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Singapore Undiagnosed Disease Program: Genomic Analysis aids Diagnosis and Clinical Management
  1. Neha S Bhatia1,2,
  2. Jiin Ying Lim1,
  3. Carine Bonnard3,
  4. Jyn-Ling Kuan1,4,
  5. Maggie Brett5,
  6. Heming Wei5,
  7. Breana Cham1,
  8. Huilin Chin6,7,
  9. Celia Bosso-Lefevre3,6,
  10. Perumal Dharuman8,
  11. Nathalie Escande-Beillard3,
  12. Arun George Devasia8,
  13. Chew Yin Jasmine Goh1,
  14. Sylvia Kam1,4,
  15. Wendy Kein-Meng Liew1,9,
  16. Woei Kang Liew1,9,
  17. Grace Lin5,
  18. Kanika Jain1,8,
  19. Alvin Yu-Jin Ng10,
  20. Deepa Subramanian8,
  21. Min Xie8,
  22. Yuen-Ming Tan1,11,
  23. Nilesh R Tawari8,
  24. Zenia Tiang12,13,
  25. Teck Wah Ting1,14,15,
  26. Sumanty Tohari10,
  27. Cheuk Ka Tong8,
  28. Alexander Lezhava8,
  29. Sarah B Ng8,
  30. Hai Yang Law1,11,14,
  31. Byrappa Venkatesh6,10,
  32. Swati Tomar6,7,
  33. Raman Sethi6,7,
  34. Grace Tan6,7,
  35. Arthi Shanmugasundaram6,7,
  36. Denise Li-Meng Goh6,7,
  37. Poh San Lai6,7,13,
  38. Angeline Lai1,14,15,
  39. Ee Shien Tan1,14,15,
  40. Ivy Ng1,14,15,
  41. Bruno Reversades3,6,8,10,
  42. Ene Choo Tan5,14,
  43. Roger Foo6,8,12,13,16,
  44. Saumya Shekhar Jamuar1,4,14,15
  45. SUREKids Working Group
    1. 1 Department of Paediatrics, KK Women's and Children's Hospital, Singapore
    2. 2 Division of Genetics and Metabolism, Tufts Medical Center and the Floating Hospital for Children, Boston, Massachusetts, USA
    3. 3 Institute of Medical Biology, A*STAR, Singapore
    4. 4 SingHealth Duke-NUS Institute of Precision Medicine, Singapore
    5. 5 KK Research Centre, KK Women's and Children's Hospital, Singapore
    6. 6 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    7. 7 Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
    8. 8 POLARIS, Genome Institute of Singapore, Singapore
    9. 9 SBCC Baby and Child Clinic, Singapore
    10. 10 Institute of Molecular and Cell Biology, A*STAR, Singapore
    11. 11 DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, Singapore
    12. 12 Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    13. 13 Genome Institute of Singapore, A*STAR, Singapore
    14. 14 Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore
    15. 15 SingHealth Duke-NUS Genomic Medicine Centre, Singapore
    16. 16 National University Heart Centre, National University Health System, Singapore
    1. Correspondence to Dr Saumya Shekhar Jamuar, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore; saumya.s.jamuar{at}singhealth.com.sg

    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.

    • genetics
    • syndrome

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    Footnotes

    • ECT, RF and SSJ are joint corresponding co-authorship.

    • Collaborators SUREKids Working Group:

      KK Women’s and Children’s Hospital, Singapore: Saumya Jamuar, Angeline Lai, Woei Kang Liew,

      Wendy Liew, Ee Shien Tan, Mark Koh, Ene Choo Tan, Hai Yang Law, Madeline Ho, Teck Wah Ting, Ene Choo Tan, Ivy Ng, Neha Singh Bhatia, Jiin Ying Lim, Jasmine Goh, Breana Cham, Sylvia Kam, Jyn Ling Kuan, Maggie Brett, Heming Wei, Grace Lin, Kanika Jain, Yuen Ming Tan; National University Hospital Singapore: Denise Goh, Lee Bee Wah, Lynette Shek, Stacey Tay, Ng Kar Hui, Lai Poh San, Swati Tomar, Raman Sethi, Grace Tan, Arthi Shanmugasundaram, Hui-lin Chin; Genome Institute of Singapore: Patrick Tan, Roger Foo, Pauline Ng, Tony Lim, Perumal Dharuman, Devasia Arun George, Deepa Subramanian, Min Xie, Nilesh R Tiwari, Zenia Tiang, Cheuk-Ka Tong, Alexander Lezhava, Sarah B Ng; Institute of Medical Biology: Bruno Reversade, Ray Dunn, Carine Bonnard, Celia Bosso-Lefevre, Nathalie Escande-Beillard; Institute of Molecular and Cell Biology: Byrappa Venkatesh, John Connolly, Alvin Yu-Jin Ng, Sumanty Tohari; Translational Laboratory in Genetic Medicine: Mahmoud Pouladi

    • Contributors NSB: drafting of the manuscript. NSB, CB, J-LK, MB, HW, HC, CB-L, PD, NE-B, AGD, GL, KJ, Y-JAN, DS, MX,Y-MT, NRT, ZT, ST, CKT, AL, SBN, H-YL, BV, ST, RS, GT, AS, PSL, BR and ECT: sequencing and data analysis, and evaluation of genetic variants. AL, EST, IN, TWT, JYL, BC, CYJG, SK, WK-ML, WKL, DL-MG, RF and SSJ: patient recruitment and phenotypical assessment, and evaluation of genetic variants. BC, JYL, CYJG and SK: genetic counselling, patient recruitment and collection of phenotype data. ECT, RF, BR and SSJ: funding support, supervision, data analysis and drafting of the manuscript. All authors read and approved the final manuscript.

    • Funding NMRC/CG/M003/2017 and NMRC/CG/006/2013 from the Singapore Ministry of Health’s National Medical Research Council (ECT) 02/FY2016/P1/03-A14 from the SingHealth Duke-NUS Academic Medical Centre (ECT) Clinical Innovation Grant from SingHealth Duke-NUS Paediatric ACP (ECT) IAF 311019 Singapore Ministry of Health’s Biomedical Research Council- (RF and BR) Strategic Positioning Fund on Genetic Orphan Diseases from A*STAR, Singapore (BR) NMRC/CISSP/003/2016 from the Singapore Ministry of Health’s National Medical Research Council (SJ) NMRC 1056/2011 and NMRC 0021/2012 from the Singapore Ministry of Health’s National Medical Research Council (LPS).

    • Competing interests None declared.

    • Patient consent for publication Not required.

    • Provenance and peer review Not commissioned; externally peer reviewed.

    • Data availability statement Data that support the findings of this study are available from the corresponding author upon reasonable request.

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