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Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH, Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Structural polymorphism and diversity of human segmental duplications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597452. [PMID: 38895457 PMCID: PMC11185583 DOI: 10.1101/2024.06.04.597452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Segmental duplications (SDs) contribute significantly to human disease, evolution, and diversity yet have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies where the majority of SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms, we identify 173.2 Mbp of duplicated sequence (47.4 Mbp not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy number when compared to non-African samples. A comparison to a resource of 563 million full-length Iso-Seq reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
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Affiliation(s)
- Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Altos Labs, San Diego, CA, USA
| | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Gage H. Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Prenatal diagnosis and molecular cytogenetic characterization of a chromosome 15q24 microdeletion. Taiwan J Obstet Gynecol 2021; 59:432-436. [PMID: 32416893 DOI: 10.1016/j.tjog.2020.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE We present prenatal diagnosis, molecular cytogenetic characterization and genetic counseling of a chromosome 15q24 microdeletion of paternal origin. CASE REPORT A 34-year-old primigravid woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 46,XY. Simultaneous array comparative genomic hybridization (aCGH) analysis on amniotic fluid revealed a de novo 2.571-Mb microdeletion of 15q24.1-q24.2. Prenatal ultrasound findings were unremarkable except persistent left superior vena cava and enlarged coronary sinus. The woman requested repeat amniocentesis at 22 weeks of gestation, and aCGH analysis confirmed the result of arr 15q24.1q24.2 (72,963,970-75,535,330) × 1.0 [GRCh37 (hg19)] and a 15q24 microdeletion encompassing the genes of STRA6, CYP11A1, SEMA7A, ARID3B, CYP1A1, CYP1A2, CSK and CPLX3. The parents did not have such a deletion, and polymorphic DNA marker analysis confirmed a paternal origin of the de novo deletion. Metaphase fluorescence in situ hybridization analysis confirmed a 15q24 deletion. The parents elected to terminate the pregnancy, and a malformed fetus was delivered with characteristic facial dysmorphism. CONCLUSION Simultaneous aCGH analysis of uncultured amniocytes at amniocentesis may help to detect rare de novo microdeletion disorders.
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3
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Liu Y, Zhang Y, Zarrei M, Dong R, Yang X, Zhao D, Scherer SW, Gai Z. Refining critical regions in 15q24 microdeletion syndrome pertaining to autism. Am J Med Genet B Neuropsychiatr Genet 2020; 183:217-226. [PMID: 31953991 DOI: 10.1002/ajmg.b.32778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/29/2019] [Accepted: 12/16/2019] [Indexed: 12/26/2022]
Abstract
Chromosome 15q24 microdeletion syndrome is characterized by developmental delay, facial dysmorphism, hearing loss, hypotonia, recurrent infection, and other congenital malformations including microcephaly, scoliosis, joint laxity, digital anomalies, as well as sometimes having autism spectrum disorder (ASD) and attention deficit hyperactivity disorder. Here, we report a boy with a 2.58-Mb de novo deletion at chromosome 15q24. He is diagnosed with ASD and having multiple phenotypes similar to those reported in cases having 15q24 microdeletion syndrome. To delineate the critical genes and region that might be responsible for these phenotypes, we reviewed all previously published cases. We observe a potential minimum critical region of 650 kb (LCR15q24A-B) affecting NEO1 among other genes that might pertinent to individuals with ASD carrying this deletion. In contrast, a previously defined minimum critical region downstream of the 650-kb interval (LCR15q24B-D) is more likely associated with the developmental delay, facial dysmorphism, recurrent infection, and other congenital malformations. As a result, the ASD phenotype in this individual is potentially attributed by genes particularly NEO1 within the newly proposed critical region.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Yanqing Zhang
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
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4
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Liu Y, Mapow B. Coexistence of urogenital malformations in a female fetus with de novo 15q24 microdeletion and a literature review. Mol Genet Genomic Med 2020; 8:e1265. [PMID: 32400031 PMCID: PMC7336734 DOI: 10.1002/mgg3.1265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Background 15q24 microdeletion is a relatively new syndrome caused by nonallelic homologous recombination (NAHR) between low‐copy repeats (LCRs) in the 15q24 chromosome region. This syndrome is characterized by a spectrum of clinical symptoms including global developmental delay, intellectual disability, facial dysmorphisms, and congenital malformations of the extremities, eye, gastrointestinal tract, genitourinary system, and genitalia. Method Molecular cytogenetic analysis was performed using whole genome single‐nucleotide polymorphism (SNP) microarray analysis. Autopsy examination including gross and microscopic examination were performed. In addition, a thorough review of the literature on 15q24 microdeletion was completed and summarized in table format. Result Molecular cytogenetic analysis revealed a 3.88 MB interstitial deletion within 15q24.1 to 15q24.3 (74,353,735–78,228,485 bp) in our case. Autopsy examination showed congenital malformations within the genitourinary system and genitalia, including left kidney agenesis and uterus didelphys. After thorough literature review, we found a series of midline defects associated with 15q24 microdeletion syndrome. Conclusion We report the first case of coexistence of urogenital abnormalities, including left kidney agenesis and uterus didelphys, with 15q24 microdeletion syndrome, which is also associated with midline defects secondary to abnormal development. Since 15q24 microdeletion syndrome is a relatively new entity, fully characterizing its variation and severity requires additional examination of the genetics, molecular profile and structural and functional abnormalities in affected patients. Due to the limited data in the literature, statistical analysis of abnormalities in each organ system is not possible. However, we can predict that novel genetic pathways involving cell migration, adhesion, apoptosis, and embryo development might be discovered with the advanced study of 15q24 microdeletion syndrome.
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Affiliation(s)
- Yaobin Liu
- Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, USA
| | - Beth Mapow
- Department of Pathology and Laboratory Medicine, Jefferson Health New jersey, Cherry Hill, New Jersey, USA
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5
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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6
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Ochando I, Alonzo Martínez MC, Serrano AM, Urbano A, Cazorla E, Calvo D, Rueda J. Prenatal diagnosis and molecular cytogenetic characterization of a de novo duplication of 15q24.3-q26.1. APPLICATION OF CLINICAL GENETICS 2018; 11:77-80. [PMID: 30013380 PMCID: PMC6037148 DOI: 10.2147/tacg.s159377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reported cases of distal 15q interstitial duplications are uncommon and do not result in a recognizable pattern of abnormalities. Some studies report prenatal overgrowth, while others describe growth retardation. We present molecular cytogenetic characterization of a 14 Mb interstitial duplication, encompassing 81 Online Mendelian Inheritance in Man (OMIM) genes, in a fetus with single umbilical artery and short limbs. We propose that growth restriction, previously described and present in our patient, may be due to duplication of a gene or genes contained in the 15q24 region.
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Affiliation(s)
- Isabel Ochando
- Genetics Unit, Unidad de Genética, Hospital Clínica Vistahermosa, Alicante, Spain, .,Departamento de Histología y Anatomía, Universidad Miguel Hernández, Alicante, Spain,
| | - Melanie Cristine Alonzo Martínez
- Department of Obstetrics and Gynecology, Servicio de Ginecología y Obstetricia, Hospital Universitario de Torrevieja, Alicante, Spain
| | - Ana María Serrano
- Department of Obstetrics and Gynecology, Servicio de Ginecología y Obstetricia, Hospital Universitario de Torrevieja, Alicante, Spain
| | - Antonio Urbano
- Genetics Unit, Unidad de Genética, Hospital Clínica Vistahermosa, Alicante, Spain,
| | - Eduardo Cazorla
- Department of Obstetrics and Gynecology, Servicio de Ginecología y Obstetricia, Hospital Universitario de Torrevieja, Alicante, Spain
| | - Dolores Calvo
- Emergency Laboratory, Laboratorio Urgencias, Hospital Clínico Universitario, Valladolid, Spain
| | - Joaquín Rueda
- Genetics Unit, Unidad de Genética, Hospital Clínica Vistahermosa, Alicante, Spain, .,Departamento de Histología y Anatomía, Universidad Miguel Hernández, Alicante, Spain,
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7
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Prenatal Identification and Molecular Characterization of Two Simultaneous De Novo Interstitial Duplications of Chromosomal Regions 7p22.1p21.1 and 15q24.1. Case Rep Genet 2018; 2018:1513534. [PMID: 29610688 PMCID: PMC5828557 DOI: 10.1155/2018/1513534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/14/2018] [Indexed: 12/02/2022] Open
Abstract
The occurrence of simultaneous de novo chromosomal aberrations is extremely rare. Here, we describe two, previously unreported, simultaneous de novo interstitial duplications of chromosomes 7p and 15q. Amniocentesis was completed for a healthy gravida 4 para 3 woman due to her advanced maternal age and concurrent ultrasound findings of partial vermian agenesis, choroid-plexus cysts, and hypoplastic nasal bone. Cytogenetic analysis of cultured amniocytes by conventional chromosome analysis, comparative genomic hybridization, and fluorescence in situ hybridization revealed two interstitial duplications of the chromosomal regions 7p22.1p21.1 and 15q24.1, leading to partial trisomy of 7p and 15q and karyotype 46,XY,dup(7)(p22.1-p21.1),dup (15)(q24.1). Parental chromosomal analysis did not identify any heritable changes, suggesting both mutations were de novo in nature. Postnatal examination of the neonate was significant for low set ears, thick helices, flat nasal bridge, ankyloglossia, and aberrant head shape and size concerning for craniosynostosis. Postnatal MRI was consistent with Dandy-Walker variant showing hypogenesis of the inferior cerebellar vermis. To our knowledge, there are no prenatal or postnatal reports of comparable duplications involving these two regions simultaneously. Continued observation of the neonate may reveal further phenotypic consequences of these two simultaneous de novo interstitial duplications.
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8
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Huynh MT, Lambert AS, Tosca L, Petit F, Philippe C, Parisot F, Benoît V, Linglart A, Brisset S, Tran CT, Tachdjian G, Receveur A. 15q24.1 BP4-BP1 microdeletion unmasking paternally inherited functional polymorphisms combined with distal 15q24.2q24.3 duplication in a patient with epilepsy, psychomotor delay, overweight, ventricular arrhythmia. Eur J Med Genet 2018; 61:459-464. [PMID: 29549028 DOI: 10.1016/j.ejmg.2018.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/05/2017] [Accepted: 03/10/2018] [Indexed: 11/25/2022]
Abstract
15q24 microdeletion and microduplication syndromes are genetic disorders caused by non-allelic homologous recombination between low-copy repeats (LCRs) in the 15q24 chromosome region. Individuals with 15q24 microdeletion and microduplication syndromes share a common 1.2 Mb critical interval, spanning from LCR15q24B to LCR15q24C. Patients with 15q24 microdeletion syndrome exhibit distinct dysmorphic features, microcephaly, variable developmental delay, multiples congenital anomalies while individuals with reciprocal 15q24 microduplication syndrome show mild developmental delay, facial dysmorphism associated with skeletal and genital abnormalities. We report the first case of a 10 year-old girl presenting mild developmental delay, psychomotor retardation, epilepsy, ventricular arrhythmia, overweight and idiopathic central precocious puberty. 180K array-CGH analysis identified a 1.38 Mb heterozygous interstitial 15q24.1 BP4-BP1 microdeletion including HCN4 combined with a concomitant 2.6 Mb heterozygous distal 15q24.2q24.3 microduplication. FISH analysis showed that both deletion and duplication occurred de novo in the proband. Of note, both copy number imbalances did not involve the 1.2 Mb minimal deletion/duplication critical interval of the 15q24.1q24.2 chromosome region (74.3-75.5 Mb). Sequencing of candidate genes for epilepsy and obesity showed that the proband was hemizygous for paternal A-at risk allele of BBS4 rs7178130 and NPTN rs7171755 predisposing to obesity, epilepsy and intellectual deficits. Our study highlights the complex interaction of functional polymorphisms and/or genetic variants leading to variable clinical manifestations in patients with submicroscopic chromosomal aberrations.
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Affiliation(s)
- Minh-Tuan Huynh
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France; Pham Ngoc Thach Medical University, Ho Chi Minh city, Viet Nam.
| | - Anne-Sophie Lambert
- APHP, Service d'Endocrinologie et de Diabétologie Pédiatrique, Hôpitaux Universitaires Paris-Sud, Hôpital Kremlin-Bicêtre, 94275 Le Kremlin-Bicêtre, France
| | - Lucie Tosca
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - François Petit
- APHP, Laboratoire de Génétique Moléculaire, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Christophe Philippe
- Laboratoire de Génétique Chromosomique et Moléculaire, Plateau technique de Biologie, CHU de Dijon, Dijon, France
| | - Frédéric Parisot
- APHP, Laboratoire de Génétique Moléculaire, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Virginie Benoît
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Agnès Linglart
- APHP, Service d'Endocrinologie et de Diabétologie Pédiatrique, Hôpitaux Universitaires Paris-Sud, Hôpital Kremlin-Bicêtre, 94275 Le Kremlin-Bicêtre, France
| | - Sophie Brisset
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - Cong Toai Tran
- Pham Ngoc Thach Medical University, Ho Chi Minh city, Viet Nam
| | - Gérard Tachdjian
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - Aline Receveur
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
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9
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Sousa AMM, Meyer KA, Santpere G, Gulden FO, Sestan N. Evolution of the Human Nervous System Function, Structure, and Development. Cell 2017; 170:226-247. [PMID: 28708995 DOI: 10.1016/j.cell.2017.06.036] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/21/2017] [Accepted: 06/22/2017] [Indexed: 12/22/2022]
Abstract
The nervous system-in particular, the brain and its cognitive abilities-is among humans' most distinctive and impressive attributes. How the nervous system has changed in the human lineage and how it differs from that of closely related primates is not well understood. Here, we consider recent comparative analyses of extant species that are uncovering new evidence for evolutionary changes in the size and the number of neurons in the human nervous system, as well as the cellular and molecular reorganization of its neural circuits. We also discuss the developmental mechanisms and underlying genetic and molecular changes that generate these structural and functional differences. As relevant new information and tools materialize at an unprecedented pace, the field is now ripe for systematic and functionally relevant studies of the development and evolution of human nervous system specializations.
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Affiliation(s)
- André M M Sousa
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
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10
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Ahram DF, Al-Sarraj Y, Taha RZ, Elhag SF, Al-Shaban FA, El-Shanti H, Kambouris M. A chromosomal microdeletion of 15q in a female patient with epilepsy, ID, and autism spectrum disorder: a case report. Clin Case Rep 2017; 5:1013-1017. [PMID: 28588858 PMCID: PMC5457985 DOI: 10.1002/ccr3.945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/19/2017] [Accepted: 03/09/2017] [Indexed: 11/15/2022] Open
Abstract
15q deletions have been described in association with intellectual disability and autism spectrum disorder (ASD). Previous reports have supported the role of 15q24 low copy repeats (LCRs) in mediating alternatively sized genomic rearrangements. Based on our reported finding of a 15q24 deletion coinciding with two LCR regions in a patient with epilepsy and ASD, we recommend that patients with 15q24 deletions be evaluated for ASD for early institution of therapy.
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Affiliation(s)
- Dina F Ahram
- Division of Nephrology College of Physicians and Surgeons Columbia University New York City New York
| | - Yasser Al-Sarraj
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Rowaida Z Taha
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Saba F Elhag
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Fouad A Al-Shaban
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Hatem El-Shanti
- Pediatrics University of Jordan Amman Jordan.,Pediatrics University of Iowa Iowa City Iowa
| | - Marios Kambouris
- Pathology-Genetics Sidra Medical and Research Center Doha Qatar.,Genetics Yale University School of Medicine New Haven Connecticut
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11
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Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SW, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat 2017; 38:669-677. [PMID: 28247551 DOI: 10.1002/humu.23207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/09/2022]
Abstract
Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 product-of-conception samples were tested for copy-number variations (CNVs) at two clinical diagnostic centers using whole-genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets. Based on Mouse Genome Informatics (MGI) and Zebrafish model organism database (ZFIN), 75% of identified genes could lead to developmental defects when mutated. Genes involved in embryonic development, gene transcription, and regulation of biological processes were significantly enriched. Especially, transcription factors and gene families sharing specific protein domains predominated, which included known developmental genes such as HOX, NKX homeodomain genes, and helix-loop-helix containing HAND2, NEUROG2, and NEUROD1 as well as potential novel developmental genes. We observed that developmental genes were denser in certain chromosomal regions, enabling identification of 31 potential genomic loci with clustered genes associated with development.
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Affiliation(s)
- Yiyun Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justin Bartanus
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Desheng Liang
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | | | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Hua Wang
- Hunan Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - Zhilin Ren
- Berry Genomics Corporation, Beijing, China
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Lingqian Wu
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | - Fuli Yu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Berry Genomics Corporation, Beijing, China
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12
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Verbitsky M, Kogon AJ, Matheson M, Hooper SR, Wong CS, Warady BA, Furth SL, Gharavi AG. Genomic Disorders and Neurocognitive Impairment in Pediatric CKD. J Am Soc Nephrol 2017; 28:2303-2309. [PMID: 28348065 DOI: 10.1681/asn.2016101108] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/22/2017] [Indexed: 12/12/2022] Open
Abstract
Children with CKD are at increased risk for neurocognitive impairment, but whether neurocognitive dysfunction is solely attributable to impaired renal function is unclear. Data from the CKD in Children Study Chronic Kidney Disease in Children (CKiD) Study indicate that a subset of children with CKD have unsuspected genomic disorders that predispose them to organ malformations and neurocognitive impairment. We therefore tested whether the CKiD Study participants with genomic disorders had impaired neurocognitive performance at enrollment. Compared with noncarriers (n=389), children with genomic disorders (n=31) scored significantly poorer on all measures of intelligence, anxiety/depressive symptoms, and executive function (differences of 0.6-0.7 SD; P=1.2×10-3-2.4×10-4). These differences persisted after controlling for known modifiers, including low birth weight, maternal education, seizure disorder, kidney disease duration, and genetically defined ancestry. The deleterious effect of genomic disorders on neurocognitive function was significantly attenuated in offspring of mothers with higher education, indicating the potential for modification by genetic and/or environmental factors. These data indicate that impaired neurocognitive function in some children with CKD may be attributable to genetic lesions that affect both kidney and neurocognitive development. Early identification of genomic disorders may provide opportunity for early diagnosis and personalized interventions to mitigate the effect on neurocognitive function.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Amy J Kogon
- Division of Pediatric Nephrology, Nationwide Children's Hospital, Columbus, Ohio
| | - Matthew Matheson
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland; Departments of
| | - Stephen R Hooper
- Allied Health Sciences and.,Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, New Mexico
| | - Bradley A Warady
- Division of Pediatric Nephrology, Children's Mercy Hospital, Kansas City, Missouri; Departments of
| | - Susan L Furth
- Pediatrics and.,Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; and.,Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ali G Gharavi
- Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, New York;
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13
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NEIL1 is a candidate gene associated with common variable immunodeficiency in a patient with a chromosome 15q24 deletion. Clin Immunol 2017; 176:71-76. [PMID: 28093361 DOI: 10.1016/j.clim.2017.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 02/07/2023]
Abstract
We report the first patient with an interstitial deletion of chromosome 15q24.1-q24.3 associated with common variable immunodeficiency (CVID). The 18-year old female patient's clinical and immunological phenotype was compared with 8 additional previously published patients with chr15q24 deletions. A CGH analysis estimated the deletion to be 3.767Mb in size (chr15: 74,410,916-78,178,418) and the result was confirmed using qRT-PCR. We defined an immune-related commonly deleted region (ICDR) within the chromosomal band 15q24.2, deleted in all four patients with different forms of antibody deficiencies. Mutations in the 14 genes within this ICDR were not identified in the remaining allele in our patient by WES and gene expression analyses showed haploinsufficiency of all the genes. Among these genes, we consider Nei Like DNA Glycosylase 1 (NEIL1) as a likely candidate gene due to its crucial role in B-cell activation and terminal differentiation.
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14
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Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism. Behav Brain Res 2016; 300:135-42. [DOI: 10.1016/j.bbr.2015.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/14/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022]
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15
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Palazón-Bru A, Ramírez-Prado D, Cortés E, Aguilar-Segura MS, Gil-Guillén VF. An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis. PeerJ 2016; 4:e1641. [PMID: 26925314 PMCID: PMC4768676 DOI: 10.7717/peerj.1641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/08/2016] [Indexed: 11/21/2022] Open
Abstract
In January 2012, a review of the cases of chromosome 15q24 microdeletion syndrome was published. However, this study did not include inferential statistics. The aims of the present study were to update the literature search and calculate confidence intervals for the prevalence of each phenotype using bootstrap methodology. Published case reports of patients with the syndrome that included detailed information about breakpoints and phenotype were sought and 36 were included. Deletions in megabase (Mb) pairs were determined to calculate the size of the interstitial deletion of the phenotypes studied in 2012. To determine confidence intervals for the prevalence of the phenotype and the interstitial loss, we used bootstrap methodology. Using the bootstrap percentiles method, we found wide variability in the prevalence of the different phenotypes (3–100%). The mean interstitial deletion size was 2.72 Mb (95% CI [2.35–3.10 Mb]). In comparison with our work, which expanded the literature search by 45 months, there were differences in the prevalence of 17% of the phenotypes, indicating that more studies are needed to analyze this rare disease.
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Affiliation(s)
- Antonio Palazón-Bru
- Department of Clinical Medicine, Miguel Hernández University, San Juan de Alicante, Alicante, Spain; Research Unit, Elda Hospital, Elda, Alicante, Spain
| | - Dolores Ramírez-Prado
- Clinical Analysis Department, Elda Hospital, Elda, Alicante, Spain; Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University, San Juan de Alicante, Alicante, Spain
| | - Ernesto Cortés
- Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University , San Juan de Alicante, Alicante , Spain
| | - María Soledad Aguilar-Segura
- Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University , San Juan de Alicante, Alicante , Spain
| | - Vicente Francisco Gil-Guillén
- Department of Clinical Medicine, Miguel Hernández University, San Juan de Alicante, Alicante, Spain; Research Unit, Elda Hospital, Elda, Alicante, Spain
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16
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Andrews JL, Fernandez-Enright F. A decade from discovery to therapy: Lingo-1, the dark horse in neurological and psychiatric disorders. Neurosci Biobehav Rev 2015; 56:97-114. [PMID: 26143511 DOI: 10.1016/j.neubiorev.2015.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 05/15/2015] [Accepted: 06/02/2015] [Indexed: 01/19/2023]
Abstract
Leucine-rich repeat and immunoglobulin domain-containing protein (Lingo-1) is a potent negative regulator of neuron and oligodendrocyte survival, neurite extension, axon regeneration, oligodendrocyte differentiation, axonal myelination and functional recovery; all processes highly implicated in numerous brain-related functions. Although playing a major role in developmental brain functions, the potential application of Lingo-1 as a therapeutic target for the treatment of neurological disorders has so far been under-estimated. A number of preclinical studies have shown that various methods of antagonizing Lingo-1 results in neuronal and oligodendroglial survival, axonal growth and remyelination; however to date literature has only detailed applications of Lingo-1 targeted therapeutics with a focus primarily on myelination disorders such as multiple sclerosis and spinal cord injury; omitting important information regarding Lingo-1 signaling co-factors. Here, we provide for the first time a complete and thorough review of the implications of Lingo-1 signaling in a wide range of neurological and psychiatric disorders, and critically examine its potential as a novel therapeutic target for these disorders.
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Affiliation(s)
- Jessica L Andrews
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong 2522, NSW, Australia; Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, NSW, Australia; Schizophrenia Research Institute, 405 Liverpool St, Darlinghurst 2010, NSW, Australia.
| | - Francesca Fernandez-Enright
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong 2522, NSW, Australia; Faculty of Social Sciences, University of Wollongong, Wollongong 2522, NSW, Australia; Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, NSW, Australia; Schizophrenia Research Institute, 405 Liverpool St, Darlinghurst 2010, NSW, Australia.
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17
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El-Hattab AW, Schaaf CP, Fang P, Roeder E, Kimonis VE, Church JA, Patel A, Cheung SW. Clinical characterization of int22h1/int22h2-mediated Xq28 duplication/deletion: new cases and literature review. BMC MEDICAL GENETICS 2015; 16:12. [PMID: 25927380 PMCID: PMC4422130 DOI: 10.1186/s12881-015-0157-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/18/2015] [Indexed: 12/21/2022]
Abstract
Background Int22h1/int22h2-mediated Xq28 duplication syndrome is caused by ~0.5 Mb chromosomal duplications mediated by nonallelic homologous recombination between intron 22 homologous region 1 (int22h1) and 2 (int22h2), which, in addition to int22h3, are also responsible for inversions disrupting the F8 gene in hemophilia A. This syndrome has recently been described in 9 males with cognitive impairment, behavioral problems, and distinctive facial features; and 6 females with milder phenotypes. The reciprocal deletion was previously reported in a mother and daughter. It was suggested that this deletion may not have phenotypic effects in females because of skewed chromosome X inactivation, but may be embryonic lethal in males. Methods Array comparative genomic hybridization analyses were performed using oligonucleotide-based chromosomal microarray. Chromosome X inactivation studies were performed at the AR (androgen receptor) and FMR1 (fragile X mental retardation 1) loci. Results We present here 5 males and 6 females with int22h1/int22h2-mediated Xq28 duplication syndrome. The males manifested cognitive impairment, behavioral problems, and distinctive facial features. Two of the six females manifested mild cognitive impairment. This duplication was maternally inherited, and skewed chromosome X inactivation was observed in the majority of females carrying the duplication. We also report the reciprocal deletion in a mother and daughter with overweight, but normal cognition. In addition, we present the first case of a prenatally diagnosed de novo int22h1/int22h2-mediated deletion in a healthy female infant. We reviewed individuals previously reported with similar or overlapping rearrangements and evaluated the potential roles of genes in the rearrangement region. Conclusions The similarity of clinical features among individuals with the int22h1/int22h2-mediated Xq28 duplication supports the notion that this duplication causes a recognizable syndrome that affects males with females exhibiting milder phenotypes. It is suggested that the observed cognitive impairment in this syndrome results from increased dosage of RAB39B gene located within the duplicated region. Increased dosage of CLIC2 may also contribute to the phenotype. The reciprocal deletion results in skewed chromosome X inactivation and no clinical phenotype in females. Review of overlapping deletions suggests that hemizygous loss of VBP1 may be the cause for the proposed male lethality associated with this deletion.
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Affiliation(s)
- Ayman W El-Hattab
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS NAB 2015, Houston, TX, 77030, U.S.A. .,Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates.
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS NAB 2015, Houston, TX, 77030, U.S.A. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Ping Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS NAB 2015, Houston, TX, 77030, U.S.A.
| | - Elizabeth Roeder
- Section of Genetics, Department of Pediatrics, Baylor College of Medicine, Children's Hospital of San Antonio, San Antonio, TX, USA.
| | - Virginia E Kimonis
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine Medical Center, Orange, CA, USA.
| | - Joseph A Church
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, and Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS NAB 2015, Houston, TX, 77030, U.S.A.
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS NAB 2015, Houston, TX, 77030, U.S.A.
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18
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Inherited 15q24 microdeletion syndrome in twins and their father with phenotypic variability. Eur J Med Genet 2015; 58:111-5. [DOI: 10.1016/j.ejmg.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 12/01/2014] [Indexed: 11/20/2022]
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19
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Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 2014; 46:1293-302. [PMID: 25326701 PMCID: PMC4244265 DOI: 10.1038/ng.3120] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into its instability, we sequenced the region in patients, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mbp. These configurations arose recently (~0.5–0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons—a ~14 kbp primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage, and independent structural changes in apes. The significant clustering (p=0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting evolutionary and disease-related instability of chromosome 15.
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20
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Abstract
Abnormal cortical circuits underlie some cognitive and psychiatric disorders, yet the molecular signals that generate normal cortical networks remain poorly understood. Semaphorin 7A (Sema7A) is an atypical member of the semaphorin family that is GPI-linked, expressed principally postnatally, and enriched in sensory cortex. Significantly, SEMA7A is deleted in individuals with 15q24 microdeletion syndrome, characterized by developmental delay, autism, and sensory perceptual deficits. We studied the role that Sema7A plays in establishing functional cortical circuitry in mouse somatosensory barrel cortex. We found that Sema7A is expressed in spiny stellate cells and GABAergic interneurons and that its absence disrupts barrel cytoarchitecture, reduces asymmetrical orientation of spiny stellate cell dendrites, and functionally impairs thalamocortically evoked synaptic responses, with reduced feed-forward GABAergic inhibition. These data identify Sema7A as a regulator of thalamocortical and local circuit development in layer 4 and provide a molecular handle that can be used to explore the coordinated generation of excitatory and inhibitory cortical circuits.
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21
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Gao X, Gotway G, Rathjen K, Johnston C, Sparagana S, Wise CA. Genomic Analyses of Patients With Unexplained Early-Onset Scoliosis. Spine Deform 2014; 2:324-332. [PMID: 27927329 PMCID: PMC4228381 DOI: 10.1016/j.jspd.2014.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 03/17/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022]
Abstract
STUDY DESIGN To test for rare genetic mutations, a cohort of patients with unexplained early-onset scoliosis (EOS) was screened using high-density microarray genotyping. A cohort of patients with adolescent idiopathic scoliosis (AIS) was similarly screened and the results were compared. SUMMARY OF BACKGROUND DATA Patients with scoliosis in infancy or early childhood (EOS) are at high risk for progressive deformity and associated problems including respiratory compromise. Early-onset scoliosis is frequently associated with genetic disorders but many patients present with nonspecific clinical features and without an associated diagnosis. The authors hypothesized that EOS in these patients may be caused by rare genetic mutations detectable by next-generation genomic methods. METHODS The researchers identified 24 patients with unexplained EOS from pediatric orthopedic clinics. They genotyped them, along with 39 connecting family members, using the Illumina OmniExpress-12, version 1.0 beadchip. Resulting genotypes were analyzed for chromosomal changes, specifically copy number variation and absence of heterozygosity. They screened 482 adolescent idiopathic scoliosis (AIS) patients and 744 healthy controls, who were similarly genotyped with the same beadchip, for chromosomal changes identified in the EOS cohort. RESULTS Copy number variation and absence of heterozygosity analyses revealed a genetic diagnosis of chromosome 15q24 microdeletion syndrome in 1 patient and maternal uniparental disomy of chromosome 14 in a second one. Prior genetic testing and clinical evaluations had been negative in both cases. A large novel chromosome 10 deletion was likely causal in a third EOS patient. These mutations identified in the EOS patients were absent in AIS patients and controls, and thus were not associated with AIS or found in asymptomatic individuals. CONCLUSIONS These data underscore the usefulness of updated genetic evaluations including high-density microarray-based genotyping and other next-generation methods in patients with unexplained EOS, even when prior genetic studies were negative. These data also suggest the intriguing possibility that other mutations detectable by whole genome sequencing, as well as epigenetic effects, await discovery in the EOS population.
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Affiliation(s)
- Xiaochong Gao
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX
| | - Garrett Gotway
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Karl Rathjen
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles Johnston
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Steven Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Carol A. Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX,To whom correspondence should be directed. Telephone: 214-559-7861 Fax: 214-559-7872
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22
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Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet 2014; 15:215-244. [PMID: 24773319 DOI: 10.1146/annurev-genom-091212-153408] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal abnormalities, including microdeletions and microduplications, have long been associated with abnormal developmental outcomes. Early discoveries relied on a common clinical presentation and the ability to detect chromosomal abnormalities by standard karyotype analysis or specific assays such as fluorescence in situ hybridization. Over the past decade, the development of novel genomic technologies has allowed more comprehensive, unbiased discovery of microdeletions and microduplications throughout the human genome. The ability to quickly interrogate large cohorts using chromosome microarrays and, more recently, next-generation sequencing has led to the rapid discovery of novel microdeletions and microduplications associated with disease, including very rare but clinically significant rearrangements. In addition, the observation that some microdeletions are associated with risk for several neurodevelopmental disorders contributes to our understanding of shared genetic susceptibility for such disorders. Here, we review current knowledge of microdeletion/duplication syndromes, with a particular focus on recurrent rearrangement syndromes.
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Affiliation(s)
- Corey T Watson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra/CSIC, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Centro Nacional de Análisis Genómico, 08023 Barcelona, Spain
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington 98195
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23
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Peddibhotla S, Nagamani SCS, Erez A, Hunter JV, Holder JL, Carlin ME, Bader PI, Perras HMF, Allanson JE, Newman L, Simpson G, Immken L, Powell E, Mohanty A, Kang SHL, Stankiewicz P, Bacino CA, Bi W, Patel A, Cheung SW. Delineation of candidate genes responsible for structural brain abnormalities in patients with terminal deletions of chromosome 6q27. Eur J Hum Genet 2014; 23:54-60. [PMID: 24736736 DOI: 10.1038/ejhg.2014.51] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 01/29/2014] [Accepted: 01/31/2014] [Indexed: 11/09/2022] Open
Abstract
Patients with terminal deletions of chromosome 6q present with structural brain abnormalities including agenesis of corpus callosum, hydrocephalus, periventricular nodular heterotopia, and cerebellar malformations. The 6q27 region harbors genes that are important for the normal development of brain and delineation of a critical deletion region for structural brain abnormalities may lead to a better genotype-phenotype correlation. We conducted a detailed clinical and molecular characterization of seven unrelated patients with deletions involving chromosome 6q27. All patients had structural brain abnormalities. Using array comparative genomic hybridization, we mapped the size, extent, and genomic content of these deletions. The smallest region of overlap spans 1.7 Mb and contains DLL1, THBS2, PHF10, and C6orf70 (ERMARD) that are plausible candidates for the causation of structural brain abnormalities. Our study reiterates the importance of 6q27 region in normal development of brain and helps identify putative genes in causation of structural brain anomalies.
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Affiliation(s)
- Sirisha Peddibhotla
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayelet Erez
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, TX, USA
| | - J Lloyd Holder
- 1] Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA [2] Texas Children's Hospital, Houston, TX, USA
| | - Mary E Carlin
- Department of Pediatrics, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - Patricia I Bader
- Parkview Cytogenetics and Northeast Indiana Genetic Counseling Center, Fort Wayne, IN, USA
| | - Helene M F Perras
- Regional Genetics Program, Conseillère en génétique agréée, Programme régional de Génétique, Ottawa, Ontario, Canada
| | - Judith E Allanson
- Regional Genetics Program, Conseillère en génétique agréée, Programme régional de Génétique, Ottawa, Ontario, Canada
| | | | | | | | - Erin Powell
- Department of Pediatrics, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Aaron Mohanty
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Sung-Hae L Kang
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Allina Medical Laboratories, Minneapolis, MN, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau W Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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24
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Somatic mosaicism detected by exon-targeted, high-resolution aCGH in 10,362 consecutive cases. Eur J Hum Genet 2014; 22:969-78. [PMID: 24398791 PMCID: PMC4350600 DOI: 10.1038/ejhg.2013.285] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 11/08/2013] [Accepted: 11/20/2013] [Indexed: 11/09/2022] Open
Abstract
Somatic chromosomal mosaicism arising from post-zygotic errors is known to cause several well-defined genetic syndromes as well as contribute to phenotypic variation in diseases. However, somatic mosaicism is often under-diagnosed due to challenges in detection. We evaluated 10 362 patients with a custom-designed, exon-targeted whole-genome oligonucleotide array and detected somatic mosaicism in a total of 57 cases (0.55%). The mosaicism was characterized and confirmed by fluorescence in situ hybridization (FISH) and/or chromosome analysis. Different categories of abnormal cell lines were detected: (1) aneuploidy, including sex chromosome abnormalities and isochromosomes (22 cases), (2) ring or marker chromosomes (12 cases), (3) single deletion/duplication copy number variations (CNVs) (11 cases), (4) multiple deletion/duplication CNVs (5 cases), (5) exonic CNVs (4 cases), and (6) unbalanced translocations (3 cases). Levels of mosaicism calculated based on the array data were in good concordance with those observed by FISH (10–93%). Of the 14 cases evaluated concurrently by chromosome analysis, mosaicism was detected solely by the array in 4 cases (29%). In summary, our exon-targeted array further expands the diagnostic capability of high-resolution array comparative genomic hybridization in detecting mosaicism for cytogenetic abnormalities as well as small CNVs in disease-causing genes.
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Wiszniewski W, Hunter J, Hanchard N, Willer J, Shaw C, Tian Q, Illner A, Wang X, Cheung S, Patel A, Campbell IM, Gelowani V, Hixson P, Ester A, Azamian M, Potocki L, Zapata G, Hernandez P, Ramocki M, Santos-Cortez R, Wang G, York M, Justice MJ, Chu Z, Bader P, Omo-Griffith L, Madduri N, Scharer G, Crawford H, Yanatatsaneejit P, Eifert A, Kerr J, Bacino C, Franklin A, Goin-Kochel RP, Simpson G, Immken L, Haque M, Stosic M, Williams M, Morgan T, Pruthi S, Omary R, Boyadjiev S, Win K, Thida A, Hurles M, Hibberd M, Khor C, Van Vinh Chau N, Gallagher T, Mutirangura A, Stankiewicz P, Beaudet A, Maletic-Savatic M, Rosenfeld J, Shaffer L, Davis E, Belmont J, Dunstan S, Simmons CP, Bonnen PE, Leal S, Katsanis N, Lupski J, Lalani S. TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. Am J Hum Genet 2013; 93:197-210. [PMID: 23810381 DOI: 10.1016/j.ajhg.2013.05.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/07/2013] [Accepted: 05/30/2013] [Indexed: 11/26/2022] Open
Abstract
White matter hyperintensities (WMHs) of the brain are important markers of aging and small-vessel disease. WMHs are rare in healthy children and, when observed, often occur with comorbid neuroinflammatory or vasculitic processes. Here, we describe a complex 4 kb deletion in 2q36.3 that segregates with early childhood communication disorders and WMH in 15 unrelated families predominantly from Southeast Asia. The premature brain aging phenotype with punctate and multifocal WMHs was observed in ~70% of young carrier parents who underwent brain MRI. The complex deletion removes the penultimate exon 3 of TM4SF20, a gene encoding a transmembrane protein of unknown function. Minigene analysis showed that the resultant net loss of an exon introduces a premature stop codon, which, in turn, leads to the generation of a stable protein that fails to target to the plasma membrane and accumulates in the cytoplasm. Finally, we report this deletion to be enriched in individuals of Vietnamese Kinh descent, with an allele frequency of about 1%, embedded in an ancestral haplotype. Our data point to a constellation of early language delay and WMH phenotypes, driven by a likely toxic mechanism of TM4SF20 truncation, and highlight the importance of understanding and managing population-specific low-frequency pathogenic alleles.
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Carvill GL, Mefford HC. Microdeletion syndromes. Curr Opin Genet Dev 2013; 23:232-9. [PMID: 23664828 DOI: 10.1016/j.gde.2013.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/11/2013] [Accepted: 03/25/2013] [Indexed: 01/11/2023]
Abstract
The recent explosion in the implementation of genome-wide microarray technology to discover rare, pathogenic genomic rearrangements in a variety of diseases has led to the discovery of numerous microdeletion syndromes. It is now clear that these microdeletions are associated with extensive phenotypic heterogeneity and incomplete penetrance. A subset of recurrent microdeletions underpin diverse phenotypes, including intellectual disability, autism, epilepsy and neuropsychiatric disorders. Recent studies highlight a role for additional low frequency variants, or 'second hits' to account for this variability. The implementation of massively parallel sequencing and epigenetic models may provide a powerful prospective approach to the delineation of microdeletion syndrome phenotypes.
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Affiliation(s)
- Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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Bi W, Borgan C, Pursley AN, Hixson P, Shaw CA, Bacino CA, Lalani SR, Patel A, Stankiewicz P, Lupski JR, Beaudet AL, Cheung SW. Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosome analysis in today’s genomic array era? Genet Med 2012; 15:450-7. [DOI: 10.1038/gim.2012.152] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Small genomic rearrangements involving FMR1 support the importance of its gene dosage for normal neurocognitive function. Neurogenetics 2012; 13:333-9. [DOI: 10.1007/s10048-012-0340-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
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Nagamani SCS, Erez A, Ben-Zeev B, Frydman M, Winter S, Zeller R, El-Khechen D, Escobar L, Stankiewicz P, Patel A, Cheung SW. Detection of copy-number variation in AUTS2 gene by targeted exonic array CGH in patients with developmental delay and autistic spectrum disorders. Eur J Hum Genet 2012; 21:343-6. [PMID: 22872102 DOI: 10.1038/ejhg.2012.157] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Small genomic rearrangements and copy-number variations (CNVs) involving a single gene have been associated recently with many neurocognitive phenotypes, including intellectual disability (ID), behavioral abnormalities, and autistic spectrum disorders (ASDs). Such small CNVs in the Autism susceptibility candidate 2 (AUTS2) gene have been shown to be associated with seizures, ID, and ASDs. We report four patients with small CNVs ranging in size between 133-319 kb that disrupt AUTS2. Two patients have duplications involving single exons, whereas two have deletions that removed multiple exons. All patients had developmental delay, whereas two patients had a diagnosis of ASDs. The CNVs were detected by an exon-targeted array CGH with dense oligonucleotide coverage in exons of genes known or hypothesized to be causative of multiple human phenotypes. Our report further shows that disruption of AUTS2 results in a variety of neurobehavioral phenotypes. More importantly, it demonstrates the utility of targeted exon array as a highly sensitive clinical diagnostic tool for the detection of small genomic rearrangements in the clinically relevant regions of the human genome.
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Affiliation(s)
- Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Celestino-Soper PBS, Skinner C, Schroer R, Eng P, Shenai J, Nowaczyk MMJ, Terespolsky D, Cushing D, Patel GS, Immken L, Willis A, Wiszniewska J, Matalon R, Rosenfeld JA, Stevenson RE, Kang SHL, Cheung SW, Beaudet AL, Stankiewicz P. Deletions in chromosome 6p22.3-p24.3, including ATXN1, are associated with developmental delay and autism spectrum disorders. Mol Cytogenet 2012; 5:17. [PMID: 22480366 PMCID: PMC3351998 DOI: 10.1186/1755-8166-5-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/05/2012] [Indexed: 04/14/2023] Open
Abstract
Interstitial deletions of the short arm of chromosome 6 are rare and have been associated with developmental delay, hypotonia, congenital anomalies, and dysmorphic features. We used array comparative genomic hybridization in a South Carolina Autism Project (SCAP) cohort of 97 subjects with autism spectrum disorders (ASDs) and identified an ~ 5.4 Mb deletion on chromosome 6p22.3-p23 in a 15-year-old patient with intellectual disability and ASDs. Subsequent database queries revealed five additional individuals with overlapping submicroscopic deletions and presenting with developmental and speech delay, seizures, behavioral abnormalities, heart defects, and dysmorphic features. The deletion found in the SCAP patient harbors ATXN1, DTNBP1, JARID2, and NHLRC1 that we propose may be responsible for ASDs and developmental delay.
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Affiliation(s)
| | - Cindy Skinner
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, USA
| | - Richard Schroer
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, USA
| | - Patricia Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jayant Shenai
- Neonatal-Perinatal Medicine, Pediatrics, The Vanderbilt Clinic, Nashville, TN, USA
| | - Malgorzata MJ Nowaczyk
- Pathology and Molecular Medicine and Pediatrics, Hamilton Regional Laboratory Medicine Program, Hamilton, ON, Canada
| | | | | | | | | | - Alecia Willis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Reuben Matalon
- Division of General Academic Pediatrics, Department of Pediatrics, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, WA, USA
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA.
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Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JWG, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE. A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. Br J Haematol 2012; 157:180-7. [PMID: 22296450 DOI: 10.1111/j.1365-2141.2012.09028.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/21/2011] [Indexed: 11/29/2022]
Abstract
Transient myeloproliferative disorder (TMD) of the newborn and acute megakaryoblastic leukaemia (AMKL) in children with Down syndrome (DS) represent paradigmatic models of leukaemogenesis. Chromosome 21 gene dosage effects and truncating mutations of the X-chromosomal transcription factor GATA1 synergize to trigger TMD and AMKL in most patients. Here, we report the occurrence of TMD, which spontaneously remitted and later progressed to AMKL in a patient without DS but with a distinct dysmorphic syndrome. Genetic analysis of the leukaemic clone revealed somatic trisomy 21 and a truncating GATA1 mutation. The analysis of the patient's normal blood cell DNA on a genomic single nucleotide polymorphism (SNP) array revealed a de novo germ line 2·58 Mb 15q24 microdeletion including 41 known genes encompassing the tumour suppressor PML. Genomic context analysis of proteins encoded by genes that are included in the microdeletion, chromosome 21-encoded proteins and GATA1 suggests that the microdeletion may trigger leukaemogenesis by disturbing the balance of a hypothetical regulatory network of normal megakaryopoiesis involving PML, SUMO3 and GATA1. The 15q24 microdeletion may thus represent the first genetic hit to initiate leukaemogenesis and implicates PML and SUMO3 as novel components of the leukaemogenic network in TMD/AMKL.
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Affiliation(s)
- Susanne Haemmerling
- Department of Paediatric Oncology, Haematology and Immunology, University of Heidelberg Medical Centre, Heidelberg, Germany
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Magoulas PL, El-Hattab AW. Chromosome 15q24 microdeletion syndrome. Orphanet J Rare Dis 2012; 7:2. [PMID: 22216833 PMCID: PMC3275445 DOI: 10.1186/1750-1172-7-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/04/2012] [Indexed: 01/24/2023] Open
Abstract
Chromosome 15q24 microdeletion syndrome is a recently described rare microdeletion syndrome that has been reported in 19 individuals. It is characterized by growth retardation, intellectual disability, and distinct facial features including long face with high anterior hairline, hypertelorism, epicanthal folds, downslanting palpebral fissures, sparse and broad medial eyebrows, broad and/or depressed nasal bridge, small mouth, long smooth philtrum, and full lower lip. Other common findings include skeletal and digital abnormalities, genital abnormalities in males, hypotonia, behavior problems, recurrent infections, and eye problems. Other less frequent findings include hearing loss, growth hormone deficiency, hernias, and obesity. Congenital malformations, while rare, can be severe and include structural brain anomalies, cardiovascular malformations, congenital diaphragmatic hernia, intestinal atresia, imperforate anus, and myelomeningocele. Karyotypes are typically normal, and the deletions were detected in these individuals by array comparative genomic hybridization (aCGH). The deletions range in size from 1.7-6.1 Mb and usually result from nonallelic homologous recombination (NAHR) between paralogous low-copy repeats (LCRs). The majority of 15q24 deletions have breakpoints that localize to one of five LCR clusters labeled LCR15q24A, -B, -C, -D, and -E. The smallest region of overlap (SRO) spans a 1.2 Mb region between LCR15q24B to LCR15q24C. There are several candidate genes within the SRO, including CYP11A1, SEMA7A, CPLX3, ARID3B, STRA6, SIN3A and CSK, that may predispose to many of the clinical features observed in individuals with 15q24 deletion syndrome. The deletion occurred as a de novo event in all of the individuals when parents were available for testing. Parental aCGH and/or FISH studies are recommended to provide accurate genetic counseling and guidance regarding prognosis, recurrence risk, and reproductive options. Management involves a multi-disciplinary approach to care with the primary care physician and clinical geneticist playing a crucial role in providing appropriate screening, surveillance, and care for individuals with this syndrome. At the time of diagnosis, individuals should receive baseline echocardiograms, audiologic, ophthalmologic, and developmental assessments. Growth and feeding should be closely monitored. Other specialists that may be involved in the care of individuals with 15q24 deletion syndrome include immunology, endocrine, orthopedics, neurology, and urology. Chromosome 15q24 microdeletion syndrome should be differentiated from other genetic syndromes, particularly velo-cardio-facial syndrome (22q11.2 deletion syndrome), Prader-Willi syndrome, and Noonan syndrome. These conditions share some phenotypic similarity to 15q24 deletion syndrome yet have characteristic features specific to each of them that allows the clinician to distinguish between them. Molecular genetic testing and/or aCGH will be able to diagnose these conditions in the majority of individuals.
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Affiliation(s)
- Pilar L Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Abstract
During the past decade, widespread use of microarray-based technologies, including oligonucleotide array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) genotyping arrays have dramatically changed our perspective on genome-wide structural variation. Submicroscopic genomic rearrangements or copy-number variation (CNV) have proven to be an important factor responsible for primate evolution, phenotypic differences between individuals and populations, and susceptibility to many diseases. The number of diseases caused by chromosomal microdeletions and microduplications, also referred to as genomic disorders, has been increasing at a rapid pace. Microdeletions and microduplications are found in patients with a wide variety of phenotypes, including Mendelian diseases as well as common complex traits, such as developmental delay/intellectual disability, autism, schizophrenia, obesity, and epilepsy. This chapter provides an overview of common microdeletion and microduplication syndromes and their clinical phenotypes, and discusses the genomic structures and molecular mechanisms of formation. In addition, an explanation for how these genomic rearrangements convey abnormal phenotypes is provided.
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Affiliation(s)
- Lisenka E L M Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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35
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Mefford HC, Rosenfeld JA, Shur N, Slavotinek AM, Cox VA, Hennekam RC, Firth HV, Willatt L, Wheeler P, Morrow EM, Cook J, Sullivan R, Oh A, McDonald MT, Zonana J, Keller K, Hannibal MC, Ball S, Kussmann J, Gorski J, Zelewski S, Banks V, Smith W, Smith R, Paull L, Rosenbaum KN, Amor DJ, Silva J, Lamb A, Eichler EE. Further clinical and molecular delineation of the 15q24 microdeletion syndrome. J Med Genet 2011; 49:110-8. [PMID: 22180641 PMCID: PMC3261729 DOI: 10.1136/jmedgenet-2011-100499] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Chromosome 15q24 microdeletion syndrome is a rare genomic disorder characterised by intellectual disability, growth retardation, unusual facial morphology and other anomalies. To date, 20 patients have been reported; 18 have had detailed breakpoint analysis. Aim To further delineate the features of the 15q24 microdeletion syndrome, the clinical and molecular characterisation of fifteen patients with deletions in the 15q24 region was performed, nearly doubling the number of reported patients. Methods Breakpoints were characterised using a custom, high-density array comparative hybridisation platform, and detailed phenotype information was collected for each patient. Results Nine distinct deletions with different breakpoints ranging in size from 266 kb to 3.75 Mb were identified. The majority of breakpoints lie within segmental duplication (SD) blocks. Low sequence identity and large intervals of unique sequence between SD blocks likely contribute to the rarity of 15q24 deletions, which occur 8–10 times less frequently than 1q21 or 15q13 microdeletions in our series. Two small, atypical deletions were identified within the region that help delineate the critical region for the core phenotype in the 15q24 microdeletion syndrome. Conclusion The molecular characterisation of these patients suggests that the core cognitive features of the 15q24 microdeletion syndrome, including developmental delays and severe speech problems, are largely due to deletion of genes in a 1.1–Mb critical region. However, genes just distal to the critical region also play an important role in cognition and in the development of characteristic facial features associated with 15q24 deletions. Clearly, deletions in the 15q24 region are variable in size and extent. Knowledge of the breakpoints and size of deletion combined with the natural history and medical problems of our patients provide insights that will inform management guidelines. Based on common phenotypic features, all patients with 15q24 microdeletions should receive a thorough neurodevelopmental evaluation, physical, occupational and speech therapies, and regular audiologic and ophthalmologic screening.
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Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, DC 98195, USA.
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Brun A, Cailley D, Toutain J, Bouron J, Arveiler B, Lacombe D, Goizet C, Rooryck C. 1.5 Mb microdeletion in 15q24 in a patient with mild OAVS phenotype. Eur J Med Genet 2011; 55:135-9. [PMID: 22198201 DOI: 10.1016/j.ejmg.2011.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/20/2011] [Indexed: 10/14/2022]
Abstract
We report on a boy presenting with features of OAVS (Oculoauriculovertebral spectrum) and carrying a 1.5 Mb microdeletion in 15q24.1q24.2. This recurrent deletion usually leads to a broad clinical spectrum but has never been found associated with features of OAVS such as ear agenesis. This observation is in accordance with OAVS being a genetically heterogeneous disorder, and points out the importance of array-CGH screening in this disorder.
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Affiliation(s)
- Aurore Brun
- CHU Bordeaux, Department of Medical Genetics, Bordeaux, France
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Narumi Y, Shiohara M, Wakui K, Hama A, Kojima S, Yoshikawa K, Amano Y, Kosho T, Fukushima Y. Myelodysplastic syndrome in a child with 15q24 deletion syndrome. Am J Med Genet A 2011; 158A:412-6. [PMID: 22140075 DOI: 10.1002/ajmg.a.34395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 10/24/2011] [Indexed: 11/10/2022]
Abstract
15q24 deletion syndrome is a recently-described chromosomal disorder, characterized by developmental delay, growth deficiency, distinct facial features, digital abnormalities, loose connective tissue, and genital malformations in males. To date, 19 patients have been reported. We report on a 13-year-old boy with this syndrome manifesting childhood myelodysplastic syndrome (MDS). He had characteristic facial features, hypospadias, and mild developmental delay. He showed neutropenia and thrombocytopenia for several years. At age 13 years, bone marrow examination was performed, which showed a sign suggestive of childhood MDS: mild dysplasia in the myeloid, erythroid, and megakaryocytic cell lineages. Array comparative genomic hybridization (array CGH) revealed a de novo 3.4 Mb 15q24.1q24.3 deletion. Although MDS has not been described in patients with the syndrome, a boy was reported to have acute lymphoblastic leukemia (ALL). The development of MDS and hematological malignancy in the syndrome might be caused by the haploinsufficiency of deleted 15q24 segment either alone or in combination with other genetic abnormalities in hematopoietic cells. Further hematological investigation is recommended to be beneficial if physical and hematological examination results are suggestive of hematopoietic disturbance in patients with the syndrome.
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Affiliation(s)
- Yoko Narumi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.
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38
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Deak KL, Horn SR, Rehder CW. The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: variable expressivity and genomic complexity. Clin Lab Med 2011; 31:543-64, viii. [PMID: 22118736 DOI: 10.1016/j.cll.2011.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several new microdeletion and microduplication syndromes have been discovered in a genotype-first approach. Many of these disorders are caused by nonallelic homologous recombination between blocks of segmental duplication. The authors describe 9 regions for which copy number alteration is proposed to cause an abnormal phenotype. Some of these disorders have been observed in affected individuals and individuals lacking a clearly abnormal phenotype. These deletions and duplications are thought to be contributory, but not always sufficient, to elicit an abnormal outcome. Additional studies are necessary to further evaluate the penetrance and delineate the clinical spectrum associated with many of these newly described disorders.
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Affiliation(s)
- Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
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39
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Salyakina D, Cukier HN, Lee JM, Sacharow S, Nations LD, Ma D, Jaworski JM, Konidari I, Whitehead PL, Wright HH, Abramson RK, Williams SM, Menon R, Haines JL, Gilbert JR, Cuccaro ML, Pericak-Vance MA. Copy number variants in extended autism spectrum disorder families reveal candidates potentially involved in autism risk. PLoS One 2011; 6:e26049. [PMID: 22016809 PMCID: PMC3189231 DOI: 10.1371/journal.pone.0026049] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 09/16/2011] [Indexed: 02/02/2023] Open
Abstract
Copy number variations (CNVs) are a major cause of genetic disruption in the human genome with far more nucleotides being altered by duplications and deletions than by single nucleotide polymorphisms (SNPs). In the multifaceted etiology of autism spectrum disorders (ASDs), CNVs appear to contribute significantly to our understanding of the pathogenesis of this complex disease. A unique resource of 42 extended ASD families was genotyped for over 1 million SNPs to detect CNVs that may contribute to ASD susceptibility. Each family has at least one avuncular or cousin pair with ASD. Families were then evaluated for co-segregation of CNVs in ASD patients. We identified a total of five deletions and seven duplications in eleven families that co-segregated with ASD. Two of the CNVs overlap with regions on 7p21.3 and 15q24.1 that have been previously reported in ASD individuals and two additional CNVs on 3p26.3 and 12q24.32 occur near regions associated with schizophrenia. These findings provide further evidence for the involvement of ICA1 and NXPH1 on 7p21.3 in ASD susceptibility and highlight novel ASD candidates, including CHL1, FGFBP3 and POUF41. These studies highlight the power of using extended families for gene discovery in traits with a complex etiology.
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Affiliation(s)
- Daria Salyakina
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Holly N. Cukier
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Joycelyn M. Lee
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Stephanie Sacharow
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Laura D. Nations
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Deqiong Ma
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - James M. Jaworski
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Harry H. Wright
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Ruth K. Abramson
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Scott M. Williams
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ramkumar Menon
- Department of Epidemiology and Department of Obstetrics and Gynecology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- * E-mail:
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40
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L Ng IS, Chin WH, P Lim EC, Tan EC. An additional case of the recurrent 15q24.1 microdeletion syndrome and review of the literature. Twin Res Hum Genet 2011; 14:333-9. [PMID: 21787116 DOI: 10.1375/twin.14.4.333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report a 9-year-old girl with 3 Mb interstitial deletion of chromosome 15q24 identified by oligonucleotide array comparative hybridization. She is of Chinese ancestry and shared some typical features of previously reported 15q24 deletion cases such as mild dysmorphism with developmental and speech delay. She also had mild hearing loss that was reported in one other case. We compared all 19 cases that are identified from array-CGH. The deletion occurred within an 8.3 Mb region from 15q23 to 15q24.3. The minimum overlapping deleted region is less than 0.5 Mb from 72.3 Mb to 72.7 Mb. The functions of the nine annotated genes within the region and how they might contribute to the microdeletion phenotype are discussed.
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Affiliation(s)
- Ivy S L Ng
- Genetics Service, KK Women's and Children's Hospital, Singapore
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41
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Delineation of a deletion region critical for corpus callosal abnormalities in chromosome 1q43-q44. Eur J Hum Genet 2011; 20:176-9. [PMID: 21934713 DOI: 10.1038/ejhg.2011.171] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Submicroscopic deletions involving chromosome 1q43-q44 result in cognitive impairment, microcephaly, growth restriction, dysmorphic features, and variable involvement of other organ systems. A consistently observed feature in patients with this deletion are the corpus callosal abnormalities (CCAs), ranging from thinning and hypoplasia to complete agenesis. Previous studies attempting to delineate the critical region for CCAs have yielded inconsistent results. We conducted a detailed clinical and molecular characterization of seven patients with deletions of chromosome 1q43-q44. Using array comparative genomic hybridization, we mapped the size, extent, and genomic content of these deletions. Four patients had CCAs, and shared the smallest region of overlap that contains only three protein coding genes, CEP170, SDCCAG8, and ZNF238. One patient with a small deletion involving SDCCAG8 and AKT3, and another patient with an intragenic deletion of AKT3 did not have any CCA, implying that the loss of these two genes is unlikely to be the cause of CCA. CEP170 is expressed extensively in the brain, and encodes for a protein that is a component of the centrosomal complex. ZNF238 is involved in control of neuronal progenitor cells and survival of cortical neurons. Our results rule out the involvement of AKT3, and implicate CEP170 and/or ZNF238 as novel genes causative for CCA in patients with a terminal 1q deletion.
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Cukier HN, Salyakina D, Blankstein SF, Robinson JL, Sacharow S, Ma D, Wright HH, Abramson RK, Menon R, Williams SM, Haines JL, Cuccaro ML, Gilbert JR, Pericak-Vance MA. Microduplications in an autism multiplex family narrow the region of susceptibility for developmental disorders on 15q24 and implicate 7p21. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:493-501. [PMID: 21480499 PMCID: PMC5490366 DOI: 10.1002/ajmg.b.31188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 03/04/2011] [Indexed: 11/08/2022]
Abstract
Copy number variations (CNVs) play a crucial role in the intricate genetics of autism spectrum disorders. A region on chromosome 15q24 vulnerable to both deletions and duplications has been previously implicated in a range of phenotypes including autism, Asperger's syndrome, delayed development, and mild to severe mental retardation. Prior studies have delineated a minimal critical region of approximately 1.33 Mb. In this study, a multiplex autism family was evaluated for CNVs using genotyping data from the Illumina 1 M BeadChip and analyzed with the PennCNV algorithm. Variants were then identified that co-segregate with autism features in this family. Here, we report autistic first cousins who carry two microduplications concordant with disease. Both duplications were inherited maternally and found to be identical by descent. The first is an approximately 10,000 base pair microduplication within the minimal region on 15q24 that falls across a single gene, ubiquitin-like 7. This is the smallest duplication in the region to result in a neuropsychiatric disorder, potentially narrowing the critical region for susceptibility to developmental and autism spectrum disorders. The second is a novel, 352 kb tandem duplication on 7p21 that replicates part of the neurexophilin 1 and islet cell autoantigen 1 genes. The breakpoint junction falls within the intronic regions of these genes and demonstrates a microhomology of four base pairs. Each of these microduplications may contribute to the complex etiology of autism spectrum disorders.
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Affiliation(s)
- Holly N. Cukier
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Daria Salyakina
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Sarah F. Blankstein
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Joycelyn L. Robinson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Stephanie Sacharow
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Deqiong Ma
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Harry H. Wright
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina
| | - Ruth K. Abramson
- Department of Neuropsychiatry, University of South Carolina School of Medicine, Columbia, South Carolina
| | - Ramkumar Menon
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia,Department of Obstetrics and Gynecology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Scott M. Williams
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - John R. Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida,Correspondence to: Margaret A. Pericak-Vance, Ph.D., Associate Dean for Human Genomic Programs, Dr. John T. Macdonald Foundation Professor of Human Genomics, Director, John P. Hussman Institute for Human Genomics, 1501 NW 10th Avenue, BRB-314 (M860), University of Miami, Miller School of Medicine, Miami, FL 33136.
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Roetzer KM, Schwarzbraun T, Obenauf AC, Hauser E, Speicher MR. Further evidence for the pathogenicity of 15q24 microduplications distal to the minimal critical regions. Am J Med Genet A 2011; 152A:3173-8. [PMID: 21108404 DOI: 10.1002/ajmg.a.33750] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA copy number alterations in 15q24 have repeatedly been reported in patients exhibiting mild to moderate developmental delay and dysmorphic features. To date, mainly microdeletions have been described, and comparison of overlapping regions allowed the definition of minimal critical regions (MCRs) for microdeletions as well as microduplications. These MCRs are associated with distinct phenotypes. Recently, a family with a new microduplication distal to these MCRs was reported. However, for this alteration the typical phenotypical consequences could not yet be determined. Here we present another family with a nearly identical microduplication exhibiting a broad clinical spectrum including developmental delay, autistic traits and dysmorphic features. Our data suggest that microduplications adjacent and distal to the known MCRs are variable in expressivity and are associated with distinct features. They might represent a novel and recurrent microduplication syndrome.
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Early-onset seizures due to mosaic exonic deletions of CDKL5 in a male and two females. Genet Med 2011; 13:447-52. [DOI: 10.1097/gim.0b013e31820605f5] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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45
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Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J, Szafranski P, Cooper ML, Rao M, Shao L, South ST, Coleman K, Fernhoff PM, Deray MJ, Rosengren S, Roeder ER, Enciso VB, Chinault AC, Patel A, Kang SHL, Shaw CA, Lupski JR, Cheung SW. Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes. Genome Res 2011; 21:33-46. [PMID: 21205869 PMCID: PMC3012924 DOI: 10.1101/gr.111609.110] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/06/2010] [Indexed: 11/24/2022]
Abstract
Four unrelated families with the same unbalanced translocation der(4)t(4;11)(p16.2;p15.4) were analyzed. Both of the breakpoint regions in 4p16.2 and 11p15.4 were narrowed to large ∼359-kb and ∼215-kb low-copy repeat (LCR) clusters, respectively, by aCGH and SNP array analyses. DNA sequencing enabled mapping the breakpoints of one translocation to 24 bp within interchromosomal paralogous LCRs of ∼130 kb in length and 94.7% DNA sequence identity located in olfactory receptor gene clusters, indicating nonallelic homologous recombination (NAHR) as the mechanism for translocation formation. To investigate the potential involvement of interchromosomal LCRs in recurrent chromosomal translocation formation, we performed computational genome-wide analyses and identified 1143 interchromosomal LCR substrate pairs, >5 kb in size and sharing >94% sequence identity that can potentially mediate chromosomal translocations. Additional evidence for interchromosomal NAHR mediated translocation formation was provided by sequencing the breakpoints of another recurrent translocation, der(8)t(8;12)(p23.1;p13.31). The NAHR sites were mapped within 55 bp in ∼7.8-kb paralogous subunits of 95.3% sequence identity located in the ∼579-kb (chr 8) and ∼287-kb (chr 12) LCR clusters. We demonstrate that NAHR mediates recurrent constitutional translocations t(4;11) and t(8;12) and potentially many other interchromosomal translocations throughout the human genome. Furthermore, we provide a computationally determined genome-wide "recurrent translocation map."
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Affiliation(s)
- Zhishuo Ou
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhilian Xia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy M. Breman
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Brian Dawson
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joanna Wiszniewska
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - M. Lance Cooper
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mitchell Rao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lina Shao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah T. South
- Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Karlene Coleman
- Children's Healthcare of Atlanta, Atlanta, Georgia 30033, USA
| | | | - Marcel J. Deray
- Department of Neurology, Miami Children's Hospital, Miami, Florida 33155, USA
| | | | | | | | - A. Craig Chinault
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ankita Patel
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sung-Hae L. Kang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A. Shaw
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
| | - Sau W. Cheung
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Abstract
The widespread clinical utilization of array comparative genome hybridization, has led to the unraveling of many new copy number variations (CNVs). Although some of these CNVs are clearly pathogenic, the phenotypic consequences of others, such as those in 16p13.11 remain unclear. Whereas deletions of 16p13.11 have been associated with multiple congenital anomalies, the relevance of duplications of the region is still being debated. We report detailed clinical and molecular characterization of 10 patients with duplication and 4 patients with deletion of 16p13.11. We found that patients with duplication of the region have varied clinical features including behavioral abnormalities, cognitive impairment, congenital heart defects and skeletal manifestations, such as hypermobility, craniosynostosis and polydactyly. These features were incompletely penetrant. Patients with deletion of the region presented with microcephaly, developmental delay and behavioral abnormalities as previously described. The CNVs were of varying sizes and were likely mediated by non-allelic homologous recombination between low copy repeats. Our findings expand the repertoire of clinical features observed in patients with CNV in 16p13.11 and strengthen the hypothesis that this is a dosage sensitive region with clinical relevance.
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Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, Pursley AN, Kang SHL, Yang Y, Wiszniewska J, Nowakowska BA, del Gaudio D, Xia Z, Simpson-Patel G, Immken LL, Gibson JB, Tsai ACH, Bowers JA, Reimschisel TE, Schaaf CP, Potocki L, Scaglia F, Gambin T, Sykulski M, Bartnik M, Derwinska K, Wisniowiecka-Kowalnik B, Lalani SR, Probst FJ, Bi W, Beaudet AL, Patel A, Lupski JR, Cheung SW, Stankiewicz P. Detection of clinically relevant exonic copy-number changes by array CGH. Hum Mutat 2010; 31:1326-42. [PMID: 20848651 DOI: 10.1002/humu.21360] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/02/2010] [Indexed: 12/22/2022]
Abstract
Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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48
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Szafranski P, Schaaf CP, Person RE, Gibson IB, Xia Z, Mahadevan S, Wiszniewska J, Bacino CA, Lalani S, Potocki L, Kang SH, Patel A, Cheung SW, Probst FJ, Graham BH, Shinawi M, Beaudet AL, Stankiewicz P. Structures and molecular mechanisms for common 15q13.3 microduplications involving CHRNA7: benign or pathological? Hum Mutat 2010; 31:840-50. [PMID: 20506139 DOI: 10.1002/humu.21284] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have investigated four approximately 1.6-Mb microduplications and 55 smaller 350-680-kb microduplications at 15q13.2-q13.3 involving the CHRNA7 gene that were detected by clinical microarray analysis. Applying high-resolution array-CGH, we mapped all 118 chromosomal breakpoints of these microduplications. We also sequenced 26 small microduplication breakpoints that were clustering at hotspots of nonallelic homologous recombination (NAHR). All four large microduplications likely arose by NAHR between BP4 and BP5 LCRs, and 54 small microduplications arose by NAHR between two CHRNA7-LCR copies. We identified two classes of approximately 1.6-Mb microduplications and five classes of small microduplications differing in duplication size, and show that they duplicate the entire CHRNA7. We propose that size differences among small microduplications result from preexisting heterogeneity of the common BP4-BP5 inversion. Clinical data and family histories of 11 patients with small microduplications involving CHRNA7 suggest that these microduplications might be associated with developmental delay/mental retardation, muscular hypotonia, and a variety of neuropsychiatric disorders. However, we conclude that these microduplications and their associated potential for increased dosage of the CHRNA7-encoded alpha 7 subunit of nicotinic acetylcholine receptors are of uncertain clinical significance at present. Nevertheless, if they prove to have a pathological effects, their high frequency could make them a common risk factor for many neurobehavioral disorders.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Tsai ACH, Dossett CJ, Walton CS, Cramer AE, Eng PA, Nowakowska BA, Pursley AN, Stankiewicz P, Wiszniewska J, Cheung SW. Exon deletions of the EP300 and CREBBP genes in two children with Rubinstein-Taybi syndrome detected by aCGH. Eur J Hum Genet 2010; 19:43-9. [PMID: 20717166 DOI: 10.1038/ejhg.2010.121] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We demonstrate the utility of an exon coverage microarray platform in detecting intragenic deletions: one in exons 24-27 of the EP300 gene and another in exons 27 and 28 of the CREBBP gene in two patients with Rubinstein-Taybi syndrome (RSTS). RSTS is a heterogeneous disorder in which approximately 45-55% of cases result from deletion or mutations in the CREBBP gene and an unknown portion of cases result from gene changes in EP300. The first case is a 3-year-old female with an exonic deletion of the EP300 gene who has classic facial features of RSTS without the thumb and great toe anomalies, consistent with the milder skeletal phenotype that has been described in other RSTS cases with EP300 mutations. In addition, the mother of this patient also had preeclampsia during pregnancy, which has been infrequently reported. The second case is a newborn male who has the classical features of RSTS. Our results illustrate that exon-targeted array comparative genomic hybridization (aCGH) is a powerful tool for detecting clinically significant intragenic rearrangements that would be otherwise missed by aCGH platforms lacking sufficient exonic coverage or sequencing of the gene of interest.
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Affiliation(s)
- Anne Chun-Hui Tsai
- The Children's Hospital, Section of Clinical Genetics and Metabolism, Denver, UC Denver, Aurora, CO, USA
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50
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Deletion and duplication of 15q24: Molecular mechanisms and potential modification by additional copy number variants. Genet Med 2010; 12:573-86. [DOI: 10.1097/gim.0b013e3181eb9b4a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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