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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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2
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Akalin H, Sahin IO, Paskal SA, Tan B, Yalcinkaya E, Demir M, Yakubi M, Caliskan BO, Ekinci OG, Ercan M, Kucuk TY, Gokgoz G, Kiraz A, Per H, Ozgun MT, Baydilli N, Ozkul Y, Dundar M. Evaluation of chromosomal abnormalities in the postnatal cohort: A single-center study on 14,242 patients. J Clin Lab Anal 2024; 38:e24997. [PMID: 38115218 PMCID: PMC10829689 DOI: 10.1002/jcla.24997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND AND AIM Chromosomal analysis is a laboratory technique used to examine the chromosomes of an individual, offering insights into chromosome numbers, structures, and arrangements to diagnose and comprehend genetic diseases. This retrospective study provides a comprehensive understanding of the distribution by indications in a large cohort of 14,242 patients and the frequency of chromosomal abnormalities in different clinical populations. METHOD The study examined various indications for karyotype evaluation, with recurrent pregnancy loss being the most common indication, followed by intellectual disability, dysmorphic features, congenital anomalies, and developmental delay. RESULTS The overall chromosomal abnormality rate was found to be 5.4%, with numerical abnormalities accounting for the majority of cases (61.7%). Trisomies, particularly trisomy 21, were the most frequent numerical abnormalities. In terms of structural abnormalities, inversions and translocations were the most commonly identified. The rates of chromosomal anomalies varied in specific indications such as amenorrhea, disorders of sex development, and Turner syndrome. The study also highlighted significant differences between males and females in the presence of chromosomal abnormalities across certain indications. Males exhibited a higher incidence of chromosomal abnormalities in cases of Down syndrome and infertility, whereas females showed higher abnormalities in terms of recurrent pregnancy loss. CONCLUSION While this study provides valuable insights into the frequency and distribution of chromosomal abnormalities, it has limitations, including its retrospective design and reliance on data from a single medical genetics department. Nevertheless, the findings emphasize the importance of karyotype analysis in diagnosing chromosomal disorders and providing appropriate management, while also pointing to potential gender-related variations in chromosomal abnormalities that warrant further investigation.
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Affiliation(s)
- Hilal Akalin
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Seyma Aktas Paskal
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Busra Tan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Ezgi Yalcinkaya
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mikail Demir
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mustafa Yakubi
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Busra Ozguc Caliskan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Ozlem Gokce Ekinci
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Mehmet Ercan
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Tugce Yasar Kucuk
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Gizem Gokgoz
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Aslihan Kiraz
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Huseyin Per
- Department of Pediatric Neurology, Faculty of Medicine, Children's HospitalErciyes UniversityKayseriTürkiye
| | - Mahmut Tuncay Ozgun
- Department of Obstetrics and Gynecology, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Numan Baydilli
- Department of Urology, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
| | - Munis Dundar
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTürkiye
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3
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Gómez-Martín A, Fuentes JM, Jordán J, Galindo MF, Fernández-García JL. Detection of rare Genetic Variations in the promoter regions of the ATG16L gene in Parkinson's patients. Neurosci Lett 2023; 804:137195. [PMID: 36958426 DOI: 10.1016/j.neulet.2023.137195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/07/2023] [Accepted: 03/18/2023] [Indexed: 03/25/2023]
Abstract
Mutations in the ATG genes have been related to impair autophagic function, contributing to the sporadic onset of Parkinsońs Disease (PD). However, scarce studies have been performed about ins/del within the regulatory domains of the autophagy genes in sporadic PD patients. This study was aimed to found ins/del within part of the crucial core autophagy promotor gene region of the ATG16L1 in a groups of sporadic PD patients. After developing a genetic marker to find ins/del using fragment size analysis, a rare mutation by insertion (0.45%) was reported in the patients. This mutation was characterized by sequencing. No others ins/del were found. As a results, the frequency of this insertion should be considered as a rare genetic variant. An in silico analysis also highlighting the usefulness of a search GDV which revealed multiples ins/del within ATG16L1 promoter. Furthermore, these genetic insertions could be found in patients with sporadic PD in the ATG161L promoter gene. When a breakpoint as deletions, insertions or tandem duplication are located within a functional gene interruption of the gene and a loss of function was expected but removing or altering in the regulatory sequence can influence the expression or the regulation of a nearby gene which may impair healthy due to dosage effects in sporadic diseases.
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Affiliation(s)
- A Gómez-Martín
- Universidad de Extremadura, Departamento de Enfermería, Facultad de Enfermería y Terapia Ocupacional, Avda. de la Universidad s/n, 10003, Cáceres, España; Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, España.
| | - José M Fuentes
- Universidad de Extremadura, Departamento de Bioquímica y Biología Molecular y Genética. Facultad de Enfermería y Terapia Ocupacional, Avda de la Universidad s/n, 10003, Cáceres, España; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain; Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, España.
| | - J Jordán
- Departamento de Farmacología. Facultad de Medicina de Albacete. Universidad de Castilla-La Mancha, Albacete, España.
| | - M F Galindo
- Universidad de Castilla-La Mancha, Área de Farmacia y Tecnología Farmacéutica. Departamento de Farmacología, Facultad de Farmacia de Albacete, Albacete, España.
| | - José L Fernández-García
- Universidad Extremadura, Departamento de Producción animal y ciencias de los alimentos, Facultad de Veterinaria, Avda. de la Universidad, s/n, 10003, Cáceres, España
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Wan Mohamad Zamri WN, Mohd Yunus N, Abdul Aziz AA, Zulkipli NN, Sulong S. Perspectives on the Application of Cytogenomic Approaches in Chronic Lymphocytic Leukaemia. Diagnostics (Basel) 2023; 13:964. [PMID: 36900108 PMCID: PMC10001075 DOI: 10.3390/diagnostics13050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a haematological malignancy characterised by the accumulation of monoclonal mature B lymphocytes (positive for CD5+ and CD23+) in peripheral blood, bone marrow, and lymph nodes. Although CLL is reported to be rare in Asian countries compared to Western countries, the disease course is more aggressive in Asian countries than in their Western counterparts. It has been postulated that this is due to genetic variants between populations. Various cytogenomic methods, either of the traditional type (conventional cytogenetics or fluorescence in situ hybridisation (FISH)) or using more advanced technology such as DNA microarrays, next generation sequencing (NGS), or genome wide association studies (GWAS), were used to detect chromosomal aberrations in CLL. Up until now, conventional cytogenetic analysis remained the gold standard in diagnosing chromosomal abnormality in haematological malignancy including CLL, even though it is tedious and time-consuming. In concordance with technological advancement, DNA microarrays are gaining popularity among clinicians as they are faster and better able to accurately diagnose the presence of chromosomal abnormalities. However, every technology has challenges to overcome. In this review, CLL and its genetic abnormalities will be discussed, as well as the application of microarray technology as a diagnostic platform.
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Affiliation(s)
| | - Nazihah Mohd Yunus
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ahmad Aizat Abdul Aziz
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ninie Nadia Zulkipli
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Terengganu 21300, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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5
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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6
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Pattern of cytogenetic abnormalities in syndromic mental retardation/intellectual disability in Kashmir region of Jammu and Kashmir. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Xie X, Wu X, Su L, Cai M, Li Y, Huang H, Xu L. Application of Single Nucleotide Polymorphism Microarray in Prenatal Diagnosis of Fetuses with Central Nervous System Abnormalities. Int J Gen Med 2021; 14:4239-4246. [PMID: 34393503 PMCID: PMC8354765 DOI: 10.2147/ijgm.s323899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023] Open
Abstract
Background The current gold standard of karyotype analysis for prenatal diagnosis of fetuses with central nervous system (CNS) abnormalities has some limitations. Here, we assessed the value of single nucleotide polymorphism (SNP) arrays as a diagnostic tool. Methods The results of prenatal diagnosis of 344 fetuses with CNS abnormalities as determined by ultrasonographic screening were retrospectively analyzed. All fetuses underwent chromosomal karyotype analysis and genome-wide SNP array analysis simultaneously. The resultant rates and frequencies of genomic abnormalities were compared. Results Karyotype analysis found 45 (13.2%) abnormal CNS cases, while SNP array found 60 (17.4%) cases. SNP array detected 23 (6.7%) cases of submicroscopic abnormalities that karyotype analysis did not find. The detection rate of karyotype analysis was 8.1% in the group with isolated CNS anomalies, but 16.5% in the group with CNS abnormalities plus extra ultrasound anomalies. Detection rates of SNP array were 12.4% and 20.8% in these two groups, respectively. Statistical analysis showed that the detection rates of both methods were significantly higher in the group with CNS malformations and other ultrasound anomalies than in the group with isolated CNS anomalies. Abnormal chromosomes were detected most frequently in fetuses with holoprosencephaly. Conclusion Genome-wide SNP array technology can significantly improve the positive detection rate of fetuses with CNS abnormalities. Combining karyotype analysis and SNP array technology is recommended for detecting the development of fetuses with abnormal CNS.
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Affiliation(s)
- Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
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Sachdev R, Field M, Baynam GS, Beilby J, Berarducci M, Berman Y, Boughtwood T, Cusack MB, Fitzgerald V, Fletcher J, Freckmann M, Grainger N, Kirk E, Lundie B, Lunke S, McGregor L, Mowat D, Parasivam G, Tyrell V, Wallis M, White SM, S L Ma A. Paediatric genomic testing: Navigating medicare rebatable genomic testing. J Paediatr Child Health 2021; 57:477-483. [PMID: 33566436 PMCID: PMC8049061 DOI: 10.1111/jpc.15382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/30/2022]
Abstract
Genomic testing for a genetic diagnosis is becoming standard of care for many children, especially those with a syndromal intellectual disability. While previously this type of specialised testing was performed mainly by clinical genetics teams, it is increasingly being 'mainstreamed' into standard paediatric care. With the introduction of a new Medicare rebate for genomic testing in May 2020, this type of testing is now available for paediatricians to order, in consultation with clinical genetics. Children must be aged less than 10 years with facial dysmorphism and multiple congenital abnormalities or have global developmental delay or moderate to severe intellectual disability. This rebate should increase the likelihood of a genetic diagnosis, with accompanying benefits for patient management, reproductive planning and diagnostic certainty. Similar to the introduction of chromosomal microarray into mainstream paediatrics, this genomic testing will increase the number of genetic diagnoses, however, will also yield more variants of uncertain significance, incidental findings, and negative results. This paper aims to guide paediatricians through the process of genomic testing, and represents the combined expertise of educators, clinical geneticists, paediatricians and genomic pathologists around Australia. Its purpose is to help paediatricians navigate choosing the right genomic test, consenting patients and understanding the possible outcomes of testing.
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Affiliation(s)
- Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital‐RandwickSydney Children's Hospitals NetworkSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Mike Field
- Cancer GeneticsRoyal North Shore HospitalSydneyNew South WalesAustralia,GOLD ServiceHunter‐New England Health ServiceNewcastleNew South WalesAustralia
| | - Gareth S Baynam
- Department of HealthGenetic Services of Western AustraliaPerthWestern AustraliaAustralia
| | - John Beilby
- Department of Diagnostic GenomicsPathWest Laboratory MedicinePerthWestern AustraliaAustralia
| | - Maria Berarducci
- Health Education and Training Institute (HETI)NSW Health ServiceSydneyNew South WalesAustralia
| | - Yemima Berman
- Department of Clinical GeneticsRoyal North Shore HospitalSydneyNew South WalesAustralia,Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Tiffany Boughtwood
- Australian GenomicsParkvilleVictoriaAustralia,Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Marie B Cusack
- NSW Health Centre for Genetics EducationRoyal North Shore HospitalSydneyNew South WalesAustralia
| | - Vanessa Fitzgerald
- Speciality Services and Technology Evaluation Unit, Strategic Reform and Planning BranchNSW Ministry of HealthSydneyNew South WalesAustralia
| | - Jeffery Fletcher
- Department of PaediatricsThe Tweed HospitalTweed HeadsNew South WalesAustralia
| | - Mary‐Louise Freckmann
- Department of Clinical GeneticsRoyal North Shore HospitalSydneyNew South WalesAustralia
| | - Natalie Grainger
- NSW Health Centre for Genetics EducationRoyal North Shore HospitalSydneyNew South WalesAustralia
| | - Edwin Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital‐RandwickSydney Children's Hospitals NetworkSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia,Randwick Genomics LaboratoryNSW Health PathologySydneyNew South WalesAustralia
| | - Ben Lundie
- Pathology QueenslandRoyal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - Sebastian Lunke
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of PathologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Lesley McGregor
- South Australian Clinical Genetics ServiceWomen's and Children's HospitalAdelaideSouth AustraliaAustralia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital‐RandwickSydney Children's Hospitals NetworkSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Gayathri Parasivam
- NSW Health Centre for Genetics EducationRoyal North Shore HospitalSydneyNew South WalesAustralia
| | - Vanessa Tyrell
- Children's Cancer Institute. RandwickSydneyNew South WalesAustralia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health ServiceRoyal Hobart HospitalHobartTasmaniaAustralia,School of MedicineThe University of TasmaniaHobartTasmaniaAustralia
| | - Susan M White
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Alan S L Ma
- Specialty of Genomic MedicineUniversity of SydneySydneyNew South WalesAustralia,Department of Clinical Genetics, Children's Hospital WestmeadSydney Children's Hospitals NetworkSydneyNew South WalesAustralia
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Corrêa T, Feltes BC, Schinzel A, Riegel M. Network-based analysis using chromosomal microdeletion syndromes as a model. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:337-348. [PMID: 33754460 DOI: 10.1002/ajmg.c.31900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Microdeletion syndromes (MSs) are a heterogeneous group of genetic diseases that can virtually affect all functions and organs in humans. Although systems biology approaches integrating multiomics and database information into biological networks have expanded our knowledge of genetic disorders, cytogenomic network-based analysis has rarely been applied to study MSs. In this study, we analyzed data of 28 MSs, using network-based approaches, to investigate the associations between the critical chromosome regions and the respective underlying biological network systems. We identified MSs-associated proteins that were organized in a network of linked modules within the human interactome. Certain MSs formed highly interlinked self-contained disease modules. Furthermore, we observed disease modules involving proteins from other disease groups in the MSs interactome. Moreover, analysis of integrated data from 564 genes located in known chromosomal critical regions, including those contributing to topological parameters, shared pathways, and gene-disease associations, indicated that complex biological systems and cellular networks may underlie many genotype to phenotype associations in MSs. In conclusion, we used a network-based analysis to provide resources that may contribute to better understanding of the molecular pathways involved in MSs.
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Affiliation(s)
- Thiago Corrêa
- Post-Graduate Program in Genetics and Molecular Biology, Genetics Department, UFRGS, Porto Alegre, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics, Institute of Informatics, UFRGS, Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Institute of Biosciences, UFRGS, Porto Alegre, Brazil
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Mariluce Riegel
- Post-Graduate Program in Genetics and Molecular Biology, Genetics Department, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, HCPA, Porto Alegre, Brazil
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10
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Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics. Mol Biol Rep 2020; 47:9055-9073. [DOI: 10.1007/s11033-020-05895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
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11
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Sciacca FL, Ciaccio C, Fontana F, Strano C, Gilardoni F, Pantaleoni C, D'Arrigo S. Severe Phenotype in a Patient With Homozygous 15q21.2 Microdeletion Involving BCL2L10, GNB5, and MYO5C Genes, Resembling Infantile Developmental Disorder With Cardiac Arrhythmias (IDDCA). Front Genet 2020; 11:399. [PMID: 32477400 PMCID: PMC7237723 DOI: 10.3389/fgene.2020.00399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 11/29/2022] Open
Abstract
Homozygous and compound heterozygous mutations in GNB5 gene have been associated with a wide spectrum of clinical presentations, ranging from neurodevelopmental issues with or without cardiac arrhythmia (LADCI) to severe developmental delay with epileptic encephalopathy, retinal dystrophy, and heart rhythm abnormalities (IDDCA). While missense or missense/non-sense mutations usually lead to milder form, the biallelic loss of function of GNB5 gene causes the severe multisystemic IDDCA phenotype. So far, only 27 patients have been described with GNB5-associated disease. We report the first case of a patient carrying a homozygous 15q21.2 microdeletion, encompassing GNB5 and the two contiguous genes BCL2L10 and MYO5C. The clinical features of the child are consistent with the severe IDDCA phenotype, thus confirming the GNB5 loss-of-function mechanism in determining such presentation of the disease.
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Affiliation(s)
- Francesca L Sciacca
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudia Ciaccio
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Federica Fontana
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Camilla Strano
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Gilardoni
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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12
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Altıner Ş, Yürür Kutlay N. Importance of patient selection criteria in determining diagnostic copy number variations in patients with multiple congenital anomaly/mental retardation. Mol Cytogenet 2019; 12:23. [PMID: 31149029 PMCID: PMC6537423 DOI: 10.1186/s13039-019-0436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Etiology of developmental delay/intellectual disability is very heterogeneous. In recent years, genetic causes have been defined through the use of chromosomal microarray analysis as a first step genetic test. Results Samples from 30 patients with multiple congenital anomaly and/or mental retardation were analyzed with array comparative genomic hybridization in the context of this study. Before this analysis, karyotyping, subtelomeric fluorescence in situ hybridization and additionally fragment analysis for fragile X in males, had been routinely made all of which were reported to be normal. The purpose of our study was to determine the copy number variations as well as to investigate methods to increase diagnostic yield of array comparative genomic hybridization and forming a suitable flow chart decision pipeline for test indication especially for developing countries. Genomic changes were identified at a rate of about 27% in our series. Although this ratio is higher than the literature data, it could be due to the patient selection criteria. Conclusion Chromosomal microarray analysis is not easily utilized for all patients because of its high-cost. Thus, for increasing cost-effectiveness, it may be used step by step for defined targets. Along with discussing the patients with copy number variations relevant with the phenotype, we suggest a flow chart for selection of diagnostic test with the highest diagnostic rate and the lowest expenditure which is quite important for developing countries.
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Affiliation(s)
- Şule Altıner
- Department of Medical Genetics, Trabzon Kanuni Training and Research Hospital, University of Health Sciences, Topal Osman Street 7, 61290 Trabzon, Turkey.,2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
| | - Nüket Yürür Kutlay
- 2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
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13
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Belkady B, Elkhattabi L, Elkarhat Z, Zarouf L, Razoki L, Aboulfaraj J, Nassereddine S, Cadi R, Rouba H, Barakat A. Chromosomal Abnormalities in Patients with Intellectual Disability: A 21-Year Retrospective Study. Hum Hered 2019; 83:274-282. [PMID: 31064002 DOI: 10.1159/000499710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/19/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) has been defined as a considerably reduced ability to understand new or complex information and to learn new skills. It is associated with life-long intellectual and adaptive functioning impairments that have a profound impact on individuals, families, and society. It affects about 3% of the general population. ID often comes out with other mental conditions like attention deficit, hyperactivity, and autism spectrum disorders (ASD), and it can be part of a malformation syndrome that affects other organs. It may be syndromic (S-ID) or non-syndromic (NS-ID). OBJECTIVE The aims of this study were to identify the profile of intellectually disable patients being referred for cytogenetic analysis in Morocco, to determine the prevalence of chromosomal abnormalities in a Moroccan group, and to compare the results with those of analogous studies from other countries. PARTICIPANTS We included data from Moroccan patients with NS-ID and others with S-ID (mostly Down syndrome cases) who have been referred between 1996 and 2016. 1,626 patients were involved in this study, 1,200 were referred with a clinical diagnosis of Down syndrome, 37 were clinically diagnosed for ASD with ID, and 389 were suspected of NS-ID. RESULTS We identified 1,200 cases of Down syndrome. In 1,096 analyses (91.3%), a cytogenetic variant of trisomy 21 was identified: standard trisomy 21 in 1,037 cases (94.6%), a translocation in 34 cases (3.10%), and mosaicism in 25 cases (2.3%). The cytogenetic analysis among ASD with ID cases did not reveal any specific chromosomal abnormalities. The present study also shows that chromosomal abnormalities were present in 6.43% of the patients with NS-ID (25 abnormal karyotypes out of 389 NS-ID cases). Autosomal structural abnormalities were the largest proportion of chromosomal aberrations. CONCLUSION The high rate of chromosomal abnormalities found in the Moroccan patients studied demonstrates the capital importance of cytogenetic evaluation in patients who show ID or any clinical development abnormality.
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Affiliation(s)
- Boutaina Belkady
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Zouhair Elkarhat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Latifa Zarouf
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Lunda Razoki
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Jamila Aboulfaraj
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sanaa Nassereddine
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Rachida Cadi
- Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco,
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14
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Levchenko OA, Lavrov AV. [Massive parallel sequencing for molecular-genetic diagnosis of mental retardation]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 118:65-71. [PMID: 30698565 DOI: 10.17116/jnevro201811812165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene mutations occur with high frequency in children with mental retardation. Standard diagnostic methods, such as TMS, Sanger's sequencing of individual genes, MLPA analysis of deletions, and investigation of methylation status in Martin-Bell syndrome are not informative in the majority of cases that hampered further diagnostic efforts. Massive parallel sequencing (MPS) allowed physicians to continue diagnostic search in previously undiagnosed cases and to find molecular causes of disease. MPS permits to discover a large number of new genes and understand the pathogenesis of mental retardation and brain development more deeply. It became possible to perform prenatal and pre-implantation diagnostics. However, big data generate big problems with their interpretation the genetic counselor faces with. This review reflects the advantages and disadvantages of MPS. Different variants of MPS, including gene panels, whole exome and whole genome sequencing as well as sequencing of trios, are described. In addition, the authors discuss the difficulties of interpretation of the results and recommendations for obtaining the most accurate results.
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Affiliation(s)
- O A Levchenko
- Research Centre for Medical Genetics, Moscow, Russia
| | - A V Lavrov
- Research Centre for Medical Genetics, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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15
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Abstract
PURPOSE OF REVIEW Investigation for genetic causes of intellectual disability has advanced rapidly in recent years. We review the assessment of copy number variants (CNVs) and the use of next-generation sequencing based assays to identify single nucleotide variation in intellectual disability. We discuss the diagnostic yields that can be expected with the different assays. There is high co-morbidity of intellectual disability and psychiatric disorders. We review the relationship between variants which are pathogenic for intellectual disability and the risk of child and adolescent onset psychiatric disorders. RECENT FINDINGS The diagnostic yields from genome wide CNV analysis and whole exome sequence analysis are high - in the region of 15 and 40%, respectively - but vary according to exact referral criteria. Many variants pathogenic for intellectual disability, notably certain recurrent CNVs, have emerged as strong risk factors for other neurodevelopmental disorders such as autism spectrum disorders, attention deficit hyperactivity disorder, and schizophrenia. SUMMARY It is now conceivable that etiological variants could be identified in the majority of children presenting with intellectual disability using next-generation sequencing based assays. However, challenges remain in assessment of the pathogenicity of variants, reporting of incidental findings in children and determination of prognosis, particularly in relation to psychiatric disorders.
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16
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Ceroni JRM, Dutra RL, Honjo RS, Llerena JC, Acosta AX, Medeiros PFV, Galera MF, Zanardo ÉA, Piazzon FB, Dias AT, Novo-Filho GM, Montenegro MM, Madia FAR, Bertola DR, de Melo JB, Kulikowski LD, Kim CA. A Multicentric Brazilian Investigative Study of Copy Number Variations in Patients with Congenital Anomalies and Intellectual Disability. Sci Rep 2018; 8:13382. [PMID: 30190605 PMCID: PMC6127201 DOI: 10.1038/s41598-018-31754-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imbalances are the most common cause of congenital anomalies (CA) and intellectual disability (ID). The aims of this study were to identify copy number variations (CNVs) in 416 patients with CA and ID from 5 different genetics centers within 4 different states by using the Multiplex Ligation-dependent Probe Amplification (MLPA) technique and to apply the chromosomal microarray (CMA) methodology in selected cases. The samples were analyzed by MLPA kits P064, P036, P070 and P250. Positive results were found in 97/416 (23.3%) patients. CMA was applied in 14 selected cases. In 6/14 (42.85%) patients, CMA detected other copy number variations not detected by the MLPA studies. Although CMA is indispensable for genotype refinement, the technique is still unfeasible in some countries as a routine analysis due to economic and technical limitations. In these cases, clinical evaluation followed by karyotyping and MLPA analysis is a helpful and affordable solution for diagnostic purposes.
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Affiliation(s)
- J R M Ceroni
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.
| | - R L Dutra
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - R S Honjo
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
| | - J C Llerena
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - A X Acosta
- Universidade Federal da Bahia, Salvador, BA, Brazil
| | - P F V Medeiros
- Universidade Federal de Campina Grande, Campina Grande, PB, Brazil
| | - M F Galera
- Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - É A Zanardo
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F B Piazzon
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - A T Dias
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - G M Novo-Filho
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - M M Montenegro
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F A R Madia
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - D R Bertola
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.,Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil., São Paulo, SP, Brazil
| | - J B de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Faculdade de Medicina, Universidade de Coimbra, CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - L D Kulikowski
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - C A Kim
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
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17
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Suleiman J, Mundt M, Sampath S, El-Hattab A. TASP1
is deleted in an infant with developmental delay, microcephaly, distinctive facial features, and multiple congenital anomalies. Clin Genet 2018; 94:170-173. [DOI: 10.1111/cge.13258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/21/2018] [Accepted: 03/30/2018] [Indexed: 11/30/2022]
Affiliation(s)
- J. Suleiman
- Division of Neurology, Department of Pediatrics; Tawam Hospital, and Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University; Al Ain United Arab Emirates
| | - M. Mundt
- PreventionGenetics, LLC; Marshfield Wisconsin
| | - S. Sampath
- PreventionGenetics, LLC; Marshfield Wisconsin
| | - A.W. El-Hattab
- Division of Genetic and Metabolic Disorders, Department of Pediatrics; Tawam Hospital; Al Ain United Arab Emirates
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18
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Abstract
MethodPatients known to learning disability services in two health boards in southeast Scotland were cross-matched with the patients tested at the Western General Hospital in Edinburgh. Those with a positive genetic diagnosis were identified. Semi-structured interviews were conducted with senior learning disability psychiatrists and clinical genetics consultants.ResultsOf the 3323 patients with intellectual disability across both health boards, 41% have had genetic tests and 6% have an identified genetic abnormality as the cause for their intellectual disability. Of the 1349 patients who have been tested, a genetic abnormality was found in 14%. Psychiatrists named several benefits to genetic testing, but they also highlighted a number of non-medical reasons for not testing adults with intellectual disability.Clinical implicationsIdentifying genetic aetiology in intellectual disability has a number of benefits. Our study would indicate that genetic diagnoses are being missed due to a lack of genetic testing in this patient group. Adult learning disability services need to consider increasing genetic testing.
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19
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Ko JM. Chromosomal Microarray: Application for Congenital Heart Diseases. Korean Circ J 2018; 48:233-235. [PMID: 29557111 PMCID: PMC5861317 DOI: 10.4070/kcj.2018.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.
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20
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Arican P, Cavusoglu D, Gencpinar P, Ozyilmaz B, Ozdemir TR, Dundar NO. A De Novo Xp11.23 Duplication in a Girl with a Severe Phenotype: Expanding the Clinical Spectrum. J Pediatr Genet 2017; 7:74-77. [PMID: 29707408 DOI: 10.1055/s-0037-1612598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
The Xp11.22-p11.23 duplication syndrome was described in 2009 by Giorda et al and is characterized by intellectual disability, speech delay, and electroencephalography anomalies. We report a case of a 23-month-old girl who presented with epilepsy and global developmental delay and who had a small duplication at Xp11.23. The case we present here is the first case showing the clinical features of Xp11.22-p11.23 duplication syndrome only involving synovial sarcoma, X breakpoint ( SSX ) genes: SSX1 , SSX3 , SSX4 , and SSX9 . This case report contributes to an expanding clinical spectrum of Xp11.22-p11.23 duplication syndrome.
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Affiliation(s)
- Pinar Arican
- Department of Pediatric Neurology, Izmir Tepecik Education and Research Hospital, Izmir, Turkey
| | - Dilek Cavusoglu
- Department of Pediatric Neurology, Izmir Katip Celebi University, Izmir, Turkey
| | - Pinar Gencpinar
- Department of Pediatric Neurology, Izmir Katip Celebi University, Izmir, Turkey
| | - Berk Ozyilmaz
- Department of Genetics, Izmir Tepecik Education and Research Hospital, Izmir, Turkey
| | - Taha Resid Ozdemir
- Department of Genetics, Izmir Tepecik Education and Research Hospital, Izmir, Turkey
| | - Nihal Olgac Dundar
- Department of Pediatric Neurology, Izmir Katip Celebi University, Izmir, Turkey
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21
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Borlot F, Regan BM, Bassett AS, Stavropoulos DJ, Andrade DM. Prevalence of Pathogenic Copy Number Variation in Adults With Pediatric-Onset Epilepsy and Intellectual Disability. JAMA Neurol 2017; 74:1301-1311. [PMID: 28846756 DOI: 10.1001/jamaneurol.2017.1775] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Importance Copy number variation (CNV) is an important cause of neuropsychiatric disorders. Little is known about the role of CNV in adults with epilepsy and intellectual disability. Objectives To evaluate the prevalence of pathogenic CNVs and identify possible candidate CNVs and genes in patients with epilepsy and intellectual disability. Design, Setting, and Participants In this cross-sectional study, genome-wide microarray was used to evaluate a cohort of 143 adults with unexplained childhood-onset epilepsy and intellectual disability who were recruited from the Toronto Western Hospital epilepsy outpatient clinic from January 1, 2012, through December 31, 2014. The inclusion criteria were (1) pediatric seizure onset with ongoing seizure activity in adulthood, (2) intellectual disability of any degree, and (3) no structural brain abnormalities or metabolic conditions that could explain the seizures. Main Outcomes and Measures DNA screening was performed using genome-wide microarray platforms. Pathogenicity of CNVs was assessed based on the American College of Medical Genetics guidelines. The Residual Variation Intolerance Score was used to evaluate genes within the identified CNVs that could play a role in each patient's phenotype. Results Of the 2335 patients, 143 probands were investigated (mean [SD] age, 24.6 [10.8] years; 69 male and 74 female). Twenty-three probands (16.1%) and 4 affected relatives (2.8%) (mean [SD] age, 24.1 [6.1] years; 11 male and 16 female) presented with pathogenic or likely pathogenic CNVs (0.08-18.9 Mb). Five of the 23 probands with positive results (21.7%) had more than 1 CNV reported. Parental testing revealed de novo CNVs in 11 (47.8%), with CNVs inherited from a parent in 4 probands (17.4%). Sixteen of 23 probands (69.6%) presented with previously cataloged human genetic disorders and/or defined CNV hot spots in epilepsy. Eight nonrecurrent rare CNVs that overlapped 1 or more genes associated with intellectual disability, autism, and/or epilepsy were identified: 2p16.1-p15 duplication, 6p25.3-p25.1 duplication, 8p23.3p23.1 deletion, 9p24.3-p23 deletion, 10q11.22-q11.23 duplication, 12p13.33-13.2 duplication, 13q34 deletion, and 16p13.2 duplication. Five genes are of particular interest given their potential pathogenicity in the corresponding phenotypes and least tolerability to variation: ABAT, KIAA2022, COL4A1, CACNA1C, and SMARCA2. ABAT duplication was associated with Lennox-Gastaut syndrome and KIAA2022 deletion with Jeavons syndrome. Conclusions and Relevance The high prevalence of pathogenic CNVs in this study highlights the importance of microarray analysis in adults with unexplained childhood-onset epilepsy and intellectual disability. Additional studies and comparison with similar cases are required to evaluate the effects of deletions and duplications that overlap specific genes.
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Affiliation(s)
- Felippe Borlot
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Clinical Neurosciences Center, Department of Neurology, University of Utah, Salt Lake City
| | - Brigid M Regan
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - D James Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Division of Neurology, Krembil Neuroscience Centre, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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22
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Best S, Rosser E, Bajaj M. Fifteen years of genetic testing from a London developmental clinic. Arch Dis Child 2017; 102:1014-1018. [PMID: 28659270 DOI: 10.1136/archdischild-2017-312739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To evaluate genetic disease among children referred to a community paediatric clinic. DESIGN Retrospective cohort study. SETTING Community paediatric clinic, Tower Hamlets, London. PATIENTS All patients seen for first time in the Child Development Team (CDT) clinic between 1999 and 2013. INTERVENTIONS Clinical notes were reviewed. Genetic test results were obtained. Exploratory Excel analysis was performed. Patients without an identified genetic disorder were labelled 'more likely genetic cause' if they had at least two out of three risk factors: developmental delay, congenital abnormality or parental consanguinity, and 'unlikely genetic cause' if they had one or no risk factors, or an obvious alternative cause. MAIN OUTCOME MEASURES Prevalence of genetic diagnoses and parental consanguinity, undertaking of genetic tests, predicted likelihood of a genetic cause among unsolved patients. RESULTS 749 patients were included. 404 (53.9%) had undergone genetic testing and 158 of those tested (39.1%) had a confirmed genetic diagnosis. Parental relatedness was documented in 461 patients, of which 128 (27.8%) had first-cousin parents. The number of patients undergoing genetic testing increased over time. Aneuploidies and syndromic/Mendelian disorders were most common. Of the 591 patients without a genetic diagnosis, 29.9% were classified 'more likely genetic cause'. Patients with consanguineous parents were significantly more likely to have a diagnosed genetic disorder than those with non-consanguineous parents (43/128 vs 72/333), particularly an autosomal recessive condition (27/43 vs 6/72). CONCLUSIONS Genetic disease was common and genetic testing is important in evaluating children in this clinic. Consanguinity increases the likelihood of autosomal recessive disease.
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Affiliation(s)
- Sunayna Best
- Community Paediatrics, Wellington Way Centre, Barts Health NHS Trust, London, UK.,Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Monika Bajaj
- Community Paediatrics, Wellington Way Centre, Barts Health NHS Trust, London, UK
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23
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Wessel K, Suleiman J, Khalaf TE, Kishore S, Rolfs A, El-Hattab AW. 17q23.2q23.3 de novo duplication in association with speech and language disorder, learning difficulties, incoordination, motor skill impairment, and behavioral disturbances: a case report. BMC MEDICAL GENETICS 2017; 18:119. [PMID: 29070031 PMCID: PMC5657100 DOI: 10.1186/s12881-017-0479-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/12/2017] [Indexed: 11/30/2022]
Abstract
Background Chromosomal rearrangements involving 17q23 have been described rarely. Deletions at 17q23.1q23.2 have been reported in individuals with developmental delay and growth retardation, whereas duplications at 17q23.1q23.2 appear to segregate with clubfoot. Dosage alterations in the TBX2 and TBX4 genes, located in 17q23.2, have been proposed to be responsible for the phenotypes observed in individuals with 17q23.1q23.2 deletions and duplications. In this report, we present the clinical phenotype of a child with a previously unreported de novo duplication at 17q23.2q23.3 located distal to the TBX2 and TBX4 region. Case presentation We report a 7.5-year-old boy with speech and language disorder, learning difficulties, incoordination, fine motor skill impairment, infrequent seizures with abnormal EEG, and behavior disturbances (mild self-inflicted injuries, hyperactivity-inattention, and stereotyped hand movements). Chromosomal microarray revealed a 2-Mb duplication of chromosome 17q23.2q23.3. Both parents did not have the duplication indicating that this duplication is de novo in the child. Conclusions The duplicated region encompasses 16 genes. It is possible that increased dosage of one or more genes in this region is responsible for the observed phenotype. The TANC2 gene is one of the genes in the duplicated region.It encodes a member of the TANC (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing) family which includes TANC1 and TANC2. These proteins are highly expressed in brain and play major roles in synapsis regulation. Hence, it is suggestive that TANC2 is the likely candidate gene responsible for the observed phenotype as an increased TANC2 dosage can potentially alter synapsis, resulting in neuronal dysfunction and the neurobehavioral phenotype observed in this child with 17q23.2q23.3 duplication.
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Affiliation(s)
- Karen Wessel
- Centogene AG, Schillingallee, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Gehlsheimer Straße, Rostock, Germany
| | - Jehan Suleiman
- Division of Neurology, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Tamam E Khalaf
- Biochemistry, University of Toronto Mississauga, Mississauga, Canada
| | - Shivendra Kishore
- Centogene AG, Schillingallee, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Gehlsheimer Straße, Rostock, Germany
| | - Arndt Rolfs
- Centogene AG, Schillingallee, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Gehlsheimer Straße, Rostock, Germany
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates.
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24
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Wu Y, Wang Y, Tao J, Han X, Zhao X, Liu C, Gao L, Cheng W. The clinical use of chromosomal microarray analysis in detection of fetal chromosomal rearrangements: a study from China Mainland. Eur J Obstet Gynecol Reprod Biol 2017; 212:44-50. [DOI: 10.1016/j.ejogrb.2017.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/19/2017] [Accepted: 03/04/2017] [Indexed: 10/20/2022]
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25
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Szczałuba K, Jakubiuk-Tomaszuk A, Kędzior M, Bernaciak J, Zdrodowska J, Kurzątkowski W, Radkowski M, Demkow U. Cytogenomic Evaluation of Children with Congenital Anomalies: Critical Implications for Diagnostic Testing and Genetic Counseling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 912:11-9. [PMID: 26987321 DOI: 10.1007/5584_2016_234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Identification of submicroscopic chromosomal aberrations, as a cause of structural malformations, is currently performed by MLPA (multiplex ligation-dependent probe amplification) or array CGH (array comparative genomic hybridization) techniques. The aim of this study was the evaluation of diagnostic usefulness of MLPA and array CGH in patients with congenital malformations or abnormalities (at least one major or minor birth defect, including dysmorphism) with or without intellectual disability or developmental delay and the optimization of genetic counseling in the context of the results obtained. The MLPA and array CGH were performed in 91 patients diagnosed with developmental disorders and major or minor congenital anomalies. A total of 49 MLPA tests toward common microdeletion syndromes, 42 MLPA tests for subtelomeric regions of chromosomes, two tests for common aberrations in autism, and five array CGH tests were performed. Eight (9 %) patients were diagnosed with microdeletion MLPA, four (4 %) patients with subtelomeric MLPA, one (1 %) patient with autism MLPA. Further three (3 %) individuals had rearrangements diagnosed by array CGH. Altogether, chromosomal microaberrations were found in 16 patients (17 %). All the MLPA-detected rearrangements were found to be pathogenic, but none detected with array CGH could unequivocally be interpreted as pathogenic. In patients with congenital anomalies, the application of MLPA and array CGH techniques is efficient in detecting syndromic and unique microrearrangements. Consistent pre-MLPA test phenotyping leads to better post-test genetic counseling. Incomplete penetrance and unknown inheritance of detected variants are major issues in clinical interpretation of array CGH data.
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Affiliation(s)
- Krzysztof Szczałuba
- MedGen Medical Center, Warsaw, Poland.
- Medical Genetics Unit, Mastermed Medical Center, Białystok, Poland.
| | | | - Marta Kędzior
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Warsaw Medical University, Warsaw, Poland
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26
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Strunk D, Weber P, Röthlisberger B, Filges I. Autism and intellectual disability in a patient with two microdeletions in 6q16: a contiguous gene deletion syndrome? Mol Cytogenet 2016; 9:88. [PMID: 27980676 PMCID: PMC5135825 DOI: 10.1186/s13039-016-0299-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 01/19/2023] Open
Abstract
Background Copy number variations play a significant role in the aetiology of developmental disabilities including non-syndromic intellectual disability and autism. Case presentation We describe a 19-year old patient with intellectual disability and autism for whom chromosomal microarray (CMA) analysis showed the unusual finding of two de novo microdeletions in cis position on chromosome 6q16.1q16.2 and 6q16.3. The two deletions span 10 genes, including FBXL4, POU3F2, PRDM13, CCNC, COQ3 and GRIK2. We compared phenotypes of patients with similar deletions and looked at the involvement of the genes in neuronal networks in order to determine the pathogenicity of our patient’s deletions. Conclusions We suggest that both deletions on 6q are causing his disease phenotype since they harbour several genes which are implicated in pathways of neuronal development and function. Further studies regarding the interaction between PRDM13 and GRIK2 specifically may be interesting.
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Affiliation(s)
- Daniela Strunk
- Medical Genetics, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
| | - Peter Weber
- Division of Neuropediatrics and Developmental Pediatrics, University Children's Hospital, Spitalstrasse 33, CH-4056 Basel, Switzerland
| | - Benno Röthlisberger
- Medical Genetics, Department of Laboratory Medicine, Cantonal Hospital Aarau, Tellstrasse, CH-5001 Aarau, Switzerland
| | - Isabel Filges
- Medical Genetics, University Hospital Basel and University of Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
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27
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Abstract
The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.
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Affiliation(s)
- Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
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28
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Puri RD, Tuteja M, Verma IC. Genetic Approach to Diagnosis of Intellectual Disability. Indian J Pediatr 2016; 83:1141-9. [PMID: 27619815 DOI: 10.1007/s12098-016-2205-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 01/29/2023]
Abstract
Intellectual disability is a non-specific phenotype present in a genetically heterogeneous group of disorders. It is characterized by deficits in intellectual and adaptive functioning, presenting before 18 y of age. Identifying the cause of ID is important to provide treatment where available, genetic counseling, recurrence risks and reproductive options for subsequent pregnancies. Advances in technology, especially next generation sequencing and microarrays, have greatly increased the diagnostic yield of evaluation in cases of ID. This paper describes the points in history taking and examination in the evaluation of a proband, and discusses the proper use of newer diagnostic technologies.
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Affiliation(s)
- Ratna Dua Puri
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India.
| | - Moni Tuteja
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - I C Verma
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
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29
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Inherited duplication of the short arm of chromosome 18p11.32-p11.31 associated with developmental delay/intellectual disability. Clin Dysmorphol 2016; 25:19-22. [PMID: 26287558 DOI: 10.1097/mcd.0000000000000097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Duplications of 18p have been reported in the literature associated with a range of different abnormalities and also in patients with normal phenotypes. The majority of these reports are based solely on G-banded cytogenetic evaluation. The use of arrayCGH characterization has improved the ability to define regions of imbalance and is helping to identify potential underlying triplosufficiency of any duplicated genes. We report on a family where the father and his two daughters all have a duplication 18p11.32-p11.31 characterized by microarray. They present with variable levels of intellectual disability/developmental delay and behavioural difficulties without any physical anomalies. This family contributes toward the growing knowledge of pure duplications of 18p and provides information on interpretation of novel array findings in the context of family history. It also reiterates the importance of elucidating a detailed learning and developmental phenotype and family pedigree in aiding interpretation of genetic testing results.
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Abstract
Over the last half century, knowledge about genetics, genetic testing, and its complexity has flourished. Completion of the Human Genome Project provided a foundation upon which the accuracy of genetics, genomics, and integration of bioinformatics knowledge and testing has grown exponentially. What is lagging, however, are efforts to reach and engage nurses about this rapidly changing field. The purpose of this article is to familiarize nurses with several frequently ordered genetic tests including chromosomes and fluorescence in situ hybridization followed by a comprehensive review of chromosome microarray. It shares the complexity of microarray including how testing is performed and results analyzed. A case report demonstrates how this technology is applied in clinical practice and reveals benefits and limitations of this scientific and bioinformatics genetic technology. Clinical implications for maternal-child nurses across practice levels are discussed.
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31
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Wang B, Ji T, Zhou X, Wang J, Wang X, Wang J, Zhu D, Zhang X, Sham PC, Zhang X, Ma X, Jiang Y. CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens. Sci Rep 2016; 6:25954. [PMID: 27257017 PMCID: PMC4891738 DOI: 10.1038/srep25954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/06/2016] [Indexed: 12/28/2022] Open
Abstract
Rare copy number variations (CNVs) are a known genetic etiology in neurodevelopmental disorders (NDD). Comprehensive CNV analysis was performed in 287 Chinese children with mental retardation and/or development delay (MR/DD) and their unaffected parents. When compared with 5,866 ancestry-matched controls, 11~12% more MR/DD children carried rare and large CNVs. The increased CNV burden in MR/DD was predominantly due to de novo CNVs, the majority of which (62%) arose in the paternal germline. We observed a 2~3 fold increase of large CNV burden in the mothers of affected children. By implementing an evidence-based review approach, pathogenic structural variants were identified in 14.3% patients and 2.4% parents, respectively. Pathogenic CNVs in parents were all carried by mothers. The maternal transmission bias of deleterious CNVs was further replicated in a published dataset. Our study confirms the pathogenic role of rare CNVs in MR/DD, and provides additional evidence to evaluate the dosage sensitivity of some candidate genes. It also supports a population model of MR/DD that spontaneous mutations in males' germline are major contributor to the de novo mutational burden in offspring, with higher penetrance in male than female; unaffected carriers of causative mutations, mostly females, then contribute to the inherited mutational burden.
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Affiliation(s)
- Binbin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,National Research Institute of Family Planning, Beijing, China
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueya Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China.,Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Wang
- Department of Medical Genetics, The Capital Medical University, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Heifei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Xu Ma
- National Research Institute of Family Planning, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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D'Arrigo S, Gavazzi F, Alfei E, Zuffardi O, Montomoli C, Corso B, Buzzi E, Sciacca FL, Bulgheroni S, Riva D, Pantaleoni C. The Diagnostic Yield of Array Comparative Genomic Hybridization Is High Regardless of Severity of Intellectual Disability/Developmental Delay in Children. J Child Neurol 2016; 31:691-9. [PMID: 26511719 DOI: 10.1177/0883073815613562] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/22/2015] [Indexed: 12/08/2022]
Abstract
Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. The aim of the present study was to apply a clinical score previously designated by de Vries to 329 patients with intellectual disability/developmental disorder (intellectual disability/developmental delay) referred to our tertiary center and to see whether the clinical factors are associated with a positive outcome of aCGH analyses. Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. Our study showed that causative copy number variants are frequently found even in cases of mild intellectual disability (30.77%). We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization.
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Affiliation(s)
- Stefano D'Arrigo
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | - Francesco Gavazzi
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | - Enrico Alfei
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | | | - Cristina Montomoli
- Department of Public Health, Neuroscience, Experimental and Forensic Medicine, University of Pavia, Italy
| | - Barbara Corso
- Neuroscience Institute, National Research Council, Padua, Italy
| | - Erika Buzzi
- Institute of Neurological and Psychiatric Sciences of Childhood and Adolescence, University of Milan, A.O. San Paolo, Milan, Italy
| | - Francesca L Sciacca
- Medical Genetics Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | - Sara Bulgheroni
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | - Daria Riva
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Department, IRCCS Fondazione Istituto Neurologico "C. Besta," Milan, Italy
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33
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Cappuccio G, Vitiello F, Casertano A, Fontana P, Genesio R, Bruzzese D, Ginocchio VM, Mormile A, Nitsch L, Andria G, Melis D. New insights in the interpretation of array-CGH: autism spectrum disorder and positive family history for intellectual disability predict the detection of pathogenic variants. Ital J Pediatr 2016; 42:39. [PMID: 27072107 PMCID: PMC4830019 DOI: 10.1186/s13052-016-0246-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/15/2016] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND Array-CGH (aCGH) is presently used into routine clinical practice for diagnosis of patients with intellectual disability (ID), multiple congenital anomalies (MCA), and autism spectrum disorder (ASD). ACGH could detect small chromosomal imbalances, copy number variations (CNVs), and closely define their size and gene content. ACGH detects pathogenic imbalances in 14-20 % of patients with ID. The aims of this study were: to establish clinical clues potentially associated with pathogenic CNVs and to identify cytogenetic indicators to predict the pathogenicity of the variants of uncertain significance (VOUS) in a large cohort of paediatric patients. METHODS We enrolled 214 patients referred for either: ID, and/or ASD and/or MCA to genetic services at the Federico II University of Naples, Department of Translational Medicine. For each patient we collected clinical and imaging data. All the patients were tested with aCGH or as first-tier test or as part of a wider diagnostic work-up. RESULTS Pathologic data were detected in 65 individuals (30 %) and 46 CNVs revealed a known syndrome. The pathological CNVs were usually deletions showing the highest gene-dosage content. The positive family history for ID/ASD/MCA and ASD were good indicators for detecting pathological chromosomal rearrangements. Other clinical features as eyes anomalies, hearing loss, neurological signs, cutaneous dyscromia and endocrinological problems seem to be potential predictors of pathological CNVs. Among patients carrying VOUS we analyzed genetic features including CNVs size, presence of deletion or duplication, genic density, multiple CNVs, to clinical features. Higher gene density was found in patients affected by ID. This result suggest that higher gene content has more chances to include pathogenic gene involved and causing ID in these patients. CONCLUSION Our study suggest the use of aCGH as first-tier test in patients with neurdevelopmental phenotypes. The inferred results have been used for building a flow-chart to be applied for children with ID.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Francesco Vitiello
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Alberto Casertano
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Paolo Fontana
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Rita Genesio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Dario Bruzzese
- Preventive Medical Sciences, Federico II University, Naples, Italy
| | | | - Angela Mormile
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Lucio Nitsch
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Generoso Andria
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Daniela Melis
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy.
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34
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Long Y, Su Y, Ai H, Zhang Z, Yang B, Ruan G, Xiao S, Liao X, Ren J, Huang L, Ding N. A genome-wide association study of copy number variations with umbilical hernia in swine. Anim Genet 2016; 47:298-305. [PMID: 27028052 DOI: 10.1111/age.12402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 02/06/2023]
Abstract
Umbilical hernia (UH) is one of the most common congenital defects in pigs, leading to considerable economic loss and serious animal welfare problems. To test whether copy number variations (CNVs) contribute to pig UH, we performed a case-control genome-wide CNV association study on 905 pigs from the Duroc, Landrace and Yorkshire breeds using the Porcine SNP60 BeadChip and penncnv algorithm. We first constructed a genomic map comprising 6193 CNVs that pertain to 737 CNV regions. Then, we identified eight CNVs significantly associated with the risk for UH in the three pig breeds. Six of seven significantly associated CNVs were validated using quantitative real-time PCR. Notably, a rare CNV (CNV14:13030843-13059455) encompassing the NUGGC gene was strongly associated with UH (permutation-corrected P = 0.0015) in Duroc pigs. This CNV occurred exclusively in seven Duroc UH-affected individuals. SNPs surrounding the CNV did not show association signals, indicating that rare CNVs may play an important role in complex pig diseases such as UH. The NUGGC gene has been implicated in human omphalocele and inguinal hernia. Our finding supports that CNVs, including the NUGGC CNV, contribute to the pathogenesis of pig UH.
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Affiliation(s)
- Yi Long
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ying Su
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhiyan Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guorong Ruan
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.,Fujian Vocational College of Agriculture, Fuzhou, 360119, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinjun Liao
- College of Life Science of Jinggangshan University, Jian, 343009, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nengshui Ding
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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35
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Szczałuba K, Nowakowska B, Sobecka K, Smyk M, Castaneda J, Klapecki J, Kutkowska-Kaźmierczak A, Śmigiel R, Bocian E, Radkowski M, Demkow U. Application of Array Comparative Genomic Hybridization in Newborns with Multiple Congenital Anomalies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 912:1-9. [PMID: 26987320 DOI: 10.1007/5584_2016_235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Major congenital anomalies are detectable in 2-3 % of the newborn population. Some of their genetic causes are attributable to copy number variations identified by array comparative genomic hybridization (aCGH). The value of aCGH screening as a first-tier test in children with multiple congenital anomalies has been studied and consensus adopted. However, array resolution has not been agreed upon, specifically in the newborn or infant population. Moreover, most array studies have been focused on mixed populations of intellectual disability/developmental delay with or without multiple congenital anomalies, making it difficult to assess the value of microarrays in newborns. The aim of the study was to determine the optimal quality and clinical sensitivity of high-resolution array comparative genomic hybridization in neonates with multiple congenital anomalies. We investigated a group of 54 newborns with multiple congenital anomalies defined as two or more birth defects from more than one organ system. Cytogenetic studies were performed using OGT CytoSure 8 × 60 K microarray. We found ten rearrangements in ten newborns. Of these, one recurrent syndromic microduplication was observed, whereas all other changes were unique. Six rearrangements were definitely pathogenic, including one submicroscopic and five that could be seen on routine karyotype analysis. Four other copy number variants were likely pathogenic. The candidate genes that may explain the phenotype were discussed. In conclusion, high-resolution array comparative hybridization can be applied successfully in newborns with multiple congenital anomalies as the method detects a significant number of pathogenic changes, resulting in early diagnoses. We hypothesize that small changes previously considered benign or even inherited rearrangements should be classified as potentially pathogenic at least until a subsequent clinical assessment would exclude a developmental delay or dysmorphism.
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Affiliation(s)
- Krzysztof Szczałuba
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland.
| | - Beata Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Katarzyna Sobecka
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Jennifer Castaneda
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Jakub Klapecki
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Anna Kutkowska-Kaźmierczak
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Robert Śmigiel
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland.,Department of Social Pediatrics, Wroclaw Medical University, Wroclaw, Poland
| | - Ewa Bocian
- Department of Medical Genetics, Institute of Mother and Child, 17a Kasprzaka St., 01-211, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Warsaw Medical University, Warsaw, Poland
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Papoulidis I, Sotiriadis A, Siomou E, Papageorgiou E, Eleftheriades M, Papadopoulos V, Oikonomidou E, Orru S, Manolakos E, Athanasiadis A. Routine use of array comparative genomic hybridization (aCGH) as standard approach for prenatal diagnosis of chromosomal abnormalities. Clinical experience of 1763 prenatal cases. Prenat Diagn 2015; 35:1269-77. [DOI: 10.1002/pd.4685] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/16/2015] [Accepted: 08/16/2015] [Indexed: 12/31/2022]
Affiliation(s)
| | - Alexandros Sotiriadis
- Second Department of Obstetrics and Gynecology; Aristotle University of Thessaloniki; Thessaloniki Greece
| | | | | | | | - Vasilios Papadopoulos
- Department of Obstetrics and Gynecology; University of Patras Medical School; Patras Greece
| | | | - Sandro Orru
- Department of Medical Genetics; Cagliari University, Binaghi Hospital; Cagliari Italy
| | | | - Apostolos Athanasiadis
- First Department of Obstetrics and Gynecology; Aristotle University of Thessaloniki; Thessaloniki Greece
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37
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Carvill GL, Mefford HC. Next-Generation Sequencing in Intellectual Disability. J Pediatr Genet 2015; 4:128-35. [PMID: 27617123 DOI: 10.1055/s-0035-1564439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 12/19/2022]
Abstract
Next-generation sequencing technologies have revolutionized gene discovery in patients with intellectual disability (ID) and led to an unprecedented expansion in the number of genes implicated in this disorder. We discuss the strategies that have been used to identify these novel genes for both syndromic and nonsyndromic ID and highlight the phenotypic and genetic heterogeneity that underpin this condition. Finally, we discuss the future of defining the genetic etiology of ID, including the role of whole-genome sequencing, mosaicism, and the importance of diagnostic testing in ID.
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Affiliation(s)
- Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, United States
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, United States
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38
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Nguyen KV. Epigenetic Regulation in Amyloid Precursor Protein with Genomic Rearrangements and the Lesch-Nyhan Syndrome. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:674-90. [PMID: 26398526 DOI: 10.1080/15257770.2015.1071844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recently, epigenetic regulation of alternative APP pre-mRNA splicing in the Lesch-Nyhan syndrome (LNS) has been studied (see Ref. 7) and showed for the first time, the presence of several APP-mRNA isoforms encoding divers APP protein isoforms ranging from 120 to 770 amino acids (with or without mutations and/or deletions). Here, by continuing on this work, I identified, for the first time new APP-mRNA isoforms with a deletion followed by an insertion (INDELS) in LNS and LNVs patients: c.19_2295delinsG166TT…GAGTCC…CTTAGTC…TCT489,p.Leu7Valfs*2;c.19_2295 delinsG169TT…GAGACC…CTTGGTC…TCT492,p.Leu7Valfs*2;and c.16_2313delinsG84CC…CAT616,p.Leu7Hisfs*45. A role of genomic rearrangements of APP gene via the Fork Stalling and Template Switching (FoSTeS) mechanism leading to INDELS was suggested. Epistasis between mutated HPRT1 and APP genes could be one of the factors of epigenetic modifications responsible for genomic rearrangements of APP gene. My findings accounted for epigenetic mechanism in the regulation of alternative APP pre-mRNA splicing as well as for epigenetic control of genomic rearrangements of APP gene may provide therefore new directions not only for investigating the role of APP in neuropathology associated with HGprt-deficiency in LNS and LNVs patients but also for the research in neurodevelopmental and neurodegenerative disorders by which APP gene involved in the pathogenesis of the diseases such as autism, fragile X syndrome (FXS), and Alzheimer's disease (AD) with its diversity and complexity, especially for sporadic form of AD (SAD). An accurate quantification of various APP-mRNA isoforms in brain tissues for detection of initial pathological changes or pathology development is needed and antisense drugs are the potential treatments.
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Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, University of California, San Diego, School of Medicine, San Diego , La Jolla , CA , USA
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Chatzimichali EA, Brent S, Hutton B, Perrett D, Wright CF, Bevan AP, Hurles ME, Firth HV, Swaminathan GJ. Facilitating collaboration in rare genetic disorders through effective matchmaking in DECIPHER. Hum Mutat 2015. [PMID: 26220709 PMCID: PMC4832335 DOI: 10.1002/humu.22842] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DECIPHER (https://decipher.sanger.ac.uk) is a web‐based platform for secure deposition, analysis, and sharing of plausibly pathogenic genomic variants from well‐phenotyped patients suffering from genetic disorders. DECIPHER aids clinical interpretation of these rare sequence and copy‐number variants by providing tools for variant analysis and identification of other patients exhibiting similar genotype–phenotype characteristics. DECIPHER also provides mechanisms to encourage collaboration among a global community of clinical centers and researchers, as well as exchange of information between clinicians and researchers within a consortium, to accelerate discovery and diagnosis. DECIPHER has contributed to matchmaking efforts by enabling the global clinical genetics community to identify many previously undiagnosed syndromes and new disease genes, and has facilitated the publication of over 700 peer‐reviewed scientific publications since 2004. At the time of writing, DECIPHER contains anonymized data from ∼250 registered centers on more than 51,500 patients (∼18000 patients with consent for data sharing and ∼25000 anonymized records shared privately). In this paper, we describe salient features of the platform, with special emphasis on the tools and processes that aid interpretation, sharing, and effective matchmaking with other data held in the database and that make DECIPHER an invaluable clinical and research resource.
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Affiliation(s)
- Eleni A Chatzimichali
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Benjamin Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Daniel Perrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Caroline F Wright
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Andrew P Bevan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.,Cambridge University Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, CB2 2QQ, United Kingdom
| | - Ganesh J Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
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Córdova-Fletes C, Domínguez MG, Delint-Ramirez I, Martínez-Rodríguez HG, Rivas-Estilla AM, Barros-Núñez P, Ortiz-López R, Neira VA. A de novo t(10;19)(q22.3;q13.33) leads to ZMIZ1/PRR12 reciprocal fusion transcripts in a girl with intellectual disability and neuropsychiatric alterations. Neurogenetics 2015; 16:287-98. [PMID: 26163108 DOI: 10.1007/s10048-015-0452-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
Abstract
We report a girl with intellectual disability (ID), neuropsychiatric alterations, and a de novo balanced t(10;19)(q22.3;q13.33) translocation. After chromosome sorting, fine mapping of breakpoints by array painting disclosed disruptions of the zinc finger, MIZ-type containing 1 (ZMIZ1) (on chr10) and proline-rich 12 (PRR12) (on chr19) genes. cDNA analyses revealed that the translocation resulted in gene fusions. The resulting hybrid transcripts predict mRNA decay or, if translated, formation of truncated proteins, both due to frameshifts that introduced premature stop codons. Though other molecular mechanisms may be operating, these results suggest that haploinsufficiency of one or both genes accounts for the patient's phenotype. ZMIZ1 is highly expressed in the brain, and its protein product appears to interact with neuron-specific chromatin remodeling complex (nBAF) and activator protein 1 (AP-1) complexes which play a role regulating the activity of genes essential for normal synapse and dendrite growth/behavior. Strikingly, the patient's phenotype overlaps with phenotypes caused by mutations in SMARCA4 (BRG1), an nBAF subunit presumably interacting with ZMIZ1 in brain cells as suggested by our results of coimmunoprecipitation in the mouse brain. PRR12 is also expressed in the brain, and its protein product possesses domains and residues thought to be related in formation of large protein complexes and chromatin remodeling. Our observation from E15 mouse brain cells that a Prr12 isoform was confined to nucleus suggests a role as a transcription nuclear cofactor likely involved in neuronal development. Moreover, a pilot transcriptome analysis from t(10;19) lymphoblastoid cell line suggests dysregulation of genes linked to neurodevelopment processes/neuronal communication (e.g., NRCAM) most likely induced by altered PRR12. This case represents the first constitutional balanced translocation disrupting and fusing both genes and provides clues for the potential function and effects of these in the central nervous system.
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Affiliation(s)
- Carlos Córdova-Fletes
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 64460, Nuevo León, México.
| | - Ma Guadalupe Domínguez
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, 44340, México
| | - Ilse Delint-Ramirez
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 64460, Nuevo León, México
| | - Herminia G Martínez-Rodríguez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 64460, Nuevo León, México
| | - Ana María Rivas-Estilla
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 64460, Nuevo León, México
| | - Patricio Barros-Núñez
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, 44340, México
| | - Rocío Ortiz-López
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 64460, Nuevo León, México
| | - Vivian Alejandra Neira
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, 44340, México
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Rezwan FI, Docherty LE, Poole RL, Lockett GA, Arshad SH, Holloway JW, Temple IK, Mackay DJ. A statistical method for single sample analysis of HumanMethylation450 array data: genome-wide methylation analysis of patients with imprinting disorders. Clin Epigenetics 2015; 7:48. [PMID: 25918558 PMCID: PMC4410592 DOI: 10.1186/s13148-015-0081-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/06/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Illumina Infinium HumanMethylation450 BeadChip is an array-based technology for analysing DNA methylation at approximately 475,000 differentially methylated cytosines across the human genome. Hitherto, the array has been used for case-control studies, where sample numbers can be sufficient to yield statistically robust data on a genome-wide basis. We recently reported an informatic pipeline capable of yielding statistically and biologically significant results using only five cases, which expanded the use of this technology to rare disease studies. However, the clinical application of these technologies requires the ability to perform robust analysis of individual patients. RESULTS Here we report a novel informatic approach for methylation array analysis of single samples, using the Crawford-Howell t-test. We tested our approach on patients with ultra-rare imprinting disorders with aberrant DNA methylation at multiple locations across the genome, which was previously detected by targeted testing. However, array analysis outperformed targeted assays in three ways: it detected loci not normally analysed by targeted testing, detected methylation changes too subtle to detect by the targeted testing and reported broad and consistent methylation changes across genetic loci not captured by point testing. CONCLUSIONS This method has potential clinical utility for human disorders where DNA methylation change may be a biomarker of disease.
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Affiliation(s)
- Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK
| | - Louise E Docherty
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK
| | - Rebecca L Poole
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK
| | - S Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Newport, Isle of Wight PO30 5TG UK ; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah Jg Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, Hampshire SO16 6YD UK ; Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wilts SO2 8BJ UK
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Giordano L, Palestra F, Giuffrida MG, Molinaro A, Iodice A, Bernardini L, La Boria P, Accorsi P, Novelli A. 17p13.1 microdeletion: genetic and clinical findings in a new patient with epilepsy and comparison with literature. Am J Med Genet A 2015; 164A:225-30. [PMID: 24501763 DOI: 10.1002/ajmg.a.36225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Array comparative genomic hybridization is now a powerful tool to investigate patients with multiple congenital abnormalities and intellectual/motor impairment, and genomic imbalances are identified in a growing number of children with intellectual disability. Deletions in the 17p13.1 region have been reported in patients with dysmorphic features and developmental delay but a consistent phenotype has yet to emerge. Here, we report on the diagnosis of a 17p13.1 microdeletion of 829 kb in an 8-year-old girl presenting with profound cognitive disability, psychomotor delay, facial dysmorphisms, and refractory epilepsy. This deletion comprises 44 genes, including 8 OMIM morbid genes. We discuss genetic, clinical, and epileptic features comparing our patient with those previously reported in the literature.
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Nguyen KV. The human β-amyloid precursor protein: biomolecular and epigenetic aspects. Biomol Concepts 2015; 6:11-32. [DOI: 10.1515/bmc-2014-0041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/22/2015] [Indexed: 11/15/2022] Open
Abstract
AbstractBeta-amyloid precursor protein (APP) is a membrane-spanning protein with a large extracellular domain and a much smaller intracellular domain. APP plays a central role in Alzheimer’s disease (AD) pathogenesis: APP processing generates β-amyloid (Aβ) peptides, which are deposited as amyloid plaques in the brains of AD individuals; point mutations and duplications of APP are causal for a subset of early-onset familial AD (FAD) (onset age <65 years old). However, these mutations in FAD represent a very small percentage of cases (∼1%). Approximately 99% of AD cases are nonfamilial and late-onset, i.e., sporadic AD (SAD) (onset age >65 years old), and the pathophysiology of this disorder is not yet fully understood. APP is an extremely complex molecule that may be functionally important in its full-length configuration, as well as the source of numerous fragments with varying effects on neural function, yet the normal function of APP remains largely unknown. This article provides an overview of our current understanding of APP, including its structure, expression patterns, proteolytic processing and putative functions. Importantly, and for the first time, my recent data concerning its epigenetic regulation, especially in alternative APP pre-mRNA splicing and in the control of genomic rearrangements of the APP gene, are also reported. These findings may provide new directions for investigating the role of APP in neuropathology associated with a deficiency in the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGprt) found in patients with Lesch-Nyhan syndrome (LNS) and its attenuated variants (LNVs). Also, these findings may be of significance for research in neurodevelopmental and neurodegenerative disorders in which the APP gene is involved in the pathogenesis of diseases such as autism, fragile X syndrome (FXS) and AD, with its diversity and complexity, SAD in particular. Accurate quantification of various APP-mRNA isoforms in brain tissues is needed, and antisense drugs are potential treatments.
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Karam SM, Riegel M, Segal SL, Félix TM, Barros AJD, Santos IS, Matijasevich A, Giugliani R, Black M. Genetic causes of intellectual disability in a birth cohort: a population-based study. Am J Med Genet A 2015; 167:1204-14. [PMID: 25728503 PMCID: PMC4863139 DOI: 10.1002/ajmg.a.37011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/22/2015] [Indexed: 11/25/2022]
Abstract
Intellectual disability affects approximately 1–3% of the population and can be caused by genetic and environmental factors. Although many studies have investigated the etiology of intellectual disability in different populations, few studies have been performed in middle‐income countries. The present study estimated the prevalence of genetic causes related to intellectual disability in a cohort of children from a city in south Brazil who were followed from birth. Children who showed poor performance in development and intelligence tests at the ages of 2 and 4 were included. Out of 4,231 liveborns enrolled in the cohort, 214 children fulfilled the inclusion criteria. A diagnosis was established in approximately 90% of the children evaluated. Genetic causes were determined in 31 of the children and 19 cases remained unexplained even after extensive investigation. The overall prevalence of intellectual disability in this cohort due to genetic causes was 0.82%. Because this study was nested in a cohort, there were a large number of variables related to early childhood and the likelihood of information bias was minimized by collecting information with a short recall time. This study was not influenced by selection bias, allowing identification of intellectual disability and estimation of the prevalence of genetic causes in this population, thereby increasing the possibility of providing appropriate management and/or genetic counseling. © 2015 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Simone M Karam
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, UFRGS, Porto Alegre, Brazil.,Faculdade de Medicina, Universidade Federal do Rio Grande (FURG), Rio Grande, Brazil
| | - Mariluce Riegel
- Serviço de Genética Médica, HCPA, Porto Alegre, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, Brazil
| | | | - Têmis M Félix
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, UFRGS, Porto Alegre, Brazil.,Serviço de Genética Médica, HCPA, Porto Alegre, Brazil
| | | | - Iná S Santos
- Programa de Pós-Graduação em Epidemiologia, UFPel, Pelotas, Brazil
| | - Alicia Matijasevich
- Programa de Pós-Graduação em Epidemiologia, UFPel, Pelotas, Brazil.,Department of Preventive Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Roberto Giugliani
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, UFRGS, Porto Alegre, Brazil.,Serviço de Genética Médica, HCPA, Porto Alegre, Brazil.,Departamento de Genética, UFRGS, Porto Alegre, Brazil
| | - Maureen Black
- John A Scholl MD and Mary Louise Scholl MD Endowed Professor, Department of Pediatrics and Department of Epidemiology and Public Health, University of Maryland, Baltimore, Maryland
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Velázquez-Wong AC, Ruiz Esparza-Garrido R, Velázquez-Flores MÁ, Huicochea-Montiel JC, Cárdenas-Conejo A, Miguez-Muñoz CP, Araujo-Solís MA, Salamanca-Gómez F, Arenas-Aranda DJ. Clinical and molecular characterization of a patient with 15q21.2q22.2 deletion syndrome. Cytogenet Genome Res 2015; 144:183-9. [PMID: 25661042 DOI: 10.1159/000370081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2014] [Indexed: 11/19/2022] Open
Abstract
We report on a 16-year-old girl with a complex phenotype, including intellectual disability, facial dysmorphisms, and obesity. During her infancy, she presented with weak sucking, global developmental delay, and later with excessive eating with central obesity. The girl was clinically diagnosed with probable Prader-Willi syndrome. Chromosomal analysis showed a de novo deletion 46,XX,del(15)(q21q22). However, the use of the Affymetrix CytoScan HD Array defined the exact breakpoints of the deleted 15q21q22 region. The imbalance, about 10.5 Mb in size, is to date the second largest deletion ever described in this chromosomal region. In addition, our patient carries a microdeletion in the 1q44 region and a gain in 9p24. The array result was arr[hg19] 9p24.1(6,619,823-6,749,335)×3, 1q44(248,688,586-248,795,277)×1, 15q21.2 q22.2(50,848,301-61,298,006)×1. Although our patient presents additional chromosomal alterations, we provide a correlation between the clinical findings and the phenotype of the 15q21 deletion syndrome.
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Affiliation(s)
- Ana C Velázquez-Wong
- Unidad de Investigación Médica en Genética Humana, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
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Coutton C, Dieterich K, Satre V, Vieville G, Amblard F, David M, Cans C, Jouk PS, Devillard F. Array-CGH in children with mild intellectual disability: a population-based study. Eur J Pediatr 2015; 174:75-83. [PMID: 24985125 DOI: 10.1007/s00431-014-2367-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 01/24/2023]
Abstract
UNLABELLED Intellectual disability (ID) is characterized by limitation in intellectual function and adaptive behavior, with onset in childhood. Frequent identifiable causes of ID originate from chromosomal imbalances. During the last years, array-CGH has successfully contributed to improve the diagnostic detection rate of genetic abnormalities in patients with ID. Most array-CGH studies focused on patients with moderate or severe intellectual disability. Studies on genetic etiology in children with mild intellectual disability (ID) are very rare. We performed array-CGH analysis in 66 children with mild intellectual disability assessed in a population-based study and for whom no genetic etiology was identified. We found one or more copy number variations (CNVs) in 20 out of 66 (~30 %) patients with a mild ID. In eight of them (~12 %), the CNVs were certainly responsible for the phenotype and in six they were potentially pathogenic for ID. Altogether, array-CGH helped to determine the etiology of ID in 14 patients (~21 %). CONCLUSION Our results underscore the clinical relevance of array-CGH to investigate the etiology of isolated idiopathic mild ID in patients or associated with even subtle dysmorphic features or congenital malformations.
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Affiliation(s)
- Charles Coutton
- Laboratoire de Génétique Chromosomique, Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble, 38700, Grenoble, France,
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Tao VQ, Chan KYK, Chu YWY, Mok GTK, Tan TY, Yang W, Lee SL, Tang WF, Tso WWY, Lau ET, Kan ASY, Tang MH, Lau YL, Chung BHY. The clinical impact of chromosomal microarray on paediatric care in Hong Kong. PLoS One 2014; 9:e109629. [PMID: 25333781 PMCID: PMC4198120 DOI: 10.1371/journal.pone.0109629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/03/2014] [Indexed: 01/27/2023] Open
Abstract
Objective To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong. Methods We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n = 9, Level 1) or peer-reviewed publications making medical management recommendation (n = 10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n = 24); diagnostic testing (n = 25), surveillance of complications (n = 19), interventional procedure (n = 7), medication (n = 15) or lifestyle modification (n = 12). Conclusion The application of CMA in children with ID/DD, ASD, and/or MCAs in Hong Kong results in a diagnostic yield of ∼11% for pathogenic/likely pathogenic results. Importantly the yield for clinically actionable results is 8.6%. We advocate using diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility. Furthermore, it incorporates evidence-based medicine into the practice of genomic medicine. The same framework can be applied to other genomic testing strategies enabled by next-generation sequencing.
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Affiliation(s)
- Victoria Q. Tao
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kelvin Y. K. Chan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Yoyo W. Y. Chu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gary T. K. Mok
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tiong Y. Tan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Royal Children's Hospital, Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wing Fai Tang
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Winnie W. Y. Tso
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Elizabeth T. Lau
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Anita S. Y. Kan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Mary H. Tang
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yu-lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Brian H. Y. Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- * E-mail:
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D'Ambrosio V, Votino C, Cos T, Boulanger S, Dheedene A, Jani J, Keymolen K. Role of CGH array in the diagnosis of autosomal recessive disease: a case of Ellis-van Creveld syndrome. Prenat Diagn 2014; 35:97-9. [PMID: 25174843 DOI: 10.1002/pd.4490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 08/03/2014] [Accepted: 08/26/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Valentina D'Ambrosio
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Brussels, Belgium; Department of Obstetrics, Gynecology and Urologic Sciences, Sapienza University, Umberto I Hospital, Rome, Italy
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