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Bhatia NS, Lim JY, Bonnard C, Kuan JL, Brett M, Wei H, Cham B, Chin H, Bosso-Lefevre C, Dharuman P, Escande-Beillard N, Devasia AG, Goh CYJ, Kam S, Liew WKM, Liew WK, Lin G, Jain K, Ng AYJ, Subramanian D, Xie M, Tan YM, Tawari NR, Tiang Z, Ting TW, Tohari S, Tong CK, Lezhava A, Ng SB, Law HY, Venkatesh B, Tomar S, Sethi R, Tan G, Shanmugasundaram A, Goh DLM, Lai PS, Lai A, Tan ES, Ng I, Reversades B, Tan EC, Foo R, Jamuar SS. Singapore Undiagnosed Disease Program: Genomic Analysis aids Diagnosis and Clinical Management. Arch Dis Child 2021; 106:31-37. [PMID: 32819910 DOI: 10.1136/archdischild-2020-319180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Use next-generation sequencing (NGS) technology to improve our diagnostic yield in patients with suspected genetic disorders in the Asian setting. DESIGN A diagnostic study conducted between 2014 and 2019 (and ongoing) under the Singapore Undiagnosed Disease Program. Date of last analysis was 1 July 2019. SETTING Inpatient and outpatient genetics service at two large academic centres in Singapore. PATIENTS Inclusion criteria: patients suspected of genetic disorders, based on abnormal antenatal ultrasound, multiple congenital anomalies and developmental delay. EXCLUSION CRITERIA patients with known genetic disorders, either after clinical assessment or investigations (such as karyotype or chromosomal microarray). INTERVENTIONS Use of NGS technology-whole exome sequencing (WES) or whole genome sequencing (WGS). MAIN OUTCOME MEASURES (1) Diagnostic yield by sequencing type, (2) diagnostic yield by phenotypical categories, (3) reduction in time to diagnosis and (4) change in clinical outcomes and management. RESULTS We demonstrate a 37.8% diagnostic yield for WES (n=172) and a 33.3% yield for WGS (n=24). The yield was higher when sequencing was conducted on trios (40.2%), as well as for certain phenotypes (neuromuscular, 54%, and skeletal dysplasia, 50%). In addition to aiding genetic counselling in 100% of the families, a positive result led to a change in treatment in 27% of patients. CONCLUSION Genomic sequencing is an effective method for diagnosing rare disease or previous 'undiagnosed' disease. The clinical utility of WES/WGS is seen in the shortened time to diagnosis and the discovery of novel variants. Additionally, reaching a diagnosis significantly impacts families and leads to alteration in management of these patients.
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Affiliation(s)
- Neha S Bhatia
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,Division of Genetics and Metabolism, Tufts Medical Center and the Floating Hospital for Children, Boston, Massachusetts, USA
| | - Jiin Ying Lim
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | | | - Jyn-Ling Kuan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Maggie Brett
- KK Research Centre, KK Women's and Children's Hospital, Singapore
| | - Heming Wei
- KK Research Centre, KK Women's and Children's Hospital, Singapore
| | - Breana Cham
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Huilin Chin
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Celia Bosso-Lefevre
- Institute of Medical Biology, A*STAR, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | | | - Sylvia Kam
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Wendy Kein-Meng Liew
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,SBCC Baby and Child Clinic, Singapore
| | - Woei Kang Liew
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,SBCC Baby and Child Clinic, Singapore
| | - Grace Lin
- KK Research Centre, KK Women's and Children's Hospital, Singapore
| | - Kanika Jain
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,POLARIS, Genome Institute of Singapore, Singapore
| | | | | | - Min Xie
- POLARIS, Genome Institute of Singapore, Singapore
| | - Yuen-Ming Tan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, Singapore
| | | | - Zenia Tiang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore
| | - Teck Wah Ting
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | | | | | - Sarah B Ng
- POLARIS, Genome Institute of Singapore, Singapore
| | - Hai Yang Law
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore
| | - Byrappa Venkatesh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Grace Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Arthi Shanmugasundaram
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Denise Li-Meng Goh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore.,Genome Institute of Singapore, A*STAR, Singapore
| | - Angeline Lai
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Ee Shien Tan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Ivy Ng
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Bruno Reversades
- Institute of Medical Biology, A*STAR, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,POLARIS, Genome Institute of Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Ene Choo Tan
- KK Research Centre, KK Women's and Children's Hospital, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore
| | - Roger Foo
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,POLARIS, Genome Institute of Singapore, Singapore.,Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore.,National University Heart Centre, National University Health System, Singapore
| | - Saumya Shekhar Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore .,SingHealth Duke-NUS Institute of Precision Medicine, Singapore.,Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore
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Ler GYL, Liew WKM, Lim J, Lim JY, Ong LY, Tang PH, Low D, Lim T, Jamuar SS. Teaching NeuroImages: Hypothalamic hamartoma and polydactyly: Think Pallister-Hall syndrome. Neurology 2019; 93:e1016-e1017. [PMID: 31792112 DOI: 10.1212/wnl.0000000000008580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Grace Yan Ling Ler
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Wendy Kein-Meng Liew
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Jocelyn Lim
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Jin Ying Lim
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Lin Yin Ong
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Phua Hwee Tang
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - David Low
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Tchoyoson Lim
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore
| | - Saumya Shekhar Jamuar
- From the Departments of Paediatrics (G.Y.L.L., W.K.-M.L., J.L., J.Y.L., S.S.J.), Paediatric Surgery (L.Y.O.), Radiology (P.H.T.), and Neurosurgery (D.L.), KK Women's and Children's Hospital; Neurology Centre (W.K.-M.L.), Singapore Baby and Child Clinic; Paediatric Academic Medical Programme (J.L.), Institute of Precision Medicine (S.S.J.), Duke-NUS Medical School; and Department of Radiology (T.L.), National Neuroscience Institute, Singapore.
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