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Kekis M, Deeg C, Hashimoto S, McKinney A, Erdman L, Green-Geer C, Shuss C, Hickey S, Astbury C, Pyatt RE. Partial tetrasomy 11q resulting from an intrachromosomal triplication of a 22 Mb region of chromosome 11. Am J Med Genet A 2017; 173:1056-1060. [PMID: 28328127 DOI: 10.1002/ajmg.a.38098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/28/2016] [Indexed: 02/01/2023]
Abstract
Intrachromosomal triplications are complex chromosomal rearrangements which arise during meiosis or mitosis and lead to a tetrasomic dose of the affected genomic regions. We describe a female patient harboring an intrachromosomal triplication who presented to the Genetics clinic with dysmorphic features, including telecanthus, flat facial profile, and prognathism, short stature, widely spaced nipples, multiple allergy complaints, loose bowel movements, and mild speech delay. Microarray analysis showed a copy number gain of a 22.37 Mb region of chromosome 11 between bands 11q14.1 and 11q22.1. This region contains 95 genes and seven microRNAs, none of which have been implicated in a disease resulting from increased gene dosage. FISH analysis using a probe targeted to the middle of the segment of the copy number gain yielded a pattern indicative of a tetrasomy via an intrachromosomal triplication, with three signals on the long arm of one homologue of chromosome 11 and the fourth on the other homologue. Subsequent FISH analysis showed that the middle triplicated fragment was positioned in an inverted orientation relative to the outer fragments. To investigate the mechanism by which the intrachromosomal triplication occurred, SNP microarray analysis was performed. These results were consistent with the presence of multiple haplotypes in the tetrasomic region and suggest that the intrachromosomal triplication in our patient arose in one parent during meiosis. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mariana Kekis
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Carol Deeg
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Sayaka Hashimoto
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Aimee McKinney
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Linda Erdman
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Cecelia Green-Geer
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Christine Shuss
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio
| | - Scott Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio
| | - Caroline Astbury
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Robert E Pyatt
- Departmentof Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
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Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. Am J Hum Genet 2015; 96:208-20. [PMID: 25640679 DOI: 10.1016/j.ajhg.2014.12.017] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/15/2014] [Indexed: 11/23/2022] Open
Abstract
Interpreting the genomic and phenotypic consequences of copy-number variation (CNV) is essential to understanding the etiology of genetic disorders. Whereas deletion CNVs lead obviously to haploinsufficiency, duplications might cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci, and in some cases these copy-number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has yet to be investigated on a large scale. Here we fine-mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). Moreover, we predicted six in-frame fusion genes at sequenced duplication breakpoints; four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These unique fusion genes could be related to clinical phenotypes and warrant further study. Although most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that might not be predicted by conventional copy-number assays. Therefore, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.
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Connolly JJ, Glessner JT, Almoguera B, Crosslin DR, Jarvik GP, Sleiman PM, Hakonarson H. Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts. Front Genet 2014; 5:51. [PMID: 24672537 PMCID: PMC3957100 DOI: 10.3389/fgene.2014.00051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/18/2014] [Indexed: 12/18/2022] Open
Abstract
The goal of this paper is to review recent research on copy number variations (CNVs) and their association with complex and rare diseases. In the latter part of this paper, we focus on how large biorepositories such as the electronic medical record and genomics (eMERGE) consortium may be best leveraged to systematically mine for potentially pathogenic CNVs, and we end with a discussion of how such variants might be reported back for inclusion in electronic medical records as part of medical history.
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Affiliation(s)
- John J Connolly
- The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA
| | - Berta Almoguera
- The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA
| | - David R Crosslin
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center Seattle, WA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center Seattle, WA, USA
| | - Patrick M Sleiman
- The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA
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Hehir-Kwa JY, Pfundt R, Veltman JA, de Leeuw N. Pathogenic or not? Assessing the clinical relevance of copy number variants. Clin Genet 2013; 84:415-21. [PMID: 23895381 DOI: 10.1111/cge.12242] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 02/04/2023]
Abstract
The availability of commercially produced genomic microarrays has resulted in the wide spread implementation of genomic microarrays, often as a first-tier diagnostic test for copy number variant (CNV) screening of patients who are suspected for chromosomal aberrations. Patients with intellectual disability (ID) and/or multiple congenital anomalies (MCA) were traditionally the main focus for this microarray-based CNV screening, but the application of microarrays to other (neurodevelopmental) disorders and tumor diagnostics has also been explored and implemented. The diagnostic workflow for patients with ID is now well established, relying on the identification of rare CNVs and determining their inheritance patterns. However, experience gained through screening large numbers of samples has revealed many subtleties and complexities of CNV interpretation. This has resulted in a better understanding of the contribution of CNVs to genomic disorders not only via de novo occurrence, but also via X-linked and recessive inheritance models as well as through models taking into account mosaicisms, imprinting, and digenic inheritance. In this review, we discuss CNV interpretation within the context of these different genetic disease models and common pitfalls that can occur when searching for supportive evidence that a CNV is clinically relevant.
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Affiliation(s)
- J Y Hehir-Kwa
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
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Beri S, Bonaglia MC, Giorda R. Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements. Eur J Hum Genet 2013; 21:757-61. [PMID: 23073313 PMCID: PMC3722940 DOI: 10.1038/ejhg.2012.235] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 08/07/2012] [Accepted: 09/12/2012] [Indexed: 01/30/2023] Open
Abstract
Submicroscopic structural variations, including deletions, duplications, inversions and more complex rearrangements, are widespread in normal human genomes. Inverted segmental duplications or highly identical low-copy repeat (LCR) sequences can mediate the formation of inversions and more complex structural rearrangements through non-allelic homologous recombination. In a patient with 7q36 inverted duplication/terminal deletion, we demonstrated the central role of a pair of short inverted LCRs in the vasoactive intestinal peptide receptor gene (VIPR2)-LCRs in generating the rearrangement. We also revealed a relatively common VIPR2-LCR-associated inversion polymorphism disrupting the gene in almost 1% of healthy subjects, and a small number of complex duplications/triplications. In genome-wide studies of several thousand patients, a significant association of rare microduplications with variable size, all involving VIPR2, with schizophrenia was recently described, suggesting that altered vasoactive intestinal peptide signaling is likely implicated in the pathogenesis of schizophrenia. Genetic testing for VIPR2-LCR-associated inversions should be performed on available cohorts of psychiatric patients to evaluate their potential pathogenic role.
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Affiliation(s)
- Silvana Beri
- Molecular Biology Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
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Combined deletion 18q22.2 and duplication/triplication 18q22.1 causes microcephaly, mental retardation and leukencephalopathy. Gene 2013; 523:92-8. [DOI: 10.1016/j.gene.2013.03.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/05/2013] [Accepted: 03/15/2013] [Indexed: 11/23/2022]
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