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Pezzani L, Pezzoli L, Rosina E, Scatigno A, Cereda A, Lucca C, Bellini M, Marchetti D, Maino M, Mangili G, Selicorni A, Iascone M. Double somatic mosaicism in Cornelia de Lange syndrome. Am J Med Genet A 2024; 194:e63512. [PMID: 38135466 DOI: 10.1002/ajmg.a.63512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Post-zygotic mosaicism is a well-known biological phenomenon characterized by the presence of genetically distinct lineages of cells in the same individual due to post-zygotic de novo mutational events. It has been identified in about 13% of Cornelia de Lange (CdLS) syndrome patients with a molecular diagnosis, an unusual high frequency. Here, we report the case of a patient affected by classic CdLS harboring post-zygotic mosaicism for two different likely pathogenic variants at the same nucleotide position in NIPBL. Double somatic mosaicism has never been reported in CdLS and only rarely recognized in human diseases. Possible pathogenetic mechanisms are discussed.
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Affiliation(s)
- Lidia Pezzani
- Pediatria, ASST Papa Giovanni XXIII, Bergamo, Italy
- Genetica Clinica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Laura Pezzoli
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Erica Rosina
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Anna Cereda
- Pediatria, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Camilla Lucca
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Matteo Bellini
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Marchetti
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Marzia Maino
- Patologia Neonatale, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
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Schierbaum LM, Schneider S, Herms S, Sivalingam S, Fabian J, Reutter H, Weber S, Merz WM, Tkaczyk M, Miklaszewska M, Sikora P, Szmigielska A, Krzemien G, Zachwieja K, Szczepanska M, Taranta-Janusz K, Kroll P, Polok M, Zaniew M, Hilger AC. Genome-Wide Survey for Microdeletions or -Duplications in 155 Patients with Lower Urinary Tract Obstructions (LUTO). Genes (Basel) 2021; 12:genes12091449. [PMID: 34573432 PMCID: PMC8468665 DOI: 10.3390/genes12091449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/28/2023] Open
Abstract
Lower urinary tract obstruction (LUTO) is, in most cases, caused by anatomical blockage of the bladder outlet. The most common form are posterior urethral valves (PUVs), a male-limited phenotype. Here, we surveyed the genome of 155 LUTO patients to identify disease-causing CNVs. Raw intensity data were collected for CNVs detected in LUTO patients and 4.392 healthy controls using CNVPartition, QuantiSNP and PennCNV. Overlapping CNVs between patients and controls were discarded. Additional filtering implicated CNV frequency in the database of genomic variants, gene content and final visual inspection detecting 37 ultra-rare CNVs. After, prioritization qPCR analysis confirmed 3 microduplications, all detected in PUV patients. One microduplication (5q23.2) occurred de novo in the two remaining microduplications found on chromosome 1p36.21 and 10q23.31. Parental DNA was not available for segregation analysis. All three duplications comprised 11 coding genes: four human specific lncRNA and one microRNA. Three coding genes (FBLIM1, SLC16A12, SNCAIP) and the microRNA MIR107 have previously been shown to be expressed in the developing urinary tract of mouse embryos. We propose that duplications, rare or de novo, contribute to PUV formation, a male-limited phenotype.
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Affiliation(s)
- Luca M. Schierbaum
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Sophia Schneider
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Stefan Herms
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Sugirthan Sivalingam
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany;
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Julia Fabian
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Stefanie Weber
- Department of Pediatrics, University Hospital Marburg, 35033 Marburg, Germany;
| | - Waltraut M. Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, 53127 Bonn, Germany;
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute of Lodz, 93-428 Łódź, Poland;
- Department of Pediatrics, Cardiology and Immunology, Medical University of Łódź, 93-428 Łódź, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, 20-059 Lublin, Poland;
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, 40-055 Katowice, Poland;
| | - Katarzyna Taranta-Janusz
- Department of Pediatrics and Nephrology, Medical University of Białystok, 15-089 Białystok, Poland;
| | - Pawel Kroll
- Neurourology Unit, Pediatric Surgery and Urology Clinic, 61-701 Poznań, Poland;
- Neurourology Unit, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Marcin Polok
- Department of Pediatric Surgery and Urology, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Alina C. Hilger
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
- Correspondence:
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3
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Muir AM, King C, Schneider AL, Buttar AS, Scheffer IE, Sadleir LG, Mefford HC. Double somatic mosaicism in a child with Dravet syndrome. NEUROLOGY-GENETICS 2019; 5:e333. [PMID: 31086826 PMCID: PMC6481227 DOI: 10.1212/nxg.0000000000000333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/18/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Alison M Muir
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Chontelle King
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Amy L Schneider
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Aman S Buttar
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Ingrid E Scheffer
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Lynette G Sadleir
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
| | - Heather C Mefford
- Division of Genetic Medicine (A.M.M., A.S.B., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Paediatrics and Child Health (C.K.), University of Otago, Wellington, New Zealand; Department of Medicine (A.L.S., I.E.S.), Epilepsy Research Centre, The University of Melbourne, Austin Health, Heidelberg, Australia; The Florey Institute and Murdoch Children's Research Institute (I.E.S.), Parkville, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Australia; and Department of Paediatrics and Child Health (L.G.S.), University of Otago, Wellington, New Zealand
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4
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High frequency of mosaic pathogenic variants in genes causing epilepsy-related neurodevelopmental disorders. Genet Med 2017; 20:403-410. [PMID: 28837158 PMCID: PMC5895461 DOI: 10.1038/gim.2017.114] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022] Open
Abstract
Purpose Mosaicism probably represents an underreported cause of genetic disorders due to detection challenges during routine molecular diagnostics. The purpose of this study was to evaluate the frequency of mosaicism detected by next-generation sequencing in genes associated with epilepsy-related neurodevelopmental disorders. Methods We conducted a retrospective analysis of 893 probands with epilepsy who had a multigene epilepsy panel or whole-exome sequencing performed in a clinical diagnostic laboratory and were positive for a pathogenic or likely pathogenic variant in one of nine genes (CDKL5, GABRA1, GABRG2, GRIN2B, KCNQ2, MECP2, PCDH19, SCN1A, or SCN2A). Parental results were available for 395 of these probands. Results Mosaicism was most common in the CDKL5, PCDH19, SCN2A, and SCN1A genes. Mosaicism was observed in GABRA1, GABRG2, and GRIN2B, which previously have not been reported to have mosaicism, and also in KCNQ2 and MECP2. Parental mosaicism was observed for pathogenic variants in multiple genes including KCNQ2, MECP2, SCN1A, and SCN2A. Conclusion Mosaic pathogenic variants were identified frequently in nine genes associated with various neurological conditions. Given the potential clinical ramifications, our findings suggest that next-generation sequencing diagnostic methods may be utilized when testing these genes in a diagnostic laboratory.
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Ocular Pathology of Oculocerebrorenal Syndrome of Lowe: Novel Mutations and Genotype-Phenotype Analysis. Sci Rep 2017; 7:1442. [PMID: 28473699 PMCID: PMC5431454 DOI: 10.1038/s41598-017-01447-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/28/2017] [Indexed: 12/02/2022] Open
Abstract
Mutations in the OCRL1 gene result in the oculocerebrorenal syndrome of Lowe, with symptoms including congenital bilateral cataracts, glaucoma, renal failure, and neurological impairments. OCRL1 encodes an inositol polyphosphate 5-phosphatase which preferentially dephosphorylates phosphatidylinositide 4,5 bisphosphate (PI(4,5)P2). We have identified two novel mutations in two unrelated Lowe syndrome patients with congenital glaucoma. Novel deletion mutations are detected at c.739-742delAAAG in Lowe patient 1 and c.1595-1631del in Lowe patient 2. End stage glaucoma in patient 2 resulted in the enucleation of the eye, which on histology demonstrated corneal keloid, fibrous infiltration of the angle, ectropion uvea, retinal gliosis, and retinal ganglion cell loss. We measured OCRL protein levels in patient keratinocytes and found that Lowe 1 patient cells had significantly reduced OCRL protein as compared to the control keratinocytes. Genotype-phenotype correlation of OCRL1 mutations associated with congenital glaucoma revealed clustering of missense and deletion mutations in the 5-phosphatase domain and the RhoGAP-like domain. In conclusion, we report novel OCRL1 mutations in Lowe syndrome patients and the corresponding histopathologic analysis of one patient’s ocular pathology.
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6
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Ikemoto Y, Takayama Y, Fujii K, Masuda M, Kato C, Hatsuse H, Fujitani K, Nagao K, Kameyama K, Ikehara H, Toyoda M, Umezawa A, Miyashita T. Somatic mosaicism containing double mutations in PTCH1 revealed by generation of induced pluripotent stem cells from nevoid basal cell carcinoma syndrome. J Med Genet 2017; 54:579-584. [PMID: 28363938 DOI: 10.1136/jmedgenet-2016-104490] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder characterised by developmental defects and tumorigenesis, such as medulloblastomas and basal cell carcinomas, caused by mutations of the patched-1 (PTCH1) gene. In this article, we seek to demonstrate a mosaicism containing double mutations in PTCH1 in an individual with NBCCS. METHODS AND RESULTS A de novo germline mutation of PTCH1 (c.272delG) was detected in a 31-year-old woman with NBCCS. Gene analysis of two out of four induced pluripotent stem cell (iPSC) clones established from the patient unexpectedly revealed an additional mutation, c.274delT. Deep sequencing confirmed a low-prevalence somatic mutation (5.5%-15.6% depending on the tissue) identical to the one found in iPSC clones. CONCLUSIONS This is the first case of mosaicism unequivocally demonstrated in NBCCS. Furthermore, the mosaicism is unique in that the patient carries one normal and two mutant alleles. Because these mutations are located in close proximity, reversion error is likely to be involved in this event rather than a spontaneous mutation. In addition, this study indicates that gene analysis of iPSC clones can contribute to the detection of mosaicism containing a minor population carrying a second mutation.
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Affiliation(s)
- Yu Ikemoto
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoshinaga Takayama
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Department of Molecular Genetics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Katsunori Fujii
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Mokuri Masuda
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
| | - Chise Kato
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
| | - Hiromi Hatsuse
- Department of Molecular Genetics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kazuko Fujitani
- Gene Analysis Center, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kazuaki Nagao
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Department of Molecular Genetics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kohzoh Kameyama
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Department of Molecular Genetics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Hajime Ikehara
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Masashi Toyoda
- Research Team for Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Miyashita
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Department of Molecular Genetics, Kitasato University School of Medicine, Sagamihara, Japan
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7
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von Lowtzow C, Hofmann A, Zhang R, Marsch F, Ebert AK, Rösch W, Stein R, Boemers TM, Hirsch K, Marcelis C, Feitz WFJ, Brusco A, Migone N, Di Grazia M, Moebus S, Nöthen MM, Reutter H, Ludwig M, Draaken M. CNV analysis in 169 patients with bladder exstrophy-epispadias complex. BMC MEDICAL GENETICS 2016; 17:35. [PMID: 27138190 PMCID: PMC4852408 DOI: 10.1186/s12881-016-0299-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 04/22/2016] [Indexed: 12/28/2022]
Abstract
Background The bladder exstrophy-epispadias complex (BEEC) represents the severe end of the congenital uro-rectal malformation spectrum. Initial studies have implicated rare copy number variations (CNVs), including recurrent duplications of chromosomal region 22q11.21, in BEEC etiology. Methods To detect further CNVs, array analysis was performed in 169 BEEC patients. Prior to inclusion, 22q11.21 duplications were excluded using multiplex ligation-dependent probe amplification. Results Following the application of stringent filter criteria, seven rare CNVs were identified: n = 4, not present in 1307 in-house controls; n = 3, frequency of <0.002 in controls. These CNVs ranged from 1 to 6.08 Mb in size. To identify smaller CNVs, relaxed filter criteria used in the detection of previously reported BEEC associated chromosomal regions were applied. This resulted in the identification of six additional rare CNVs: n = 4, not present in 1307 in-house controls; n = 2, frequency <0.0008 in controls. These CNVs ranged from 0.03–0.08 Mb in size. For 10 of these 13 CNVs, confirmation and segregation analyses were performed (5 of maternal origin; 5 of paternal origin). Interestingly, one female with classic bladder extrophy carried a 1.18 Mb duplication of 22q11.1, a chromosomal region that is associated with cat eye syndrome. Conclusions A number of rare CNVs were identified in BEEC patients, and these represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial BEEC phenotypes.
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Affiliation(s)
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Rong Zhang
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Florian Marsch
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Wolfgang Rösch
- Department of Pediatric Urology, St. Hedwig Hospital Barmherzige Brüder, Regensburg, Germany
| | - Raimund Stein
- Department of Pediatric and Adolescent Urology, University of Mannheim, Mannheim, Germany
| | - Thomas M Boemers
- Department of Pediatric Surgery and Pediatric Urology, Children's Hospital of Cologne, Cologne, Germany
| | - Karin Hirsch
- Department of Urology, Division of Pediatric Urology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Wouter F J Feitz
- Pediatric Urology Center, Department of Urology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Alfredo Brusco
- Department of Medical Sciences and Medical Genetics Unit, Città della Salute e della Scienza University Hospital, University of Torino, Torino, Italy
| | - Nicola Migone
- Department of Medical Sciences and Medical Genetics Unit, Città della Salute e della Scienza University Hospital, University of Torino, Torino, Italy
| | - Massimo Di Grazia
- Institute for Maternal and Child Health, IRCCS Burlo Garofalo, Trieste, Italy
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry, and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Sigmund-Freud-Str. 25, Bonn, D-53127, Germany.
| | - Markus Draaken
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, Bonn, Germany
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8
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Schumann M, Hofmann A, Krutzke SK, Hilger AC, Marsch F, Stienen D, Gembruch U, Ludwig M, Merz WM, Reutter H. Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs. J Neurodev Disord 2016; 8:11. [PMID: 27087860 PMCID: PMC4832534 DOI: 10.1186/s11689-016-9144-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/15/2016] [Indexed: 11/21/2022] Open
Abstract
Background The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations. Methods Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations. Identified putative disease-causing CNVs were confirmed using quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification. Results Based on their de novo occurrence and/or their established association with congenital brain malformations, we detected five disease-causing CNVs in four fetuses involving chromosomal regions 6p25.1-6p25.3 (FOXC1), 6q27, 16p12.3, Xp22.2-Xp22.32 (MID1), and Xp22.32-Xp22.33. Furthermore, we detected a probably disease-causing CNV involving chromosomal region 3p26.3 in one fetus, and in addition, we detected 12 CNVs in nine fetuses of unknown clinical significance. All CNVs except for two were absent in 1307 healthy in-house controls (frequency <0.0008). Each of the two CNVs present in in-house controls was present only once (frequency = 0.0008). Furthermore, our data suggests the involvement of CNTN6 and KLHL15 in the etiology of agenesis of the corpus callosum, the involvement of RASD1 and PTPRD in Dandy-Walker malformation, and the involvement of ERMARD in ventriculomegaly. Conclusions Our study suggests that CNVs play an important role in the etiology of isolated brain malformations.
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Affiliation(s)
- Madita Schumann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Florian Marsch
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Neonatology and Pediatric Intensive Care & Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
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Krutzke SK, Engels H, Hofmann A, Schumann MM, Cremer K, Zink AM, Hilger A, Ludwig M, Gembruch U, Reutter H, Merz WM. Array-based molecular karyotyping in fetal brain malformations: Identification of novel candidate genes and chromosomal regions. ACTA ACUST UNITED AC 2015; 106:16-26. [PMID: 26680650 DOI: 10.1002/bdra.23458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/17/2015] [Accepted: 09/07/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND For the majority of congenital brain malformations, the underlying cause remains unknown. Recent studies have implicated rare copy number variations (CNVs) in their etiology. METHODS Here, we used array-based molecular karyotyping to search for causative CNVs in 33 fetuses of terminated pregnancies with prenatally detected brain malformations and additional extracerebral anomalies. RESULTS In 11 fetuses, we identified 15 CNVs (0.08 Mb to 29.59 Mb), comprising four duplications and eleven deletions. All larger CNVs (> 5 Mb) had also been detected by prenatal conventional karyotyping. None of these CNVs was present in our 1307 healthy in-house controls (frequency < 0.0008). Among these CNVs, we prioritized six chromosomal regions (1q25.1, 5q35.1, 6q25.3-qter, 11p14.3, 15q11.2-q13.1, 18q21.1) due to their previous association with human brain malformations or owing to the presence of a single gene expressed in human brain. Prioritized genes within these regions were UBTD2, SKA1, SVIP, and, most convincingly, GPR52. However, re-sequencing of GPR52 in 100 samples from fetuses with brain malformations or patients with intellectual disability and brain malformations revealed no disease-causing mutation. CONCLUSION Our study suggests chromosomal regions 1q25.1, 5q35.1, 6q25.3-qter, 11p14.3, 15q11.2-q13.1, and 18q21.1 to be involved in human brain development. Within three of these regions, we suggest UBTD2, GPR52, and SKA1 as possible candidate genes. Because the overall detection rate of array-based molecular karyotyping was slightly higher (23%) than that of conventional prenatal karyotyping (20%), we suggest it's use for prenatal diagnostic testing in fetuses with nonisolated brain malformations.
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Affiliation(s)
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Alina Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn, Germany
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10
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Recker F, Zaniew M, Böckenhauer D, Miglietti N, Bökenkamp A, Moczulska A, Rogowska-Kalisz A, Laube G, Said-Conti V, Kasap-Demir B, Niemirska A, Litwin M, Siteń G, Chrzanowska KH, Krajewska-Walasek M, Sethi SK, Tasic V, Anglani F, Addis M, Wasilewska A, Szczepańska M, Pawlaczyk K, Sikora P, Ludwig M. Characterization of 28 novel patients expands the mutational and phenotypic spectrum of Lowe syndrome. Pediatr Nephrol 2015; 30:931-43. [PMID: 25480730 DOI: 10.1007/s00467-014-3013-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/07/2014] [Accepted: 11/11/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND The oculocerebrorenal syndrome of Lowe (OCRL) is a rare X-linked multi-systemic disorder, almost always characterized by the triad of congenital cataract, cognitive and behavioral impairment and a proximal tubulopathy. METHODS Twenty-eight novel patients with suspected Lowe syndrome were studied. RESULTS All patients carried OCRL gene defects with mutational hot spots at CpG dinucleotides. Mutations previously unknown in Lowe syndrome were observed in ten of the 28 patients, and carriership was identified in 30.4 % of the mothers investigated. Mapping the exact breakpoints of a complete OCRL gene deletion revealed involvement of several flanking repeat elements. We noted a similar pattern of documented clinically relevant symptoms, and even though the patient cohort comprised relatively young patients, 32 % of these patients already showed advanced chronic kidney disease. Thrombocytopenia was seen in several patients, and hyperosmia and/or hyperacusis were reported recurrently. A p.Asp523Asn mutation in a Polish patient, associated with the typical cerebrorenal spectrum but with late cataract (10 year), was also evident in two milder affected Italian brothers with ocular involvement of similar progression. CONCLUSIONS We have identified clinical features in 28 patients with suspected Lowe syndrome that had not been recognized in Lowe syndrome prior to our study. We also provide further evidence that OCRL mutations cause a phenotypic continuum with selective and/or time-dependent organ involvement. At least some of these mutants might exhibit a genotype-phenotype correlation.
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Affiliation(s)
- Florian Recker
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
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11
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Dworschak GC, Draaken M, Hilger AC, Schramm C, Bartels E, Schmiedeke E, Grasshoff-Derr S, Märzheuser S, Holland-Cunz S, Lacher M, Jenetzky E, Zwink N, Schmidt D, Nöthen MM, Ludwig M, Reutter H. Genome-wide mapping of copy number variations in patients with both anorectal malformations and central nervous system abnormalities. ACTA ACUST UNITED AC 2014; 103:235-42. [DOI: 10.1002/bdra.23321] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/06/2014] [Accepted: 08/29/2014] [Indexed: 12/31/2022]
Affiliation(s)
| | - Markus Draaken
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics, Life and Brain Center; University of Bonn; Bonn Germany
| | - Alina C. Hilger
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | | | - Enrika Bartels
- Institute of Human Genetics, University of Bonn; Bonn Germany
| | - Eberhard Schmiedeke
- Department of Pediatric Surgery and Urology; Center for Child and Adolescent Health; Hospital Bremen-Mitte Bremen Germany
| | | | - Stefanie Märzheuser
- Department of Pediatric Surgery; Campus Virchow Clinic, Charité University Hospital Berlin; Berlin Germany
| | - Stefan Holland-Cunz
- Department of Pediatric Surgery; Children's University Hospital Basel; Basel Switzerland
| | - Martin Lacher
- Center of Pediatric Surgery Hannover; Hannover Medical School; Hannover Germany
| | - Ekkehart Jenetzky
- Division of Clinical Epidemiology and Aging Research; German Cancer Research Center; Heidelberg Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy; Johannes-Gutenberg University; Mainz Germany
| | - Nadine Zwink
- Division of Clinical Epidemiology and Aging Research; German Cancer Research Center; Heidelberg Germany
| | - Dominik Schmidt
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Pediatric Surgery; Campus Virchow Clinic, Charité University Hospital Berlin; Berlin Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics, Life and Brain Center; University of Bonn; Bonn Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology; University of Bonn; Bonn Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Neonatology; Children's Hospital, University of Bonn; Bonn Germany
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12
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Dworschak GC, Draaken M, Marcelis C, de Blaauw I, Pfundt R, van Rooij IALM, Bartels E, Hilger A, Jenetzky E, Schmiedeke E, Grasshoff-Derr S, Schmidt D, Märzheuser S, Hosie S, Weih S, Holland-Cunz S, Palta M, Leonhardt J, Schäfer M, Kujath C, Rissmann A, Nöthen MM, Zwink N, Ludwig M, Reutter H. De novo 13q deletions in two patients with mild anorectal malformations as part of VATER/VACTERL and VATER/VACTERL-like association and analysis of EFNB2 in patients with anorectal malformations. Am J Med Genet A 2013; 161A:3035-41. [PMID: 24038947 DOI: 10.1002/ajmg.a.36153] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/25/2013] [Indexed: 12/13/2022]
Abstract
Anorectal malformations (ARMs) comprise a broad spectrum of conditions ranging from mild anal anomalies to complex cloacal malformations. In 40-50% of cases, ARM occurs within the context of defined genetic syndromes or complex multiple congenital anomalies, such as VATER/VACTERL (vertebral defects [V], ARMs [A], cardiac defects [C], tracheoesophageal fistula with or without esophageal atresia [TE], renal malformations [R], and limb defects [L]) association. Here, we report the identification of deletions at chromosome 13q using single nucleotide polymorphism-based array analysis in two patients with mild ARM as part of VATER/VACTERL and VATER/VACTERL-like associations. Both deletions overlap the previously defined critical region for ARM. Heterozygous Efnb2 murine knockout models presenting with mild ARM suggest EFNB2 as an excellent candidate gene in this region. Our patients showed a mild ARM phenotype, closely resembling that of the mouse. We performed a comprehensive mutation analysis of the EFNB2 gene in 331 patients with isolated ARM, or ARM as part of VATER/VACTERL or VATER/VACTERL-like associations. However, we did not identify any disease-causing mutations. Given the convincing argument for EFNB2 as a candidate gene for ARM, analyses of larger samples and screening of functionally relevant non-coding regions of EFNB2 are warranted. In conclusion, our report underlines the association of chromosome 13q deletions with ARM, suggesting that routine molecular diagnostic workup should include the search for these deletions. Despite the negative results of our mutation screening, we still consider EFNB2 an excellent candidate gene for contributing to the development of ARM in humans.
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DWORSCHAK GABRIELC, DRAAKEN MARKUS, HILGER ALINA, BORN MARK, REUTTER HEIKO, LUDWIG MICHAEL. An incompletely penetrant novel MAFB (p.Ser56Phe) variant in autosomal dominant multicentric carpotarsal osteolysis syndrome. Int J Mol Med 2013; 32:174-8. [DOI: 10.3892/ijmm.2013.1373] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/16/2013] [Indexed: 11/06/2022] Open
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14
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Hilger A, Schramm C, Pennimpede T, Wittler L, Dworschak GC, Bartels E, Engels H, Zink AM, Degenhardt F, Müller AM, Schmiedeke E, Grasshoff-Derr S, Märzheuser S, Hosie S, Holland-Cunz S, Wijers CHW, Marcelis CLM, van Rooij IALM, Hildebrandt F, Herrmann BG, Nöthen MM, Ludwig M, Reutter H, Draaken M. De novo microduplications at 1q41, 2q37.3, and 8q24.3 in patients with VATER/VACTERL association. Eur J Hum Genet 2013; 21:1377-82. [PMID: 23549274 DOI: 10.1038/ejhg.2013.58] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 11/09/2022] Open
Abstract
The acronym VATER/VACTERL association describes the combination of at least three of the following congenital anomalies: vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), renal malformations (R), and limb defects (L). We aimed to identify highly penetrant de novo copy number variations (CNVs) that contribute to VATER/VACTERL association. Array-based molecular karyotyping was performed in a cohort of 41 patients with VATER/VACTERL association and 6 patients with VATER/VACTERL-like phenotype including all of the patients' parents. Three de novo CNVs were identified involving chromosomal regions 1q41, 2q37.3, and 8q24.3 comprising one (SPATA17), two (CAPN10, GPR35), and three (EPPK1, PLEC, PARP10) genes, respectively. Pre-existing data from the literature prompted us to choose GPR35 and EPPK1 for mouse expression studies. Based on these studies, we prioritized GPR35 for sequencing analysis in an extended cohort of 192 patients with VATER/VACTERL association and VATER/VACTERL-like phenotype. Although no disease-causing mutation was identified, our mouse expression studies suggest GPR35 to be involved in the development of the VATER/VACTERL phenotype. Follow-up of GPR35 and the other genes comprising the identified duplications is warranted.
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Affiliation(s)
- Alina Hilger
- 1] Institute of Human Genetics, University of Bonn, Bonn, Germany [2] Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany [3] Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
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15
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Draaken M, Mughal SS, Pennimpede T, Wolter S, Wittler L, Ebert AK, Rösch W, Stein R, Bartels E, Schmidt D, Boemers TM, Schmiedeke E, Hoffmann P, Moebus S, Herrmann BG, Nöthen MM, Reutter H, Ludwig M. Isolated bladder exstrophy associated with a de novo 0.9 Mb microduplication on chromosome 19p13.12. ACTA ACUST UNITED AC 2013; 97:133-9. [PMID: 23359465 DOI: 10.1002/bdra.23112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/12/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND The exstrophy-epispadias complex (BEEC) is a urogenital birth defect of varying severity. The causes of the BEEC are likely to be heterogeneous, with individual environmental or genetic risk factors still being largely unknown. In this study, we aimed to identify de novo causative copy number variations (CNVs) that contribute to the BEEC. METHODS Array-based molecular karyotyping was performed to screen 110 individuals with BEEC. Promising CNVs were tested for de novo occurrence by investigating parental DNAs. Genes located in regions of rearrangements were prioritized through expression analysis in mice to be sequenced in the complete cohort, to identify high-penetrance mutations involving small sequence changes. RESULTS A de novo 0.9 Mb microduplication involving chromosomal region 19p13.12 was identified in a single patient. This region harbors 20 validated RefSeq genes, and in situ hybridization data showed specific expression of the Wiz gene in regions surrounding the cloaca and the rectum between GD 9.5 and 13.5. Sanger sequencing of the complete cohort did not reveal any pathogenic alterations affecting the coding region of WIZ. CONCLUSIONS The present study suggests chromosomal region 19p13.12 as possibly involved in the development of CBE, but further studies are needed to prove a causal relation. The spatiotemporal expression patterns determined for the genes encompassed suggest a role for Wiz in the development of the phenotype. Our mutation screening, however, could not confirm that WIZ mutations are a frequent cause of CBE, although rare mutations might be detectable in larger patient samples. 19p13.12, microduplication, bladder exstrophy-epispadias complex, array-based molecular karyotyping, in situ hybridization analysis, copy number variations, WIZ gene.
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Affiliation(s)
- Markus Draaken
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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16
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Ke YH, He JW, Fu WZ, Zhang ZL. Identification of two novel mutations in the OCRL1 gene in two Chinese families with Lowe syndrome. Nephrology (Carlton) 2012; 17:20-5. [PMID: 21854507 DOI: 10.1111/j.1440-1797.2011.01514.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM Lowe syndrome is a rare, multisystem, X-linked disorder characterized by anomalies affecting the eyes, the nervous system and the kidneys. The objective of this study was to identify and characterize the clinical manifestations of mutations of the causative gene in two Chinese families with Lowe syndrome. METHODS Lowe syndrome was diagnosed based on the clinical manifestations and laboratory and imaging findings. Altogether, 164 DNA samples, including samples from three affected subjects, five family members (from two families) and 156 healthy donors, were analyzed to identify the mutations in the OCRL1 gene. RESULTS In family 1, proband 1 had a novel nonsense mutation (c.880G>T) in exon 10 of the OCRL1. This mutation led to a premature termination of the OCRL1 protein (p.Glu294X). In family 2, a novel insertion mutation (c.2626dupA) in exon 24 of OCRL1 was found in proband 2 and his affected elder brother. This mutation likely results in the degradation of the OCRL1 protein (p.Met876AsnfsX8). Both probands' mothers were identified as carriers of the respective mutations. These mutations were not found in the unrelated controls. CONCLUSIONS Our study suggests that the novel nonsense mutation (c.880G>T) in exon 10 and the novel insertion mutation (c.2626dupA) in exon 24 of the OCRL1 gene cause Lowe syndrome in these two Chinese families.
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Affiliation(s)
- Yao-Hua Ke
- Metabolic Bone Disease and Genetic Research Unit, The Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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