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The Singapore National Precision Medicine Strategy. Nat Genet 2023; 55:178-186. [PMID: 36658435 DOI: 10.1038/s41588-022-01274-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/30/2022] [Indexed: 01/21/2023]
Abstract
Precision medicine promises to transform healthcare for groups and individuals through early disease detection, refining diagnoses and tailoring treatments. Analysis of large-scale genomic-phenotypic databases is a critical enabler of precision medicine. Although Asia is home to 60% of the world's population, many Asian ancestries are under-represented in existing databases, leading to missed opportunities for new discoveries, particularly for diseases most relevant for these populations. The Singapore National Precision Medicine initiative is a whole-of-government 10-year initiative aiming to generate precision medicine data of up to one million individuals, integrating genomic, lifestyle, health, social and environmental data. Beyond technologies, routine adoption of precision medicine in clinical practice requires social, ethical, legal and regulatory barriers to be addressed. Identifying driver use cases in which precision medicine results in standardized changes to clinical workflows or improvements in population health, coupled with health economic analysis to demonstrate value-based healthcare, is a vital prerequisite for responsible health system adoption.
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2
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Cheung R, Jolly S, Vimal M, Kim HL, McGonigle I. Who's afraid of genetic tests?: An assessment of Singapore's public attitudes and changes in attitudes after taking a genetic test. BMC Med Ethics 2022; 23:5. [PMID: 35081954 PMCID: PMC8791081 DOI: 10.1186/s12910-022-00744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a consequence of precision medicine initiatives, genomic technologies have rapidly spread around the world, raising questions about genetic privacy and the ethics of data sharing. Previous scholarship in bioethics and science and technology studies has made clear that different nations have varying expectations about trust, transparency, and public reason in relation to emerging technologies and their governance. The key aims of this article are to assess genetic literacy, perceptions of genetic testing, privacy concerns, and governing norms amongst the Singapore population by collecting surveys. METHODS This study investigated genetic literacy and broad public attitudes toward genetic tests in Singapore with an online public survey (n = 560). To assess potential changes in attitudes following receipt of results from a genetic test, we also surveyed undergraduate students who underwent a genetic screen as part of a university class before and after they received their test results (n = 25). RESULTS Public participants showed broad support for the use of genetic tests; scored an average of 48.9% in genetic literacy; and expressed privacy concerns over data sharing and a desire for control over their genetic data. After taking a genetic test and receiving genetic test results, students reported less fear of genetic tests while other attitudes did not change significantly. CONCLUSION These findings highlight the potential of genetic education and active engagement with genetic testing to increase support and participation in genomic projects, PM, and biobanking initiatives; and they suggest that data privacy protections could potentially reduce discrimination by giving participants control over who can access their data. More specifically, these findings and the dataset we provide may be helpful in formulating culturally sensitive education programs and regulations concerning genomic technologies and data privacy.
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Affiliation(s)
- Ross Cheung
- School of Social Sciences, Nanyang Technological University, 48 Nanyang Avenue, Singapore, Singapore, 639818
| | - Shreshtha Jolly
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore, 637551
| | - Manoj Vimal
- School of Social Sciences, Nanyang Technological University, 48 Nanyang Avenue, Singapore, Singapore, 639818
| | - Hie Lim Kim
- Asian School of the Environment, Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore, Singapore, 637459
| | - Ian McGonigle
- School of Social Sciences, Nanyang Technological University, 48 Nanyang Avenue, Singapore, Singapore, 639818.
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Yoon S, Goh H, Fung SM, Tang S, Matchar D, Ginsburg GS, Orlando LA, Ngeow J, Wu RR. Experience and Perceptions of a Family Health History Risk Assessment Tool among Multi-Ethnic Asian Breast Cancer Patients. J Pers Med 2021; 11:jpm11101046. [PMID: 34683187 PMCID: PMC8536959 DOI: 10.3390/jpm11101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
A family health history-based risk assessment is particularly valuable for guiding cancer screening and treatment strategies, yet an optimal implementation depends upon end-users' values and needs. This is not only true prior to disease development, but also for those already affected. The aim of this study is to explore perceptions of the value of knowing one's family health history (FHH)-based risk, experience using a patient-facing FHH tool and the potential of the tool for wider implementation. Twenty multi-ethnic Asian patients undergoing breast cancer treatment in Singapore completed an FHH-based risk assessment. Semi-structured one-on-one interviews were conducted and data were thematically analyzed. All participants were female and slightly more than half were Chinese. The acceptance and usage of an FHH risk assessment tool for cancers and its broader implementation was affected by a perceived importance of personal control over early detection, patient concerns of anxiety for themselves and their families due to risk results, concerns for genetic discrimination, adequacy of follow-up care plans and Asian cultural beliefs toward disease and dying. This study uniquely sheds light on the factors affecting Asian breast cancer patients' perceptions about undergoing an FHH-based risk assessment, which should inform steps for a broader implementation in Asian healthcare systems.
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Affiliation(s)
- Sungwon Yoon
- Health Services and Systems Research, Center for Population Health Research Institute, Duke-NUS Medical School, Singapore Health Services, 8 College Road, Singapore 169857, Singapore;
| | - Hendra Goh
- Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore; (H.G.); (S.T.); (D.M.)
| | - Si Ming Fung
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore; (S.M.F.); (J.N.)
| | - Shihui Tang
- Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore; (H.G.); (S.T.); (D.M.)
| | - David Matchar
- Health Services and Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore; (H.G.); (S.T.); (D.M.)
- Department of Medicine, Duke University School of Medicine, Durham, NC 27708, USA
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27708, USA; (G.S.G.); (L.A.O.)
| | - Lori A. Orlando
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27708, USA; (G.S.G.); (L.A.O.)
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore; (S.M.F.); (J.N.)
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Rebekah Ryanne Wu
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, 304 Research Dr. Box 90141, Office 264, Durham, NC 27708, USA
- Correspondence:
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4
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Learning from scaling up ultra-rapid genomic testing for critically ill children to a national level. NPJ Genom Med 2021; 6:5. [PMID: 33510162 PMCID: PMC7843635 DOI: 10.1038/s41525-020-00168-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022] Open
Abstract
In scaling up an ultra-rapid genomics program, we used implementation science principles to design and investigate influences on implementation and identify strategies required for sustainable “real-world” services. Interviews with key professionals revealed the importance of networks and relationship building, leadership, culture, and the relative advantage afforded by ultra-rapid genomics in the care of critically ill children. Although clinical geneticists focused on intervention characteristics and the fit with patient-centered care, intensivists emphasized the importance of access to knowledge, in particular from clinical geneticists. The relative advantage of ultra-rapid genomics and trust in consistent and transparent delivery were significant in creating engagement at initial implementation, with appropriate resourcing highlighted as important for longer term sustainability of implementation. Our findings demonstrate where common approaches can be used and, significantly, where there is a need to tailor support by professional role and implementation phase, to maximize the potential of ultra-rapid genomic testing to improve patient care.
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5
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Bylstra Y, Lim WK, Kam S, Tham KW, Wu RR, Teo JX, Davila S, Kuan JL, Chan SH, Bertin N, Yang CX, Rozen S, Teh BT, Yeo KK, Cook SA, Jamuar SS, Ginsburg GS, Orlando LA, Tan P. Family history assessment significantly enhances delivery of precision medicine in the genomics era. Genome Med 2021; 13:3. [PMID: 33413596 PMCID: PMC7791763 DOI: 10.1186/s13073-020-00819-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/07/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Family history has traditionally been an essential part of clinical care to assess health risks. However, declining sequencing costs have precipitated a shift towards genomics-first approaches in population screening programs rendering the value of family history unknown. We evaluated the utility of incorporating family history information for genomic sequencing selection. METHODS To ascertain the relationship between family histories on such population-level initiatives, we analysed whole genome sequences of 1750 research participants with no known pre-existing conditions, of which half received comprehensive family history assessment of up to four generations, focusing on 95 cancer genes. RESULTS Amongst the 1750 participants, 866 (49.5%) had high-quality standardised family history available. Within this group, 73 (8.4%) participants had an increased family history risk of cancer (increased FH risk cohort) and 1 in 7 participants (n = 10/73) carried a clinically actionable variant inferring a sixfold increase compared with 1 in 47 participants (n = 17/793) assessed at average family history cancer risk (average FH risk cohort) (p = 0.00001) and a sevenfold increase compared to 1 in 52 participants (n = 17/884) where family history was not available (FH not available cohort) (p = 0.00001). The enrichment was further pronounced (up to 18-fold) when assessing only the 25 cancer genes in the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes. Furthermore, 63 (7.3%) participants had an increased family history cancer risk in the absence of an apparent clinically actionable variant. CONCLUSIONS These findings demonstrate that the collection and analysis of comprehensive family history and genomic data are complementary and in combination can prioritise individuals for genomic analysis. Thus, family history remains a critical component of health risk assessment, providing important actionable data when implementing genomics screening programs. TRIAL REGISTRATION ClinicalTrials.gov NCT02791152 . Retrospectively registered on May 31, 2016.
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Affiliation(s)
- Yasmin Bylstra
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Center, Singapore Health Services, Singapore, Singapore
| | - Sylvia Kam
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Koei Wan Tham
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,Department of Physiology, National University of Singapore, Singapore, Singapore
| | - R Ryanne Wu
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore
| | - Sonia Davila
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Center, Singapore Health Services, Singapore, Singapore.,Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Jyn Ling Kuan
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Nicolas Bertin
- Centre for Big Data and Integrative Genomics, Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Cheng Xi Yang
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Steve Rozen
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Bin Tean Teh
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,National Cancer Centre Singapore, Singapore, Singapore
| | - Khung Keong Yeo
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.,Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Stuart Alexander Cook
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.,Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Center, Singapore Health Services, Singapore, Singapore.,Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Lori A Orlando
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
| | - Patrick Tan
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore, Singapore. .,Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore. .,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
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6
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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] [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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7
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Lysaght T, Ballantyne A, Xafis V, Ong S, Schaefer GO, Ling JMT, Newson AJ, Khor IW, Tai ES. "Who is watching the watchdog?": ethical perspectives of sharing health-related data for precision medicine in Singapore. BMC Med Ethics 2020; 21:118. [PMID: 33213433 PMCID: PMC7678103 DOI: 10.1186/s12910-020-00561-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We aimed to examine the ethical concerns Singaporeans have about sharing health-data for precision medicine (PM) and identify suggestions for governance strategies. Just as Asian genomes are under-represented in PM, the views of Asian populations about the risks and benefits of data sharing are under-represented in prior attitudinal research. METHODS We conducted seven focus groups with 62 participants in Singapore from May to July 2019. They were conducted in three languages (English, Mandarin and Malay) and analysed with qualitative content and thematic analysis. RESULTS Four key themes emerged: nuanced understandings of data security and data sensitivity; trade-offs between data protection and research benefits; trust (and distrust) in the public and private sectors; and governance and control options. Participants were aware of the inherent risks associated with data sharing for research. Participants expressed conditional support for data sharing, including genomic sequence data and information contained within electronic medical records. This support included sharing data with researchers from universities and healthcare institutions, both in Singapore and overseas. Support was conditional on the perceived social value of the research and appropriate de-identification and data security processes. Participants suggested that a data sharing oversight body would help strengthen public trust and comfort in data research for PM in Singapore. CONCLUSION Maintenance of public trust in data security systems and governance regimes can enhance participation in PM and data sharing for research. Contrary to themes in much prior research, participants demonstrated a sophisticated understanding of the inherent risks of data sharing, analysed trade-offs between risks and potential benefits of PM, and often adopted an international perspective.
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Affiliation(s)
- Tamra Lysaght
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Angela Ballantyne
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Primary Health Care and General Practice, University of Otago, Dunedin, New Zealand
| | - Vicki Xafis
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Serene Ong
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerald Owen Schaefer
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Ainsley J Newson
- Sydney Health Ethics, Faculty of Medicine and Health, Sydney School of Public Health, University of Sydney, Camperdown, Australia
| | - Ing Wei Khor
- Department of Medicine,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
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8
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Mehandziska S, Stajkovska A, Stavrevska M, Jakovleva K, Janevska M, Rosalia R, Kungulovski I, Mitrev Z, Kungulovski G. Workflow for the Implementation of Precision Genomics in Healthcare. Front Genet 2020; 11:619. [PMID: 32695137 PMCID: PMC7338716 DOI: 10.3389/fgene.2020.00619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 05/21/2020] [Indexed: 12/04/2022] Open
Abstract
To enable the implementation of precise genomics in a local healthcare system, we devised a pipeline for filtering and reporting of relevant genetic information to healthy individuals based on exome or genome data. In our analytical pipeline, the first tier of filtering is variant-centric, and it is based on the selection of annotated pathogenic, protective, risk factor, and drug response variants, and their one-by-one detailed evaluation. This is followed by a second-tier gene-centric deconstruction and filtering of virtual gene lists associated with diseases, and VUS-centric filtering according to ACMG pathogenicity criteria and pre-defined deleteriousness criteria. By applying this filtering protocol, we were able to provide valuable insights regarding the carrier status, pharmacogenetic profile, actionable cardiovascular and cancer predispositions, and potentially pathogenic variants of unknown significance to our patients. Our experience demonstrates that genomic profiling can be implemented into routine healthcare and provide information of medical significance.
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9
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Lanillos J, Santos M, Carcajona M, Roldan-Romero JM, Martinez AM, Calsina B, Monteagudo M, Leandro-García LJ, Montero-Conde C, Cascón A, Maietta P, Alvarez S, Robledo M, Rodriguez-Antona C. A Novel Approach for the Identification of Pharmacogenetic Variants in MT-RNR1 through Next-Generation Sequencing Off-Target Data. J Clin Med 2020; 9:jcm9072082. [PMID: 32630724 PMCID: PMC7408883 DOI: 10.3390/jcm9072082] [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: 06/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Specific genetic variants in the mitochondrially encoded 12S ribosomal RNA gene (MT-RNR1) cause aminoglycoside-induced irreversible hearing loss. Mitochondrial DNA is usually not included in targeted sequencing experiments; however, off-target data may deliver this information. Here, we extract MT-RNR1 genetic variation, including the most relevant ototoxicity variant m.1555A>G, using the off-target reads of 473 research samples, sequenced through a capture-based, custom-targeted panel and whole exome sequencing (WES), and of 1245 diagnostic samples with clinical WES. Sanger sequencing and fluorescence-based genotyping were used for genotype validation. There was a correlation between off-target reads and mitochondrial coverage (rcustomPanel = 0.39, p = 2 × 10−13 and rWES = 0.67, p = 7 × 10−21). The median read depth of MT-RNR1 m.1555 was similar to the average mitochondrial genome coverage, with saliva and blood samples giving comparable results. The genotypes from 415 samples, including three m.1555G carriers, were concordant with fluorescence-based genotyping data. In clinical WES, median MT-RNR1 coverage was 56×, with 90% of samples having ≥20 reads at m.1555 position, and one m.1494T and three m.1555G carriers were identified with no evidence for heteroplasmy. Altogether, this study shows that obtaining MT-RNR1 genotypes through off-target reads is an efficient strategy that can impulse preemptive pharmacogenetic screening of this mitochondrial gene.
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Affiliation(s)
- Javier Lanillos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - María Santos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | | | - Juan María Roldan-Romero
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Angel M. Martinez
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - María Monteagudo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Paolo Maietta
- Nimgenetics, 28049 Madrid, Spain; (M.C.); (P.M.); (S.A.)
| | - Sara Alvarez
- Nimgenetics, 28049 Madrid, Spain; (M.C.); (P.M.); (S.A.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (J.L.); (M.S.); (J.M.R.-R.); (A.M.M.); (B.C.); (M.M.); (L.J.L.-G.); (C.M.-C.); (A.C.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-732-8000 (ext. 3321)
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Evaluation of family health history collection methods impact on data and risk assessment outcomes. Prev Med Rep 2020; 18:101072. [PMID: 32181122 PMCID: PMC7066218 DOI: 10.1016/j.pmedr.2020.101072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/17/2020] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
Information technology applications for patient-collection of family health history (FHH) increase identification of elevated-risk individuals compared to usual care. It is unknown if the method of collection impacts data collected or if simply going directly to the patient is what makes the difference. The objective of this study was to examine differences in data detail and risk identification rates between FHH collection directly from individuals using paper-based forms and an interactive web-based platform. This is a non-randomized epidemiologic study in Singaporean population from 2016 to 2018. Intervention was paper-based versus web-based interactive platform for FHH collection. Participant demographics, FHH detail, and risk assessment results were analyzed. 882 participants enrolled in the study, 481 in the paper-based group and 401 in the web-based group with mean (SD) age of 45.4 (12.98) years and 47.5% male. Web-based FHH collection participants had an increased number of conditions per relative (p-value <0.001), greater frequency of reporting age of onset (p-value <0.001), and greater odds of receiving ≥1 risk recommendation both overall (OR: 3.99 (2.41, 6.59)) and within subcategories of genetic counselling for hereditary cancer syndromes (p-value = 0.041) and screening and prevention for breast (p-value = 0.002) and colon cancer (p-value = 0.005). This has significant implications for clinical care and research efforts where FHH is being assessed. Using interactive information technology platforms to collect FHH can improve the completeness of the data collected and result in increased rates of risk identification. Methods of data collection to maximize benefit should be taken into account in future studies and clinical care.
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Desai R, Ali Khan MZ, Farheen N, Varakantam VR. Six times higher odds of coronary heart disease-related hospitalizations in Asian American and Pacific Islanders with a positive family history. Int J Cardiol 2019; 297:14. [PMID: 31839194 DOI: 10.1016/j.ijcard.2019.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 08/27/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Rupak Desai
- Division of Cardiology, Atlanta VA Medical Center, Decatur, GA, USA.
| | | | - Nazia Farheen
- Family Medicine, Lake America Family Physicians, Clermont, FL, USA
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Abstract
Genetic testing has an increasingly important role in the diagnosis and management of cardiac disorders, where it confirms the diagnosis, aids prognostication and risk stratification and guides treatment. A genetic diagnosis in the proband also enables clarification of the risk for family members by cascade testing. Genetics in cardiac disorders is complex where epigenetic and environmental factors might come into interplay. Incomplete penetrance and variable expressivity is also common. Genetic results in cardiac conditions are mostly probabilistic and should be interpreted with all available clinical information. With this complexity in cardiac genetics, testing is only indicated in patients with a strong suspicion of an inheritable cardiac disorder after a full clinical evaluation. In this review we discuss the genetics underlying the major cardiomyopathies and channelopathies, and the practical aspects of diagnosing these conditions in the laboratory.
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