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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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2
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Pfeiffer D, Chen B, Schlicht K, Ginsbach P, Abboud S, Bersano A, Bevan S, Brandt T, Caso V, Debette S, Erhart P, Freitag-Wolf S, Giacalone G, Grau AJ, Hayani E, Jern C, Jiménez-Conde J, Kloss M, Krawczak M, Lee JM, Lemmens R, Leys D, Lichy C, Maguire JM, Martin JJ, Metso AJ, Metso TM, Mitchell BD, Pezzini A, Rosand J, Rost NS, Stenman M, Tatlisumak T, Thijs V, Touzé E, Traenka C, Werner I, Woo D, Del Zotto E, Engelter ST, Kittner SJ, Cole JW, Grond-Ginsbach C, Lyrer PA, Lindgren A. Genetic Imbalance Is Associated With Functional Outcome After Ischemic Stroke. Stroke 2019; 50:298-304. [PMID: 30661490 DOI: 10.1161/strokeaha.118.021856] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background and Purpose- We sought to explore the effect of genetic imbalance on functional outcome after ischemic stroke (IS). Methods- Copy number variation was identified in high-density single-nucleotide polymorphism microarray data of IS patients from the CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) and SiGN (Stroke Genetics Network)/GISCOME (Genetics of Ischaemic Stroke Functional Outcome) networks. Genetic imbalance, defined as total number of protein-coding genes affected by copy number variations in an individual, was compared between patients with favorable (modified Rankin Scale score of 0-2) and unfavorable (modified Rankin Scale score of ≥3) outcome after 3 months. Subgroup analyses were confined to patients with imbalance affecting ohnologs-a class of dose-sensitive genes, or to those with imbalance not affecting ohnologs. The association of imbalance with outcome was analyzed by logistic regression analysis, adjusted for age, sex, stroke subtype, stroke severity, and ancestry. Results- The study sample comprised 816 CADISP patients (age 44.2±10.3 years) and 2498 SiGN/GISCOME patients (age 67.7±14.2 years). Outcome was unfavorable in 122 CADISP and 889 SiGN/GISCOME patients. Multivariate logistic regression analysis revealed that increased genetic imbalance was associated with less favorable outcome in both samples (CADISP: P=0.0007; odds ratio=0.89; 95% CI, 0.82-0.95 and SiGN/GISCOME: P=0.0036; odds ratio=0.94; 95% CI, 0.91-0.98). The association was independent of age, sex, stroke severity on admission, stroke subtype, and ancestry. On subgroup analysis, imbalance affecting ohnologs was associated with outcome (CADISP: odds ratio=0.88; 95% CI, 0.80-0.95 and SiGN/GISCOME: odds ratio=0.93; 95% CI, 0.89-0.98) whereas imbalance without ohnologs lacked such an association. Conclusions- Increased genetic imbalance was associated with poorer functional outcome after IS in both study populations. Subgroup analysis revealed that this association was driven by presence of ohnologs in the respective copy number variations, suggesting a causal role of the deleterious effects of genetic imbalance.
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Affiliation(s)
- Dorothea Pfeiffer
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Bowang Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China (B.C.)
| | - Kristina Schlicht
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Philip Ginsbach
- School of Informatics, University of Edinburgh, United Kingdom (P.G.)
| | - Sherine Abboud
- Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium (S.A.)
| | - Anna Bersano
- Cerebrovascular Unit IRCCS Foundation C. Besta Neurological Institute, Milan, Italy (A.B.)
| | - Steve Bevan
- School of Life Science, University of Lincoln, United Kingdom (S.B.)
| | - Tobias Brandt
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.).,Suva/Swiss National Accident Insurance Fund, Lucerne, Switzerland (T.B.)
| | - Valeria Caso
- Stroke Unit, Perugia University Hospital, Italy (V.C.)
| | - Stéphanie Debette
- Inserm, Bordeaux Population Health Research Center, UMR 1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, France (S.D.)
| | - Philipp Erhart
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Germany (P.E.)
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Giacomo Giacalone
- Department of Neurology, San Raffaele University Hospital, Milan, Italy (G.G.)
| | - Armin J Grau
- Department of Neurology, Klinikum Ludwigshafen, Germany (A.J.G.)
| | - Eyad Hayani
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Christina Jern
- The Sahlgrenska Academy, University of Gothenburg, Sweden (C.J.).,Sahlgrenska University Hospital, Sweden (C.J.)
| | | | - Manja Kloss
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, St Louis, MO (J.-M.L.)
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven, University of Leuven, Belgium (R.L.).,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium (R.L.).,Department of Neurology, University Hospitals Leuven, Belgium (R.L.)
| | - Didier Leys
- Department of Neurology, University of Lille, France (D.L.)
| | | | - Jane M Maguire
- Faculty of Health, University of Technology Sydney, Australia (J.M.M.).,Hunter Medical Research Institute, Priority Research Centre for Stroke and Traumatic Brain Injury, University of Newcastle, Australia (J.M.M.)
| | - Juan J Martin
- Department of Neurology, Sanatorio Allende, Cordoba, Argentina (J.J.M.)
| | - Antti J Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Tiina M Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore (B.D.M.).,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD (B.D.M.)
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Jonathan Rosand
- Center for Genomic Medicine (J.R.), Massachusetts General Hospital, Boston
| | - Natalia S Rost
- Department of Neurology (N.S.R.), Massachusetts General Hospital, Boston
| | - Martin Stenman
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
| | - Turgut Tatlisumak
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.).,Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Sweden (T.T.).,Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden (T.T.)
| | - Vincent Thijs
- Stroke Division, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia (V.T.).,Department of Neurology, Austin Health, Heidelberg, Victoria, Australia (V.T.)
| | - Emmanuel Touzé
- Paris Descartes University, INSERM UMR S894, Department of Neurology, Sainte-Anne Hospital, Paris, France (E.T.).,Normandie Université, Université Caen-Normandie, Inserm U1237, CHU Côte de Nacre, Service de Neurologie, Caen, France (E.T.)
| | - Christopher Traenka
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Inge Werner
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, OH (D.W.)
| | - Elisabetta Del Zotto
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Stefan T Engelter
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.).,Neurorehabilitation Unit, University of Basel, Switzerland (S.T.E.).,University Center for Medicine of Aging, Felix Platter Hospital, Basel, Switzerland (S.T.E.)
| | - Steven J Kittner
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - John W Cole
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - Caspar Grond-Ginsbach
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Philippe A Lyrer
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Arne Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
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Dutta UR, Rao SN, Pidugu VK, V.S. V, Bhattacherjee A, Bhowmik AD, Ramaswamy SK, Singh KG, Dalal A. Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing. Genomics 2019; 111:1108-1114. [DOI: 10.1016/j.ygeno.2018.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/21/2018] [Accepted: 07/06/2018] [Indexed: 01/20/2023]
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Ceroni JRM, Dutra RL, Honjo RS, Llerena JC, Acosta AX, Medeiros PFV, Galera MF, Zanardo ÉA, Piazzon FB, Dias AT, Novo-Filho GM, Montenegro MM, Madia FAR, Bertola DR, de Melo JB, Kulikowski LD, Kim CA. A Multicentric Brazilian Investigative Study of Copy Number Variations in Patients with Congenital Anomalies and Intellectual Disability. Sci Rep 2018; 8:13382. [PMID: 30190605 PMCID: PMC6127201 DOI: 10.1038/s41598-018-31754-2] [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: 03/09/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imbalances are the most common cause of congenital anomalies (CA) and intellectual disability (ID). The aims of this study were to identify copy number variations (CNVs) in 416 patients with CA and ID from 5 different genetics centers within 4 different states by using the Multiplex Ligation-dependent Probe Amplification (MLPA) technique and to apply the chromosomal microarray (CMA) methodology in selected cases. The samples were analyzed by MLPA kits P064, P036, P070 and P250. Positive results were found in 97/416 (23.3%) patients. CMA was applied in 14 selected cases. In 6/14 (42.85%) patients, CMA detected other copy number variations not detected by the MLPA studies. Although CMA is indispensable for genotype refinement, the technique is still unfeasible in some countries as a routine analysis due to economic and technical limitations. In these cases, clinical evaluation followed by karyotyping and MLPA analysis is a helpful and affordable solution for diagnostic purposes.
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Affiliation(s)
- J R M Ceroni
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.
| | - R L Dutra
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - R S Honjo
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
| | - J C Llerena
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - A X Acosta
- Universidade Federal da Bahia, Salvador, BA, Brazil
| | - P F V Medeiros
- Universidade Federal de Campina Grande, Campina Grande, PB, Brazil
| | - M F Galera
- Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - É A Zanardo
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F B Piazzon
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - A T Dias
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - G M Novo-Filho
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - M M Montenegro
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F A R Madia
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - D R Bertola
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.,Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil., São Paulo, SP, Brazil
| | - J B de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Faculdade de Medicina, Universidade de Coimbra, CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - L D Kulikowski
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - C A Kim
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
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Cheung SW, Bi W. Novel applications of array comparative genomic hybridization in molecular diagnostics. Expert Rev Mol Diagn 2018; 18:531-542. [PMID: 29848116 DOI: 10.1080/14737159.2018.1479253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.
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Affiliation(s)
- Sau W Cheung
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Weimin Bi
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Baylor Genetics , Houston , TX , USA
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Dong Z, Wang H, Chen H, Jiang H, Yuan J, Yang Z, Wang WJ, Xu F, Guo X, Cao Y, Zhu Z, Geng C, Cheung WC, Kwok YK, Yang H, Leung TY, Morton CC, Cheung SW, Choy KW. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics. Genet Med 2017; 20:697-707. [PMID: 29095815 PMCID: PMC5932280 DOI: 10.1038/gim.2017.170] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/14/2017] [Indexed: 02/04/2023] Open
Abstract
Purpose Recent studies demonstrate that whole-genome sequencing (WGS) enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in The 1000 Genomes Project without knowing affected bands. Methods The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparently BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold). Results Our approach detected four reciprocal balanced translocations and four inversions ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and PCR studies. One of DNAs has a subtle translocation that is not readily identified by chromosome analysis due to similar banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene. Conclusions Our study demonstrates the extension of utilizing low-coverage WGS for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,BGI-Shenzhen, Shenzhen, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huilin Wang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jianying Yuan
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhenjun Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenzhen Zhu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Chunyu Geng
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wan Chee Cheung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Harvard Medical School, Boston, Massachusetts, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Center, Manchester, UK.
| | - Sau Wai Cheung
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
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7
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Martin CL, Ledbetter DH. Molecular cytogenetic analysis of telomere rearrangements. CURRENT PROTOCOLS IN HUMAN GENETICS 2015; 84:8.11.1-8.11.15. [PMID: 25599669 PMCID: PMC4410364 DOI: 10.1002/0471142905.hg0811s84] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an introductory section describing advances in the discipline that have taken place since the original publication.
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Affiliation(s)
- Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
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8
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D'Amours G, Langlois M, Mathonnet G, Fetni R, Nizard S, Srour M, Tihy F, Phillips MS, Michaud JL, Lemyre E. SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay. BMC Med Genomics 2014; 7:70. [PMID: 25539807 PMCID: PMC4299176 DOI: 10.1186/s12920-014-0070-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy number variation (CNV) in 10-14% of them. High-resolution microarrays combining molecular karyotyping and single nucleotide polymorphism (SNP) genotyping were recently introduced to the market. In addition to identifying CNVs, these platforms detect loss of heterozygosity (LOH), which can indicate the presence of a homozygous mutation or uniparental disomy. Since these abnormalities can be associated with ID and/or MCA, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection has not been established. Methods We selected 21 children affected with ID, with or without congenital malformations, for whom standard genetic analyses failed to provide a diagnosis. We performed high-resolution SNP array analysis with four platforms (Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix Cytogenetics Whole-Genome 2.7 M array, Illumina HumanOmni1-Quad BeadChip, and Illumina HumanCytoSNP-12 DNA Analysis BeadChip) on whole-blood samples obtained from children and their parents to detect pathogenic CNVs and LOHs, and compared the results with those obtained on a moderate resolution array-based comparative genomic hybridization platform (NimbleGen CGX-12 Cytogenetics Array), already used in the clinical setting. Results We identified a total of four pathogenic CNVs in three patients, and all arrays successfully detected them. With the SNP arrays, we also identified a LOH containing a gene associated with a recessive disorder consistent with the patient’s phenotype (i.e., an informative LOH) in four children (including two siblings). A homozygous mutation within the informative LOH was found in three of these patients. Therefore, we were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. Conclusions This study shows the clinical usefulness of SNP arrays in children with ID, since they successfully detect pathogenic CNVs, identify informative LOHs that can lead to the diagnosis of a recessive disorder. It also highlights some challenges associated with the use of SNP arrays in a clinical laboratory. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0070-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guylaine D'Amours
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Mathieu Langlois
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | | | - Raouf Fetni
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Département de pathologie, CHU Sainte-Justine, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Nizard
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Myriam Srour
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada.
| | - Frédérique Tihy
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Michael S Phillips
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | - Jacques L Michaud
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Emmanuelle Lemyre
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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9
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Behjati F, Ghasemi Firouzabadi S, Sajedi F, Kahrizi K, Najafi M, Ebrahimizade Ghasemlou B, Shafeghati Y, Behnia F, Mohammadi Arya AR, Karimi H, Hadipour F, Hadipour Z, Jamali P, Kariminejad R, Darvish H, Bahman I, Bagherizadeh E, Najmabadi H, Vameghi R. Identification of Chromosome Abnormalities in Subtelomeric Regions Using Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 Iranian Patients With Idiopathic Mental Retardation. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 15:e8221. [PMID: 24693374 PMCID: PMC3950786 DOI: 10.5812/ircmj.8221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 06/14/2013] [Indexed: 11/16/2022]
Abstract
Background Mental retardation/Developmental delay (MR/DD) is present in 1 - 3% of the general
population (1, 2). MR is defined as a significant impairment of both cognitive (IQ <
70) and social adaptive functions, with onset before 18 years of age. Objectives The purpose was to determine the results of subtelomeric screening by the Multiplex
Ligation Dependent Probe Amplification (MLPA) Technique in 100 selected patients with
idiopathic mental retardation (IMR) in Iran. Materials and Methods A number of 100 patients with IMR, normal karyotypes and negative fragile-X and
metabolic tests were screened for subtelomeric abnormalities using MLPA technique. Results Nine of 100 patients showed subtelomeric abnormalities with at least one of the two
MLPA kits. Deletion in a single region was found in 3 patients, and in two different
subtelomeric regions in 1 patient. Duplication was only single and was present in 2
patients. Three patients were found to have both a deletion and duplication.MLPA testing
in the parental samples of 7 patients which was accessible showed that 4 patients were
de novo, 2 patients had inherited from a clinically normal mother, and one had inherited
from a clinically normal father. Screening with the two MLPA kits (SALSA P036 and SALSA
P070) proved abnormality in only five of the 9 patients. Conclusions So, the prevalence rate of abnormal subtelomeres using MLPA technique in patients with
idiopathic MR in our study was 5 - 9%, the higher limit referring to the positive
results of one of the two MLPA kits, and the lower limit representing the results of
positive double-checking with the two MLPA kits.
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Affiliation(s)
- Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Firoozeh Sajedi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Mostafa Najafi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Yousef Shafeghati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | - Fatemeh Behnia
- Department of Occupational Therapy, University of Social
Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | | | | | | | - Zahra Hadipour
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | | | | | - Hossein Darvish
- Department of Medical Genetics, Shahid Beheshti University
of Medical Sciences, Tehran, IR Iran
| | - Ideh Bahman
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Roshanak Vameghi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
- Corresponding author: Roshanak Vameghi, Pediatric
Neurorehabilitation Research Center, University of Social Welfare and Rehabilitation
Sciences, Tehran, IR Iran. Tel/Fax: +9821-22180099, E-mail:
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10
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Multiplex ligation-dependent probe amplification to subtelomeric rearrangements in idiopathic intellectual disability in Colombia. Pediatr Neurol 2014; 50:250-4. [PMID: 24412240 DOI: 10.1016/j.pediatrneurol.2013.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 10/06/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND A cause cannot be determined in 30% to 50% of patients with intellectual disability. Determining the etiology of intellectual disability is important and useful for pediatric neurologists, geneticists, pediatricians, and patients' families because it allows assessment of recurrence risk, appropriate genetic counseling, and focus on treatment options and prognosis. This study aims to determine the prevalence, origin, and characterization of subtelomeric rearrangements through the Multiplex Ligation-Dependent Probe Amplification method in pediatric patients with idiopathic intellectual disability. METHODS A cross-sectional descriptive study was undertaken with patients seen in consultation at the neuropediatrics or genetic service of the Central Military Hospital, the Mercy' Hospital, or the Genetics Institute National University of Colombia. Patients were diagnosed with idiopathic intellectual disability between December 2010 and September 2011 and underwent a complete medical history, physical examination, and assessment to rule out other etiologies of intellectual disability. Then we applied the genetic test of Multiplex Ligation-Dependent Probe Amplification to each patient's sample of peripheral blood to determine subtelomeric rearrangements. RESULTS We studied a group of 119 patients with idiopathic intellectual disability; Multiplex Ligation-Dependent Probe Amplification showed subtelomeric rearrangements in five. In the group with subtelomeric rearrangements, the most frequent results were de novo rearrangements (80%), deletion type (60%), moderate and severe intellectual disability (80%), minor phenotypic abnormalities (80%), and family history of neurological disorders (80%). No dependence relationship was observed between subtelomeric rearrangements and family history of neurological disorders, family history of intellectual disability, severity of intellectual disability, phenotypic abnormalities, and consanguinity. CONCLUSIONS This study determined a prevalence of subtelomeric rearrangements of 4.2% in a group of Colombian pediatric patients with idiopathic intellectual disability using the genetic test Multiplex Ligation-Dependent Probe Amplification.
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11
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Wei Y, Xu F, Li P. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation. J Genet Genomics 2013; 40:1-14. [DOI: 10.1016/j.jgg.2012.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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12
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Müller P, Ramel C, Franke K, Riedel S, Junge A, Reichenbach H. Autoimmunerkrankungen, mentale Retardierung und Dysmorphien. Monatsschr Kinderheilkd 2012. [DOI: 10.1007/s00112-012-2701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Abstract
AbstractA wide range of developmental disorders present with characteristic psychopathologies and behaviors, with diagnoses including, inter alia, cognitive disorders and learning disabilities, epilepsies, autism, and schizophrenia. Each, to varying extent, has a genetic component to etiology and is associated with cytogenetic abnormalities. Technological developments, particularly array-based comparative genome hybridization and single nucleotide polymorphism chips, has revealed a wide range of rare recurrent and de novo copy number variants (CNVs) to be associated with disorder and psychopathology. It is surprising that many apparently similar CNVs are identified across two or more disorders hitherto considered unrelated. This article describes the characteristics of CNVs and current technological restrictions that make accurately identifying small events difficult. It summarizes the latest discoveries for individual diagnostic categories and considers the implications for a shared neurobiology. It examines likely developments in the knowledge base as well as addressing the clinical implications going forward.
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14
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Grayton HM, Fernandes C, Rujescu D, Collier DA. Copy number variations in neurodevelopmental disorders. Prog Neurobiol 2012; 99:81-91. [DOI: 10.1016/j.pneurobio.2012.07.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/20/2011] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
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15
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Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization. Hum Genet 2012; 131:1895-910. [PMID: 22890305 DOI: 10.1007/s00439-012-1216-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/01/2012] [Indexed: 12/19/2022]
Abstract
Constitutional deletions of distal 9q34 encompassing the EHMT1 (euchromatic histone methyltransferase 1) gene, or loss-of-function point mutations in EHMT1, are associated with the 9q34.3 microdeletion syndrome, also known as Kleefstra syndrome [MIM#610253]. We now report further evidence for genomic instability of the subtelomeric 9q34.3 region as evidenced by copy number gains of this genomic interval that include duplications, triplications, derivative chromosomes and complex rearrangements. Comparisons between the observed shared clinical features and molecular analyses in 20 subjects suggest that increased dosage of EHMT1 may be responsible for the neurodevelopmental impairment, speech delay, and autism spectrum disorders revealing the dosage sensitivity of yet another chromatin remodeling protein in human disease. Five patients had 9q34 genomic abnormalities resulting in complex deletion-duplication or duplication-triplication rearrangements; such complex triplications were also observed in six other subtelomeric intervals. Based on the specific structure of these complex genomic rearrangements (CGR) a DNA replication mechanism is proposed confirming recent findings in Caenorhabditis elegans telomere healing. The end-replication challenges of subtelomeric genomic intervals may make them particularly prone to rearrangements generated by errors in DNA replication.
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16
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Ruiz Esparza-Garrido R, Velázquez-Wong AC, Araujo-Solís MA, Huicochea-Montiel JC, Velázquez-Flores MÁ, Salamanca-Gómez F, Arenas-Aranda DJ. Duplication of the Miller-Dieker Critical Region in a Patient with a Subtelomeric Unbalanced Translocation t(10;17)(p15.3;p13.3). Mol Syndromol 2012; 3:82-8. [PMID: 23326253 DOI: 10.1159/000339639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2012] [Indexed: 01/01/2023] Open
Abstract
Submicroscopic duplications in the Miller-Dieker critical region have been recently described as new genomic disorders. To date, only a few cases have been reported with overlapping 17p13.3 duplications in this region. Also, small deletions that affect chromosome region 10p14→pter are rarely described in the literature. In this study, we describe, to our knowledge for the first time, a 5-year-old female patient with intellectual disability who has an unbalanced 10;17 translocation inherited from the father. The girl was diagnosed by subtelomeric FISH and array-CGH, showing a 4.43-Mb heterozygous deletion on chromosome 10p that involved 14 genes and a 3.22-Mb single-copy gain on chromosome 17p, which includes the critical region of the Miller-Dieker syndrome and 61 genes. The patient's karyotype was established as 46,XX.arr 10p15.3p15.1(138,206-4,574,436)x1,17p13.3(87,009-3,312,600)x3. Because our patient exhibits a combination of 2 imbalances, she has phenotypic features of both chromosome abnormalities, which have been reported separately. Interestingly, the majority of patients who carry the deletion 10p have visual and auditory deficiencies that are attributed to loss of the GATA3 gene. However, our patient also presents severe hearing and visual problems even though GATA3 is present, suggesting the involvement of different genes that affect the development of the visual and auditory systems.
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Affiliation(s)
- R Ruiz Esparza-Garrido
- Unidad de Investigación Médica en Genética Humana (UIMGH), Hospital de Pediatría, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
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17
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Abstract
Mutations in more than 450 different genes have been associated with intellectual disability (ID) and related cognitive disorders (CDs), such as autism. It is to be expected that this number will increase three to fourfold in the next years due to the rapid implementation of innovative high-throughput sequencing technology in genetics labs. Numerous functional relationships have been identified between the products of individual ID genes, and common molecular and cellular pathways onto which these networks converge are beginning to emerge. Prominent examples are genes involved in synaptic plasticity, Ras and Rho GTPase signaling, and epigenetic genes that encode modifiers of the chromatin structure. It thus seems that there might be common pathological patterns in ID, despite its bewildering genetic heterogeneity. These common pathways provide attractive opportunities for knowledge-based therapeutic interventions.
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Affiliation(s)
- Hans van Bokhoven
- Molecular Neurogenetics Unit, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands.
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18
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Luo Y, Hermetz KE, Jackson JM, Mulle JG, Dodd A, Tsuchiya KD, Ballif BC, Shaffer LG, Cody JD, Ledbetter DH, Martin CL, Rudd MK. Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements. Hum Mol Genet 2011; 20:3769-78. [PMID: 21729882 DOI: 10.1093/hmg/ddr293] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.
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Affiliation(s)
- Yue Luo
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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19
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D'Amours G, Kibar Z, Mathonnet G, Fetni R, Tihy F, Désilets V, Nizard S, Michaud JL, Lemyre E. Whole-genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype. Clin Genet 2011; 81:128-41. [PMID: 21496010 DOI: 10.1111/j.1399-0004.2011.01687.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite a wide range of clinical tools, the etiology of mental retardation and multiple congenital malformations remains unknown for many patients. Array-based comparative genomic hybridization (aCGH) has proven to be a valuable tool in these cases, as its pangenomic coverage allows the identification of chromosomal aberrations that are undetectable by other genetic methods targeting specific genomic regions. Therefore, aCGH is increasingly used in clinical genetics, both in the postnatal and the prenatal settings. While the diagnostic yield in the postnatal population has been established at 10-12%, studies investigating fetuses have reported variable results. We used whole-genome aCGH to investigate fetuses presenting at least one major malformation detected on ultrasound, but for whom standard genetic analyses (including karyotype) failed to provide a diagnosis. We identified a clinically significant chromosomal aberration in 8.2% of tested fetuses (4/49), and a result of unclear clinical significance in 12.2% of tested fetuses (6/49). Our results document the value of whole-genome aCGH as a prenatal diagnostic tool and highlight the interpretation difficulties associated with copy number variations of unclear significance.
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Affiliation(s)
- G D'Amours
- Service de Génétique Médicale, CHU Sainte-Justine, Montréal, QC, Canada
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20
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Jezela-Stanek A, Ciara E, Juszczak M, Pelc M, Materna-Kiryluk A, Krajewska-Walasek M. Cryptic x; autosome translocation in a boy--delineation of the phenotype. Pediatr Neurol 2011; 44:221-4. [PMID: 21310340 DOI: 10.1016/j.pediatrneurol.2010.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 08/19/2010] [Accepted: 10/01/2010] [Indexed: 11/25/2022]
Abstract
Chromosome X-to-autosome translocations [t(X;A)] are rare rearrangements with an estimated occurrence of 1 to 3 per 10,000 live births. Occurrences of Xq duplications have been observed in male and female subjects in whom the X chromosome segment escapes inactivation and results in functional disomy. We report a case of X;6 translocation in a 7-year-old boy with severe mental retardation, hypotonia, and recurrent respiratory tract infections. High-resolution chromosome analyses (fluorescence in situ hybridization, multiplex ligation probe-dependent amplification, and whole-genome array) revealed a terminal duplication of chromosome X at q28-qter (approximately 3.246 Mb in size) involving gene MECP2 and a terminal deletion (approximately 1.89 Mb) with the breakpoint at 6q27. This is the second report of a boy with a cryptic unbalanced Xq-autosome translocation. This case increases our understanding of mental disability caused by terminal Xq duplication.
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Affiliation(s)
- Aleksandra Jezela-Stanek
- Department of Medical Genetics, The Children's Memorial Health Institute, Aleja Dzieci Polskich 20, 04-736 Warsaw, Poland.
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Abstract
Intellectual disability (ID) is the leading socio-economic problem of health care, but compared to autism and schizophrenia, it has received very little public attention. Important risk factors for ID are malnutrition, cultural deprivation, poor health care, and parental consanguinity. In the Western world, fetal alcohol exposure is the most common preventable cause. Most severe forms of ID have genetic causes. Cytogenetically detectable and submicroscopic chromosomal rearrangements account for approximately 25% of all cases. X-linked gene defects are responsible in 10-12% of males with ID; to date, 91 of these defects have been identified. In contrast, autosomal gene defects have been largely disregarded, but due to coordinated efforts and the advent of next-generation DNA sequencing, this is about to change. As shown for Fra(X) syndrome, this renewed focus on autosomal gene defects will pave the way for molecular diagnosis and prevention, shed more light on the pathogenesis of ID, and reveal new opportunities for therapy.
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22
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Kaufman L, Ayub M, Vincent JB. The genetic basis of non-syndromic intellectual disability: a review. J Neurodev Disord 2010; 2:182-209. [PMID: 21124998 PMCID: PMC2974911 DOI: 10.1007/s11689-010-9055-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/25/2010] [Indexed: 11/06/2022] Open
Abstract
Intellectual disability (ID), also referred to as mental retardation (MR), is frequently the result of genetic mutation. Where ID is present together with additional clinical symptoms or physical anomalies, there is often sufficient information available for the diagnosing physician to identify a known syndrome, which may then educe the identification of the causative defect. However, where co-morbid features are absent, narrowing down a specific gene can only be done by ‘brute force’ using the latest molecular genetic techniques. Here we attempt to provide a systematic review of genetic causes of cases of ID where no other symptoms or co-morbid features are present, or non-syndromic ID. We attempt to summarize commonalities between the genes and the molecular pathways of their encoded proteins. Since ID is a common feature of autism, and conversely autistic features are frequently present in individuals with ID, we also look at possible overlaps in genetic etiology with non-syndromic ID.
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Holoprosencephaly: An update on cytogenetic abnormalities. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2010; 154C:86-92. [DOI: 10.1002/ajmg.c.30250] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Affiliation(s)
- Natasha Shur
- Rhode Island Hospital and Alpert Medical School, Brown University, Providene, RI 02906, USA.
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25
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Nine patients with a microdeletion 15q11.2 between breakpoints 1 and 2 of the Prader-Willi critical region, possibly associated with behavioural disturbances. Eur J Med Genet 2009; 52:108-15. [PMID: 19328872 DOI: 10.1016/j.ejmg.2009.03.010] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 03/18/2009] [Indexed: 11/21/2022]
Abstract
Behavioural differences have been described in patients with type I deletions (between breakpoints 1 and 3 (BP1-BP3)) or type II deletions (between breakpoints 2 and 3) of the 15q11.2 Prader-Willi/Angelman region. The larger type I deletions appear to coincide with more severe behavioural problems (autism, ADHD, obsessive-compulsive disorder). The non-imprinted chromosomal segment between breakpoints 1 and 2 involves four highly conserved genes, TUBGCP5, NIPA1, NIPA2, and CYFIP1; the latter three are widely expressed in the central nervous system, while TUBGCP5 is expressed in the subthalamic nuclei. These genes might explain the more severe behavioural problems seen in type I deletions. We describe nine cases with a microdeletion at 15q11.2 between BP1-BP2, thus having a haploinsufficiency for TUBGCP5, NIPA1, NIPA2, and CYFIP1 without Prader-Willi/Angelman syndrome. The clinical significance of a pure BP1-BP2 microdeletion has been debated, however, our patients shared several clinical features, including delayed motor and speech development, dysmorphisms and behavioural problems (ADHD, autism, obsessive-compulsive behaviour). Although the deletion often appeared to be inherited from a normal or mildly affected parent, it was de novo in two cases and we did not find it in 350 healthy unrelated controls. Our results suggest a pathogenic nature for the BP1-BP2 microdeletion and, although there obviously is an incomplete penetrance, they support the existence of a novel microdeletion syndrome in 15q11.2.
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26
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Yatsenko SA, Brundage EK, Roney EK, Cheung SW, Chinault AC, Lupski JR. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet 2009; 18:1924-36. [PMID: 19293338 DOI: 10.1093/hmg/ddp114] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We characterized at the molecular level the genomic rearrangements in 28 unrelated patients with 9q34.3 subtelomeric deletions. Four distinct categories were delineated: terminal deletions, interstitial deletions, derivative chromosomes and complex rearrangements; each results in haploinsufficiency of the EHMT1 gene and a characteristic phenotype. Interestingly, 25% of our patients had de novo interstitial deletions, 25% were found with derivative chromosomes and complex rearrangements and only 50% were bona fide terminal deletions. In contrast to genomic disorders that are often associated with recurrent rearrangements, breakpoints involving the 9q34.3 subtelomere region are highly variable. Molecular studies identified three regions of breakpoint grouping. Interspersed repetitive elements such as Alu, LINE, long-terminal repeats and simple tandem repeats are frequently observed at the breakpoints. Such repetitive elements may play an important role by providing substrates with a specific DNA secondary structure that stabilizes broken chromosomes or assist in either DNA double-strand break repair or repair of single double-strand DNA ends generated by collapsed forks. Sequence analyses of the breakpoint junctions suggest that subtelomeric deletions can be stabilized by both homologous and nonhomologous recombination mechanisms, through a telomere-capture event, by de novo telomere synthesis, or multistep breakage-fusion-bridge cycles.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Auber B, Bruemmer V, Zoll B, Burfeind P, Boehm D, Liehr T, Brockmann K, Wilichowski E, Argyriou L, Bartels I. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation. Mol Cytogenet 2009; 2:10. [PMID: 19284615 PMCID: PMC2660352 DOI: 10.1186/1755-8166-2-10] [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: 01/19/2009] [Accepted: 03/12/2009] [Indexed: 01/04/2023] Open
Abstract
Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.
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Affiliation(s)
- Bernd Auber
- Institute of Human Genetics, Georg August University, Göttingen, Germany.
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D'Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum Genet 2009; 125:551-63. [PMID: 19271239 DOI: 10.1007/s00439-009-0650-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 02/25/2009] [Indexed: 12/23/2022]
Abstract
The mechanisms involved in the formation of subtelomeric rearrangements are now beginning to be elucidated. Breakpoint sequencing analysis of 1p36 rearrangements has made important contributions to this line of inquiry. Despite the unique architecture of segmental duplications inherent to human subtelomeres, no common mechanism has been identified thus far and different nonexclusive recombination-repair mechanisms seem to predominate. In order to gain further insights into the mechanisms of chromosome breakage, repair, and stabilization mediating subtelomeric rearrangements in humans, we investigated the constitutional rearrangements of 1p36. Cloning of the breakpoint junctions in a complex rearrangement and three non-reciprocal translocations revealed similarities at the junctions, such as microhomology of up to three nucleotides, along with no significant sequence identity in close proximity to the breakpoint regions. All the breakpoints appeared to be unique and their occurrence was limited to non-repetitive, unique DNA sequences. Several recombination- or cleavage-associated motifs that may promote non-homologous recombination were observed in close proximity to the junctions. We conclude that NHEJ is likely the mechanism of DNA repair that generates these rearrangements. Additionally, two apparently pure terminal deletions were also investigated, and the refinement of the breakpoint regions identified two distinct genomic intervals ~25-kb apart, each containing a series of 1p36 specific segmental duplications with 90-98% identity. Segmental duplications can serve as substrates for ectopic homologous recombination or stimulate genomic rearrangements.
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Affiliation(s)
- Carla S D'Angelo
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, SP CEP, Brazil.
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Stumm M, Tönnies H. Fluorescence in situ hybridization techniques in medical diagnostics. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2008; 2:1381-1390. [PMID: 23496784 DOI: 10.1517/17530050802558899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Fluorescence in situ hybridization (FISH) has become a well-established method in medical diagnostics. FISH methods complement conventional cytogenetic banding techniques and offer extra clinical applications. FISH is based on the binding of complementary, single-stranded fluorescence-labeled nucleic acid sequences to the fixed and denatured target DNA of metaphases, interphase nuclei or isolated DNA sequences (BACs, oligonucleotides). OBJECTIVE The intent of this article is to review the development of molecular cytogenetic techniques available at present and to summarize the most efficient and appropriate use of these techniques in medical diagnostics. The technical aspects and most important applications of FISH assays are described. CONCLUSION FISH is bridging the gap between conventional cytogenetic banding analysis and molecular genetic DNA studies. The use of FISH techniques enhances the correct interpretation of numerical and structural chromosome aberrations.
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Affiliation(s)
- Markus Stumm
- Centre for Prenatal Diagnosis, Kudamm 199, Berlin 10719, Germany
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Friedman JM. High-resolution array genomic hybridization in prenatal diagnosis. Prenat Diagn 2008; 29:20-8. [DOI: 10.1002/pd.2129] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Piccione M, Antona V, Piro E, Cavani S, Malacarne M, Pierluigi M, Corsello G. 10qter deletion: A new case. Am J Med Genet A 2008; 146A:2435-8. [DOI: 10.1002/ajmg.a.32467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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