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Array-comparative Genomic Hybridization Results in Clinically Affected Cases with Apparently Balanced Chromosomal Rearrangements. Balkan J Med Genet 2021; 23:25-34. [PMID: 33816069 PMCID: PMC8009573 DOI: 10.2478/bjmg-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carriers of apparently balanced chromosomal rearrangements (ABCRs) have a 2-3-fold higher risk of carrying an abnormal phenotype, when compared to the average population. Apparently balanced chromosomal rearrangements can be imbalanced at the submicroscopic level, and changes in the gene structure, formation of a new chimeric gene, gain or loss of function of the genes and altered imprinting pattern may also affect the phenotype. Chromosomal microarray (CMA) is an efficient tool to detect submicroscopic imbalances at the breakpoints as well as in the whole genome. We aimed to determine the effectiveness of array-comparative genomic hybridization (aCGH) application in phenotypically affected cases with ABCRs at a single center from Turkey. Thirty-four affected cases (13 prenatal, 21 postnatal) carrying ABCRs were investigated with CMA. In postnatal series, ABCRs were familial in 7 and de novo in 14 cases. Seven de novo cases were imbalanced (in postnatal series 33.3% and in de novo cases 50.0%). Out of 13 prenatal cases, five were familial and eight were de novo in origin and two de novo cases were imbalanced (in 15.4% prenatal series and in 25.0% de novo cases). No cryptic imbalance was observed in familial cases. The anomaly rates with array studies ranged between 14.3-25.0% in familial and between 20.0-57.5% in de novo cases of postnatal series in the literature. Studies focused on prenatal ABCR cases with abnormal ultrasound findings are limited and no submicroscopic imbalance was reported in the cohorts. When de novo postnatal or prenatal results were combined, the percentage of abnormalities detected by CMA was 40.9%. Taking this contribution into consideration, all ABCRs should be investigated by CMA even if the fetal ultrasound findings are normal.
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Miura M, Ishiyama A, Nakagawa E, Sasaki M, Kurosawa K, Inoue K, Goto YI. 13q13.3 microdeletion associated with apparently balanced translocation of 46,XX,t(7;13) suggests NBEA involvement. Brain Dev 2020; 42:581-586. [PMID: 32507666 DOI: 10.1016/j.braindev.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Deletion of 13q13.3 is an extremely rare event. CASE We report on a 25-month-old girl with neurodevelopmental disorder and intellectual disability. She had dysmorphic facies characterized by synophrys, long and narrow palpebral fissures; and a large, round face with small organs such as the eyes and mouth positioned near the center. She was hypotonic and had autism-like behaviors. Blood tests and brain MRI revealed no specific findings. However, G-banding chromosome analysis showed an apparently balanced translocation: 46,XX,t(7,13)(q11.23;q12.3). Both parents had normal karyotypes. Furthermore, her abnormal phenotype and chromosomal breakpoint lesion were suspected to be associated. Hence, we conducted array comparative genomic hybridization, which revealed a 3.2 Mb novel pathological microdeletion at 13q13.3 involving 17 genes including neurobeachin (NBEA), a neurodevelopment disorder gene. Furthermore, fluorescence in situ hybridization using probes adjacent to the microdeletion suggested a concomitant occurrence of the deletion and translocation as the structural basis of this rare genomic variant. CONCLUSION NBEA may have roles in her neurodevelopmental phenotypes, whereas other genes within the 13q13.3 microdeletion may contribute to her dysmorphic features.
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Affiliation(s)
- Masaki Miura
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.
| | - Eiji Nakagawa
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, NCNP, Tokyo, Japan
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Lovrecic L, Remec ZI, Volk M, Rudolf G, Writzl K, Peterlin B. Clinical utility of array comparative genomic hybridisation in prenatal setting. BMC MEDICAL GENETICS 2016; 17:81. [PMID: 27846804 PMCID: PMC5111187 DOI: 10.1186/s12881-016-0345-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 11/06/2016] [Indexed: 12/16/2022]
Abstract
Background The objective of reported study was to evaluate the clinical utility of prenatal microarray testing for submicroscopic genomic imbalances in routine prenatal settings and to stratify the findings according to the type of fetal ultrasound anomaly. Methods From July 2012 to October 2015 chromosomal microarray testing was performed in 218 fetuses with varying indications for invasive prenatal diagnosis: abnormal karyotype, ultrasound anomalies, pathogenic variant in previous pregnancy or carriership in a parent. Results The detection rate in the group of fetuses with ultrasound anomalies was 10,0% for pathogenic copy number variants (CNVs), five of them being larger than 8 Mb and expected to be seen on prenatal karyotype. If only those pathogenic CNVs below the classical karyotype resolution are considered, chromosomal microarray testing provided an additional 7,7% diagnostic yield in here reported series. When stratified according to the ultrasound anomalies, the highest percentage of pathogenic CNVs were detected in the group of fetuses with multiple congenital anomalies (16,7%) and lowest in the group of isolated in utero growth restriction (6,3%). In the group of cases with isolated increased nuchal translucency we identified a small interstitial deletion of 16p24.1 involving FOXF1 gene. Prenatal aCGH also provided important insights into cases with seemingly balanced chromosomal rearrangements found on prenatal karyotype, where additional pathogenic CNV were discovered. Conclusion Prenatal chromosomal microarray testing significantly increases the diagnostic yield when compared with conventional karyotyping. The highest added value is shown in prenatal diagnostics in fetuses with abnormal ultrasound results. Variants of unknown significance and risk factor CNVs present important challenges and should be discussed with parents in advance, therefore pretest counseling prior to prenatal testing is very important.
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Affiliation(s)
- Luca Lovrecic
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia.
| | - Ziga Iztok Remec
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia
| | - Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia
| | - Gorazd Rudolf
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Slajmerjeva 3, SI-1000, Ljubljana, Slovenia
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Ordulu Z, Kammin T, Brand H, Pillalamarri V, Redin CE, Collins RL, Blumenthal I, Hanscom C, Pereira S, Bradley I, Crandall BF, Gerrol P, Hayden MA, Hussain N, Kanengisser-Pines B, Kantarci S, Levy B, Macera MJ, Quintero-Rivera F, Spiegel E, Stevens B, Ulm JE, Warburton D, Wilkins-Haug LE, Yachelevich N, Gusella JF, Talkowski ME, Morton CC. Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis. Am J Hum Genet 2016; 99:1015-1033. [PMID: 27745839 PMCID: PMC5097935 DOI: 10.1016/j.ajhg.2016.08.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 08/26/2016] [Indexed: 12/27/2022] Open
Abstract
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care. Herein, we present and evaluate sequencing results of balanced chromosomal rearrangements in ten prenatal subjects with respect to the location of regulatory chromatin domains (topologically associated domains [TADs]). The genomic material from all subjects was interpreted to be "normal" by microarray analyses, and their rearrangements would not have been detected by cell-free DNA (cfDNA) screening. The findings of our systematic approach correlate with phenotypes of both pregnancies with untoward outcomes (5/10) and with healthy newborns (3/10). Two pregnancies, one with a chromosomal aberration predicted to be of unknown clinical significance and another one predicted to be likely benign, were terminated prior to phenotype-genotype correlation (2/10). We demonstrate that the clinical interpretation of structural rearrangements should not be limited to interruption, deletion, or duplication of specific genes and should also incorporate regulatory domains of the human genome with critical ramifications for the control of gene expression. As detailed in this study, our molecular approach to both detecting and interpreting the breakpoints of structural rearrangements yields unparalleled information in comparison to other commonly used first-tier diagnostic methods, such as non-invasive cfDNA screening and microarray analysis, to provide improved genetic counseling for phenotypic outcome in the prenatal setting.
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Affiliation(s)
- Zehra Ordulu
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Harrison Brand
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Claire E Redin
- Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA
| | - Ryan L Collins
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shahrin Pereira
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - India Bradley
- Department of Psychiatry, Prenatal Diagnosis Center, David Geffen School of Medicine, University of California, Los Angeles, Medical Plaza, Los Angeles, CA 90095, USA
| | - Barbara F Crandall
- Department of Psychiatry, Prenatal Diagnosis Center, David Geffen School of Medicine, University of California, Los Angeles, Medical Plaza, Los Angeles, CA 90095, USA
| | - Pamela Gerrol
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Mark A Hayden
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Naveed Hussain
- Department of Pediatrics, Connecticut Children's Medical Center, University of Connecticut, Farmington, CT 06030, USA
| | | | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Michael J Macera
- New York Presbyterian Hospital, Columbia University Medical Center, New York, NY 10032, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erica Spiegel
- Department of Maternal Fetal Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Blair Stevens
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Janet E Ulm
- Regional Obstetrical Consultants, Chattanooga, TN 37403, USA
| | - Dorothy Warburton
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Louise E Wilkins-Haug
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Yachelevich
- Department of Pediatrics, Clinical Genetics Services, New York University School of Medicine, New York, NY 10003, USA
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Genetics, Harvard Medical School, Boson, MA 02115, USA
| | - Michael E Talkowski
- Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Departments of Psychiatry and Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Evolution and Genomic Science, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Center, Manchester 03101, UK.
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Ben Khelifa H, Soyah N, Labalme A, Guilbert H, Sanlaville D, Saad A, Mougou-Zerelli S. Genomic Microarray in Intellectual Disability: The Usefulness of Existing Systems in the Interpretation of Copy Number Variation. J Pediatr Genet 2016; 6:84-91. [PMID: 28496995 DOI: 10.1055/s-0036-1588027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
Whole genome array technology is an essential tool for the detection of a large number of copy number variants (CNVs) in patients with ID and/or multiple congenital anomalies. However, the clinical significance of some microimbalances is not known. In this article, we succeeded to detect seven new variations of unknown significance (dup12p13.33, dup2p16.3, dupXq13.2, del12q24.33, dup16p13.11, trip4q22.1, and dup9p21.3), one CNV classified as known pathogenic syndrome (del22q13.31-q33), and one CNV classified as potentially pathogenic (del11q24.3). We emphasize the role of comparative genomic hybridization arrays in the investigation of intellectual disability and evaluate the usefulness of existing systems in the interpretation of CNVs.
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Affiliation(s)
- Hela Ben Khelifa
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Najla Soyah
- Department of Pediatric, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Audrey Labalme
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Helene Guilbert
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Service de Cytogénétique Constitutionnelle, Lyon, France
| | - Ali Saad
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Soumaya Mougou-Zerelli
- Department of Cytogenetic and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
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Rosenfeld JA, Patel A. Chromosomal Microarrays: Understanding Genetics of Neurodevelopmental Disorders and Congenital Anomalies. J Pediatr Genet 2016; 6:42-50. [PMID: 28180026 DOI: 10.1055/s-0036-1584306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes. Advances in CMA technology allow CNV identification at increasingly finer scales, improving detection of pathogenic changes, although these sometimes are difficult to distinguish from normal population variation. This paper confronts some of the challenges uncovered by CMA testing while reviewing advances in genetics and the clinical use of this test that has replaced standard karyotyping in most genetic evaluations.
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Affiliation(s)
- Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
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Poot M, Haaf T. Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. Mol Syndromol 2015; 6:110-34. [PMID: 26732513 DOI: 10.1159/000438812] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 01/08/2023] Open
Abstract
Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Rigola MA, Baena N, Català V, Lozano I, Gabau E, Guitart M, Fuster C. A 11.7-Mb Paracentric Inversion in Chromosome 1q Detected in Prenatal Diagnosis Associated with Familial Intellectual Disability. Cytogenet Genome Res 2015; 146:109-114. [PMID: 26280689 DOI: 10.1159/000437127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2015] [Indexed: 11/19/2022] Open
Abstract
Most apparent balanced chromosomal inversions are usually clinically asymptomatic; however, infertility, miscarriages, and mental retardation have been reported in inversion carriers. We present a small family with a paracentric inversion 1q42.13q43 detected in routine prenatal diagnosis. Molecular cytogenetic methods defined the size of the inversion as 11.7 Mb and excluded other unbalanced chromosomal alterations in the patients. Our findings suggest that intellectual disability is caused by dysfunction, disruption, or position effects of genes located at or near the breakpoints involved in this inversion.
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Affiliation(s)
- Maria A Rigola
- Unitat de Biologia Cel∙lular i Genètica Mèdica, Departament de Biologia Cel∙lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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9
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Tabet AC, Verloes A, Pilorge M, Delaby E, Delorme R, Nygren G, Devillard F, Gérard M, Passemard S, Héron D, Siffroi JP, Jacquette A, Delahaye A, Perrin L, Dupont C, Aboura A, Bitoun P, Coleman M, Leboyer M, Gillberg C, Benzacken B, Betancur C. Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder. Mol Autism 2015; 6:19. [PMID: 25844147 PMCID: PMC4384291 DOI: 10.1186/s13229-015-0015-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. Methods Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. Results We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. Conclusions These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings.
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Affiliation(s)
- Anne-Claude Tabet
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Alain Verloes
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Marion Pilorge
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Elsa Delaby
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Richard Delorme
- Department of Child and Adolescent Psychiatry, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Françoise Devillard
- Département de Génétique et Procréation, CHU de Grenoble, Hôpital Couple-Enfant, avenue du Maquis du Grésivaudan, 38043 Grenoble, France
| | - Marion Gérard
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Sandrine Passemard
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Neurology Unit, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Delphine Héron
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Jean-Pierre Siffroi
- Service de Génétique et d'Embryologie Médicales, AP-HP, Trousseau Hospital, 26 avenue du Docteur Arnold Netter, 75012 Paris, France
| | - Aurelia Jacquette
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Andrée Delahaye
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Laurence Perrin
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Céline Dupont
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Azzedine Aboura
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Pierre Bitoun
- Medical Genetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France
| | - Mary Coleman
- Foundation for Autism Research, 3081 Quail Hollow, Sarasota, FL 34235 USA
| | - Marion Leboyer
- Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France ; Department of Psychiatry, AP-HP, Henri Mondor-Albert Chenevier Hospital, 40 rue de Mesly, 94000 Créteil, France ; INSERM U955, Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, 8 rue du Général Sarrail, 94000 Créteil, France ; Faculty of Medicine, University Paris-Est Créteil, 8 rue du Général Sarrail, 94000 Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Brigitte Benzacken
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Catalina Betancur
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
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10
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Al-Qattan SM, Wakil SM, Anazi S, Alazami AM, Patel N, Shaheen R, Shamseldin HE, Hagos ST, AlDossari HM, Salih MA, El Khashab HY, Kentab AY, AlNasser MN, Bashiri FA, Kaya N, Hashem MO, Alkuraya FS. The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population. Genet Med 2014; 17:719-25. [PMID: 25503496 DOI: 10.1038/gim.2014.184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Molecular karyotyping has rapidly become the test of choice in patients with neurocognitive phenotypes, but studies of its clinical utility have largely been limited to outbred populations. In consanguineous populations, single-gene recessive causes of neurocognitive phenotypes are expected to account for a relatively high percentage of cases, thus diminishing the yield of molecular karyotyping. The aim of this study was to test the clinical yield of molecular karyotyping in the highly consanguineous population of Saudi Arabia. METHODS We have reviewed the data of 584 patients with neurocognitive phenotypes (mainly referred from pediatric neurology clinics), all evaluated by a single clinical geneticist. RESULTS At least 21% of tested cases had chromosomal aberrations that are likely disease-causing. These changes include both known and novel deletion syndromes. The higher yield of molecular karyotyping in this study as compared with the commonly cited 11% can be explained by our ability to efficiently identify single-gene disorders, thus enriching the samples that underwent molecular karyotyping for de novo chromosomal aberrations. We show that we were able to identify a causal mutation in 37% of cases on a clinical basis with the help of autozygome analysis, thus bypassing the need for molecular karyotyping. CONCLUSION Our study confirms the clinical utility of molecular karyotyping even in highly consanguineous populations.
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Affiliation(s)
- Sarah M Al-Qattan
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haya M AlDossari
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, Children Hospital, Ain Shams University, Cairo, Egypt
| | - Amal Y Kentab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed N AlNasser
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad A Bashiri
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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11
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Castiglione A, Guaran V, Astolfi L, Orioli E, Zeri G, Gemmati D, Bovo R, Montaldi A, Alghisi A, Martini A. Karyotype-phenotype correlation in partial trisomies of the short arm of chromosome 6: a family case report and review of the literature. Cytogenet Genome Res 2013; 141:243-59. [PMID: 23942271 DOI: 10.1159/000353846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
The first child (proband) of nonconsanguineous Caucasian parents underwent genetic investigation because she was affected with congenital choanal atresia, heart defects and kidney hyposplasia with mild transient renal insufficiency. The direct DNA sequencing after PCR of the CHD7 gene, which is thought to be responsible for approximately 60-70% of the cases of CHARGE syndrome/association, found no mutations. The cytogenetic analysis (standard GTG banding karyotype) revealed the presence of extrachromosomal material on 10q. The chromosome analysis was completed with array CGH (30 kb resolution), MLPA and FISH, which allowed the identification of three 6p regions (6p.25.3p23 × 3): 2 of these regions are normally located on chromosome 6, and the third region is translocated to the long arm of chromosome 10. The same chromosomal rearrangement was subsequently found in the father, who was affected with congenital ptosis and progressive hearing loss, and in the proband's sister, the second child, who presented at birth with choanal atresia and congenital heart defects. The mutated karyotypes, which were directly inherited, are thought to be responsible for a variable phenotype, including craniofacial dysmorphisms, choanal atresia, congenital ptosis, sensorineural hearing loss, heart defects, developmental delay, and renal dysfunction. Nevertheless, to achieve a complete audiological assessment of the father, he underwent further investigation that revealed an increased level of the coagulation factor XIII (300% increased activity), fluctuating levels of fibrin D-dimer degradation products (from 296 to 1,587 ng/ml) and a homoplasmic mitochondrial DNA mutation: T961G in the MTRNR1 (12S rRNA) gene. He was made a candidate for cochlear implantation. Preoperative high-resolution computed tomography and magnetic resonance imaging of the temporal bone revealed the presence of an Arnold-Chiari malformation type I. To the best of our knowledge, this study is the second report on partial 6p trisomy that involves the 10q terminal region. Furthermore, we report the first case of documented Arnold-Chiari malformation type I and increased factor XIII activity associated with 6p trisomy. We present a comprehensive report of the familial cases and an exhaustive literature review.
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Affiliation(s)
- A Castiglione
- Department of Neurosciences, Complex Operative Unit of Otorhinolaryngology and Otosurgery, Padua University Hospital, Padua, Italy
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12
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Sinnerbrink IB, Sherwen A, Meiser B, Halliday J, Amor DJ, Waters E, Rea F, Evans E, Rahman B, Kirk EP. Long-term health and development of children diagnosed prenatally with a de novo
apparently balanced chromosomal rearrangement. Prenat Diagn 2013; 33:831-8. [DOI: 10.1002/pd.4131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/03/2013] [Accepted: 03/19/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Ingrid B. Sinnerbrink
- School of Women's and Children's Health; University of New South Wales; Kensington NSW 2051 Australia
| | - Amanda Sherwen
- Murdoch Children's Research Institute; Royal Children's Hospital; Parkville Victoria 3052 Australia
| | - Bettina Meiser
- Prince of Wales Clinical School; University of New South Wales; Kensington NSW 2051 Australia
| | - Jane Halliday
- Murdoch Children's Research Institute; Royal Children's Hospital; Parkville Victoria 3052 Australia
- Department of Paediatrics; University of Melbourne, Royal Children's Hospital; Parkville Victoria 3052 Australia
| | - David J. Amor
- Murdoch Children's Research Institute; Royal Children's Hospital; Parkville Victoria 3052 Australia
- Department of Paediatrics; University of Melbourne, Royal Children's Hospital; Parkville Victoria 3052 Australia
| | - Elizabeth Waters
- Jack Brockhoff Child Health and Wellbeing Program, Melbourne School of Population Health; University of Melbourne; Victoria 3010 Australia
| | - Felicity Rea
- Prince of Wales Clinical School; University of New South Wales; Kensington NSW 2051 Australia
| | - Elizabeth Evans
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry; University of New South Wales; Kensington NSW 2051 Australia
| | - Belinda Rahman
- Prince of Wales Clinical School; University of New South Wales; Kensington NSW 2051 Australia
| | - Edwin P. Kirk
- School of Women's and Children's Health; University of New South Wales; Kensington NSW 2051 Australia
- Department of Medical Genetics; Sydney Children's Hospital; Randwick NSW 2031 Australia
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13
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Oliveira R, Dória S, Madureira C, Lima V, Almeida C, Pinho MJ, Ramalho C, Matoso E, Barros A, Carreira IM, Moura CP. Inv21p12q22del21q22 and intellectual disability. Gene 2013; 517:120-4. [PMID: 23266646 DOI: 10.1016/j.gene.2012.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/02/2012] [Indexed: 11/26/2022]
Abstract
Chromosomal rearrangements are common in humans. Pericentric inversions are among the most frequent aberrations (1-2%). Most inversions are balanced and do not cause problems in carriers unless one of the breakpoints disrupts important functional genes, has near submicroscopic copy number variants or hosts "cryptic" complex chromosomal rearrangements. Pericentric inversions can lead to imbalance in offspring. Less than 3% of Down syndrome patients have duplication as a result of parental pericentric inversion of chromosome 21. We report a family with an apparently balanced pericentric inversion of chromosome 21. The proband, a 23-year-old female was referred for prenatal diagnosis at 16 weeks gestation because of increased nuchal translucency. She has a familial history of Down's syndrome and moderate intellectual disability, a personal history of four spontaneous abortions and learning difficulties. Peripheral blood and amniotic fluid samples were collected to perform proband's and fetus' cytogenetic analyses. Additionally, another six family members were evaluated and cytogenetic analysis was performed. Complementary FISH and MLPA studies were carried out. An apparent balanced chromosome 21 pericentric inversion was observed in four family members, two revealed a recombinant chromosome 21 with partial trisomy, and one a full trisomy 21 with an inverted chromosome 21. Array CGH analysis was performed in the mother and the brother's proband. MLPA and aCGH studies identified a deletion of about 1.7 Mb on the long arm of inverted chromosome 21q22.11. We believe the cause of the intellectual disability/learning difficulties observed in the members with the inversion is related to this deletion. The recombinant chromosome 21 has a partial trisomy including the DSCR with no deletion. The risk for carriers of having a child with multiple malformations/intellectual disability is about 30% depending on whether and how this rearrangement interferes with meiosis.
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Affiliation(s)
- Renata Oliveira
- Dept. of Human Genetics, Faculty of Medicine, University of Porto/Hospital São João, Portugal.
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14
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Balanced into array: genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis. Eur J Hum Genet 2011; 19:1152-60. [PMID: 21712853 DOI: 10.1038/ejhg.2011.120] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
High-resolution genome-wide array analysis enables detailed screening for cryptic and submicroscopic imbalances of microscopically balanced de novo rearrangements in patients with developmental delay and/or congenital abnormalities. In this report, we added the results of genome-wide array analysis in 54 patients to data on 117 patients from seven other studies. A chromosome imbalance was detected in 37% of all patients with two-breakpoint rearrangements. In 49% of these patients, the imbalances were located in one or both breakpoint regions. Imbalances were more frequently (90%) found in complex rearrangements, with the majority (81%) having deletions in the breakpoint regions. The size of our own cohort enabled us to relate the presence of an imbalance to the clinical features of the patients by using a scoring system, the De Vries criteria, that indicates the complexity of the phenotype. The median De Vries score was significantly higher (P=0.002) in those patients with an imbalance (5, range 1-9) than in patients with a normal array result (3, range 0-7). This study provides accurate percentages of cryptic imbalances that can be detected by genome-wide array analysis in simple and complex de novo microscopically balanced chromosome rearrangements and confirms that these imbalances are more likely to occur in patients with a complex phenotype.
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