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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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2
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Zuffardi O, Fichera M, Bonaglia MC. The embryo battle against adverse genomes: Are de novo terminal deletions the rescue of unfavorable zygotic imbalances? Eur J Med Genet 2022; 65:104532. [PMID: 35724817 DOI: 10.1016/j.ejmg.2022.104532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 04/02/2022] [Accepted: 05/21/2022] [Indexed: 11/03/2022]
Abstract
De novo distal deletions are structural variants considered to be already present in the zygote. However, investigations especially in the prenatal setting have documented that they are often in mosaic with cell lines in which the same deleted chromosome shows different types of aberrations such as: 1) neutral copy variants with loss of heterozygosity that replace the deleted region with equivalent portions of the homologous chromosome and create distal uniparental disomy (UPD); 2) derivative chromosomes where the deleted one ends with the distal region of another chromosome or has the shape of a ring; 3) U-type mirror dicentric or inv-dup del rearrangements. Unstable dicentrics had already been entailed as causative of terminal deletions even when no trace of the reciprocal inv-dup del had been detected. To clarify the mechanism of origin of distal deletions, we examined PubMed using as keywords: complex/mosaic chromosomal deletions, distal UPD, U-type dicentrics, inv-dup del chromosomes, excluding the recurrent inv-dup del(8p)s which are known to originate by NAHR at the maternal meiosis. The literature has shown that U-type dicentrics leading to nearly complete trisomy and therefore incompatible with zygotic survival underlie many types of de novo unbalanced rearrangements, including terminal deletions. In the early embryo, the position of the postzygotic breaks of the dicentric, the different ways of acquiring telomeres by the broken portions and the selection of the most favorable cell lines in the different tissues determine the prevalence of one or the other rearrangement. Multiple lines with simple terminal deletions, inv-dup dels, unbalanced translocations and segmental UPDs can coexist in various mosaic combinations although it is rare to identify them all in the blood. Regarding the origin of the dicentric, among the 30 cases of non-recurrent inv-dup del with sufficient genotyping information, paternal origin was markedly prevalent with consistently identical polymorphisms within the duplication region, regardless of parental origin. The non-random parental origin made any postzygotic origin unlikely and suggested the occurrence of these dicentrics mainly in spermatogenesis. This study strengthens the evidence that non-recurrent de novo structural rearrangements are often secondary to the rescue of a zygotic genome incompatible with embryo survival.
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Affiliation(s)
- Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy; Oasi Research Institute-IRCCS, Troina, Italy.
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy.
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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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Vibert R, Mignot C, Keren B, Chantot-Bastaraud S, Portnoï MF, Nouguès MC, Moutard ML, Faudet A, Whalen S, Haye D, Garel C, Chatron N, Rossi M, Vincent-Delorme C, Boute O, Delobel B, Andrieux J, Devillard F, Coutton C, Puechberty J, Pebrel-Richard C, Colson C, Gerard M, Missirian C, Sigaudy S, Busa T, Doco-Fenzy M, Malan V, Rio M, Doray B, Sanlaville D, Siffroi JP, Héron D, Heide S. Neurodevelopmental phenotype in 36 new patients with 8p inverted duplication-deletion: Genotype-phenotype correlation for anomalies of the corpus callosum. Clin Genet 2021; 101:307-316. [PMID: 34866188 DOI: 10.1111/cge.14096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/26/2022]
Abstract
Inverted duplication deletion 8p [invdupdel(8p)] is a complex and rare chromosomal rearrangement that combines a distal deletion and an inverted interstitial duplication of the short arm of chromosome 8. Carrier patients usually have developmental delay and intellectual disability (ID), associated with various cerebral and extra-cerebral malformations. Invdupdel(8p) is the most common recurrent chromosomal rearrangement in ID patients with anomalies of the corpus callosum (AnCC). Only a minority of invdupdel(8p) cases reported in the literature to date had both brain cerebral imaging and chromosomal microarray (CMA) with precise breakpoints of the rearrangements, making genotype-phenotype correlation studies for AnCC difficult. In this study, we report the clinical, radiological, and molecular data from 36 new invdupdel(8p) cases including three fetuses and five individuals from the same family, with breakpoints characterized by CMA. Among those, 97% (n = 32/33) of patients presented with mild to severe developmental delay/ID and 34% had seizures with mean age of onset of 3.9 years (2 months-9 years). Moreover, out of the 24 patients with brain MRI and 3 fetuses with neuropathology analysis, 63% (n = 17/27) had AnCC. We review additional data from 99 previously published patients with invdupdel(8p) and compare data of 17 patients from the literature with both CMA analysis and brain imaging to refine genotype-phenotype correlations for AnCC. This led us to refine a region of 5.1 Mb common to duplications of patients with AnCC and discuss potential candidate genes within this region.
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Affiliation(s)
- Roseline Vibert
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
| | - Boris Keren
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
| | | | - Marie-France Portnoï
- Department of Cytogenetics, Armand Trousseau Hospital, APHP-Sorbonne Université, Paris, France
| | - Marie-Christine Nouguès
- Service of Pediatric Neurology, Armand Trousseau Hospital, APHP-Sorbonne Université, Paris, France
| | - Marie-Laure Moutard
- Service of Pediatric Neurology, Armand Trousseau Hospital, APHP-Sorbonne Université, Paris, France
| | - Anne Faudet
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
| | - Sandra Whalen
- UF de Génétique Clinique et Centre de Référence Maladies Rares des Anomalies du Développement et Syndromes Malformatifs, Hôpital Armand Trousseau, ERN ITHACA, APHP-Sorbonne Université, Paris, France
| | - Damien Haye
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
| | - Catherine Garel
- Department of Radiology, Armand Trousseau Hospital, APHP-Sorbonne Université, Paris, France
| | - Nicolas Chatron
- Departments of Genetics, Lyon University Hospitals, Lyon, France
| | - Massimiliano Rossi
- Genetics Department, Referral Centre for Developmental Abnormalities, Lyon University Hospital, and INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Centre, GENDEV Team, Claude Bernard Lyon 1 University, Bron, France
| | | | - Odile Boute
- Service of Clinical Genetic, Jeanne de Flandre Hospital, Lille, France
| | - Bruno Delobel
- Service of Cytogenetics, Institut Catholique de Lille, Lille, France
| | - Joris Andrieux
- Institute of Medical Genetics, Jeanne de Flandre Hospital, Lille, France
| | - Françoise Devillard
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, 38700 La Tronche, France; INSERM 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Charles Coutton
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, 38700 La Tronche, France; INSERM 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Jacques Puechberty
- Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Céline Pebrel-Richard
- Service of Cytogenetic, Clermont-Ferrand's University Hospital, Clermont-Ferrand, France
| | - Cindy Colson
- Service of Clinical Genetic, Caen's University Hospital, Caen, France
| | - Marion Gerard
- Service of Clinical Genetic, Caen's University Hospital, Caen, France
| | - Chantal Missirian
- APHM, Laboratory of Genetic, Timone Enfants' Hospital, Marseille, France
| | - Sabine Sigaudy
- Department of Medical Genetics, Timone Enfants' Hospital, Marseille, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Enfants' Hospital, Marseille, France
| | | | - Valérie Malan
- APHP, Service de Médecine Génomique, Hôpital Necker-Enfants Malades, Paris, Université de Paris, Paris, France
| | - Marlène Rio
- Department of Genetics, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Bérénice Doray
- Service of Genetic, Felix Guyon Hospital, La Réunion, France
| | | | - Jean-Pierre Siffroi
- Department of Cytogenetics, Armand Trousseau Hospital, APHP-Sorbonne Université, Paris, France
| | - Delphine Héron
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
| | - Solveig Heide
- Département de Génétique, Hôpital Armand-Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP-Sorbonne Université, Paris, France
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Lo Bianco M, Vecchio D, Timpanaro TA, Arena A, Macchiaiolo M, Bartuli A, Sciuto L, Presti S, Sciuto S, Sapuppo A, Fiumara A, Marino L, Messina G, Pavone P. Deciphering the Invdupdel(8p) Genotype-Phenotype Correlation: Our Opinion. Brain Sci 2020; 10:brainsci10070451. [PMID: 32679641 PMCID: PMC7408450 DOI: 10.3390/brainsci10070451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/05/2020] [Accepted: 07/10/2020] [Indexed: 01/30/2023] Open
Abstract
The 8p inverted duplication/deletion is a rare chromosomal rearrangement clinically featuring neurodevelopmental delay, mild to severe cognitive impairment, heart congenital defects and brain abnormalities. Patients affected also present typical facial dysmorphisms and skeletal malformations, and it is thought that the composite clinical picture may fall into the chromosomal rearrangement architecture. With the major aim of better framing its related clinical and diagnostic paths, we describe a patient carrying a de novo invdupde[8p] whose clinical features have not been described so far. Hence, through an extensive genotype-phenotype correlation analysis and by reviewing the dedicated scientific literature, we compared our patient's features with those reported in other patients, which allows us to place our proband's expressiveness in an intermediate area, widening the scope of the already known invdupde[8p] genotype-phenotype relationship.
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Affiliation(s)
- Manuela Lo Bianco
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
- Correspondence: (M.L.B.); (P.P.); Tel.: +39-3401841225 (M.L.B.); +39-0953781193 (P.P.)
| | - Davide Vecchio
- Rare Disease and Medical Genetics, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, 00146 Rome, Italy; (D.V.); (M.M.); (A.B.)
| | - Tiziana A. Timpanaro
- Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (T.A.T.); (A.A.); (A.F.)
| | - Alessia Arena
- Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (T.A.T.); (A.A.); (A.F.)
| | - Marina Macchiaiolo
- Rare Disease and Medical Genetics, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, 00146 Rome, Italy; (D.V.); (M.M.); (A.B.)
| | - Andrea Bartuli
- Rare Disease and Medical Genetics, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, 00146 Rome, Italy; (D.V.); (M.M.); (A.B.)
| | - Laura Sciuto
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Santiago Presti
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Sarah Sciuto
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Annamaria Sapuppo
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Agata Fiumara
- Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (T.A.T.); (A.A.); (A.F.)
| | - Lidia Marino
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Giulia Messina
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (L.S.); (S.P.); (S.S.); (A.S.); (L.M.); (G.M.)
| | - Piero Pavone
- Department of Clinical and Experimental Medicine, University of Catania, 95100 Catania, Italy; (T.A.T.); (A.A.); (A.F.)
- Correspondence: (M.L.B.); (P.P.); Tel.: +39-3401841225 (M.L.B.); +39-0953781193 (P.P.)
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6
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Pendina AA, Shilenkova YV, Talantova OE, Efimova OA, Chiryaeva OG, Malysheva OV, Dudkina VS, Petrova LI, Serebryakova EA, Shabanova ES, Mekina ID, Komarova EM, Koltsova AS, Tikhonov AV, Tral TG, Tolibova GK, Osinovskaya NS, Krapivin MI, Petrovskaia-Kaminskaia AV, Korchak TS, Ivashchenko TE, Glotov OS, Romanova OV, Shikov AE, Urazov SP, Tsay VV, Eismont YA, Scherbak SG, Sagurova YM, Vashukova ES, Kozyulina PY, Dvoynova NM, Glotov AS, Baranov VS, Gzgzyan AM, Kogan IY. Reproductive History of a Woman With 8p and 18p Genetic Imbalance and Minor Phenotypic Abnormalities. Front Genet 2019; 10:1164. [PMID: 31824569 PMCID: PMC6880252 DOI: 10.3389/fgene.2019.01164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/23/2019] [Indexed: 02/04/2023] Open
Abstract
We report on the phenotype and the reproductive history of an adult female patient with an unbalanced karyotype: 8p23 and 18p11.3 terminal deletions and 8p22 duplication. The indication for karyotyping of the 28-year-old patient was a structural rearrangement in her miscarriage specimen: 45,ХХ,der(8;18)t(8;18)(p23;p11.3). Unexpectedly, the patient had the same karyotype with only one normal chromosome 8, one normal chromosome 18, and a derivative chromosome, which was a product of chromosomes 8 and 18 fusion with loss of their short arm terminal regions. Fluorescence in situ hybridization revealed that derivative chromosome was a pseudodicentric with an active centromere of chromosome 8. Array comparative genomic hybridization confirmed 8p and 18p terminal deletions and additionally revealed 8p22 duplication with a total of 43 OMIM annotated genes being affected by the rearrangement. The patient had minor facial and cranial dysmorphia and no pronounced physical or mental abnormalities. She was socially normal, had higher education and had been married since the age of 26 years. Considering genetic counseling, the patient had decided to conceive the next pregnancy through in vitro fertilization (IVF) with preimplantation genetic testing for structural chromosomal aberrations (PGT-SR). She underwent four IVF/PGT-SR cycles with a total of 25 oocytes obtained and a total of 10 embryos analyzed. Only one embryo was balanced regarding chromosomes 8 and 18, while the others were unbalanced and demonstrated different combinations of the normal chromosomes 8 and 18 and the derivative chromosome. The balanced embryo was transferred, but the pregnancy was not registered. After four unsuccessful IVF/PGT-SR cycles, the patient conceived naturally. Non-invasive prenatal testing showed additional chromosome 18. The prenatal cytogenetic analysis of chorionic villi revealed an abnormal karyotype: 46,ХХ,der(8;18)t(8;18)(p23;p11.3)mat,+18. The pregnancy was terminated for medical reasons. The patient has a strong intention to conceive a karyotypically normal fetus. However, genetic counseling regarding this issue is highly challenging. Taking into account a very low chance of balanced gametes, emotional stress caused by numerous unsuccessful attempts to conceive a balanced embryo and increasing age of the patient, an IVF cycle with a donor oocyte should probably be considered.
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Affiliation(s)
- Anna A. Pendina
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Yulia V. Shilenkova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Olga E. Talantova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Olga A. Efimova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Olga G. Chiryaeva
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Olga V. Malysheva
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Vera S. Dudkina
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Lubov' I. Petrova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Elena A. Serebryakova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Elena S. Shabanova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Irina D. Mekina
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Evgeniia M. Komarova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Alla S. Koltsova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Andrei V. Tikhonov
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Tatyana G. Tral
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Gulrukhsor Kh. Tolibova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Natalia S. Osinovskaya
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Mikhail I. Krapivin
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiia V. Petrovskaia-Kaminskaia
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Taisia S. Korchak
- St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Tatyana E. Ivashchenko
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Oleg S. Glotov
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- City Hospital №40, St. Petersburg, Russia
| | | | | | | | | | | | - Sergei G. Scherbak
- St. Petersburg State University, St. Petersburg, Russia
- City Hospital №40, St. Petersburg, Russia
| | | | - Elena S. Vashukova
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Polina Y. Kozyulina
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | | | - Andrey S. Glotov
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Vladislav S. Baranov
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
- St. Petersburg State University, St. Petersburg, Russia
| | - Alexander M. Gzgzyan
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
| | - Igor Yu. Kogan
- D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, St. Petersburg, Russia
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Chromosome 3p Inverted Duplication with Terminal Deletion: Second Postnatal Case Report with Additional Clinical Features. Case Rep Genet 2019; 2019:5384295. [PMID: 31428485 PMCID: PMC6683815 DOI: 10.1155/2019/5384295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 12/05/2022] Open
Abstract
Distal deletions and duplications of 3p are individually well-characterized chromosome abnormalities. Here, we report an inverted duplication of 3p with an adjacent terminal 3p deletion in a 17-month-old girl who had prenatal intrauterine growth restriction and cardiac defects. Other findings included hemangiomas, neutropenia, umbilical hernia, hypotonia, gross motor delay, microcephaly, and ptosis. Family history was noncontributory. Microarray analysis revealed a 5.37 Mb deletion of chromosome bands 3p26.1 to 3p26.3 and a 13.68 Mb duplication of 3p24.3 to 3p26.1. FISH analysis confirmed that the duplication was inverted. Upon literature review, only one postnatal patient and one second trimester pregnancy have been reported with this finding. Many of our patient's features are present in both 3p deletion and 3p duplication syndromes, including congenital heart disease, growth restriction, microcephaly, hypotonia, and developmental delay. Our patient has additional features not commonly reported in 3p deletion or duplication patients, such as aortic dilation, hemangiomas, and neutropenia. The identification of this patient contributes to additional understanding of features associated with concurrent deletion and inverted duplication in the distal 3p chromosome. This report may assist clinicians working with patients who have constellations of similar features or similar cytogenomic abnormalities.
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8
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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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9
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Akkurt MO, Higgs A, Turan OT, Turan OM, Turan S. Prenatal diagnosis of inverted duplication deletion 8p syndrome mimicking trisomy 18. Am J Med Genet A 2017; 173:776-779. [PMID: 28211984 DOI: 10.1002/ajmg.a.38074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/14/2016] [Indexed: 11/06/2022]
Abstract
Inverted duplication deletion of 8p (invdupdel[8p]) is a well-described and uncommon chromosomal rearrangement. The majority of the reported cases have revealed no life-threatening malformations. Although the invdupdel[8p] syndrome in children with central nervous system abnormalities has been reported before, we present the first prenatal microarray diagnosis of invdupdel[8p] syndrome mimicking trisomy 18 due to similar sonographic features. Contrary to reported cases with invdupdel[8p] syndrome, the present case had severe polyvalvular dysplasia and the infant deceased at day 12 of life. In this case, we also emphasize the diagnostic power of microarray analysis in detecting the underlying genetic causes for fetuses with multiple congenital anomalies. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mehmet Ozgur Akkurt
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland, Baltimore, Maryland
| | - Amanda Higgs
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland, Baltimore, Maryland
| | - Ozerk T Turan
- College of Arts and Sciences, University of Miami, Coral Gables, Florida
| | - Ozhan M Turan
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland, Baltimore, Maryland
| | - Sifa Turan
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland, Baltimore, Maryland
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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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11
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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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12
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Moog U, Bierhals T, Brand K, Bautsch J, Biskup S, Brune T, Denecke J, de Die-Smulders CE, Evers C, Hempel M, Henneke M, Yntema H, Menten B, Pietz J, Pfundt R, Schmidtke J, Steinemann D, Stumpel CT, Van Maldergem L, Kutsche K. Phenotypic and molecular insights into CASK-related disorders in males. Orphanet J Rare Dis 2015; 10:44. [PMID: 25886057 PMCID: PMC4449965 DOI: 10.1186/s13023-015-0256-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/20/2015] [Indexed: 12/05/2022] Open
Abstract
Background Heterozygous loss-of-function mutations in the X-linked CASK gene cause progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH) and severe intellectual disability (ID) in females. Different CASK mutations have also been reported in males. The associated phenotypes range from nonsyndromic ID to Ohtahara syndrome with cerebellar hypoplasia. However, the phenotypic spectrum in males has not been systematically evaluated to date. Methods We identified a CASK alteration in 8 novel unrelated male patients by targeted Sanger sequencing, copy number analysis (MLPA and/or FISH) and array CGH. CASK transcripts were investigated by RT-PCR followed by sequencing. Immunoblotting was used to detect CASK protein in patient-derived cells. The clinical phenotype and natural history of the 8 patients and 28 CASK-mutation positive males reported previously were reviewed and correlated with available molecular data. Results CASK alterations include one nonsense mutation, one 5-bp deletion, one mutation of the start codon, and five partial gene deletions and duplications; seven were de novo, including three somatic mosaicisms, and one was familial. In three subjects, specific mRNA junction fragments indicated in tandem duplication of CASK exons disrupting the integrity of the gene. The 5-bp deletion resulted in multiple aberrant CASK mRNAs. In fibroblasts from patients with a CASK loss-of-function mutation, no CASK protein could be detected. Individuals who are mosaic for a severe CASK mutation or carry a hypomorphic mutation still showed detectable amount of protein. Conclusions Based on eight novel patients and all CASK-mutation positive males reported previously three phenotypic groups can be distinguished that represent a clinical continuum: (i) MICPCH with severe epileptic encephalopathy caused by hemizygous loss-of-function mutations, (ii) MICPCH associated with inactivating alterations in the mosaic state or a partly penetrant mutation, and (iii) syndromic/nonsyndromic mild to severe ID with or without nystagmus caused by CASK missense and splice mutations that leave the CASK protein intact but likely alter its function or reduce the amount of normal protein. Our findings facilitate focused testing of the CASK gene and interpreting sequence variants identified by next-generation sequencing in cases with a phenotype resembling either of the three groups. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Kristina Brand
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Jan Bautsch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | | | - Thomas Brune
- Universitätskinderklinik, Universitätsklinikum Magdeburg, Magdeburg, Germany.
| | - Jonas Denecke
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Neuropädiatrie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| | - Christine E de Die-Smulders
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht UMC+, Maastricht, The Netherlands.
| | - Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Marco Henneke
- Klinik für Kinder- und Jugendmedizin, Universitätsmedizin Göttingen, Göttingen, Germany.
| | - Helger Yntema
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
| | - Joachim Pietz
- Section of Neuropediatrics, Center for Child and Adolescent Medicine, Heidelberg, Germany.
| | - Rolph Pfundt
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Jörg Schmidtke
- Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover, Germany.
| | - Doris Steinemann
- Institut für Zell- und Molekularpathologie, Medizinische Hochschule Hannover, Hannover, Germany.
| | - Constance T Stumpel
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht UMC+, Maastricht, The Netherlands.
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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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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15
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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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16
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Auger J, Bonnet C, Valduga M, Philippe C, Bertolo-Houriez E, Beri-Dexheimer M, Schweitzer C, Leheup B, Jonveaux P. De novo complex X chromosome rearrangement unmasking maternally inherited CSF2RA deletion in a girl with pulmonary alveolar proteinosis. Am J Med Genet A 2013; 161A:2594-9. [PMID: 23918747 DOI: 10.1002/ajmg.a.36097] [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] [Received: 03/07/2013] [Accepted: 05/20/2013] [Indexed: 11/11/2022]
Abstract
We report on a 3-year-old girl with a de novo complex X chromosome rearrangement associated with congenital pulmonary alveolar proteinosis (PAP) and short stature. Array comparative genome hybridization and FISH analyses contributed to characterize the complex rearrangement consisting of a 7.37 Mb terminal deletion of Xp22.33p22.2, a 17.3 Mb interstitial inverted duplication of Xp22.2p21.3, and a 10.14 Mb duplication of Xq27.3q28. PCR analysis of microsatellite markers supported a paternal origin of the X chromosome rearrangement. A pre-meiotic two-step mechanism may explain the occurrence of this complex X rearrangement: an inverted duplication deletion event on Xp, and duplication of the Xq27.3qter region through a telomere capture event stabilizing the broken chromosome Xp end. The girl has also inherited from her healthy mother an X chromosome with a colony stimulating factor 2 receptor, alpha (CSF2RA) gene deletion. Consistent with the recessive mode of inheritance, the de novo paternal Xp22.33p22.2 deletion combined to the maternally inherited CSF2RA gene deletion led to homozygous deletion of CSF2RA and PAP diagnosis in the girl. The Xp deletion encompasses the pseudoautosomal region 1 (PAR1) which contains genes that escape X inactivation. Short stature homeobox (SHOX) haploinsufficiency explains growth retardation. Absence of other symptoms in relation to the X deletion/amplification is most probably due to skewed X inactivation. Finally, inherited deletions may unmask rare pathogenic genomic rearrangement and contribute to clinical phenotypes by a recessive mode of gene action.
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Affiliation(s)
- Julie Auger
- Laboratoire de Génétique Médicale, Centre Hospitalier Universitaire de Nancy, Vandoeuvre-les-Nancy, France; Service de Médecine Infantile 3 et Génétique Clinique, Centre Hospitalier Universitaire de Nancy, Vandoeuvre-les-Nancy, France
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Trachoo O, Assanatham M, Jinawath N, Nongnuch A. Chromosome 20p inverted duplication deletion identified in a Thai female adult with mental retardation, obesity, chronic kidney disease and characteristic facial features. Eur J Med Genet 2013; 56:319-24. [PMID: 23542666 DOI: 10.1016/j.ejmg.2013.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/11/2013] [Indexed: 11/18/2022]
Abstract
We report on a 21-year-old Thai woman presenting with mental retardation, developmental delays, selective mutism, distinctive facial features, sensorineural hearing loss, single right kidney, uterine didelphys and obesity. A longitudinal clinical course beginning in childhood revealed excessive weight gain, poor language skills and poor school performance. Chronic kidney disease stage 4, with elevated blood pressure, was first noted in adulthood. Array comparative genomic hybridization detected a copy loss at 20p13 co-existing with a copy gain at 20p13-20p11.22. A conventional cytogenetic study revealed the complex structural rearrangement of chromosome 20 [der (20) dup (20) (p11.2p13) del (20) (p13.pter)]. A FISH analysis, using probes against duplication and deletion regions, confirmed that there was an inverted duplication of p11.2-p13 and a deletion in the subtelomere region. Previous reports have identified this cytogenetic characterization in a Caucasian boy. Therefore, this is the first reported case of chromosome 20p inverted duplication deletion syndrome in an adult from the Southeast Asian population group.
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Affiliation(s)
- Objoon Trachoo
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Chen CP, Su YN, Chern SR, Hsu CY, Tsai FJ, Wu PC, Lee CC, Chen YT, Lee MS, Wang W. Inv dup del(9p): prenatal diagnosis and molecular cytogenetic characterization by fluorescence in situ hybridization and array comparative genomic hybridization. Taiwan J Obstet Gynecol 2011; 50:67-73. [PMID: 21482378 DOI: 10.1016/j.tjog.2011.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2010] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE To present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 9p, or inv dup del(9p). MATERIALS, METHODS, AND RESULTS A 35-year-old primigravid woman underwent amniocentesis at 16 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 9, or der(9) with additional material at the end of the short arm of one chromosome 9. Parental karyotypes were normal. Level II ultrasound showed ventriculomegaly and normal male external genitalia. Repeated amniocentesis was performed at 20 weeks of gestation. Array comparative genomic hybridization revealed a 0.70-Mb deletion at 9p24.3 and an 18.36-Mb duplication from 9p24.3 to 9p22.1. The distal 9p deletion encompassed the genes of DOCK8, ANKRD15, FOXD4, DMRT1, and DMRT3. Fluorescence in situ hybridization analysis using bacterial artificial chromosome clone probes specific for 9p confirmed that the der(9) was derived from the inv dup del(9p). The karyotype of the fetus was 46,XY,inv dup del(9)(:p22.1-->p24.3::p24.3-->qter)dn or 46,XY,der(9) del(9)(p24.3) inv dup(9)(p22.1p24.3)dn. Polymorphic DNA marker analysis determined a maternal origin of the inv dup del(9p). A 512-g male fetus was subsequently terminated at 22 weeks of gestation with facial dysmorphism. The fetus had normal male external genitalia without sex reversal. CONCLUSION Fluorescence in situ hybridization and array comparative genomic hybridization are useful to determine the nature of a prenatally detected aberrant chromosome derived from the inv dup del. Male fetuses with inv dup del(9p) and haploinsufficiency of DMRT1 and DMRT3 may present normal male external genitalia without sex reversal.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
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19
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Genotype-phenotype association studies of chromosome 8p inverted duplication deletion syndrome. Behav Genet 2011; 41:373-80. [PMID: 21259039 DOI: 10.1007/s10519-011-9447-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 01/07/2011] [Indexed: 10/18/2022]
Abstract
Individuals diagnosed with chromosome 8p inverted duplication deletion (invdupdel(8p)) manifest a wide range of clinical features and cognitive impairment. The purpose of this study is to employ array CGH technology to define more precisely the cytogenetic breakpoints and regions of copy number variation found in several individuals with invdupdel(8p), and compare these results with their neuropsychological characteristics. We examined the cognitive-behavioral features of two male and two female children, ages 3-15 years, with invdupdel(8p). We noted cognitive deficits that ranged from mild to severe, and adaptive behavior composites that ranged from significantly to substantially lower than adequate levels. CARS scores, a measure of autistic behavior, identified three children with autism or autistic-like features. Three of the four children exhibited attention deficits and hyperactivity consistent with a DSM-IV-TR diagnosis of ADHD. One child showed extreme emotional lability. Interestingly, intellectual disability was not correlated with deletion size, nor was the deletion location associated with the autistic phenotype. On the other hand, the duplication length in 8p21.1/8p22 was associated with cognitive deficit. In addition, a small locus of over-expression in 8p21.3 was common for all three participants diagnosed as autistic. A limitation of the study is its small sample size. Further analyses of the deleted and over-expressed regions are needed to ascertain the genes involved in cognitive function and, possibly, autism.
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20
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Vera-Carbonell A, López-Expósito I, Bafalliu JA, Ballesta-Martínez M, Glóver G, Llópis C, Moya-Quiles R, Suela J, Fernández A, Guillén-Navarro E. Molecular characterization of a new patient with a non-recurrent inv dup del 2q and review of the mechanisms for this rearrangement. Am J Med Genet A 2010; 152A:2670-80. [PMID: 20799321 DOI: 10.1002/ajmg.a.33613] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report on newborn baby with microcephaly, facial anomalies, congenital heart defects, hypotonia, wrist contractures, long fingers, adducted thumbs, and club feet. Cytogenetic studies revealed an inverted duplication with terminal deletion (inv dup del) of 2q in the patient and a paternal 2qter deletion polymorphism. Microsatellite markers demonstrated that the inv dup del was maternal in origin and intrachromosomal. Intra or interchromosomal rearrangements may cause this aberration either by a U-type exchange (end-to-end fusion), an unequal crossover between inverted repeats (non-allelic homologous recombination: NAHR), or through breakage-fusion-bridge (BFB) cycles leading to a sister chromatid fusion by non-homologous end joining (NHEJ). A high-resolution oligo array-CGH (244 K) defined the breakpoints and did not detect a single copy region with a size exceeding 12.93 Kb in the fusion site. The size of the duplicated segment was 38.75 Mb, extending from 2q33.1 to 2q37.3 and the size of the terminal deletion was 2.85 Mb in 2q37.3. Our results indicate that the inv dup del (2q) is likely a non-recurrent chromosomal rearrangement generated by a NHEJ mechanism. The major clinical characteristics associated with this 2q rearrangement overlap with those commonly found in patients with 2q duplication reported in the literature.
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Affiliation(s)
- Ascensión Vera-Carbonell
- Sección de Citogenética, Centro de Bioquímica y Genética Clínica, Hospital U. Virgen de la Arrixaca, Murcia, Spain
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21
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Chen JM, Cooper DN, Férec C, Kehrer-Sawatzki H, Patrinos GP. Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 2010; 20:222-33. [PMID: 20541013 DOI: 10.1016/j.semcancer.2010.05.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/22/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Genomic rearrangements in inherited disease and cancer involve gross alterations of chromosomes or large chromosomal regions and can take the form of deletions, duplications, insertions, inversions or translocations. The characterization of a considerable number of rearrangement breakpoints has now been accomplished at the nucleotide sequence level, thereby providing an invaluable resource for the detailed study of the mutational mechanisms which underlie genomic recombination events. A better understanding of these mutational mechanisms is vital for improving the design of mutation detection strategies. At least five categories of mutational mechanism are known to give rise to genomic rearrangements: (i) homologous recombination including non-allelic homologous recombination (NAHR), gene conversion, single strand annealing (SSA) and break-induced replication (BIR), (ii) non-homologous end joining (NHEJ), (iii) microhomology-mediated replication-dependent recombination (MMRDR), (iv) long interspersed element-1 (LINE-1 or L1)-mediated retrotransposition and (v) telomere healing. Focussing on the first three of these general mechanisms, we compare and contrast their hallmark characteristics, and discuss the role of various local DNA sequence features (e.g. recombination-promoting motifs, repetitive sequences and sequences capable of non-B DNA formation) in mediating the recombination events that underlie gross genomic rearrangements. Finally, we explore how studies both at the level of the gene (using the neurofibromatosis type-1 gene as an example) and the whole genome (using data derived from cancer genome sequencing studies) are shaping our understanding of the impact of genomic rearrangements as a cause of human genetic disease.
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Affiliation(s)
- Jian-Min Chen
- Etablissement Français du Sang (EFS) - Bretagne, Brest, France.
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22
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Genomic profile of copy number variants on the short arm of human chromosome 8. Eur J Hum Genet 2010; 18:1114-20. [PMID: 20461109 DOI: 10.1038/ejhg.2010.66] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We evaluated 966 consecutive pediatric patients with various developmental disorders by high-resolution microarray-based comparative genomic hybridization and found 10 individuals with pathogenic copy number variants (CNVs) on the short arm of chromosome 8 (8p), representing approximately 1% of the patients analyzed. Two patients with 8p terminal deletion associated with interstitial inverted duplication (inv dup del(8p)) had different mechanisms leading to the formation of a dicentric intermediate during meiosis. Three probands carried an identical ∼5.0 Mb interstitial duplication of chromosome 8p23.1. Four possible hotspots within 8p were observed at nucleotide coordinates of ∼10.45, 24.32-24.82, 32.19-32.77, and 38.94-39.72 Mb involving the formation of recurrent genomic rearrangements. Other CNVs with deletion- or duplication-specific start or stop coordinates on the 8p provide useful information for exploring the basic mechanisms of complex structural rearrangements in the human genome.
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23
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Zuffardi O, Bonaglia M, Ciccone R, Giorda R. Inverted duplications deletions: underdiagnosed rearrangements?? Clin Genet 2009; 75:505-13. [PMID: 19508415 DOI: 10.1111/j.1399-0004.2009.01187.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular techniques led to the discovery that several chromosome rearrangements interpreted as terminal duplications were in fact inverted duplications contiguous to terminal deletions. Inv dup del rearrangements originate through a symmetric dicentric chromosome that, after asymmetric breakage, generates an inv dup del and a deleted chromosome. In recurrent inverted duplications the dicentric chromosome is formed at meiosis through non-allelic homologous recombination. In non-recurrent inv dup del cases, dicentric intermediates are formed by non-homologous end joining or intrastrand annealing. Some authors hypothesized that in these cases the dicentric may have been formed directly in the zygote. Healing of the broken dicentric chromosomes can occur not only in a telomerase-dependent way but also through telomere capture and circularization thus creating translocated or ring inv dup del chromosomes. In all the cases reported up to now, the duplicated region was always longer than the deleted one, but we can safely assume that there is another group of rearrangements where the deleted region is longer than the duplicated portion. In general, in these cases, the cytogeneticist will suspect the presence of a deletion and confirm it by FISH with a subtelomeric probe, but he/she will almost certainly miss the duplication. It is likely that the conventional analysis techniques used until now have led to a substantial underestimate of the frequency of inv dup del rearrangements and that the widespread use of array-CGH in routine analysis will allow a more realistic estimate. Obviously, the concomitant presence of deletion and duplication has important consequences in genotype/phenotype correlations.
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Affiliation(s)
- O Zuffardi
- Biologia Generale e Genetica Medica, Università di Pavia, Pavia, Italy.
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24
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Aktas D, Weise A, Utine E, Alehan D, Mrasek K, von Eggeling F, Thieme H, Tuncbilek E, Liehr T. Clinically abnormal case with paternally derived partial trisomy 8p23.3 to 8p12 including maternal isodisomy of 8p23.3: a case report. Mol Cytogenet 2009; 2:14. [PMID: 19566937 PMCID: PMC2715415 DOI: 10.1186/1755-8166-2-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/30/2009] [Indexed: 01/30/2023] Open
Abstract
Background Because of low copy repeats (LCRs) and common inversion polymorphisms, the human chromosome 8p is prone to a number of recurrent rearrangements. Each of these rearrangements is associated with several phenotypic features. We report on a patient with various clinical malformations and developmental delay in connection with an inverted duplication event, involving chromosome 8p. Methods Chromosome analysis, multicolor banding analysis (MCB), extensive fluorescence in situ hybridization (FISH) analysis and microsatellite analysis were performed. Results The karyotype was characterized in detail by multicolor banding (MCB), subtelomeric and centromere-near probes as 46,XY,dup(8)(pter->p23.3::p12->p23.3::p23.3->qter). Additionally, microsatellite analysis revealed the paternal origin of the duplication and gave hints for a mitotic recombination involving about 6 MB in 8p23.3. Conclusion A comprehensive analysis of the derivative chromosome 8 suggested a previously unreported mechanism of formation, which included an early mitotic aberration leading to maternal isodisomy, followed by an inverted duplication of the 8p12p23.3 region.
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Affiliation(s)
- Dilek Aktas
- Hacettepe University Faculty of Medicine, Department of Genetics, 06100 Sihhiye, Ankara, Turkey.
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