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Jo YH, Choi SH, Yoo HW, Kwak MJ, Park KH, Kong J, Lee YJ, Nam SO, Lee BL, Chung WY, Oh SH, Kim YM. Clinical use of whole exome sequencing in children with developmental delay/intellectual disability. Pediatr Neonatol 2024:S1875-9572(24)00004-4. [PMID: 38281861 DOI: 10.1016/j.pedneo.2023.05.015] [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: 10/18/2022] [Revised: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Identifying the underlying etiology of developmental delay/intellectual disability (DD/ID) is challenging but important. The genetic diagnosis of unexplained DD/ID helps in the treatment and prognosis of the disability in patients. In this study, we reported our experience of using whole exome sequencing (WES) of children with unexplained DD/ID. METHODS We conducted a retrospective analysis of WES results of children under 19 years of age with unexplained DD/ID between January 2020 and December 2021. The demographic data of all patients and variants identified through WES were evaluated. Furthermore, we evaluated the clinical characteristics that influenced the identification of genetic causes. RESULTS Forty-one patients with DD/ID were included, of whom 21 (51.2 %) were male. The average age at symptom onset was 1.6 ± 1.3 years, and the duration from symptom onset to diagnosis was 3.1 ± 3.7 years. Hypotonia was the most common symptom (17 patients, 41.5 %), and epilepsy was confirmed in 10 patients (24.4 %). Twenty-two pathogenic/likely pathogenic variants were identified in 20 patients, and three variants of uncertain significance were identified in three patients. Family-based trio Sanger sequencing for candidate variants of 12 families was conducted; 10 variants were de novo, one variant paternally inherited, and two variants compound heterozygous. The diagnostic yield of WES for DD/ID was 48.8 % and was significantly high in patients with an early onset of DD/ID and facial dysmorphism. In contrast, patients with autism spectrum disorder (ASD) were more likely to have negative WES results compared with others without ASD. CONCLUSION The diagnostic yield of WES was 48.8 %. We conclude that patients' characteristics, such as dysmorphic features and the age of symptom onset, can predict the likelihood that WES will identify a causal variant of a phenotype.
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Affiliation(s)
- Yoon Hee Jo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Soo Han Choi
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Hye Won Yoo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Min Jung Kwak
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Kyung Hee Park
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Juhyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Yun-Jin Lee
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Bo Lyun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea.
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Kim J, Lee J, Jang DH. Combining chromosomal microarray and clinical exome sequencing for genetic diagnosis of intellectual disability. Sci Rep 2023; 13:22807. [PMID: 38129582 PMCID: PMC10739828 DOI: 10.1038/s41598-023-50285-z] [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: 06/21/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the current widespread use of chromosomal microarray analysis (CMA) and exome/genome sequencing for the genetic diagnosis of unexplained intellectual disability (ID) in children, gaining improved diagnostic yields and defined guidelines remains a significant challenge. This is a cohort study of children with unexplained ID. We analyzed the diagnostic yield and its correlation to clinical phenotypes in children with ID who underwent concurrent CMA and clinical exome sequencing (CES). A total of 154 children were included (110 [71.4%] male; mean [SD] age, 51.9 [23.1] months). The overall diagnosis yield was 26.0-33.8%, with CMA contributing 12.3-14.3% and CES contributing 13.6-19.4%, showing no significant difference. The diagnostic rate was significantly higher when gross motor delay (odds ratio, 6.69; 95% CI, 3.20-14.00; P < 0.001), facial dysmorphism (odds ratio, 9.34; 95% CI 4.29-20.30; P < 0.001), congenital structural anomaly (odds ratio 3.62; 95% CI 1.63-8.04; P = 0.001), and microcephaly or macrocephaly (odds ratio 4.87; 95% CI 2.05-11.60; P < 0.001) were presented. Patients with only ID without any other concomitant phenotype (63/154, 40.9%) exhibited a 6.3-11.1% diagnostic rate.
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Affiliation(s)
- Jaewon Kim
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaewoong Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dae-Hyun Jang
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Gerik-Celebi HB, Aydin H, Bolat H, Unsel-Bolat G. Clinical and Genetic Characteristics of Patients with Unexplained Intellectual Disability/Developmental Delay without Epilepsy. Mol Syndromol 2023; 14:208-218. [PMID: 37323201 PMCID: PMC10267527 DOI: 10.1159/000529018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/05/2023] [Indexed: 10/21/2023] Open
Abstract
Introduction Global developmental delay (DD), intellectual disability (ID), and autism spectrum disorder (ASD) are mainly evaluated under the neurodevelopmental disorder framework. In this study, we aimed to determine the genetic diagnosis yield using step-by-step genetic analysis in 38 patients with unexplained ID/DD and/or ASD. Methods In 38 cases (27 male, 11 female) with unexplained ID/DD and/or ASD, chromosomal microarray (CMA) analysis, clinical exome sequencing (CES), and whole-exome sequencing (WES) analysis were applied, respectively. Results We found a diagnostic rate of only CMA analysis as 21% (8/38) presenting 8 pathogenic and likely pathogenic CNVs. The rate of patients diagnosed with CES/WES methods was 32.2% (10/31). When all pathogenic and likely pathogenic variants were evaluated, the diagnosis rate was 44.7% (17/38). A dual diagnosis was obtained in a case with 16p11.2 microduplication and de novo SNV. We identified eight novel variants: TUBA1A (c.787C>G), TMEM63A (c.334-2A>G), YY1AP1 (c.2051_2052del), ABCA13 (c.12064C>T), ABCA13 (c.13187G>A), USP9X (c.1189T>C), ANKRD17 (c.328_330dup), and GRIA4 (c.17G>A). Conclusion We present diagnostic rates of a complementary approach to genetic analysis (CMA, CES, and WES). The combined use of genetic analysis methods in unexplained ID/DD and/or ASD cases has contributed significantly to diagnosis rates. Also, we present detailed clinical characteristics to improve genotype-phenotype correlation in the literature for rare and novel variants.
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Affiliation(s)
| | - Hilal Aydin
- Department of Pediatrics, Division of Child Neurology, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Gul Unsel-Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
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Sun Y, Peng J, Liang D, Ye X, Xu N, Chen L, Yan D, Zhang H, Xiao B, Qiu W, Shen Y, Pang N, Liu Y, Liang C, Qin Z, Luo J, Chen F, Wang J, Zhang Z, Wei H, Du J, Yan H, Duan R, Wang J, Zhang Y, Liao S, Sun K, Wu L, Yu Y. Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: a prospective study. Hum Mutat 2022; 43:568-581. [PMID: 35143101 DOI: 10.1002/humu.24347] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
Genome sequencing(GS) has been used in the diagnosis of global developmental delay(GDD)/intellectual disability(ID). However, the performance of GS in patients with inconclusive results from chromosomal microarray analysis(CMA) and exome sequencing(ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test prior to enrollment. Reanalysis of their CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 21%. Seven cases could have been solved with reanalysis of ES data. Thirteen families were missed by previous CMA/ES due to improper methodology. Two remained unsolved after ES reanalysis due to complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this undiagnosed GDD/ID cohort, detecting a wide range of variant types of different sizes in a single workflow. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, 410008, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, 410008, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Xiantao Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Na Xu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Linlin Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Dan Yan
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, 410008, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, 410008, Changsha, China
| | - Yingdi Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Chen Liang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, 529000, Jiangmen, China
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Zhixin Zhang
- International Medical Services, China-Japan Friendship Hospital, 100029, Beijing, China
| | - Haiyan Wei
- Department of Endocrinologic and Inherited Metabolic, Childen's Hospital affiliated to Zhengzhou University, 450018, Zhengzhou, China
| | - Juan Du
- Reproductive and Genetic Hospital of CITIC-Xiangya, 410078, Changsha, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Junyu Wang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Yu Zhang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Shixiu Liao
- Provincial People's Hospital, Medical Genetics Institute of Henan Province, 450003, Zhengzhou, Henan Province, China
| | - Kun Sun
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
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