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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [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: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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Oud MS, Smits RM, Smith HE, Mastrorosa FK, Holt GS, Houston BJ, de Vries PF, Alobaidi BKS, Batty LE, Ismail H, Greenwood J, Sheth H, Mikulasova A, Astuti GDN, Gilissen C, McEleny K, Turner H, Coxhead J, Cockell S, Braat DDM, Fleischer K, D’Hauwers KWM, Schaafsma E, Nagirnaja L, Conrad DF, Friedrich C, Kliesch S, Aston KI, Riera-Escamilla A, Krausz C, Gonzaga-Jauregui C, Santibanez-Koref M, Elliott DJ, Vissers LELM, Tüttelmann F, O’Bryan MK, Ramos L, Xavier MJ, van der Heijden GW, Veltman JA. A de novo paradigm for male infertility. Nat Commun 2022; 13:154. [PMID: 35013161 PMCID: PMC8748898 DOI: 10.1038/s41467-021-27132-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/02/2021] [Indexed: 12/29/2022] Open
Abstract
De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10-5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10-4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.
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Affiliation(s)
- M. S. Oud
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - R. M. Smits
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - H. E. Smith
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - F. K. Mastrorosa
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. S. Holt
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - B. J. Houston
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - P. F. de Vries
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - B. K. S. Alobaidi
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L. E. Batty
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - H. Ismail
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - J. Greenwood
- grid.420004.20000 0004 0444 2244Department of Genetic Medicine, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - H. Sheth
- Foundation for Research in Genetics and Endocrinology, Institute of Human Genetics, Ahmedabad, India
| | - A. Mikulasova
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. D. N. Astuti
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands ,grid.412032.60000 0001 0744 0787Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - C. Gilissen
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - K. McEleny
- grid.420004.20000 0004 0444 2244Newcastle Fertility Centre, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - H. Turner
- grid.420004.20000 0004 0444 2244Department of Cellular Pathology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - J. Coxhead
- grid.1006.70000 0001 0462 7212Genomics Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - S. Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences New, castle University, Newcastle upon Tyne, UK
| | - D. D. M. Braat
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - K. Fleischer
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - K. W. M. D’Hauwers
- grid.10417.330000 0004 0444 9382Department of Urology, Radboudumc, Nijmegen, The Netherlands
| | - E. Schaafsma
- grid.10417.330000 0004 0444 9382Department of Pathology, Radboudumc, Nijmegen, The Netherlands
| | | | - L. Nagirnaja
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - D. F. Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - C. Friedrich
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - S. Kliesch
- grid.16149.3b0000 0004 0551 4246Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - K. I. Aston
- grid.223827.e0000 0001 2193 0096Department of Surgery, Division of Urology, University of Utah School of Medicine, Salt Lake City, UT USA
| | - A. Riera-Escamilla
- grid.418813.70000 0004 1767 1951Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain
| | - C. Krausz
- grid.8404.80000 0004 1757 2304Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - C. Gonzaga-Jauregui
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - M. Santibanez-Koref
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - D. J. Elliott
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - L. E. L. M. Vissers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - F. Tüttelmann
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - M. K. O’Bryan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - L. Ramos
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - M. J. Xavier
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - G. W. van der Heijden
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboudumc, Nijmegen, The Netherlands
| | - J. A. Veltman
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Barros II, Leão V, Santis JO, Rosa RCA, Brotto DB, Storti CB, Siena ÁDD, Molfetta GA, Silva WA. Non-Syndromic Intellectual Disability and Its Pathways: A Long Noncoding RNA Perspective. Noncoding RNA 2021; 7:ncrna7010022. [PMID: 33799572 PMCID: PMC8005948 DOI: 10.3390/ncrna7010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Non-syndromic intellectual disability (NS-ID or idiopathic) is a complex neurodevelopmental disorder that represents a global health issue. Although many efforts have been made to characterize it and distinguish it from syndromic intellectual disability (S-ID), the highly heterogeneous aspect of this disorder makes it difficult to understand its etiology. Long noncoding RNAs (lncRNAs) comprise a large group of transcripts that can act through various mechanisms and be involved in important neurodevelopmental processes. In this sense, comprehending the roles they play in this intricate context is a valuable way of getting new insights about how NS-ID can arise and develop. In this review, we attempt to bring together knowledge available in the literature about lncRNAs involved with molecular and cellular pathways already described in intellectual disability and neural function, to better understand their relevance in NS-ID and the regulatory complexity of this disorder.
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Affiliation(s)
- Isabela I. Barros
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Vitor Leão
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Jessica O. Santis
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Reginaldo C. A. Rosa
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Danielle B. Brotto
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Camila B. Storti
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Ádamo D. D. Siena
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Greice A. Molfetta
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Wilson A. Silva
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
- National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell Based Therapy, Ribeirão Preto Medical School, University of São Paulo, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto 14051-140, Brazil
- Center for Integrative Systems Biology-CISBi, NAP/USP, Ribeirão Preto Medical School, University of São Paulo, Rua Catão Roxo, 2501, Monte Alegre, Ribeirão Preto 14051-140, Brazil
- Department of Medicine at the Midwest State University of Paraná-UNICENTRO, and Guarapuava Institute for Cancer Research, Rua Fortim Atalaia, 1900, Cidade dos Lagos, Guarapuava 85100-000, Brazil
- Correspondence: ; Tel.: +55-16-3315-3293
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