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Aspell N, Goldsteen A, Renwick R. Dicing with data: the risks, benefits, tensions and tech of health data in the iToBoS project. Front Digit Health 2024; 6:1272709. [PMID: 38357640 PMCID: PMC10864635 DOI: 10.3389/fdgth.2024.1272709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
This paper will discuss the European funded iToBoS project, tasked by the European Commission to develop an AI diagnostic platform for the early detection of skin melanoma. The paper will outline the project, provide an overview of the data being processed, describe the impact assessment processes, and explain the AI privacy risk mitigation methods being deployed. Following this, the paper will offer a brief discussion of some of the more complex aspects: (1) the relatively low population clinical trial study cohort, which poses risks associated with data distinguishability and the masking ability of the applied anonymisation tools, (2) the project's ability to obtain informed consent from the study cohort given the complexity of the technologies, (3) the project's commitment to an open research data strategy and the additional privacy risk mitigations required to protect the multi-modal study data, and (4) the ability of the project to adequately explain the outputs of the algorithmic components to a broad range of stakeholders. The paper will discuss how the complexities have caused tension which are reflective of wider tensions in the health domain. A project level solution includes collaboration with a melanoma patient network, as an avenue for fair and representative qualification of risks and benefits with the patient stakeholder group. However, it is unclear how scalable this process is given the relentless pursuit of innovation within the health domain, accentuated by the continued proliferation of artificial intelligence, open data strategies, and the integration of multi-modal data sets inclusive of genomics.
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Affiliation(s)
- Niamh Aspell
- Innovation & Research, Trilateral Research Ltd., Waterford, Ireland
| | | | - Robin Renwick
- Innovation & Research, Trilateral Research Ltd., Waterford, Ireland
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2
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Gandaeva L, Sonicheva-Paterson N, McKenna WJ, Savostyanov K, Myasnikov R, Pushkov A, Zhanin I, Barskiy V, Zharova O, Silnova I, Kaverina V, Sdvigova N, Fisenko A, Arad M, Basargina E. Clinical features of pediatric Danon disease and the importance of early diagnosis. Int J Cardiol 2023; 389:131189. [PMID: 37454822 DOI: 10.1016/j.ijcard.2023.131189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Successful therapy in a cohort with early onset Danon disease (DD) highlights the potential importance of earlier disease recognition. We present experience from the largest National Pediatric Center in Russia for cardiomyopathy patients. This report focuses on identification of early clinical features of DD in the pediatric population by detailed pedigree analysis and review of medical records. RESULTS: Nine patients (3 females) were identified with DD at the Russian National Medical Research Center of Children's Health ("National Pediatric Center") aged birth to 16 years. At presentation/evaluation: all patients had left ventricular hypertrophy (LVH), ECG features of Wolff-Parkinson-White (WPW), and an increase in hepatic enzymes (particularly lactate dehydrogenase (LDH)); three had marked increase in NT-proBNP; two had HCM with impaired LV function; one had LVH with LV noncompaction; five had arrhythmia with paroxysmal supraventricular and/or ventricular tachycardia. Two teenagers died at ages 16-17 from refractory heart failure and two underwent heart transplantation. All patients were found to have a pathogenic/likely pathogenic variant in the LAMP2 gene, six patients had no family history and a de novo evolvement was documented in 4/6 of those available for genetic tested. Retrospective review related to family background and earlier clinical evaluations revealed a definitive or highly suspicious family history of DD in 3, early clinical presentation with cardiac abnormalities (ECG, echo) in 3, and cerebral, hepatic and/or neuromuscular symptoms in 5. Abnormalities were detected 9,5 months to 5,8 years, median 3,5 years prior to referral to the National Pediatric Center. CONCLUSION: The earliest clinical manifestations of Danon disease occur in the first 12 years of life with symptoms of skeletal muscle and cerebral disease, raised hepatic enzymes, and evidence of cardiac disease on ECG/echo.
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Affiliation(s)
- Leila Gandaeva
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia.
| | | | - William J McKenna
- University College London, London, United Kingdom; Grupo de Investigación Cardiovascular (GRINCAR), Universidad de A Coruña, Spain.
| | - Kirill Savostyanov
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Roman Myasnikov
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Alexander Pushkov
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Ilya Zhanin
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Vladimir Barskiy
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Olga Zharova
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Irina Silnova
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Valentina Kaverina
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Natalia Sdvigova
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia
| | - Andrey Fisenko
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia.
| | - Michael Arad
- Cardiomyopathy Clinic and Heart Failure Institute, Leviev Heart Center, Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Israel.
| | - Elena Basargina
- National Medical Research Center for Children's Health, Moscow, Lomonosov Avenue, 2, 119991, Russia.
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3
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Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. N Engl J Med 2023; 388:1559-1571. [PMID: 37043637 PMCID: PMC7614484 DOI: 10.1056/nejmoa2209046] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
BACKGROUND Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. METHODS We conducted a large-scale sequencing study involving more than 13,500 families with probands with severe, probably monogenic, difficult-to-diagnose developmental disorders from 24 regional genetics services in the United Kingdom and Ireland. Standardized phenotypic data were collected, and exome sequencing and microarray analyses were performed to investigate novel genetic causes. We developed an iterative variant analysis pipeline and reported candidate variants to clinical teams for validation and diagnostic interpretation to inform communication with families. Multiple regression analyses were performed to evaluate factors affecting the probability of diagnosis. RESULTS A total of 13,449 probands were included in the analyses. On average, we reported 1.0 candidate variant per parent-offspring trio and 2.5 variants per singleton proband. Using clinical and computational approaches to variant classification, we made a diagnosis in approximately 41% of probands (5502 of 13,449). Of 3599 probands in trios who received a diagnosis by clinical assertion, approximately 76% had a pathogenic de novo variant. Another 22% of probands (2997 of 13,449) had variants of uncertain significance in genes that were strongly linked to monogenic developmental disorders. Recruitment in a parent-offspring trio had the largest effect on the probability of diagnosis (odds ratio, 4.70; 95% confidence interval [CI], 4.16 to 5.31). Probands were less likely to receive a diagnosis if they were born extremely prematurely (i.e., 22 to 27 weeks' gestation; odds ratio, 0.39; 95% CI, 0.22 to 0.68), had in utero exposure to antiepileptic medications (odds ratio, 0.44; 95% CI, 0.29 to 0.67), had mothers with diabetes (odds ratio, 0.52; 95% CI, 0.41 to 0.67), or were of African ancestry (odds ratio, 0.51; 95% CI, 0.31 to 0.78). CONCLUSIONS Among probands with severe, probably monogenic, difficult-to-diagnose developmental disorders, multimodal analysis of genomewide data had good diagnostic power, even after previous attempts at diagnosis. (Funded by the Health Innovation Challenge Fund and Wellcome Sanger Institute.).
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Affiliation(s)
- Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter UK, EX2 5DW
| | - Patrick Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - V. Kartik Chundru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Sarah J. Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Katrina Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Juliet Hampstead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Kaitlin E. Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Rachel J. Hobson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Michael J. Parker
- Wellcome Centre for Ethics and Humanities/Ethox Centre, Oxford Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, UK, OX3 7LF
| | - Hilary C. Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
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4
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Horton R, Lucassen A. Ethical Considerations in Research with Genomic Data. New Bioeth 2023; 29:37-51. [PMID: 35484929 DOI: 10.1080/20502877.2022.2060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Our ability to generate genomic data is currently well ahead of our ability to understand what they mean, raising challenges about how best to engage with them. This article considers ethical aspects of work with such data, focussing on research contexts that are intertwined with clinical care. We discuss the identifying nature of genomic data, the medical information intrinsic within them, and their linking of people within a biological family. We go on to consider what this means for consent, the importance of thoughtful sharing of genomic data, the challenge of constructing meaningful findings, and the legacy of unequal representation in genomic datasets. We argue that the ongoing success of genomic data research relies on public trust in the enterprise: to justify this trust, we need to ensure robust stewarding, and wide engagement about the ethical issues inherent in such practices.
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Affiliation(s)
- Rachel Horton
- Centre for Personalised Medicine, St Anne's College, University of Oxford, Oxford, UK.,Clinical Ethics, Law and Society, University of Southampton, Southampton, UK
| | - Anneke Lucassen
- Centre for Personalised Medicine, St Anne's College, University of Oxford, Oxford, UK.,Clinical Ethics, Law and Society, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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5
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Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality-that benefits clearly outweigh associated risks-and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
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6
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Rethinking the ethical principles of genomic medicine services. Eur J Hum Genet 2019; 28:147-154. [PMID: 31534213 PMCID: PMC6974588 DOI: 10.1038/s41431-019-0507-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 08/02/2019] [Indexed: 01/10/2023] Open
Abstract
Clinical genome and exome sequencing is currently used in only a small fraction of patients, yet large scale genomic initiatives are becoming more embedded in clinical services. This paper examines the ethical principles that should guide regulatory processes regarding consent and data sharing in this context. We argue that a genomic dataset administered by the health system carries substantial societal benefits, and that the collective nature of this initiative means that at least those patients who benefit from genome sequencing have an ethical obligation to share their health information. This obligation is grounded in considerations of fairness. Furthermore, we argue that the use of genomic data for the advancement of medical knowledge should be permitted without explicit consent and that international and other bodies should be granted access to these data, provided certain conditions are satisfied.
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7
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Wright CF, Ware JS, Lucassen AM, Hall A, Middleton A, Rahman N, Ellard S, Firth HV. Genomic variant sharing: a position statement. Wellcome Open Res 2019; 4:22. [PMID: 31886409 PMCID: PMC6913213 DOI: 10.12688/wellcomeopenres.15090.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Sharing de-identified genetic variant data is essential for the practice of genomic medicine and is demonstrably beneficial to patients. Robust genetic diagnoses that inform medical management cannot be made accurately without reference to genetic test results from other patients, as well as population controls. Errors in this process can result in delayed, missed or erroneous diagnoses, leading to inappropriate or missed medical interventions for the patient and their family. The benefits of sharing individual genetic variants, and the harms of not sharing them, are numerous and well-established. Databases and mechanisms already exist to facilitate deposition and sharing of pseudonomised genetic variants, but clarity and transparency around best practice is needed to encourage widespread use, prevent inconsistencies between different communities, maximise individual privacy and ensure public trust. We therefore recommend that widespread sharing of a small number of individual genetic variants associated with limited clinical information should become standard practice in genomic medicine. Information robustly linking genetic variants with specific conditions is fundamental biological knowledge, not personal information, and therefore should not require consent to share. For additional case-level detail about individual patients or more extensive genomic information, which is often essential for clinical interpretation, it may be more appropriate to use a controlled-access model for data sharing, with the ultimate aim of making as much information as open and de-identified as possible with appropriate consent.
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Affiliation(s)
- Caroline F. Wright
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - James S. Ware
- National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Anneke M. Lucassen
- Department of Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Anna Middleton
- Faculty of Education, University of Cambridge, Cambridge, UK
- Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, UK, London, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Helen V. Firth
- Department of Clinical Genetics, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
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8
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Wright CF, Ware JS, Lucassen AM, Hall A, Middleton A, Rahman N, Ellard S, Firth HV. Genomic variant sharing: a position statement. Wellcome Open Res 2019. [DOI: 10.12688/wellcomeopenres.15090.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sharing de-identified genetic variant data is essential for the practice of genomic medicine and is demonstrably beneficial to patients. Robust genetic diagnoses that inform medical management cannot be made accurately without reference to genetic test results from other patients, as well as population controls. Errors in this process can result in delayed, missed or erroneous diagnoses, leading to inappropriate or missed medical interventions for the patient and their family. The benefits of sharing individual genetic variants, and the harms of not sharing them, are numerous and well-established. Databases and mechanisms already exist to facilitate deposition and sharing of pseudonomised genetic variants, but clarity and transparency around best practice is needed to encourage widespread use, prevent inconsistencies between different communities, maximise individual privacy and ensure public trust. We therefore recommend that widespread sharing of a small number of individual genetic variants associated with limited clinical information should become standard practice in genomic medicine. Information robustly linking genetic variants with specific conditions is fundamental biological knowledge, not personal information, and therefore should not require consent to share. For additional case-level detail about individual patients or more extensive genomic information, which is often essential for clinical interpretation, it may be more appropriate to use a controlled-access model for data sharing, with the ultimate aim of making as much information as open and de-identified as possible with appropriate consent.
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9
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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Abstract
Over its 30 or so years of existence, the genomic commons-the worldwide collection of publicly accessible repositories of human and nonhuman genomic data-has enjoyed remarkable, perhaps unprecedented, success. Thanks to the rapid public data release policies initiated by the Human Genome Project, free access to a vast array of scientific data is now the norm, not only in genomics, but in scientific disciplines of all descriptions. And far from being a monolithic creation of bureaucratic fiat, the genomic commons is an exemplar of polycentric, multistakeholder governance. But like all dynamic and rapidly evolving systems, the genomic commons is not without its challenges. Issues involving scientific priority, intellectual property, individual privacy, and informed consent, in an environment of data sets of exponentially expanding size and complexity, must be addressed in the near term. In this review, we describe the characteristics and unique history of the genomic commons, then address some of the trends, challenges, and opportunities that we envision for this valuable public resource in the years to come.
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Affiliation(s)
- Jorge L Contreras
- S.J. Quinney College of Law and School of Medicine, University of Utah, Salt Lake City, Utah 84112, USA;
| | - Bartha M Knoppers
- Centre of Genomics and Policy and Department of Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada;
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11
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Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders. Genet Med 2018; 20:1216-1223. [PMID: 29323667 PMCID: PMC5912505 DOI: 10.1038/gim.2017.246] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/20/2017] [Indexed: 12/15/2022] Open
Abstract
Purpose Given the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalysing previously generated genomic sequence data in light of new knowledge. Methods We tested this hypothesis in the UK-wide Deciphering Developmental Disorders Study, where in 2014 we reported a diagnostic yield of 27% through whole exome sequencing of 1133 children with severe developmental disorders and their parents. We reanalysed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes. Results We are now able to diagnose an additional 182 individuals, taking our overall diagnostic yield to 454/1133 (40%), and another 43 (4%) have a finding of uncertain clinical significance. The majority of these new diagnoses are due to novel developmental disorder-associated genes discovered since our original publication. Conclusion This study highlights the importance of coupling large-scale research with clinical practice, and of discussing the possibility of iterative reanalysis and recontact with patients and health professionals at an early stage. We estimate that implementing parent-offspring whole exome sequencing as a first line diagnostic test for developmental disorders would diagnose >50% of patients.
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12
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Bowman P, Flanagan SE, Hattersley AT. Future Roadmaps for Precision Medicine Applied to Diabetes: Rising to the Challenge of Heterogeneity. J Diabetes Res 2018; 2018:3061620. [PMID: 30599002 PMCID: PMC6288579 DOI: 10.1155/2018/3061620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Precision medicine, the concept that specific treatments can be targeted to groups of individuals with specific genetic, cellular, or molecular features, is a key aspect of modern healthcare, and its use is rapidly expanding. In diabetes, the application of precision medicine has been demonstrated in monogenic disease, where sulphonylureas are used to treat patients with neonatal diabetes due to mutations in ATP-dependent potassium (KATP) channel genes. However, diabetes is highly heterogeneous, both between and within polygenic and monogenic subtypes. Making the correct diagnosis and using the correct treatment from diagnosis can be challenging for clinicians, but it is crucial to prevent long-term morbidity and mortality. To facilitate precision medicine in diabetes, research is needed to develop a better understanding of disease heterogeneity and its impact on potential treatments for specific subtypes. Animal models have been used in diabetes research, but they are not translatable to humans in the majority of cases. Advances in molecular genetics and functional laboratory techniques and availability and sharing of large population data provide exciting opportunities for human studies. This review will map the key elements of future diabetes research in humans and its potential for clinical translation to promote precision medicine in all diabetes subtypes.
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Affiliation(s)
- P. Bowman
- University of Exeter Medical School, Exeter, UK
- Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - A. T. Hattersley
- University of Exeter Medical School, Exeter, UK
- Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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13
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Abstract
Introduction Effective data sharing does not occur in the UK despite being essential for the delivery of high-quality genomic services to patients across clinical specialities and to optimize advances in genomic medicine. Sources of data Original papers, reviews, guidelines, policy papers and web-resources. Areas of agreement Data sharing for genomic medicine requires appropriate infrastructure and policies, together with acceptance by health professionals and the public of the necessity of data sharing for clinical care. Areas of controversy There is ongoing debate around the different technical approaches and safeguards that could be used to facilitate data sharing while minimizing the risks to individuals of identification. Lack of consensus undermines trust and confidence. Growing points Ongoing policy developments around genomics and health data create opportunities to ensure systems and policies are in place to support proportionate, effective and safeguarded data sharing. Areas timely for developing research Mechanisms to improve public trust.
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Affiliation(s)
- Sobia Raza
- PHG Foundation, 2 Worts Causeway, Cambridge, CB1 8RN, UK
| | - Alison Hall
- PHG Foundation, 2 Worts Causeway, Cambridge, CB1 8RN, UK
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14
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Wright CF, Middleton A, Barrett JC, Firth HV, FitzPatrick DR, Hurles ME, Parker M. Returning genome sequences to research participants: Policy and practice. Wellcome Open Res 2017; 2:15. [PMID: 28317033 PMCID: PMC5351846 DOI: 10.12688/wellcomeopenres.10942.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2017] [Indexed: 12/18/2022] Open
Abstract
Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support. In addition, we identify a number of ethico-legal issues that require careful consideration, including returning data to family members, mitigating against unintended consequences, and ensuring appropriate governance. Finally, recognising that there is an opportunity cost to addressing these issues, we make some specific pragmatic suggestions for studies that are considering whether to share individual genomic datasets with individual study participants. If data are shared, research should be undertaken into the personal, familial and societal impact of receiving individual genome sequence data.
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Affiliation(s)
- Caroline F. Wright
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anna Middleton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Helen V. Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
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Raza S, Luheshi L. Big data or bust: realizing the microbial genomics revolution. Microb Genom 2016; 2:e000046. [PMID: 28348842 PMCID: PMC5320582 DOI: 10.1099/mgen.0.000046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/16/2015] [Indexed: 12/29/2022] Open
Abstract
Pathogen genomics has the potential to transform the clinical and public health management of infectious diseases through improved diagnosis, detection and tracking of antimicrobial resistance and outbreak control. However, the wide-ranging benefits of this technology can only fully be realized through the timely collation, integration and sharing of genomic and clinical/epidemiological metadata by all those involved in the delivery of genomic-informed services. As part of our review on bringing pathogen genomics into ‘health-service’ practice, we undertook extensive stakeholder consultation to examine the factors integral to achieving effective data sharing and integration. Infrastructure tailored to the needs of clinical users, as well as practical support and policies to facilitate the timely and responsible sharing of data with relevant health authorities and beyond, are all essential. We propose a tiered data sharing and integration model to maximize the immediate and longer term utility of microbial genomics in healthcare. Realizing this model at the scale and sophistication necessary to support national and international infection management services is not uncomplicated. Yet the establishment of a clear data strategy is paramount if failures in containing disease spread due to inadequate knowledge sharing are to be averted, and substantial progress made in tackling the dangers posed by infectious diseases.
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