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Ranieri A, La Monica I, Di Iorio MR, Lombardo B, Pastore L. Genetic Alterations in a Large Population of Italian Patients Affected by Neurodevelopmental Disorders. Genes (Basel) 2024; 15:427. [PMID: 38674362 PMCID: PMC11050211 DOI: 10.3390/genes15040427] [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: 02/21/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Neurodevelopmental disorders are a group of complex multifactorial disorders characterized by cognitive impairment, communication deficits, abnormal behaviour, and/or motor skills resulting from abnormal neural development. Copy number variants (CNVs) are genetic alterations often associated with neurodevelopmental disorders. We evaluated the diagnostic efficacy of the array-comparative genomic hybridization (a-CGH) method and its relevance as a routine diagnostic test in patients with neurodevelopmental disorders for the identification of the molecular alterations underlying or contributing to the clinical manifestations. In the present study, we analysed 1800 subjects with neurodevelopmental disorders using a CGH microarray. We identified 208 (7%) pathogenetic CNVs, 2202 (78%) variants of uncertain significance (VOUS), and 504 (18%) benign CNVs in the 1800 patients analysed. Some alterations contain genes potentially related to neurodevelopmental disorders including CHRNA7, ANKS1B, ANKRD11, RBFOX1, ASTN2, GABRG3, SHANK2, KIF1A SETBP1, SNTG2, CTNNA2, TOP3B, CNTN4, CNTN5, and CNTN6. The identification of interesting significant genes related to neurological disorders with a-CGH is therefore an essential step in the diagnostic procedure, allowing a better understanding of both the pathophysiology of these disorders and the mechanisms underlying their clinical manifestations.
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Affiliation(s)
- Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Maria Rosaria Di Iorio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
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Wayhelova M, Vallova V, Broz P, Mikulasova A, Smetana J, Dynkova Filkova H, Machackova D, Handzusova K, Gaillyova R, Kuglik P. Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders. Orphanet J Rare Dis 2024; 19:41. [PMID: 38321498 PMCID: PMC10845791 DOI: 10.1186/s13023-024-03056-6] [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: 06/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses. RESULTS In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system. CONCLUSION Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.
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Affiliation(s)
- Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic.
| | - Vladimira Vallova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Petr Broz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Dynkova Filkova
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Dominika Machackova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristina Handzusova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
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Kubota N, Takeda R, Kobayashi J, Hidaka E, Nishi E, Takano K, Wakui K. Reanalysis of Chromosomal Microarray Data Using a Smaller Copy Number Variant Call Threshold Identifies Four Cases with Heterozygous Multiexon Deletions of ARID1B, EHMT1, and FOXP1 Genes. Mol Syndromol 2023; 14:394-404. [PMID: 37901861 PMCID: PMC10601822 DOI: 10.1159/000530252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/16/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Chromosomal microarray (CMA) is a highly accurate and established method for detecting copy number variations (CNVs) in clinical genetic testing. CNVs are important etiological factors for disorders such as intellectual disability, developmental delay, and multiple congenital anomalies. Recently developed analytical methods have facilitated the identification of smaller CNVs. Therefore, reanalyzing CMA data using a smaller CNV calling threshold may yield useful information. However, this method was left to the discretion of each institution. Methods We reanalyzed the CMA data of 131 patients using a smaller CNV call threshold: 50 kb 50 probes for gain and 25 kb 25 probes for loss. We interpreted the reanalyzed CNVs based on the most recently available information. In the reanalysis, we filtered the data using the Clinical Genome Resource dosage sensitivity gene list as an index to quickly and efficiently check morbid genes. Results The number of copy number loss was approximately 20 times greater, and copy number gain was approximately three times greater compared to those in the previous analysis. We detected new likely pathogenic CNVs in four participants: a 236.5 kb loss within ARID1B, a 50.6 kb loss including EHMT1, a 46.5 kb loss including EHMT1, and an 89.1 kb loss within the FOXP1 gene. Conclusion The method employed in this study is simple and effective for CMA data reanalysis using a smaller CNV call threshold. Thus, this method is efficient for both ongoing and repeated analyses. This study may stimulate further discussion of reanalysis methodology in clinical laboratories.
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Affiliation(s)
- Noriko Kubota
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Ryojun Takeda
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Jun Kobayashi
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eiko Hidaka
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eriko Nishi
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Kyoko Takano
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Keiko Wakui
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
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Yu L, Ding H, Liu M, Liu L, Zhang Q, Lu J, Guo F, Zhang Y. A novel 1p13.2 deletion associates with neurodevelopmental disorders in a three-generation pedigree. BMC Med Genomics 2023; 16:114. [PMID: 37221554 DOI: 10.1186/s12920-023-01534-7] [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: 01/03/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND A multitude of studies have highlighted that copy number variants (CNVs) are associated with neurodevelopmental disorders (NDDs) characterized by a wide range of clinical characteristics. Benefiting from CNV calling from WES data, WES has emerged as a more powerful and cost-effective molecular diagnostic tool, which has been widely used for the diagnosis of genetic diseases, especially NDDs. To our knowledge, isolated deletions on chromosome 1p13.2 are rare. To date, only a few patients were reported with 1p13.2 deletions and most of them were sporadic. Besides, the correlation between 1p13.2 deletions and NDDs remained unclear. CASE PRESENTATION Here, we first reported five members in a three-generation Chinese family who presented with NDDs and carried a novel 1.41 Mb heterozygous 1p13.2 deletion with precise breakpoints. The diagnostic deletion contained 12 protein-coding genes and was observed to segregate with NDDs among the members of our reported family. Whether those genes contribute to the patient's phenotypes is still inconclusive. CONCLUSIONS We hypothesized that the NDD phenotype of our patients was caused by the diagnostic 1p13.2 deletion. However, further in-depth functional experiments are still needed to establish a 1p13.2 deletion-NDDs relationship. Our study might supplement the spectrum of 1p13.2 deletion-NDDs.
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Affiliation(s)
- Lihua Yu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Hongke Ding
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Min Liu
- Prenatal diagnostic center, Huizhou No2 Maternal and Children's Healthcare Hospital, Huizhou, China
| | - Ling Liu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Qi Zhang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Jian Lu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Fangfang Guo
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yan Zhang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility. Heliyon 2023; 9:e13923. [PMID: 36879971 PMCID: PMC9984859 DOI: 10.1016/j.heliyon.2023.e13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.
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Streață I, Caramizaru A, Riza AL, Șerban-Sosoi S, Pîrvu A, Cara ML, Cucu MG, Dobrescu AM, Shelby ES, Albeanu A, Burada F, Ioana M. Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort. Diagnostics (Basel) 2022; 12:diagnostics12123137. [PMID: 36553144 PMCID: PMC9777762 DOI: 10.3390/diagnostics12123137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.
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Affiliation(s)
- Ioana Streață
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Alexandru Caramizaru
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Simona Șerban-Sosoi
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai-Gabriel Cucu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Amelia Mihaela Dobrescu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Ro-NMCA-ID Group
- The Ro-NMCA-ID (RoNetwork Multiple Congenital Abnormalities with ID) Member of European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA) [EU Framework Partnership Agreement ID: 3HP-HP-FPA ERN-01-2016/739516], 400011 Timisoara, Romania
| | | | | | - Elena-Silvia Shelby
- National University Center for Children’s Neurorehabilitation “Dr. Nicolae Robănescu”, 44 Dumitru Mincă Street, District 4, 041408 Bucharest, Romania
| | - Adriana Albeanu
- Department of Pediatric Neurology, Clinical Emergency Children Hospital Brasov, Nicopole Street No. 45, 500063 Brasov, Romania
| | - Florin Burada
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
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Lengyel A, Pinti É, Pikó H, Kristóf Á, Abonyi T, Némethi Z, Fekete G, Haltrich I. Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort. Mol Cytogenet 2022; 15:47. [PMID: 36320065 PMCID: PMC9623912 DOI: 10.1186/s13039-022-00623-z] [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: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders are genetically heterogeneous pediatric conditions. The first tier diagnostic method for uncovering copy number variations (CNVs), one of the most common genetic etiologies in affected individuals, is chromosomal microarray (CMA). However, this methodology is not yet a routine molecular cytogenetic test in many parts of the world, including Hungary. Here we report clinical and genetic data of the first, relatively large Hungarian cohort of patients whose genetic testing included CMA. METHODS Clinical data were retrospectively collected for 78 children who were analyzed using various CMA platforms. Phenotypes of patients with disease-causing variants were compared to patients with negative results using the chi squared/Fisher exact tests. RESULTS A total of 30 pathogenic CNVs were identified in 29 patients (37.2%). Postnatal growth delay (p = 0.05564), pectus excavatum (p = 0.07484), brain imaging abnormalities (p = 0.07848), global developmental delay (p = 0.08070) and macrocephaly (p = 0.08919) were more likely to be associated with disease-causing CNVs. CONCLUSION Our results allow phenotypic expansion of 14q11.2 microdeletions encompassing SUPT16H and CHD8 genes. Variants of unknown significance (n = 24) were found in 17 patients. We provide detailed phenotypic and genetic data of these individuals to facilitate future classification efforts, and spotlight two patients with potentially pathogenic alterations. Our results contribute to unraveling the diagnostic value of rare CNVs.
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Affiliation(s)
- Anna Lengyel
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Éva Pinti
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Henriett Pikó
- grid.11804.3c0000 0001 0942 9821Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Árvai Kristóf
- grid.11804.3c0000 0001 0942 9821Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Tünde Abonyi
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zaránd Némethi
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
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Lichtenstein P, Tideman M, Sullivan PF, Serlachius E, Larsson H, Kuja-Halkola R, Butwicka A. Familial risk and heritability of intellectual disability: a population-based cohort study in Sweden. J Child Psychol Psychiatry 2022; 63:1092-1102. [PMID: 34921396 DOI: 10.1111/jcpp.13560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Intellectual disability (ID) aggregates in families, but factors affecting individual risk and heritability estimates remain unknown. METHODS A population-based family cohort study of 4,165,785 individuals born 1973-2013 in Sweden, including 37,787 ID individuals and their relatives. The relative risks (RR) of ID with 95% confidence intervals (95% CI) were obtained from stratified Cox proportional-hazards models. Relatives of ID individuals were compared to relatives of unaffected individuals. Structural equation modeling was used to estimate heritability. RESULTS Relatives of ID individuals were at increased risk of ID compared to individuals with unaffected relatives. The RR of ID among relatives increased proportionally to the degree of genetic relatedness with ID probands; 256.70(95% CI 161.30-408.53) for monozygotic twins, 16.47(13.32-20.38) for parents, 14.88(12.19-18.16) for children, 7.04(4.67-10.61) for dizygotic twins, 8.38(7.97-8.83) for full siblings, 4.56(4.02-5.16) for maternal, 2.90(2.49-3.37) for paternal half-siblings, 3.03(2.61-3.50) for nephews/nieces, 2.84(2.45-3.29) for uncles/aunts, and 2.04(1.91-2.20) for cousins. Lower RRs were observed for siblings of probands with chromosomal abnormalities (RR 5.53, 4.74-6.46) and more severe ID (mild RR 9.15, 8.55-9.78, moderate RR 8.13, 7.28-9.08, severe RR 6.80, 5.74-8.07, and profound RR 5.88, 4.52-7.65). Male sex of relative and maternal line of relationship with proband was related to higher risk (RR 1.33, 1.25-1.41 for brothers vs. sisters and RR 1.49, 1.34-1.68 for maternal vs. paternal half-siblings). ID was substantially heritable with 0.95(95% CI 0.93-0.98) of the variance in liability attributed to genetic influences. CONCLUSIONS The risk estimates will benefit researchers, clinicians, families in understanding the risk of ID in the family and the whole population. The higher risk of ID related to male sex and maternal linage will be of value for planning and interpreting etiological studies in ID.
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Affiliation(s)
- Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Tideman
- School of Health and Social Science, Halmstad University, Halmstad, Sweden
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,UNC Center for Psychiatric Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eva Serlachius
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Service, Region Stockholm, Stockholm, Sweden
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,School of Medical sciences, Örebro University, Örebro, Sweden
| | - Ralf Kuja-Halkola
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Agnieszka Butwicka
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Child and Adolescent Psychiatry Stockholm, Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.,Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland.,Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
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9
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Kamath V, Yoganathan S, Thomas MM, Gowri M, Chacko MP. Utility of Chromosomal Microarray in Children with Unexplained Developmental Delay/Intellectual Disability. Fetal Pediatr Pathol 2022; 41:208-218. [PMID: 32701375 DOI: 10.1080/15513815.2020.1791292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
ObjectiveTo evaluate the chromosomal microarray (CMA) yield among children who presented with global developmental delay/intellectual disability (GDD/ID) with/without co-occurring conditions. Methods: The pathogenic copy number variation (pCNVs) findings on CMA of all children who presented with unexplained GDD/ID were categorized based on the clinical features. The karyotype results were compared with CMA. Results: The overall pCNV yield in children presenting with GDD/ID with or without comorbid conditions constituted 20.9%. Among the 17 pCNVs, 13 were losses and four were gains. Cardiac defect was the only co-morbidity in our study that demonstrated statistically significant prediction for pCNV (odds ratio 6.13, p value- 0.031). Six children who were karyotyped prior to CMA testing showed a structural abnormality. Conclusions: In our study, 20.9% of children with GDD/ID showed pCNVs on CMA. Cardiac defect alongside GDD/ID, emerged as the single strongest phenotype associated with pCNVs. CMA also provided vital information in previously karyotyped patients.
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Affiliation(s)
- Vandana Kamath
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
| | - Sangeetha Yoganathan
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Maya Mary Thomas
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Mahasampath Gowri
- Department of Biostatistics, Christian Medical College and Hospital, Vellore, India
| | - Mary Purna Chacko
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
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Jezkova J, Heath J, Williams A, Barrell D, Norton J, Collinson MN, Beal SJ, Corrin S, Morgan S. Exon-focused targeted oligonucleotide microarray design increases detection of clinically relevant variants across multiple NHS genomic centres. NPJ Genom Med 2020; 5:28. [PMID: 32714564 PMCID: PMC7374691 DOI: 10.1038/s41525-020-0136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
In recent years, chromosomal microarrays have been widely adopted by clinical diagnostic laboratories for postnatal constitutional genome analysis and have been recommended as the first-line test for patients with intellectual disability, developmental delay, autism and/or congenital abnormalities. Traditionally, array platforms have been designed with probes evenly spaced throughout the genome and increased probe density in regions associated with specific disorders with a resolution at the level of whole genes or multiple exons. However, this level of resolution often cannot detect pathogenic intragenic deletions or duplications, which represent a significant disease-causing mechanism. Therefore, new high-resolution oligonucleotide comparative genomic hybridisation arrays (oligo-array CGH) have been developed with probes targeting single exons of disease relevant genes. Here we present a retrospective study on 27,756 patient samples from a consortium of state-funded diagnostic UK genomic centres assayed by either oligo-array CGH of a traditional design (Cytosure ISCA v2) or by an oligo-array CGH with enhanced exon-level coverage of genes associated with developmental disorders (CytoSure Constitutional v3). The new targeted design used in Cytosure v3 array has been designed to capture intragenic aberrations that would have been missed on the v2 array. To assess the relative performance of the two array designs, data on a subset of samples (n = 19,675), generated only by laboratories using both array designs, were compared. Our results demonstrate that the new high-density exon-focused targeted array design that uses updated information from large scale genomic studies is a powerful tool for detection of intragenic deletions and duplications that leads to a significant improvement in diagnostic yield.
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Affiliation(s)
- Jana Jezkova
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Jade Heath
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Angharad Williams
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Deborah Barrell
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Jessica Norton
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK.,Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Sarah J Beal
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
| | - Sian Morgan
- All Wales Medical Genomics Service, Cardiff and Vale University Health Board, NHS Wales, Cardiff, UK
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