abstract
Foldback inversions, also called inverted duplications, have been observed in human genetic diseases and cancers. Here, we used a Saccharomyces cerevisiae genetic system that generates gross chromosomal rearrangements (GCRs) mediated by foldback inversions combined with whole-genome sequencing to study their formation. Foldback inversions were mediated by formation of single-stranded DNA hairpins. Two types of hairpins were identified: small-loop hairpins that were suppressed by MRE11, SAE2, SLX1, and YKU80 and large-loop hairpins that were suppressed by YEN1, TEL1, SWR1, and MRC1. Analysis of CRISPR/Cas9-induced double strand breaks (DSBs) revealed that long-stem hairpin-forming sequences could form foldback inversions when proximal or distal to the DSB, whereas short-stem hairpin-forming sequences formed foldback inversions when proximal to the DSB. Finally, we found that foldback inversion GCRs were stabilized by secondary rearrangements, mostly mediated by different homologous recombination mechanisms including single-strand annealing; however, POL32-dependent break-induced replication did not appear to be involved forming secondary rearrangements.
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Affiliation(s)
- Bin-Zhong Li
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States.,Departments of Medicine, University of California School of Medicine, San Diego, San Diego, United States
| | - Richard David Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, San Diego, United States.,Cellular and Molecular Medicine, University of California School of Medicine, San Diego, San Diego, United States.,Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, San Diego, United States.,Institute of Genomic Medicine, University of California School of Medicine, San Diego, San Diego, United States
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10
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Kato T, Inagaki H, Miyai S, Suzuki F, Naru Y, Shinkai Y, Kato A, Kanyama K, Mizuno S, Muramatsu Y, Yamamoto T, Shinya M, Tazaki Y, Hiwatashi S, Ikeda T, Ozaki M, Kurahashi H. The involvement of U-type dicentric chromosomes in the formation of terminal deletions with or without adjacent inverted duplications. Hum Genet 2020; 139:1417-1427. [PMID: 32488466 DOI: 10.1007/s00439-020-02186-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/22/2020] [Indexed: 11/28/2022]
Abstract
An inverted duplication with a terminal deletion (inv-dup-del) is one of the complex constitutional structural rearrangements that can occur in a chromosome. Although breakages of dicentric chromosome have been suggested, the precise mechanism of this is yet to be fully understood. In our present study, we investigated the genomic structure of 10 inv-dup-del cases to elucidate this mechanism. Two recurrent 8p inv-dup-del cases harbored a large copy-number-neutral region between the duplication and deletion in common. Although the other non-recurrent cases did not appear to have this copy-number-neutral region, refined sequencing analysis identified that they contained a small intervening region at the junction between the inverted and non-inverted segment. The size of this small intervening region ranged from 1741 to 3728 bp. Combined with a presence of microhomology at the junction, a resolution of the replication fork stalling through template switching within the same replication fork is suggested. We further observed two cases with mosaicism of the dicentric chromosome and various structural rearrangements related to the dicentric chromosome. Refined analysis allowed us to identify different breakpoints on the same chromosome in the same case, implicating multiple rounds of U-type formation and its breakage. From these results, we propose that a replication-based mechanism generates unstable dicentric chromosomes and that their breakage leads to the formation of inv-dup-dels and other related derivative chromosomes.
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Affiliation(s)
- Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Syunsuke Miyai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Fumihiko Suzuki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yuki Naru
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Asuka Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Kazuo Kanyama
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Kasugai, Japan
| | - Yukako Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Shinjuku, Japan
| | - Mitsuhisa Shinya
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Yukiko Tazaki
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Sayuri Hiwatashi
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Toshiro Ikeda
- Genetic Counseling Room, Kagoshima University Hospital, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima, Japan
| | - Mamoru Ozaki
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan. .,Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Kasugai, Japan.
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11
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Chai H, Grommisch B, DiAdamo A, Wen J, Hui P, Li P. Inverted duplication, triplication and quintuplication through sequential breakage-fusion-bridge events induced by a terminal deletion at 5p in a case of spontaneous abortion. Mol Genet Genomic Med 2019; 7:e00965. [PMID: 31478360 PMCID: PMC6785443 DOI: 10.1002/mgg3.965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Integrated chromosome, fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) analyses have been effective in defining unbalanced chromosomal rearrangements. Discordant chromosome and aCGH results are rarely reported. Methods Routine cytogenomic analyses and literature review were performed in the study of a case from products of conception (POC). Results Chromosome and FISH analysis revealed a mosaic pattern consisting of a primary aberration of an inverted duplication of 5p and derived secondary and tertiary aberrations from sequential triplication and quintuplication of 5p, respectively. The aCGH analysis detected only a 1.521 Mb terminal deletion at 5p15.33 with no other pathogenic copy number variants in the genome. This mosaic karyotypic pattern likely resulted from chromosome instability induced by sequential breakage‐fusion‐bridge events during in vitro cell culture. A review of literature found heterogeneous distal deletion and inverted duplication of 5p in prenatal and pediatric cases. Conclusion This is the first case reported in POC with a unique mosaic pattern and discordant chromosome and aCGH results. Caution should be applied in reporting and interpreting these discordant results and further analysis for underlying mechanism should be considered.
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Affiliation(s)
- Hongyan Chai
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Brittany Grommisch
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn DiAdamo
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Jiadi Wen
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Peining Li
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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12
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Orru S, Papoulidis I, Siomou E, Papadimitriou DT, Sotiriou S, Nikolaidis P, Eleftheriades M, Papanikolaou E, Thomaidis L, Manolakos E. Autism spectrum disorder, anxiety and severe depression in a male patient with deletion and duplication in the 21q22.3 region: A case report. Biomed Rep 2019; 1:1-5. [PMID: 31258897 DOI: 10.3892/br.2019.1210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
In this report, a patient carrying a 650 kb deletion and a 759 kb duplication of chromosomal 21q22.3 region was described. Facial dysmorphic features, hypotonia, short stature, learning impairment, autism spectrum disorder, anxiety and depression were observed clinical characteristics. Mentioned copy number variants were the shortest in length reported so far. The current study hypothesized that the presence of a susceptibility locus for autism spectrum disorder associated with depression and anxiety may be located in a 200 kb region between the PCNT and PRMT2 genes. The current study aimed to provide insight into the human genome morbidity map of chromosome 21.
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Affiliation(s)
- Sandro Orru
- Department of Medical Genetics, University of Cagliari, Binaghi Hospital, I-09126 Cagliari, Italy
| | | | - Elisavet Siomou
- ATG P.C., Clinical Laboratory Genetics, Athens 11528, Greece
| | - Dimitrios T Papadimitriou
- Department of Pediatric Endocrinology and Diabetes, Athens Medical Center, Athens 15125, Greece.,Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa 41334, Greece
| | - Sotirios Sotiriou
- Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa 41334, Greece
| | | | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, Aretaieio Hospital, Medical School, National and Kapodistrian University of Athens, Athens 11528, Greece
| | - Evaggelos Papanikolaou
- Third Department in Obstetrics and Gynecology, Ippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54642, Greece
| | - Loretta Thomaidis
- Developmental Assessment Unit, Second Department of Pediatrics, 'P. & A. Kyriakou' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Emmanouil Manolakos
- Department of Medical Genetics, University of Cagliari, Binaghi Hospital, I-09126 Cagliari, Italy.,ATG P.C., Clinical Laboratory Genetics, Athens 11528, Greece.,Developmental Assessment Unit, Second Department of Pediatrics, 'P. & A. Kyriakou' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens 11527, Greece
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13
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De novo unbalanced translocations have a complex history/aetiology. Hum Genet 2018; 137:817-829. [DOI: 10.1007/s00439-018-1941-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
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14
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A Heterochromatin Domain Forms Gradually at a New Telomere and Is Dynamic at Stable Telomeres. Mol Cell Biol 2018; 38:MCB.00393-17. [PMID: 29784772 PMCID: PMC6048312 DOI: 10.1128/mcb.00393-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 05/09/2018] [Indexed: 02/03/2023] Open
Abstract
Heterochromatin domains play important roles in chromosome biology, organismal development, and aging, including centromere function, mammalian female X chromosome inactivation, and senescence-associated heterochromatin foci. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin contains histone H3 that is dimethylated at lysine 9. Heterochromatin domains play important roles in chromosome biology, organismal development, and aging, including centromere function, mammalian female X chromosome inactivation, and senescence-associated heterochromatin foci. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin contains histone H3 that is dimethylated at lysine 9. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin. To form a new heterochromatic region in S. pombe, an inducible DNA double-strand break (DSB) was engineered next to 48 bp of telomere repeats in euchromatin, which caused formation of a new telomere and the establishment and gradual spreading of a new heterochromatin domain. However, spreading was dynamic even after the telomere had reached its stable length, with reporter genes within the heterochromatin domain showing variegated expression. The system also revealed the presence of repeats located near the boundaries of euchromatin and heterochromatin that are oriented to allow the efficient healing of a euchromatic DSB to cap the chromosome end with a new telomere. Telomere formation in S. pombe therefore reveals novel aspects of heterochromatin dynamics and fail-safe mechanisms to repair subtelomeric breaks, with implications for similar processes in metazoan genomes.
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15
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dos Santos A, Campagnari F, Krepischi ACV, Ribeiro Câmara MDL, de Arruda Brasil RDCE, Vieira L, Vianna-Morgante AM, Otto PA, Pearson PL, Rosenberg C. Insight into the mechanisms and consequences of recurrent telomere capture associated with a sub-telomeric deletion. Chromosome Res 2018; 26:191-198. [DOI: 10.1007/s10577-018-9578-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/28/2022]
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16
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Knijnenburg J, Uytdewilligen ME, van Hassel DA, Oostenbrink R, Eussen BH, de Klein A, Brooks AS, van Zutven LJ. Postzygotic telomere capture causes segmental UPD, duplication and deletion of chromosome 8p in a patient with intellectual disability and obesity. Eur J Med Genet 2017; 60:445-450. [DOI: 10.1016/j.ejmg.2017.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/13/2017] [Accepted: 06/06/2017] [Indexed: 01/30/2023]
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17
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Sánchez-Casillas AL, Rivera H, Castro-Martínez AG, García-Ortiz JE, Córdova-Fletes C, Mendoza-Pérez P. De Novo San Luis Valley Syndrome-like der(8) Chromosome With a Concomitant dup(8p22) in a Mexican Girl. Ann Lab Med 2017; 37:88-91. [PMID: 27834075 PMCID: PMC5107627 DOI: 10.3343/alm.2017.37.1.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/01/2016] [Accepted: 08/29/2016] [Indexed: 01/30/2023] Open
Affiliation(s)
- Alma Laura Sánchez-Casillas
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jal., México
| | - Horacio Rivera
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jal., México.,Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jal., México
| | | | - José Elías García-Ortiz
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jal., México
| | - Carlos Córdova-Fletes
- Laboratorio de Citogenómica y Microarreglos, Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, N.L., México.
| | - Paul Mendoza-Pérez
- Laboratorio de Citogenómica y Microarreglos, Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, N.L., México
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18
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Unbalanced karyotype with X;11 translocation associated with SHOX duplication and 11q partial deletion in a girl with amenorrhea and mild mental retardation detected by array CGH: Case Report. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Bi W, Cheung SW, Breman AM, Bacino CA. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions. Am J Med Genet A 2016; 170:2540-50. [DOI: 10.1002/ajmg.a.37796] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/30/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Weimin Bi
- Department of Molecular and Human Genetics; Baylor College of Medicine; One Baylor Plaza; Houston Texas
| | - Sau-Wai Cheung
- Department of Molecular and Human Genetics; Baylor College of Medicine; One Baylor Plaza; Houston Texas
| | - Amy M. Breman
- Department of Molecular and Human Genetics; Baylor College of Medicine; One Baylor Plaza; Houston Texas
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics; Baylor College of Medicine; One Baylor Plaza; Houston Texas
- Texas Children's Hospital; Houston Texas
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20
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Tabet AC, Verloes A, Pilorge M, Delaby E, Delorme R, Nygren G, Devillard F, Gérard M, Passemard S, Héron D, Siffroi JP, Jacquette A, Delahaye A, Perrin L, Dupont C, Aboura A, Bitoun P, Coleman M, Leboyer M, Gillberg C, Benzacken B, Betancur C. Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder. Mol Autism 2015; 6:19. [PMID: 25844147 PMCID: PMC4384291 DOI: 10.1186/s13229-015-0015-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. Methods Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. Results We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. Conclusions These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings.
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Affiliation(s)
- Anne-Claude Tabet
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Alain Verloes
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Marion Pilorge
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Elsa Delaby
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Richard Delorme
- Department of Child and Adolescent Psychiatry, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Françoise Devillard
- Département de Génétique et Procréation, CHU de Grenoble, Hôpital Couple-Enfant, avenue du Maquis du Grésivaudan, 38043 Grenoble, France
| | - Marion Gérard
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Sandrine Passemard
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Neurology Unit, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Delphine Héron
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Jean-Pierre Siffroi
- Service de Génétique et d'Embryologie Médicales, AP-HP, Trousseau Hospital, 26 avenue du Docteur Arnold Netter, 75012 Paris, France
| | - Aurelia Jacquette
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Andrée Delahaye
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Laurence Perrin
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Céline Dupont
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Azzedine Aboura
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Pierre Bitoun
- Medical Genetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France
| | - Mary Coleman
- Foundation for Autism Research, 3081 Quail Hollow, Sarasota, FL 34235 USA
| | - Marion Leboyer
- Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France ; Department of Psychiatry, AP-HP, Henri Mondor-Albert Chenevier Hospital, 40 rue de Mesly, 94000 Créteil, France ; INSERM U955, Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, 8 rue du Général Sarrail, 94000 Créteil, France ; Faculty of Medicine, University Paris-Est Créteil, 8 rue du Général Sarrail, 94000 Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Brigitte Benzacken
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Catalina Betancur
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
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García-Santiago FA, Martínez-Glez V, Santos F, García-Miñaur S, Mansilla E, Meneses AG, Rosell J, Granero ÁP, Vallespín E, Fernández L, Sierra B, Oliver-Bonet M, Palomares M, de Torres ML, Mori MÁ, Nevado J, Heath KE, Delicado A, Lapunzina P. Analysis of invdupdel(8p) rearrangement: Clinical, cytogenetic and molecular characterization. Am J Med Genet A 2015; 167A:1018-25. [DOI: 10.1002/ajmg.a.36879] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/22/2014] [Indexed: 01/30/2023]
Affiliation(s)
- Fe Amalia García-Santiago
- Cytogenetics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
| | - Víctor Martínez-Glez
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Fernando Santos
- Clinical Gentics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Sixto García-Miñaur
- Clinical Gentics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Elena Mansilla
- Cytogenetics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | | | - Jordi Rosell
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
- Genetics Unit; Hospital Son Espases; Palma de Mallorca; Spain
| | | | - Elena Vallespín
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Luis Fernández
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Blanca Sierra
- Genetics Unit; Hospital Son Espases; Palma de Mallorca; Spain
| | | | - María Palomares
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - María Luisa de Torres
- Cytogenetics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - María Ángeles Mori
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Julián Nevado
- Functional and Structural Genomics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Karen E. Heath
- Molecular Endocrinology Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Alicia Delicado
- Cytogenetics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
| | - Pablo Lapunzina
- Clinical Gentics Unit, Institute of Medical and Molecular Genetics (INGEMM); IdiPAZ, Hospital Universitario La Paz; Madrid Spain
- CIBERER; Centro de Investigación Biomédica en Red de Enfermedades Raras; ISCIII; Madrid Spain
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Papenhausen PR, Kelly CA, Zvereff V, Schwartz S. Four-copy number intervals in SNP microarray analysis: unique patterns and positions. Cytogenet Genome Res 2014; 144:92-103. [PMID: 25401283 DOI: 10.1159/000368859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2014] [Indexed: 11/19/2022] Open
Abstract
Over the past several years, the utility of microarray technology in delineating copy number changes has become well established. In the past 4 years, we have used the SNP array to detect and analyze allele ratios in 150 cases with 4-copy intervals, confirmed by FISH, offering insight into the underlying mechanisms of formation. These cases may be divided into 5 allele patterns--the first 4 of which involve a single homologue--as detected by the genotyping aspects of the microarray: (1) triplications combining homozygous and heterozygous alleles, with a 3:1 ratio of heterozygotes; (2) triplications with allele patterns combining homozygous and heterozygous alleles, with heterozygote ratios of both 3:1 and 2:2; (3) triplications that have homozygous alleles combined with only 2:2 heterozygous alleles; (4) triplications that are completely homozygous; and (5) homozygous duplications on each homologue with no heterozygous alleles. The implications of copy number variants with diverse allelic segregations are presented in this study.
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Affiliation(s)
- Peter R Papenhausen
- Department of Cytogenetics, Laboratory Corporation of America, Research Triangle Park, N.C., USA
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23
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Milosevic J, El Khattabi L, Roubergue A, Coussement A, Doummar D, Cuisset L, Le Tessier D, Flageul B, Viot G, Lebbar A, Dupont JM. Inverted duplication with deletion: first interstitial case suggesting a novel undescribed mechanism of formation. Am J Med Genet A 2014; 164A:3180-6. [PMID: 25257167 DOI: 10.1002/ajmg.a.36777] [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: 02/24/2014] [Accepted: 08/23/2014] [Indexed: 11/09/2022]
Abstract
Inverted duplications with terminal deletions are a well-defined family of complex rearrangements already observed for most of chromosome extremities. Several mechanisms have been suggested which could lead to their occurrence, either through non-homologous end joining, non-allelic homologous recombination, or more recently through an intrastrand fold-back mechanism. We describe here a patient with intellectual disability and pharmacoresistant epilepsy, for which array CGH analysis showed the first interstitial case of inverted duplication with deletion on chromosome 1p. Furthermore, SNP array analysis revealed an associated segmental isodisomy for the distal part of 1p, which led us to consider a replicative mechanism to explain this abnormality. This observation extends the range of this once telomeric rearrangement.
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Affiliation(s)
- J Milosevic
- Faculté de Médecine, Laboratoire de Cytogénétique Constitutionnelle, Hôpital Cochin, APHP, Université Paris Descartes, Paris, France
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24
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Quelin C, Spaggiari E, Khung-Savatovsky S, Dupont C, Pasquier L, Loeuillet L, Jaillard S, Lucas J, Marcorelles P, Journel H, Pluquailec-Bilavarn K, Bazin A, Verloes A, Delezoide AL, Aboura A, Guimiot F. Inversion duplication deletions involving the long arm of chromosome 13: phenotypic description of additional three fetuses and genotype-phenotype correlation. Am J Med Genet A 2014; 164A:2504-9. [PMID: 24975584 DOI: 10.1002/ajmg.a.36658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 05/28/2014] [Indexed: 11/09/2022]
Abstract
Inversion duplication and terminal deletion of the long arm of chromosome 13 (inv dup del 13q) is a rare chromosomal rearrangement: only five patients have been reported, mostly involving a ring chromosome 13. We report on additional three fetuses with pure inv dup del 13q: Patient 1 had macrosomia, enlarged kidneys, hypersegmented lungs, unilateral moderate ventriculomegaly, and a mild form of hand and feet preaxial polydactyly; Patient 2 had intrauterine growth retardation, widely spaced eyes, left microphthalmia, right anophthalmia, short nose, bilateral absent thumbs, cutaneous syndactyly of toes 4 and 5, bifid third metacarpal, a small left kidney, hyposegmented lungs, and partial agenesis of the corpus callosum; Patient 3 had widely spaced eyes, long and smooth philtrum, low-set ears, median notch in the upper alveolar ridge, bifid tongue, cutaneous syndactyly of toes 2 and 3, enlarged kidneys and pancreas, arhinencephaly, and partial agenesis of the corpus callosum. We compared the phenotypes of these patients to those previously reported for ring chromosome 13, pure 13q deletions and duplications. We narrowed some critical regions previously reported for lung, kidney and fetal growth, and for thumb, cerebral, and eye anomalies.
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Affiliation(s)
- Chloe Quelin
- Department of Developmental Biology, AP-HP, Robert Debré University Hospital, Paris and Diderot University, Paris, France; Clinical Genetics Unit, Rennes Sud University Hospital, Rennes, France
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25
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Chen CP, Lin SP, Chern SR, Kuo YL, Wu PS, Chen YT, Lee MS, Wang W. Array CGH characterization of an unbalanced X-autosome translocation associated with Xq27.2–qter deletion, 11q24.3–qter duplication and Xq22.3–q27.1 duplication in a girl with primary amenorrhea and mental retardation. Gene 2014; 535:88-92. [DOI: 10.1016/j.gene.2013.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 10/31/2013] [Accepted: 11/13/2013] [Indexed: 10/26/2022]
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26
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Hermetz KE, Newman S, Conneely KN, Martin CL, Ballif BC, Shaffer LG, Cody JD, Rudd MK. Large inverted duplications in the human genome form via a fold-back mechanism. PLoS Genet 2014; 10:e1004139. [PMID: 24497845 PMCID: PMC3907307 DOI: 10.1371/journal.pgen.1004139] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022] Open
Abstract
Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “fold-back” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes. Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children. These chromosome rearrangements typically involve hundreds of genes, leading to significant changes in gene dosage. Though inverted duplications adjacent to terminal deletions are a relatively common type of chromosomal imbalance, the DNA repair mechanism responsible for their formation is not known. In this study, we analyze the genomic organization of the largest collection of human inverted duplications. We find a common inverted duplication structure, consistent with a model that requires DNA to fold back and form a dicentric chromosome intermediate. These data provide insight into the formation of nonrecurrent inverted duplications in the human genome.
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Affiliation(s)
- Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Scott Newman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America ; Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Christa L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Blake C Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America ; The Chromosome 18 Registry and Research Society, San Antonio, Texas, United States of America
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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27
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Mackinnon RN, Wall M, Zordan A, Nutalapati S, Mercer B, Peverall J, Campbell LJ. Genome organization and the role of centromeres in evolution of the erythroleukaemia cell line HEL. EVOLUTION MEDICINE AND PUBLIC HEALTH 2013; 2013:225-40. [PMID: 24481202 PMCID: PMC3868402 DOI: 10.1093/emph/eot020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND OBJECTIVES The human erythroleukaemia (HEL) cell line has a highly rearranged genome. We matched whole chromosome analysis with cytogenomic microarray data to build a detailed description of these rearrangements. METHODOLOGY We used a combination of single nucleotide polymorphism array and multiple fluorescence in situ hybridization approaches, and compared our array data with publicly available data for different sublines of HEL. B allele frequencies revealed the fate of each homologue for most chromosomes. RESULTS At least two instances of the breakage-fusion-bridge cycle appear to have facilitated amplification of oncogenes and deletion of tumour suppressor genes. Because our study included centromere identification, we found that some abnormal chromosomes had centromeres that did not match the identity of the rest of the chromosome. CONCLUSIONS AND IMPLICATIONS This study highlights the variety of complementary methods required to understand remodelling of the genome in cancer and uncover some of the mechanisms involved. We present evidence of centromere capture as a means of preserving broken chromosome segments. Testing for another highly repetitive DNA region, the nucleolus organizer region, helped identify the steps involved in chromosome 9 copy number aberrations. Increased use of techniques for identifying centromeres and other repetitive DNA regions will add to our understanding of genome remodelling and evolution. The pattern of chromosome 20 aberration in HEL supports an association of 20q11.21 amplification with erythroleukaemia (acute myeloid leukaemia subtype M6) in the context of 20q12 deletion. The differences between the karyotypes in different HEL sublines highlight the constantly evolving genomes of cultured cell lines.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Melbourne, Fitzroy, Vic, Australia; Department of Medicine, St Vincent's Hospital, University of Melbourne, Melbourne, Vic, Australia; and PathWest Department of Diagnostic Genomics, QEII Medical Centre, Nedlands, WA, Australia
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28
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Nakane T, Kousuke N, Sonoko H, Yuko K, Sato H, Kubota T, Sugita K. 6p subtelomere deletion with congenital glaucoma, severe mental retardation, and growth impairment. Pediatr Int 2013; 55:376-81. [PMID: 23782370 DOI: 10.1111/j.1442-200x.2012.03729.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/03/2012] [Accepted: 08/21/2012] [Indexed: 12/21/2022]
Abstract
Submicroscopic deletion of the 6p subtelomere has recently been recognized as a clinically identifiable syndrome. A distinct phenotype has emerged consisting of developmental delay/mental retardation, language impairment, hearing loss, and ophthalmologic, cardiac, and craniofacial abnormalities, including hypertelorism, midface hypoplasia, small nose, and high arched palate. We describe here a patient with 6p subtelomere deletion associated with congenital glaucoma, severe mental retardation, and growth impairment. Fluorescent in situ hybridization analysis revealed only one 6p25.3 signal. Array comparative genomic hybridization assay showed 2.1 Mb deletion and 4.14 Mb duplication in the 6p25 region. Generally, developmental delay and language impairment are common findings in patients with 6p subtelomere deletion syndrome, but growth impairment is not. Compared to that, the present patient showed atypically severe developmental delay and growth impairment.
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Affiliation(s)
- Takaya Nakane
- Department of Pediatrics, University of Yamanashi, Chuo, Japan.
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29
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The role of ATM in the deficiency in nonhomologous end-joining near telomeres in a human cancer cell line. PLoS Genet 2013; 9:e1003386. [PMID: 23555296 PMCID: PMC3610639 DOI: 10.1371/journal.pgen.1003386] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
Abstract
Telomeres distinguish chromosome ends from double-strand breaks (DSBs) and prevent chromosome fusion. However, telomeres can also interfere with DNA repair, as shown by a deficiency in nonhomologous end joining (NHEJ) and an increase in large deletions at telomeric DSBs. The sensitivity of telomeric regions to DSBs is important in the cellular response to ionizing radiation and oncogene-induced replication stress, either by preventing cell division in normal cells, or by promoting chromosome instability in cancer cells. We have previously proposed that the telomeric protein TRF2 causes the sensitivity of telomeric regions to DSBs, either through its inhibition of ATM, or by promoting the processing of DSBs as though they are telomeres, which is independent of ATM. Our current study addresses the mechanism responsible for the deficiency in repair of DSBs near telomeres by combining assays for large deletions, NHEJ, small deletions, and gross chromosome rearrangements (GCRs) to compare the types of events resulting from DSBs at interstitial and telomeric DSBs. Our results confirm the sensitivity of telomeric regions to DSBs by demonstrating that the frequency of GCRs is greatly increased at DSBs near telomeres and that the role of ATM in DSB repair is very different at interstitial and telomeric DSBs. Unlike at interstitial DSBs, a deficiency in ATM decreases NHEJ and small deletions at telomeric DSBs, while it increases large deletions. These results strongly suggest that ATM is functional near telomeres and is involved in end protection at telomeric DSBs, but is not required for the extensive resection at telomeric DSBs. The results support our model in which the deficiency in DSB repair near telomeres is a result of ATM-independent processing of DSBs as though they are telomeres, leading to extensive resection, telomere loss, and GCRs involving alternative NHEJ.
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30
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Independent post-zygotic breaks of a dicentric chromosome result in mosaicism for an inverted duplication deletion 9p and terminal deletion 9p. Eur J Med Genet 2013; 56:229-35. [PMID: 23416622 DOI: 10.1016/j.ejmg.2013.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/22/2013] [Indexed: 01/30/2023]
Abstract
Mosaicism with two cell lines having different rearrangements of the same chromosome is rare. Only a few cases of mosaicism have been described in association with chromosomal inverted duplication deletion (inv dup del) rearrangements. A well-established mechanism of formation of inv dup del rearrangements involves a dicentric intermediate, which undergoes breakage during cell division, generating cells with either an inv dup del or a simple deletion. A patient with developmental delay and dysmorphic features was found to carry two cell lines with rearrangements of 9p: an inv dup del 9p and a terminal deletion 9p. Microarray and FISH analysis showed that these cell lines do not constitute the reciprocal products of a single dicentric breakage event. We propose that independent post-zygotic breaks of a dicentric chromosome as a likely mechanism leading to the generation of the observed cell lines. The post-zygotic origin of the inv dup del rearrangements and the associated mosaicism can be a more frequent phenomenon than currently appreciated. Therefore, genotype-phenotype correlations in the inv dup del rearrangements need to take into account the possible presence of other abnormal cell lines during early development.
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31
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Muraki K, Nyhan K, Han L, Murnane JP. Mechanisms of telomere loss and their consequences for chromosome instability. Front Oncol 2012; 2:135. [PMID: 23061048 PMCID: PMC3463808 DOI: 10.3389/fonc.2012.00135] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/19/2012] [Indexed: 12/17/2022] Open
Abstract
The ends of chromosomes in mammals, called telomeres, are composed of a 6-bp repeat sequence, TTAGGG, which is added on by the enzyme telomerase. In combination with a protein complex called shelterin, these telomeric repeat sequences form a cap that protects the ends of chromosomes. Due to insufficient telomerase expression, telomeres shorten gradually with each cell division in human somatic cells, which limits the number of times they can divide. The extensive cell division involved in cancer cell progression therefore requires that cancer cells must acquire the ability to maintain telomeres, either through expression of telomerase, or through an alternative mechanism involving recombination. It is commonly thought that the source of many chromosome rearrangements in cancer cells is a result of the extensive telomere shortening that occurs prior to the expression of telomerase. However, despite the expression of telomerase, tumor cells can continue to show chromosome instability due to telomere loss. Dysfunctional telomeres in cancer cells can result from oncogene-induced replication stress, which results in double-strand breaks (DSBs) at fragile sites, including telomeres. DSBs near telomeres are especially prone to chromosome rearrangements, because telomeric regions are deficient in DSB repair. The deficiency in DSB repair near telomeres is also an important mechanism for ionizing radiation-induced replicative senescence in normal human cells. In addition, DSBs near telomeres can result in chromosome instability in mouse embryonic stem cells, suggesting that telomere loss can contribute to heritable chromosome rearrangements. Consistent with this possibility, telomeric regions in humans are highly heterogeneous, and chromosome rearrangements near telomeres are commonly involved in human genetic disease. Understanding the mechanisms of telomere loss will therefore provide important insights into both human cancer and genetic disease.
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Affiliation(s)
- Keiko Muraki
- Department of Radiation Oncology, University of California at San Francisco San Francisco, CA, USA
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32
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Chen CP, Chen M, Su YN, Huang JP, Ma GC, Chang SP, Chern SR, Chen YT, Su JW, Lee CC, Town DD, Wang W. Inv dup del(10q): Identification by fluorescence in situ hybridization and array comparative genomic hybridization in a fetus with two concurrent chromosomal rearrangements. Taiwan J Obstet Gynecol 2012; 51:245-52. [DOI: 10.1016/j.tjog.2012.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2012] [Indexed: 10/28/2022] Open
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33
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Zhang HZ, Xu F, Seashore M, Li P. Unique genomic structure and distinct mitotic behavior of ring chromosome 21 in two unrelated cases. Cytogenet Genome Res 2012; 136:180-7. [PMID: 22398511 DOI: 10.1159/000336978] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2012] [Indexed: 12/26/2022] Open
Abstract
A ring chromosome replacing a normal chromosome could involve variable structural rearrangements and mitotic instability. However, most previously reported cases lacked further genomic characterization. High-resolution oligonucleotide array comparative genomic hybridization with single-nucleotide polymorphism typing (aCGH+SNP) was used to study 2 unrelated cases with a ring chromosome 21. Case 1 had severe myopia, hypotonia, joint hypermobility, speech delay, and dysmorphic features. aCGH detected a 1.275-Mb duplication of 21q22.12-q22.13 and a 6.731-Mb distal deletion at 21q22.2. Case 2 showed severe growth and developmental retardations, intractable seizures, and dysmorphic features. aCGH revealed a contiguous pattern of a 3.612- Mb deletion of 21q22.12-q22.2, a 4.568-Mb duplication of 21q22.2-q22.3, and a 2.243-Mb distal deletion at 21q22.3. Mitotic instability was noted in 13, 30, and 76% of in vitro cultured metaphase cells, interphase cells, and leukocyte DNA, respectively. The different phenotypes of these 2 cases are likely associated with the unique genomic structure and distinct mitotic behavior of their ring chromosome 21. These 2 cases represent a subtype of ring chromosome 21 probably involving somatic dicentric ring breakage and reunion. A cytogenomic approach is proposed for characterizing the genomic structure and mitotic instability of ring chromosome abnormalities.
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Affiliation(s)
- H Z Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520-8005, USA
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Rodríguez L, Nevado J, Vallespin E, Palomares M, Golmayo L, Bonaglia MC, Delicado A, Abarca E. Molecular characterization of an atypical inv dup del 8q. Proposal of a mechanism of formation. Am J Med Genet A 2011; 155A:915-9. [PMID: 21412979 DOI: 10.1002/ajmg.a.33924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 01/10/2011] [Indexed: 11/07/2022]
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35
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Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons. PLoS Genet 2011; 7:e1002016. [PMID: 21437266 PMCID: PMC3060070 DOI: 10.1371/journal.pgen.1002016] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Bonita J Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
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