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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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Dharmadhikari AV, Pereira EM, Andrews CC., Macera M, Harkavy N, Wapner R, Jobanputra V, Levy B, Ganapathi M, Liao J. Case Report: Prenatal Identification of a De Novo Mosaic Neocentric Marker Resulting in 13q31.1→qter Tetrasomy in a Mildly Affected Girl. Front Genet 2022; 13:906077. [PMID: 35928455 PMCID: PMC9343796 DOI: 10.3389/fgene.2022.906077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Partial tetrasomy of distal 13q has a reported association with a variable phenotype including microphthalmia, ear abnormalities, hypotelorism, facial dysmorphisms, urogenital defects, pigmentation and skin defects, and severe learning difficulties. A wide range of mosaicism has been reported, which may, to some extent, account for the variable spectrum of observed phenotypes. We report here a pregnancy conceived using intrauterine insemination in a 32-year-old female with a history of infertility. Non-invasive prenatal screening (NIPS) was performed in the first trimester which reported an increased risk for trisomy 13. Follow-up cytogenetic workup using chorionic villus sampling (CVS) and amniotic fluid samples showed a mosaic karyotype with a small supernumerary marker chromosome (sSMC). Chromosomal microarray analysis (CMA) identified a mosaic 31.34 Mb terminal gain on chr13q31.1q34 showing the likely origin of the sSMC to distal chromosome 13q. Follow-up metaphase FISH testing suggested an inverted duplication rearrangement involving 13q31q34 in the marker chromosome and the presence of a neocentromere. At 21 months of age, the proband has a history of gross motor delay, hypotonia, left microphthalmia, strabismus, congenital anomaly of the right optic nerve, hemangiomas, and a tethered spinal cord. Postnatal chromosome analyses in buccal, peripheral blood, and spinal cord ligament tissues were consistent with the previous amniocentesis and CVS findings, and the degree of mosaicism varied from 25 to 80%. It is often challenging to pinpoint the chromosomal identity of sSMCs using banding cytogenetics. A combination of low-pass genome sequencing of cell-free DNA, chromosomal microarray, and FISH enabled the identification of the precise chromosomal rearrangement in this patient. This study adds to the growing list of clinically identified neocentric marker chromosomes and is the first described instance of partial tetrasomy 13q31q34 identified in a mosaic state prenatally. Since NIPS is now being routinely performed along with invasive testing for advanced maternal age, an increased prenatal detection rate for mosaic sSMCs in otherwise normal pregnancies is expected. Future studies investigating how neocentromeres mediate gene expression changes could help identify potential epigenetic targets as treatment options to rescue or reverse the phenotypes seen in patients with congenital neocentromeres.
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Affiliation(s)
- Avinash V. Dharmadhikari
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Elaine M. Pereira
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Carli C . Andrews
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Michael Macera
- Clinical Cytogenetics Laboratory, New York Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Nina Harkavy
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Jun Liao
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- *Correspondence: Jun Liao,
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Barra V, Fachinetti D. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat Commun 2018; 9:4340. [PMID: 30337534 PMCID: PMC6194107 DOI: 10.1038/s41467-018-06545-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Abstract
Centromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer.
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Affiliation(s)
- V Barra
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France
| | - D Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France.
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Sequence Composition and Evolution of Mammalian B Chromosomes. Genes (Basel) 2018; 9:genes9100490. [PMID: 30309007 PMCID: PMC6211034 DOI: 10.3390/genes9100490] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
B chromosomes (Bs) revealed more than a hundred years ago remain to be some of the most mysterious elements of the eukaryotic genome. Their origin and evolution, DNA composition, transcriptional activity, impact on adaptiveness, behavior in meiosis, and transfer to the next generation require intensive investigations using modern methods. Over the past years, new experimental techniques have been applied and helped us gain a deeper insight into the nature of Bs. Here, we consider mammalian Bs, taking into account data on their DNA sequencing, transcriptional activity, positions in nuclei of somatic and meiotic cells, and impact on genome functioning. Comparative cytogenetics of Bs suggests the existence of different mechanisms of their formation and evolution. Due to the long and complicated evolvement of Bs, the similarity of their morphology could be explained by the similar mechanisms involved in their development while the difference between Bs even of the same origin could appear due to their positioning at different stages of their evolution. A complex analysis of their DNA composition and other features is required to clarify the origin and evolutionary history of Bs in the species studied. The intraspecific diversity of Bs makes this analysis a very important element of B chromosome studies.
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Tesner P, Drabova J, Stolfa M, Kudr M, Kyncl M, Moslerova V, Novotna D, Kremlikova Pourova R, Kocarek E, Rasplickova T, Sedlacek Z, Vlckova M. A boy with developmental delay and mosaic supernumerary inv dup(5)(p15.33p15.1) leading to distal 5p tetrasomy - case report and review of the literature. Mol Cytogenet 2018; 11:29. [PMID: 29760779 PMCID: PMC5941596 DOI: 10.1186/s13039-018-0377-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/20/2018] [Indexed: 01/01/2023] Open
Abstract
Background With only 11 patients reported, 5p tetrasomy belongs to rare postnatal findings. Most cases are due to small supernumerary marker chromosomes (sSMCs) or isochromosomes. The patients share common but unspecific symptoms such as developmental delay, seizures, ventriculomegaly, hypotonia, and fifth finger clinodactyly. Simple interstitial duplications leading to trisomies of parts of 5p are much more frequent and better described. Duplications encompassing 5p13.2 cause a defined syndrome with macrocephaly, distinct facial phenotype, heart defects, talipes equinovarus, feeding difficulties, respiratory distress and anomalies of the central nervous system, developmental delay and hypotonia. Case presentation We present a boy with dysmorphic features, developmental delay, intellectual disability and congenital anomalies, and a mosaic sSMC inv dup(5)(p15.33p15.1). He is the fourth and the oldest reported patient with distal 5p tetrasomy. His level of mosaicism was significantly different in lymphocytes (13.2%) and buccal cells (64.7%). The amplification in our patient is smaller than that in the three previously published patients but the only phenotype difference is the absence of seizures in our patient. Conclusions Our observations indicate that for the assessment of prognosis, especially with respect to intellectual functioning, the level of mosaicism could be more important than the extent of amplification and the number of extra copies. Evaluation of the phenotypical effect of rare chromosomal aberrations is challenging and each additional case is valuable for refinement of the genotype-phenotype correlation. Moreover, our patient demonstrates that if the phenotype is severe and if the level of sSMC mosaicism is low in lymphocytes, other tissues should be tested. Electronic supplementary material The online version of this article (10.1186/s13039-018-0377-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavel Tesner
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Jana Drabova
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Miroslav Stolfa
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Martin Kudr
- 2Department of Paediatric Neurology, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Martin Kyncl
- 3Department of Radiology, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Veronika Moslerova
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Drahuse Novotna
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Radka Kremlikova Pourova
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Eduard Kocarek
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Tereza Rasplickova
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Zdenek Sedlacek
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Marketa Vlckova
- 1Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic
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6
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Pristyazhnyuk IE, Menzorov AG. Ring chromosomes: from formation to clinical potential. PROTOPLASMA 2018; 255:439-449. [PMID: 28894962 DOI: 10.1007/s00709-017-1165-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Ring chromosomes (RCs) are circular DNA molecules, which occur rarely in eukaryotic nuclear genomes. Lilian Vaughan Morgan first described them in the fruit fly. Human embryos very seldom have RCs, about 1:50,000. Carriers of RCs may have varying degrees of symptoms, from healthy phenotype to serious pathologies in physical and intellectual development. Many authors describe common symptoms of RC presence: short stature and some developmental delay that could be described as a "ring chromosome syndrome." As a rule, RCs arise de novo through the end-joining of two DNA double-strand breaks, telomere-subtelomere junction, or inv dup del rearrangement in both meiosis and mitosis. There are family cases of RC inheritance. The presence of RCs causes numerous secondary chromosome rearrangements in vivo and in vitro. RCs can change their size, become lost, or increase their copy number and cause additional deletions, duplication, and translocations, affecting both RCs and other chromosomes. In this review, we examine RC inheritance, instability, mechanisms of formation, and potential clinical applications of artificially created RCs for large-scale chromosome rearrangement treatment.
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Affiliation(s)
- Inna E Pristyazhnyuk
- Sector of Genomic Mechanisms of Ontogenesis, Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090.
| | - Aleksei G Menzorov
- Sector of Cell Collections, Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090
- Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia, 630090
- Research Institute of Medical Genetics, Tomsk National Research Medical Center Russian Academy of Sciences, Tomsk, Russia, 634050
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7
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Poot M. Neocentromeres to the Rescue of Acentric Chromosome Fragments. Mol Syndromol 2017; 8:279-281. [PMID: 29230156 DOI: 10.1159/000481332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 11/19/2022] Open
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8
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Alesi V, Dentici ML, Restaldi F, Orlando V, Liambo MT, Calacci C, Capolino R, Digilio MC, El Hachem M, Novelli A, Diociaiuti A, Dallapiccola B. Unclassifiable pattern of hypopigmentation in a patient with mosaic partial 12p tetrasomy without Pallister-Killian syndrome. Am J Med Genet A 2017; 173:1943-1946. [PMID: 28489314 DOI: 10.1002/ajmg.a.38269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/03/2017] [Indexed: 12/19/2022]
Abstract
Pallister-Killian syndrome (PKS-#OMIM601803) is a multisystem developmental disorder typically due to the presence of an aneuploidy cell line, consisting of a supernumerary tetrasomic chromosomal marker (SCM) arisen from the short arm of chromosome 12 (12p isochromosome). The clinical phenotype, which is strictly related to the percentage and tissue distribution of aneuploid cells, is characterized by craniofacial dysmorphisms, pigmentary skin anomalies, limb shortening, congenital heart defects, diaphragmatic hernia, hypotonia, intellectual disability, and epilepsy. We report on a 4 year-old girl harboring a 12p partial isochromosome, involving the PKS critical region, affecting about 70% of circulating lymphocytes, urine, and saliva cells and fibroblast from a hyperpigmented skin spot, and 100% of fibroblasts from a hypopigmented skin spot. Interestingly, despite the high proportion of affected cells this patient did not present with PKS, and a pattern of linear and patchy pigmentary mosaicism was the sole clinical manifestation. The present observation suggests that partial 12p SCM can also result in mild phenotypes, and its prevalence in the human population could have been underestimated. Accurate dermatologic evaluation could be a major handle for genetic testing.
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Affiliation(s)
- Viola Alesi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria L Dentici
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabrizia Restaldi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Orlando
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria T Liambo
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Calacci
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria C Digilio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - May El Hachem
- Dermatology Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Diociaiuti
- Dermatology Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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9
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Weckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. Trends Genet 2015; 31:587-599. [PMID: 26209074 PMCID: PMC4600437 DOI: 10.1016/j.tig.2015.05.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023]
Abstract
Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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10
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Ma R, Peng Y, Zhang Y, Xia Y, Tang G, Chang J, Guo R, Gui B, Huang Y, Chen C, Liang D, Wu L. Partial trisomy 2q33.3-q37.3 in a patient with an inverted duplicated neocentric marker chromosome. Mol Cytogenet 2015; 8:10. [PMID: 25774219 PMCID: PMC4359772 DOI: 10.1186/s13039-015-0111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/15/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Increasing number of cases with small supernumerary marker chromosomes (sSMCs) without centromeric DNA and dozens of cases with trisomy 2q3 have been reported in recent years. However, cases of simultaneous sSMC and partial trisomy of chromosome 2q have been rarely described. RESULTS We report the case of a young girl patient with growth retardation and mild facial features due to a partial trisomy 2q33.3-37.3. The 34.3 Mb-duplication of the 2q33.3 to q37.3 region found in the patient constituted a supernumerary inverted duplicated neocentric marker chromosome. CONCLUSIONS This is the first case of a patient with partial trisomy 2q33.3-37.3 presenting an inverted duplicated neocentric marker chromosome. Based on the case, this study will help further understanding the genotype/phenotype correlations of partial 2q3 duplication and exploring the relationship between neocentric sSMC and human diseases.
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Affiliation(s)
- Ruiyu Ma
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Ying Peng
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yanghui Zhang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yan Xia
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Guizhi Tang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Jiazhen Chang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Ruolan Guo
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Baoheng Gui
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Yanru Huang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Chen Chen
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
- />Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan P.R China
| | - Desheng Liang
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
| | - Lingqian Wu
- />State Key Laboratory of Medical Genetics, Central South University, 110 Xiangya Rd, Changsha, Hunan 410078 China
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11
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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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12
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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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13
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Ou J, Wang W, Liehr T, Klein E, Hamid AB, Wang F, Duan C, Li H. Characterization of three small supernumerary marker chromosomes (sSMC) in humans. J Matern Fetal Neonatal Med 2012; 26:106-8. [PMID: 23013067 DOI: 10.3109/14767058.2012.732129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, three prenatally detected small supernumerary marker chromosomes (sSMC) were identified by banding cytogenetics and characterized in detail by molecular cytogenetics. In one case an sSMC(10) leading to a pericentric partial trisomy and in two cases heterochromatic sSMC derived from chromosome 22 were characterized. Outcomes were reportedly normal for two of the three cases for whom this information was known.
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Affiliation(s)
- Jian Ou
- Nanjing Medical University Affiliated Suzhou Hospital, Suzhou Municipal Hospital, Jiangsu, China
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14
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Córdova-Fletes C, Domínguez M, Vázquez-Cárdenas A, Figuera L, Neira V, Rojas-Martínez A, Ortiz-López R. A de novo sSMC(22) Characterized by High-Resolution Arrays in a Girl with Cat-Eye Syndrome without Coloboma. Mol Syndromol 2012; 3:131-135. [PMID: 23112755 PMCID: PMC3473349 DOI: 10.1159/000341632] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2012] [Indexed: 11/19/2022] Open
Abstract
Cat-eye syndrome (CES) results from trisomy or tetrasomy of proximal 22q originated by a small supernumerary marker chromosome (sSMC). Two critical regions for the major clinical features of CES (CESCRs) have been suggested; however, CES clinical presentation often does not correlate with the sSMC genetic content. We report here a CES girl without coloboma and carrier of a de novo type I sSMC(22) as determined by G- and C-banding, NOR staining and microarrays. This sSMC included 6 distal genes outside the original CESCR and led to a tetrasomy for 22q11.1-22q11.21. The patient's final karyotype was 47,XX,+psu dic(22)(q11.21).arr 22q11.1q11.21(15,250,000-17,035,860)×4 dn. The amplified region outside of CESCR included some genes that may be related to neurologic, heart and renal abnormalities. Conversely, even though the amplification included the CECR2 gene, a major candidate for eye features, there was no coloboma in the patient. The genetic delineation of the present sSMC further strengthens that the CES clinical presentation does not fit completely with the duplicated genetic content and that CES is actually a genomic disorder. Furthermore, since we observed no mosaicism, we believe that other mechanisms might be behind the variability of CES phenotypes as well, mainly those related with functional interactions among amplified genes.
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Affiliation(s)
- C. Córdova-Fletes
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
- Unidad de Biología Molecular, Genómica y Secuenciación, Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
| | - M.G. Domínguez
- División de Genética, Centro de Investigación Biomédica de Occidente, CMNO-IMSS, Guadalajara, México
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - A. Vázquez-Cárdenas
- Departamento de Genética, Instituto de Ciencias Biológicas, Universidad Autónoma de Guadalajara, Guadalajara, México
| | - L.E. Figuera
- División de Genética, Centro de Investigación Biomédica de Occidente, CMNO-IMSS, Guadalajara, México
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - V.A. Neira
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - A. Rojas-Martínez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
- Unidad de Biología Molecular, Genómica y Secuenciación, Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
| | - R. Ortiz-López
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
- Unidad de Biología Molecular, Genómica y Secuenciación, Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Guadalajara, México
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15
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George-Abraham JK, Zimmerman SL, Hinton RB, Marino BS, Witte DP, Hopkin RJ. Tetrasomy 15q25.2 → qter identified with SNP microarray in a patient with multiple anomalies including complex cardiovascular malformation. Am J Med Genet A 2012; 158A:1971-6. [DOI: 10.1002/ajmg.a.35428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 03/28/2012] [Indexed: 11/08/2022]
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16
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Rossi E, Giorda R, Bonaglia MC, Candia SD, Grechi E, Franzese A, Soli F, Rivieri F, Patricelli MG, Saccilotto D, Bonfante A, Giglio S, Beri S, Rocchi M, Zuffardi O. De novo unbalanced translocations in Prader-Willi and Angelman syndrome might be the reciprocal product of inv dup(15)s. PLoS One 2012; 7:e39180. [PMID: 22720067 PMCID: PMC3375265 DOI: 10.1371/journal.pone.0039180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/21/2012] [Indexed: 11/30/2022] Open
Abstract
The 15q11-q13 region is characterized by high instability, caused by the presence of several paralogous segmental duplications. Although most mechanisms dealing with cryptic deletions and amplifications have been at least partly characterized, little is known about the rare translocations involving this region. We characterized at the molecular level five unbalanced translocations, including a jumping one, having most of 15q transposed to the end of another chromosome, whereas the der(15)(pter->q11-q13) was missing. Imbalances were associated either with Prader-Willi or Angelman syndrome. Array-CGH demonstrated the absence of any copy number changes in the recipient chromosome in three cases, while one carried a cryptic terminal deletion and another a large terminal deletion, already diagnosed by classical cytogenetics. We cloned the breakpoint junctions in two cases, whereas cloning was impaired by complex regional genomic architecture and mosaicism in the others. Our results strongly indicate that some of our translocations originated through a prezygotic/postzygotic two-hit mechanism starting with the formation of an acentric 15qter->q1::q1->qter representing the reciprocal product of the inv dup(15) supernumerary marker chromosome. An embryo with such an acentric chromosome plus a normal chromosome 15 inherited from the other parent could survive only if partial trisomy 15 rescue would occur through elimination of part of the acentric chromosome, stabilization of the remaining portion with telomere capture, and formation of a derivative chromosome. All these events likely do not happen concurrently in a single cell but are rather the result of successive stabilization attempts occurring in different cells of which only the fittest will finally survive. Accordingly, jumping translocations might represent successful rescue attempts in different cells rather than transfer of the same 15q portion to different chromosomes. We also hypothesize that neocentromerization of the original acentric chromosome during early embryogenesis may be required to avoid its loss before cell survival is finally assured.
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Affiliation(s)
- Elena Rossi
- Medical Genetics, University of Pavia, Pavia, Italy
| | - Roberto Giorda
- Scientific Institute Eugenio Medea, Bosisio Parini, Lecco, Italy
| | | | - Stefania Di Candia
- Department of Pediatrics, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Grechi
- Department of Pediatrics, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | | | - Fiorenza Soli
- Medical Genetics Department, APSS Trento, Trento, Italy
| | | | - Maria Grazia Patricelli
- Biologia Molecolare Clinica e Citogenetica, Diagnostica e Ricerca, San Raffaele SPA, Milan, Italy
| | | | - Aldo Bonfante
- Genetica Medica, Ospedale Civile, Bassano del Grappa, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's Hospital, University of Firenze, Firenze, Italy
| | - Silvana Beri
- Scientific Institute Eugenio Medea, Bosisio Parini, Lecco, Italy
| | | | - Orsetta Zuffardi
- Medical Genetics, University of Pavia, Pavia, Italy
- IRCCS “C. Mondino National Neurological Institute” Foundation, Pavia, Italy
- * E-mail:
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17
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Hemmat M, Wang BT, Warburton PE, Yang X, Boyar FZ, El Naggar M, Anguiano A. Neocentric X-chromosome in a girl with Turner-like syndrome. Mol Cytogenet 2012; 5:29. [PMID: 22682421 PMCID: PMC3477003 DOI: 10.1186/1755-8166-5-29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 04/11/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Neocentromeres are rare human chromosomal aberrations in which a new centromere has formed in a previously non-centromeric location. We report the finding of a structurally abnormal X chromosome with a neocentromere in a 15-year-old girl with clinical features suggestive of Turner syndrome, including short stature and primary amenorrhea. RESULT G-banded chromosome analysis revealed a mosaic female karyotype involving two abnormal cell lines. One cell line (84% of analyzed metaphases) had a structurally abnormal X chromosome (duplication of the long arm and deletion of the short arm) and a normal X chromosome. The other cell line (16% of cells) exhibited monosomy X. C-banding studies were negative for the abnormal X chromosome. FISH analysis revealed lack of hybridization of the abnormal X chromosome with both the X centromere-specific probe and the "all human centromeres" probe, a pattern consistent with lack of the X chromosome endogenous centromere. A FISH study using an XIST gene probe revealed the presence of two XIST genes, one on each long arm of the iso(Xq), required for inactivation of the abnormal X chromosome. R-banding also demonstrated inactivation of the abnormal X chromosome. An assay for centromeric protein C (CENP-C) was positive on both the normal and the abnormal X chromosomes. The position of CENP-C in the abnormal X chromosome defined a neocentromere, which explains its mitotic stability. The karyotype is thus designated as 46,X,neo(X)(qter- > q12::q12- > q21.2- > neo- > q21.2- > qter)[42]/45,X[8], which is consistent with stigmata of Turner syndrome. The mother of this patient has a normal karyotype; however, the father was not available for study. CONCLUSION To our knowledge, this is the first case of mosaic Turner syndrome involving an analphoid iso(Xq) chromosome with a proven neocentromere among 90 previously described cases with a proven neocentromere.
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Affiliation(s)
- Morteza Hemmat
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Boris T Wang
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Peter E Warburton
- Deparment of Genetics and Genomic Sciences, Mount Sinai School of Medicine, NY, USA
| | - Xiaojing Yang
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Fatih Z Boyar
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Mohammed El Naggar
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Arturo Anguiano
- Cytogenetics Dept, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.,Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92690, USA
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18
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Hasson D, Alonso A, Cheung F, Tepperberg JH, Papenhausen PR, Engelen JJM, Warburton PE. Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres. Chromosoma 2011; 120:621-32. [PMID: 21826412 DOI: 10.1007/s00412-011-0337-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 01/02/2023]
Abstract
Endogenous human centromeres form on megabase-sized arrays of tandemly repeated alpha satellite DNA. Human neocentromeres form epigenetically at ectopic sites devoid of alpha satellite DNA and permit analysis of centromeric DNA and chromatin organization. In this study, we present molecular cytogenetic and CENP-A chromatin immunoprecipitation (ChIP) on CHIP analyses of two neocentromeres that have formed in chromosome band 8q21 each with a unique DNA and CENP-A chromatin configuration. The first neocentromere was found on a neodicentric chromosome 8 with an inactivated endogenous centromere, where the centromeric activity and CENP-A domain were repositioned to band 8q21 on a large tandemly repeated DNA. This is the first example of a neocentromere forming on repetitive DNA, as all other mapped neocentromeres have formed on single copy DNA. Quantitative fluorescent in situ hybridization (FISH) analysis showed a 60% reduction in the alpha satellite array size at the inactive centromere compared to the active centromere on the normal chromosome 8. This neodicentric chromosome may provide insight into centromere inactivation and the role of tandem DNA in centromere structure. The second neocentromere was found on a neocentric ring chromosome that contained the 8q21 tandemly repeated DNA, although the neocentromere was localized to a different genomic region. Interestingly, this neocentromere is composed of two distinct CENP-A domains in bands 8q21 and 8q24, which are brought into closer proximity on the ring chromosome. This neocentromere suggests that chromosomal rearrangement and DNA breakage may be involved in neocentromere formation. These novel examples provide insight into the formation and structure of human neocentromeres.
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Affiliation(s)
- Dan Hasson
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, Icahn Medical Institute, NY 10029, USA
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19
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Chen CP, Chen M, Ma GC, Chang SP, Chen YY, Wu PC, Chen LF, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of a small marker chromosome derived from Y chromosome. Taiwan J Obstet Gynecol 2011; 50:253-7. [PMID: 21791323 DOI: 10.1016/j.tjog.2011.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2010] [Indexed: 10/18/2022] Open
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
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20
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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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21
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Van Opstal D, Boter M, Noomen P, Srebniak M, Hamers G, Galjaard RJH. Multiplex ligation dependent probe amplification (MLPA) for rapid distinction between unique sequence positive and negative marker chromosomes in prenatal diagnosis. Mol Cytogenet 2011; 4:2. [PMID: 21235775 PMCID: PMC3033356 DOI: 10.1186/1755-8166-4-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 01/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small supernumerary marker chromosomes (sSMC) are extra structurally abnormal chromosomes that cannot be unambiguously identified with conventional chromosome banding techniques. These marker chromosomes may cause an abnormal phenotype or be harmless depending on different factors such as genetic content, chromosomal origin and level of mosaicism. When a sSMC is found during prenatal diagnosis, the main question is whether the sSMC contains euchromatin since in most cases this will lead to phenotypic abnormalities. We present the use of Multiplex Ligation Dependent probe Amplification (MLPA) for rapid distinction between non-euchromatic and euchromatic sSMC. RESULTS 29 well-defined sSMC found during prenatal diagnosis were retrospectively investigated with MLPA with the SALSA MLPA centromere kits P181 and P182 as well as with the SALSA MLPA telomere kits P036B and P070 (MRC Holland BV, Amsterdam, The Netherlands). All unique-sequence positive sSMC were correctly identified with MLPA, whereas the unique-sequence negative sSMC had normal MLPA results. CONCLUSIONS Although different techniques exist for identification of sSMC, we show that MLPA is a valuable adjunctive tool for rapidly distinguishing between unique-sequence positive and negative sSMC. In case of positive MLPA results, genetic microarray analysis or, if not available, targeted FISH can be applied for further identification and determination of the exact breakpoints, which is important for prediction of the fetal phenotype. In case of a negative MLPA result, which means that the sSMC most probably does not contain genes, the parents can already be reassured and parental karyotyping can be initiated to assess the heritability. In the mean time, FISH techniques are needed for determination of the chromosomal origin.
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Affiliation(s)
- Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Petra Noomen
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Malgorzata Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Guus Hamers
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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22
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Blom E, Heyning FH, Kroes WGM. A case of angioimmunoblastic T-cell non-Hodgkin lymphoma with a neocentric inv dup(1). ACTA ACUST UNITED AC 2010; 202:38-42. [PMID: 20804919 DOI: 10.1016/j.cancergencyto.2010.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 06/03/2010] [Accepted: 06/06/2010] [Indexed: 10/19/2022]
Abstract
Neocentromeres are rare epigenetic phenomena in which functional centromeres are formed onto novel chromosomal locations without any alpha-satellite DNA. To date, constitutional human neocentromeres have been reported in at least 90 cases. In cancer, however, the knowledge is much more limited. Acquired neocentromeres have been described in a particular class of lipomatous tumors (atypical lipomas and well-differentiated liposarcomas; ALP-WDLPS), three cases of acute myeloid leukemia (AML), one case of non-Hodgkin lymphoma (NHL), and one case of lung carcinoma. Here, we report on a 66-year-old male with angioimmunoblastic T-cell NHL. Cytogenetic analysis of his bone marrow showed multiple aberrations, including the presence of a supernumerary chromosome. Using the fluorescence in situ hybridization technique, the supernumerary chromosome was demonstrated to be entirely composed of material derived from chromosome 1. It represented an inverted duplication of the segments between 1q21 and 1qter with a neocentromere in band 1q31. To our knowledge, this is the second reported case of NHL (both T-cell) with the presence of a neocentromere. The occurrence of neocentromeres in tumor cells, however, may be underestimated because of technical limitations during the routine diagnostic chromosomal analysis. The prognostic impact is therefore currently unknown.
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Affiliation(s)
- Eric Blom
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
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23
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Scott SA, Cohen N, Brandt T, Warburton PE, Edelmann L. Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet 2010; 19:3383-93. [PMID: 20570968 PMCID: PMC2916707 DOI: 10.1093/hmg/ddq250] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/03/2010] [Accepted: 06/14/2010] [Indexed: 02/01/2023] Open
Abstract
Turner syndrome (TS) results from whole or partial monosomy X and is mediated by haploinsufficiency of genes that normally escape X-inactivation. Although a 45,X karyotype is observed in half of all TS cases, the most frequent variant TS karyotype includes the isodicentric X chromosome alone [46,X,idic(X)(p11)] or as a mosaic [46,X,idic(X)(p11)/45,X]. Given the mechanism of idic(X)(p11) rearrangement is poorly understood and breakpoint sequence information is unknown, this study sought to investigate the molecular mechanism of idic(X)(p11) formation by determining their precise breakpoint intervals. Karyotype analysis and fluorescence in situ hybridization mapping of eight idic(X)(p11) cell lines and three unbalanced Xp11.2 translocation lines identified the majority of breakpoints within a 5 Mb region, from approximately 53 to 58 Mb, in Xp11.1-p11.22, clustering into four regions. To further refine the breakpoints, a high-resolution oligonucleotide microarray (average of approximately 350 bp) was designed and array-based comparative genomic hybridization (aCGH) was performed on all 11 idic(X)(p11) and Xp11.2 translocation lines. aCGH analyses identified all breakpoint regions, including an idic(X)(p11) line with two potential breakpoints, one breakpoint shared between two idic(X)(p11) lines and two Xp translocations that shared breakpoints with idic(X)(p11) lines. Four of the breakpoint regions included large inverted repeats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of copy-number variation. These data indicate that the rearrangement sites on Xp11.2 that lead to isodicentric chromosome formation and translocations are probably not random and suggest that the complex repetitive architecture of this region predisposes it to rearrangements, some of which are recurrent.
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Affiliation(s)
| | | | | | | | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York 10029, USA
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24
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Ewers E, Yoda K, Hamid AB, Weise A, Manvelyan M, Liehr T. Centromere activity in dicentric small supernumerary marker chromosomes. Chromosome Res 2010; 18:555-62. [PMID: 20568005 DOI: 10.1007/s10577-010-9138-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 05/27/2010] [Accepted: 05/27/2010] [Indexed: 11/25/2022]
Abstract
Twenty-five dicentric small supernumerary marker chromosomes (sSMC) derived from #13/21, #14, #15, #18, and #22 were studied by immunohistochemistry for their centromeric activity. Centromere protein (CENP)-B was applied as marker for all centromeres and CENP-C to label the active ones. Three different 'predominant' activation patterns could be observed, i.e., centric fusion or either only one or all two centromeres were active. In one inherited case, the same activation pattern was found in mother and son. In acrocentric-derived sSMC, all three activation patterns could be present. In contrary, in chromosome 18-derived sSMC, only the fusion type was observed. In concordance with previous studies a certain centromeric plasticity was observed in up to 13% of the cells of an individual case. Surprisingly, the obtained data suggests a possible influence of the sSMC carrier's gender on the implementation of the predominant activation pattern; especially, only one active centromere was found more frequently in female than in male carriers. Also, it might be suggested that dicentric sSMC with one active centromere could be less stable than such with two active ones-centromeric plasticity might have an influence here, as well. Also, centromere activity in acrocentric-derived dicentrics could be influenced by heteromorphisms of the corresponding short arms. Finally, evidence is provided that the closer the centromeres of a dicentric are and if they are not fused, the more likely it was that both of them became active. In concordance and refinement with previous studies, a distance of 1.4 Mb up to about 13 Mb the two active centromere state was favored, while centromeric distance of over approximately 15 Mb lead to inactivation of one centromere. Overall, here, the first and largest ever undertaken study in dicentric sSMC is presented, providing evidence that the centromeric activation pattern is, and parental origin may be of interest for their biology. Influence of mechanisms similar or identical to meiotic imprinting in the centromeric regions of human chromosomes might be present. Furthermore, centromeric activation pattern could be at least in parts meaningful for the clinical outcome of dicentric sSMC, as sSMC stability and mosaicism can make the difference between clinically normal and abnormal phenotypes.
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Affiliation(s)
- Elisabeth Ewers
- Institute of Human Genetics and Anthropology, Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
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