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Aldosari AN, Aldosari TS. Comprehensive evaluation of the child with global developmental delays or intellectual disability. Clin Exp Pediatr 2024; 67:435-446. [PMID: 38810986 PMCID: PMC11374451 DOI: 10.3345/cep.2023.01697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/07/2024] [Indexed: 05/31/2024] Open
Abstract
Global developmental delay (GDD) and intellectual disability (ID) are relatively common neurodevelopmental disorders that significantly impact affected children, their families, and society. The etiology of GDD/ID is notably diverse, encompassing both genetic and acquired factors. Although the precise cause of most GDD/ID cases remains unclear, an estimated half of all cases can be attributed to genetic factors. Thus, a detailed medical history and comprehensive physical examination remain pivotal for guiding diagnostic investigations into the underlying causes of GDD/ID. Advancements in genetic testing have supplanted traditional methods such as karyotyping and fluorescence in situ hybridization with chromosomal micro arrays, which are now the primary genetic tests for children with idiopathic GDD/ID. Moreover, the evaluation of Fragile X and Rett syndrome should be an integral component of initial diagnostic assessments. In recent years, whole-exome sequencing and whole-genome sequ-encing have emerged as important diagnostic tools for evaluating children with GDD/ID and have substantially enhanced the diagnostic yield rates. Gene therapy has emerged as a promising avenue and is poised to become a cornerstone in addressing various genetic developmental and epilepsy disorders. Early intervention facilitated by a proficient multidisciplinary team can markedly enhance the prognosis and outcomes of GDD/ID, particularly when parents or caregivers are actively engaged in the interventional process. This review discusses risk factors and common underlying causes, explores recent evidence and recommendations for genetic evaluation, and offers management strategies for children with GDD/ID.
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Affiliation(s)
| | - T Saeed Aldosari
- Department of Special Education, Prince Sattam bin Abdulaziz University, Riyadh, Saudi Arabia
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Yatsenko SA, Aarabi M, Hu J, Surti U, Ortiz D, Madan-Khetarpal S, Saller DN, Bellissimo D, Rajkovic A. Copy number alterations involving 59 ACMG-recommended secondary findings genes. Clin Genet 2020; 98:577-588. [PMID: 33009833 DOI: 10.1111/cge.13852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/14/2020] [Accepted: 09/13/2020] [Indexed: 12/17/2022]
Abstract
In clinical exome/genome sequencing, the American College of Medical Genetics and Genomics (ACMG) recommends reporting of secondary findings unrelated to a patient's phenotype when pathogenic single-nucleotide variants (SNVs) are observed in one of 59 genes associated with a life-threatening, medically actionable condition. Little is known about the incidence and sensitivity of chromosomal microarray analysis (CMA) for detection of pathogenic copy number variants (CNVs) comprising medically-actionable genes. Clinical CMA has been performed on 8865 individuals referred for molecular cytogenetic testing. We retrospectively reviewed the CMA results to identify patients with CNVs comprising genes included in the 59-ACMG list of secondary findings. We evaluated the clinical significance of these CNVs in respect to pathogenicity, phenotypic manifestations, and heritability. We identified 23 patients (0.26%) with relevant CNV either deletions comprising the entire gene or intragenic alterations involving one or more secondary findings genes. A number of patients and/or their family members with pathogenic CNVs manifest or expected to develop an anticipated clinical phenotype and would benefit from preventive management similar to the patients with pathogenic SNVs. To improve patients' care standardization should apply to reporting of both sequencing and CNVs obtained via clinical genome-wide analysis, including chromosomal microarray and exome/genome sequencing.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mahmoud Aarabi
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jie Hu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Damara Ortiz
- Department of Medical Genetics, Childrens Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Suneeta Madan-Khetarpal
- Department of Medical Genetics, Childrens Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Devereux N Saller
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Bellissimo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Aleksandar Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, California, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
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Hyder Z, Fairclough A, Groom M, Getty J, Alexander E, van Veen EM, Makin G, Sethuraman C, Tang V, Evans DG, Maher ER, Woodward ER. Constitutional de novo deletion CNV encompassing REST predisposes to diffuse hyperplastic perilobar nephroblastomatosis (HPLN). J Med Genet 2020; 58:581-585. [PMID: 32917767 DOI: 10.1136/jmedgenet-2020-107087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Nephroblastomatosis is a recognised precursor for the development of Wilms tumour (WT), the most common childhood renal tumour. While the majority of WT is sporadic in origin, germline intragenic mutations of predisposition genes such as WT1, REST and TRIM28 have been described in apparently isolated (non-familial) WT.Despite constitutional CNVs being a well-studied cause of developmental disorders, their role in cancer predisposition is less well defined, so that the interpretation of cancer risks associated with specific CNVs can be complex. OBJECTIVE To highlight the role of a constitutional deletion CNV (delCNV) encompassing the REST tumour suppressor gene in diffuse hyperplastic perilobar nephroblastomatosis (HPLN). METHODS/RESULTS Array comparative genomic hybridisation in an infant presenting with apparently sporadic diffuse HPLN revealed a de novo germline CNV, arr[GRCh37] 4q12(57,385,330-57,947,405)x1. The REST tumour suppressor gene is located at GRCh37 chr4:57,774,042-57,802,010. CONCLUSION This delCNV encompassing REST is associated with nephroblastomatosis. Deletion studies should be included in the molecular work-up of inherited predisposition to WT/nephroblastomatosis. Detection of delCNVs involving known cancer predisposition genes can yield insights into the relationship between underlying genomic architecture and associated tumour risk.
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Affiliation(s)
- Zerin Hyder
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Adele Fairclough
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK.,NW Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Mike Groom
- NW Genomic Laboratory Hub, Liverpool Women's Hospital, Liverpool, UK
| | - Joan Getty
- NW Genomic Laboratory Hub, Liverpool Women's Hospital, Liverpool, UK
| | - Elizabeth Alexander
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Guy Makin
- Department of Paediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK.,Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Chitra Sethuraman
- Department of Paediatric Histopathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Vivian Tang
- Department of Radiology, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, Cambridgeshire, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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Talukdar S, Hawkes L, Hanson H, Kulkarni A, Brady AF, McMullan DJ, Ahn JW, Woodward E, Turnbull C. Structural Aberrations with Secondary Implications (SASIs): consensus recommendations for reporting of cancer susceptibility genes identified during analysis of Copy Number Variants (CNVs). J Med Genet 2019; 56:718-726. [DOI: 10.1136/jmedgenet-2018-105820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/19/2019] [Accepted: 03/02/2019] [Indexed: 11/04/2022]
Abstract
Clinical testing with chromosomal microarray (CMA) is most commonly undertaken for clinical indications such as intellectual disability, dysmorphic features and/or congenital abnormalities. Identification of a structural aberration (SA) involving a cancer susceptibility gene (CSG) constitutes a type of incidental or secondary finding. Laboratory reporting, risk communication and clinical management of these structural aberrations with secondary implications (SASIs) is currently inconsistent. We undertake meta-analysis of 18 622 instances of CMA performed for unrelated indications in which 106 SASIs are identified involving in total 40 different CSGs. Here we present the recommendations of a joint UK working group representing the British Society of Genomic Medicine, UK Cancer Genetics Group and UK Association for Clinical Genomic Science. SASIs are categorised into four groups, defined by the type of SA and the cancer risk. For each group, recommendations are provided regarding reflex parental testing and cancer risk management.
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Truty R, Paul J, Kennemer M, Lincoln SE, Olivares E, Nussbaum RL, Aradhya S. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genet Med 2018; 21:114-123. [PMID: 29895855 PMCID: PMC6752305 DOI: 10.1038/s41436-018-0033-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
Purpose We investigated the frequencies and characteristics of intragenic copy-number variants (CNVs) in a deep sampling of disease genes associated with monogenic disorders. Methods Subsets of 1507 genes were tested using next-generation sequencing to simultaneously detect sequence variants and CNVs in >143,000 individuals referred for genetic testing. We analyzed CNVs in gene panels for hereditary cancer syndromes and cardiovascular, neurological, or pediatric disorders. Results Our analysis identified 2844 intragenic CNVs in 384 clinically tested genes. CNVs were observed in 1.9% of the entire cohort but in a disproportionately high fraction (9.8%) of individuals with a clinically significant result. CNVs accounted for 4.7–35% of pathogenic variants, depending on clinical specialty. Distinct patterns existed among CNVs in terms of copy number, location, exons affected, clinical classification, and genes affected. Separately, analysis of de-identified data for 599 genes unrelated to the clinical phenotype yielded 4054 CNVs. Most of these CNVs were novel rare events, present as duplications, and enriched in genes associated with recessive disorders or lacking loss-of-function mutational mechanisms. Conclusion Universal intragenic CNV analysis adds substantial clinical sensitivity to genetic testing. Clinically relevant CNVs have distinct properties that distinguish them from CNVs contributing to normal variation in human disease genes.
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Affiliation(s)
| | | | | | | | | | - Robert L Nussbaum
- Invitae, San Francisco, CA, USA.,Volunteer Clinical Faculty, University of California, San Francisco, CA, USA
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