1
|
Zhao J, O'Hagan A, Salter-Townshend M. How group structure impacts the numbers at risk for coronary artery disease: polygenic risk scores and nongenetic risk factors in the UK Biobank cohort. Genetics 2024; 227:iyae086. [PMID: 38781512 DOI: 10.1093/genetics/iyae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 03/22/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The UK Biobank (UKB) is a large cohort study that recruited over 500,000 British participants aged 40-69 in 2006-2010 at 22 assessment centers from across the United Kingdom. Self-reported health outcomes and hospital admission data are 2 types of records that include participants' disease status. Coronary artery disease (CAD) is the most common cause of death in the UKB cohort. After distinguishing between prevalence and incidence CAD events for all UKB participants, we identified geographical variations in age-standardized rates of CAD between assessment centers. Significant distributional differences were found between the pooled cohort equation scores of UKB participants from England and Scotland using the Mann-Whitney test. Polygenic risk scores of UKB participants from England and Scotland and from different assessment centers differed significantly using permutation tests. Our aim was to discriminate between assessment centers with different disease rates by collecting data on disease-related risk factors. However, relying solely on individual-level predictions and averaging them to obtain group-level predictions proved ineffective, particularly due to the presence of correlated covariates resulting from participation bias. By using the Mundlak model, which estimates a random effects regression by including the group means of the independent variables in the model, we effectively addressed these issues. In addition, we designed a simulation experiment to demonstrate the functionality of the Mundlak model. Our findings have applications in public health funding and strategy, as our approach can be used to predict case rates in the future, as both population structure and lifestyle changes are uncertain.
Collapse
Affiliation(s)
- Jinbo Zhao
- Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin D04V1W8, Ireland
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin D04V1W8, Ireland
| | - Adrian O'Hagan
- Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin D04V1W8, Ireland
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin D04V1W8, Ireland
| | - Michael Salter-Townshend
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin D04V1W8, Ireland
| |
Collapse
|
2
|
Sedlić F, Sertić J, Markotić A, Primorac D, Slavica A, Zibar L, Vlahoviček K, Kušec V, Barić I, Paar V, Borovečki F, Žmak L, Kurolt IC, Canki-Klain N, Roksandić S, Rinčić I, Jurić H, Škaro V, Marjanović D, Projić P, Primorac D, Starčević A, Vujaklija D, Šikić M, Križanović K, Gamulin S. The Applied Genomics Development Strategy by the Croatian Academy of Sciences and Arts paves the way for the future development of applied genomics in Croatia. Croat Med J 2024; 65:297-302. [PMID: 38868976 PMCID: PMC11157260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Affiliation(s)
| | | | | | - Dragan Primorac
- Dragan Primorac, St. Catherine Specialty Hospital, Zagreb, Croatia,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Gaydarska H, Takashima K, Shahrier S, Raz A, Minari J. The interplay of ethics and genetic technologies in balancing the social valuation of the human genome in UNESCO declarations. Eur J Hum Genet 2024; 32:725-730. [PMID: 38355962 PMCID: PMC11153547 DOI: 10.1038/s41431-024-01549-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
This study investigates changes in the social valuation of the human genome over the more than 30 years since the establishment of the Human Genome Project. It offers a descriptive sociological analysis of the three waves of this valuation, mainly by considering three key UNESCO declarations and a relevant report. These waves represent a shifting balance between collectivism and individualism, starting with a broadly constructed valuation of the human genome as common human heritage and moving toward a valuation of dynamic applications within various social and medical contexts (e.g., personalized genomic medicine and genome editing). We seek to broaden the analytical perspective by examining how the declarations' ethical foci are framed within the context of rapidly evolving genetic technologies and their social applications. We conclude by discussing continuity and change in value balancing vis-à-vis changing genomic technologies.
Collapse
Affiliation(s)
- Hristina Gaydarska
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kayo Takashima
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shibly Shahrier
- Teesside University International Business School, Teesside University, Tees Valley, UK
| | - Aviad Raz
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beersheba, Israel.
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| |
Collapse
|
4
|
Kawakami K, Procopio F, Rimfeld K, Malanchini M, von Stumm S, Asbury K, Plomin R. Exploring the genetic prediction of academic underachievement and overachievement. NPJ SCIENCE OF LEARNING 2024; 9:39. [PMID: 38824137 PMCID: PMC11144217 DOI: 10.1038/s41539-024-00251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/10/2024] [Indexed: 06/03/2024]
Abstract
Academic underachievement refers to school performance which falls below expectations. Focusing on the pivotal first stage of education, we explored a quantitative measure of underachievement using genomically predicted achievement delta (GPAΔ), which reflects the difference between observed and expected achievement predicted by genome-wide polygenic scores. We analyzed the relationship between GPAΔ at age 7 and achievement trajectories from ages 7 to 16, using longitudinal data from 4175 participants in the Twins Early Development Study to assess empirically the extent to which students regress to their genomically predicted levels by age 16. We found that the achievement of underachievers and overachievers who deviated from their genomic predictions at age 7 regressed on average by one-third towards their genomically predicted levels. We also found that GPAΔ at age 7 was as predictive of achievement trajectories as a traditional ability-based index of underachievement. Targeting GPAΔ underachievers might prove cost-effective because such interventions seem more likely to succeed by going with the genetic flow rather than swimming upstream, helping GPAΔ underachievers reach their genetic potential as predicted by their GPS. However, this is a hypothesis that needs to be tested in intervention research investigating whether GPAΔ underachievers respond better to the intervention than other underachievers. We discuss the practicality of genomic indices in assessing underachievement.
Collapse
Affiliation(s)
- Kaito Kawakami
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
| | - Francesca Procopio
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychology, Royal Holloway, University of London, London, UK
| | - Margherita Malanchini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | | | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| |
Collapse
|
5
|
Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
Collapse
Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
6
|
Hibler EA, Szymaniak B, Abbass MA. Colorectal Cancer Risk between Mendelian and Non-Mendelian Inheritance. Clin Colon Rectal Surg 2024; 37:140-145. [PMID: 38606051 PMCID: PMC11006447 DOI: 10.1055/s-0043-1770382] [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: 04/13/2024]
Abstract
Hereditary colorectal cancer has been an area of focus for research and public health practitioners due to our ability to quantify risk and then act based on such results by enrolling patients in surveillance programs. The wide access to genetic testing and whole-genome sequencing has resulted in identifying many low/moderate penetrance genes. Above all, our understanding of the family component of colorectal cancer has been improving. Polygenic scores are becoming part of the risk assessment for many cancers, and the data about polygenic risk scores for colorectal cancer is promising. The challenge is determining how we incorporate this data in clinical care.
Collapse
Affiliation(s)
- Elizabeth A. Hibler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Brittany Szymaniak
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Mohammad Ali Abbass
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| |
Collapse
|
7
|
Valančienė J, Melaika K, Šliachtenko A, Šiaurytė-Jurgelėnė K, Ekkert A, Jatužis D. Stroke genetics and how it Informs novel drug discovery. Expert Opin Drug Discov 2024; 19:553-564. [PMID: 38494780 DOI: 10.1080/17460441.2024.2324916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION Stroke is one of the main causes of death and disability worldwide. Nevertheless, despite the global burden of this disease, our understanding is limited and there is still a lack of highly efficient etiopathology-based treatment. It is partly due to the complexity and heterogenicity of the disease. It is estimated that around one-third of ischemic stroke is heritable, emphasizing the importance of genetic factors identification and targeting for therapeutic purposes. AREAS COVERED In this review, the authors provide an overview of the current knowledge of stroke genetics and its value in diagnostics, personalized treatment, and prognostication. EXPERT OPINION As the scale of genetic testing increases and the cost decreases, integration of genetic data into clinical practice is inevitable, enabling assessing individual risk, providing personalized prognostic models and identifying new therapeutic targets and biomarkers. Although expanding stroke genetics data provides different diagnostics and treatment perspectives, there are some limitations and challenges to face. One of them is the threat of health disparities as non-European populations are underrepresented in genetic datasets. Finally, a deeper understanding of underlying mechanisms of potential targets is still lacking, delaying the application of novel therapies into routine clinical practice.
Collapse
Affiliation(s)
| | | | | | - Kamilė Šiaurytė-Jurgelėnė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Dalius Jatužis
- Center of Neurology, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
8
|
Fuat A, Adlen E, Monane M, Coll R, Groves S, Little E, Wild J, Kamali FJ, Soni Y, Haining S, Riding H, Riveros-Mckay F, Peneva I, Lachapelle A, Giner-Delgado C, Weale ME, Plagnol V, Harrison S, Donnelly P. A polygenic risk score added to a QRISK®2 cardiovascular disease risk calculator demonstrated robust clinical acceptance and clinical utility in the primary care setting. Eur J Prev Cardiol 2024; 31:716-722. [PMID: 38243727 DOI: 10.1093/eurjpc/zwae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/21/2024]
Abstract
AIMS The aim of the study was to assess the real-world feasibility, acceptability, and impact of an integrated risk tool for cardiovascular disease (CVD IRT, combining the standard QRISK®2 risk algorithm with a polygenic risk score), implemented within routine primary practice in the UK National Health Service. METHODS AND RESULTS The Healthcare Evaluation of Absolute Risk Testing Study (NCT05294419) evaluated participants undergoing primary care health checks. Both QRISK2 and CVD IRT scores were returned to the healthcare providers (HCPs), who then communicated the results to participants. The primary outcome of the study was feasibility of CVD IRT implementation. Secondary outcomes included changes in CVD risk (QRISK2 vs. CVD IRT) and impact of the CVD IRT on clinical decision-making. A total of 832 eligible participants (median age 55 years, 62% females, 97.5% White ethnicity) were enrolled across 12 UK primary care practices. Cardiovascular disease IRT scores were obtained on 100% of the blood samples. Healthcare providers stated that the CVD IRT could be incorporated into routine primary care in a straightforward manner in 90.7% of reports. Participants stated they were 'likely' or 'very likely' to recommend the use of this test to their family or friends in 86.9% of reports. Participants stated that the test was personally useful (98.8%) and that the results were easy to understand (94.6%). When CVD IRT exceeded QRISK2, HCPs planned changes in management for 108/388 (27.8%) of participants and 47% (62/132) of participants with absolute risk score changes of >2%. CONCLUSION Amongst HCPs and participants who agreed to the trial of genetic data for refinement of clinical risk prediction in primary care, we observed that CVD IRT implementation was feasible and well accepted. The CVD IRT results were associated with planned changes in prevention strategies.
Collapse
Affiliation(s)
| | - Ella Adlen
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Mark Monane
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Ruth Coll
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Sarah Groves
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | | | | | | | - Yusuf Soni
- Riverside General Practice, Stockton-on-Tees, UK
| | - Shona Haining
- Research and Evidence, NHS North of England Commissioning Support, Durham, UK
| | - Helen Riding
- Research and Evidence, NHS North of England Commissioning Support, Durham, UK
| | | | - Iliana Peneva
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | | | | | - Michael E Weale
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Vincent Plagnol
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Seamus Harrison
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Peter Donnelly
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| |
Collapse
|
9
|
Sabatello M, Bakken S, Chung WK, Cohn E, Crew KD, Kiryluk K, Kukafka R, Weng C, Appelbaum PS. Return of polygenic risk scores in research: Stakeholders' views on the eMERGE-IV study. HGG ADVANCES 2024; 5:100281. [PMID: 38414240 PMCID: PMC10950748 DOI: 10.1016/j.xhgg.2024.100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Research on polygenic risk scores (PRSs) for common, genetically complex chronic diseases aims to improve health-related predictions, tailor risk-reducing interventions, and improve health outcomes. Yet, the study and use of PRSs in clinical settings raise equity, clinical, and regulatory challenges that can be greater for individuals from historically marginalized racial, ethnic, and other minoritized communities. As part of the National Human Genome Research Institute-funded Electronic Medical Records and Genomics IV Network, we conducted online focus groups with patients/community members, clinicians, and members of institutional review boards to explore their views on key issues, including PRS research, return of PRS results, clinical translation, and barriers and facilitators to health behavioral changes in response to PRS results. Across stakeholder groups, our findings indicate support for PRS development and a strong interest in having PRS results returned to research participants. However, we also found multi-level barriers and significant differences in stakeholders' views about what is needed and possible for successful implementation. These include researcher-participant interaction formats, health and genomic literacy, and a range of structural barriers, such as financial instability, insurance coverage, and the absence of health-supporting infrastructure and affordable healthy food options in poorer neighborhoods. Our findings highlight the need to revisit and implement measures in PRS studies (e.g., incentives and resources for follow-up care), as well as system-level policies to promote equity in genomic research and health outcomes.
Collapse
Affiliation(s)
- Maya Sabatello
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, NY, USA; Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY, USA.
| | - Suzanne Bakken
- School of Nursing and Department of Biomedical Informatic, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Cohn
- Northwell Health 600 Community Drive, Manhasset, NY, USA
| | - Katherine D Crew
- Department of Medicine and Epidemiology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Rita Kukafka
- Departments of Biomedical Informatics and Sociomedical Sciences, Columbia University, New York, NY 10032, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
| |
Collapse
|
10
|
Wouters RHP, van der Horst MZ, Aalfs CM, Bralten J, Luykx JJ, Zinkstok JR. The ethics of polygenic scores in psychiatry: minefield or opportunity for patient-centered psychiatry? Psychiatr Genet 2024; 34:31-36. [PMID: 38441147 DOI: 10.1097/ypg.0000000000000363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Recent advancements in psychiatric genetics have sparked a lively debate on the opportunities and pitfalls of incorporating polygenic scores into clinical practice. Yet, several ethical concerns have been raised, casting doubt on whether further development and implementation of polygenic scores would be compatible with providing ethically responsible care. While these ethical issues warrant thoughtful consideration, it is equally important to recognize the unresolved need for guidance on heritability among patients and their families. Increasing the availability of genetic counseling services in psychiatry should be regarded as a first step toward meeting these needs. As a next step, future integration of novel genetic tools such as polygenic scores into genetic counseling may be a promising way to improve psychiatric counseling practice. By embedding the exploration of polygenic psychiatry into the supporting environment of genetic counseling, some of the previously identified ethical pitfalls may be prevented, and opportunities to bolster patient empowerment can be seized upon. To ensure an ethically responsible approach to psychiatric genetics, active collaboration with patients and their relatives is essential, accompanied by educational efforts to facilitate informed discussions between psychiatrists and patients.
Collapse
Affiliation(s)
- Roel H P Wouters
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Psychiatry, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marte Z van der Horst
- GGNet Mental Health, Warnsveld, The Netherlands
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
| | - Cora M Aalfs
- Department of Clinical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Janita Bralten
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Jurjen J Luykx
- GGNet Mental Health, Warnsveld, The Netherlands
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
| | - Janneke R Zinkstok
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry, University Centre Nijmegen, Nijmegen, The Netherlands
| |
Collapse
|
11
|
Yanes T, Tiller J, Haining CM, Wallingford C, Otlowski M, Keogh L, McInerney-Leo A, Lacaze P. Future implications of polygenic risk scores for life insurance underwriting. NPJ Genom Med 2024; 9:25. [PMID: 38555372 PMCID: PMC10981684 DOI: 10.1038/s41525-024-00407-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 03/08/2024] [Indexed: 04/02/2024] Open
Affiliation(s)
- Tatiane Yanes
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia.
| | - Jane Tiller
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Casey M Haining
- Centre for Health Equity, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Courtney Wallingford
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
| | - Margaret Otlowski
- Centre for Law and Genetics, Faculty of Law, University of Tasmania, Churchill Avenue, Hobart, Tasmania, Australia
| | - Louise Keogh
- Centre for Health Equity, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Aideen McInerney-Leo
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| |
Collapse
|
12
|
Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E. Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis. Nat Commun 2024; 15:2568. [PMID: 38531883 PMCID: PMC10966072 DOI: 10.1038/s41467-023-44512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/15/2023] [Indexed: 03/28/2024] Open
Abstract
Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.
Collapse
Affiliation(s)
- Pooja Middha
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lydia Yao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zoe Quandt
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Cardenas
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina J Falcon
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew A Gubens
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University of Medicine, Stanford, CA, USA
| | - Khaleeq Khan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Min Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Megan H Murray
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kristin Werking
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luna Jia Zhan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Temerty School of Medicine, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Center for Genes, Environment and Health, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
13
|
Andreoli L, Peeters H, Van Steen K, Dierickx K. Taking the risk. A systematic review of ethical reasons and moral arguments in the clinical use of polygenic risk scores. Am J Med Genet A 2024:e63584. [PMID: 38450933 DOI: 10.1002/ajmg.a.63584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
Debates about the prospective clinical use of polygenic risk scores (PRS) have grown considerably in the last years. The potential benefits of PRS to improve patient care at individual and population levels have been extensively underlined. Nonetheless, the use of PRS in clinical contexts presents a number of unresolved ethical challenges and consequent normative gaps that hinder their optimal implementation. Here, we conducted a systematic review of reasons of the normative literature discussing ethical issues and moral arguments related to the use of PRS for the prevention and treatment of common complex diseases. In total, we have included and analyzed 34 records, spanning from 2013 to 2023. The findings have been organized in three major themes: in the first theme, we consider the potential harms of PRS to individuals and their kin. In the theme "Threats to health equity," we consider ethical concerns of social relevance, with a focus on justice issues. Finally, the theme "Towards best practices" collects a series of research priorities and provisional recommendations to be considered for an optimal clinical translation of PRS. We conclude that the use of PRS in clinical care reinvigorates old debates in matters of health justice; however, open questions, regarding best practices in clinical counseling, suggest that the ethical considerations applicable in monogenic settings will not be sufficient to face PRS emerging challenges.
Collapse
Affiliation(s)
- Lara Andreoli
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Kris Dierickx
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| |
Collapse
|
14
|
Siermann M, Valcke O, Vermeesch JR, Raivio T, Tšuiko O, Borry P. "Are we not going too far?": Socio-ethical considerations of preimplantation genetic testing using polygenic risk scores according to healthcare professionals. Soc Sci Med 2024; 343:116599. [PMID: 38244362 DOI: 10.1016/j.socscimed.2024.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
The recent introduction of polygenic risk scores within preimplantation genetic testing (PGT-P) has been met with many concerns. To get more insights into the perspectives of relevant stakeholders on the socio-ethical aspects of PGT-P, an interview study with 31 healthcare professionals involved in reproductive medicine and genetics in Europe and North-America was performed. Healthcare professionals in our study were concerned that PGT-P was going too far in terms of selection, with regards to both medical conditions and non-medical traits. Healthcare professionals were worried about the ethical 'slippery slope' of PGT-P, the increasing medicalization of reproductive health, the commercial context of PGT-P, and potential stigmatization and discrimination. There were also concerns that the availability and the 'technological imperative' of PGT-P could lead to pressure and a sense of responsibility for parents to use PGT-P. Additionally, it could cause new anxieties about the child's health before the child has even been born. Since PGT-P provides polygenic risk scores before birth, the autonomy of the child has to be considered. These socio-ethical concerns heighten existing debates regarding reproductive genetic technologies and show that the specifics of PGT-P make this screening option especially ethically controversial.
Collapse
Affiliation(s)
- Maria Siermann
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 7 - Box 7001, 3000, Leuven, Belgium; Department of Physiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (P.O. Box 63), 00014, Helsinki, Finland.
| | - Ophelia Valcke
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 7 - Box 7001, 3000, Leuven, Belgium
| | - Joris Robert Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, ON1 Herestraat 49 - Bus 606, 3000, Leuven, Belgium
| | - Taneli Raivio
- Department of Physiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (P.O. Box 63), 00014, Helsinki, Finland
| | - Olga Tšuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, ON1 Herestraat 49 - Bus 606, 3000, Leuven, Belgium; Reproductive Genetics Unit, Center for Human Genetics, UZ Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 7 - Box 7001, 3000, Leuven, Belgium
| |
Collapse
|
15
|
Bentz M, Saperstein A, Fullerton SM, Shim JK, Lee SSJ. Conflating race and ancestry: Tracing decision points about population descriptors over the precision medicine research life course. HGG ADVANCES 2024; 5:100243. [PMID: 37771152 PMCID: PMC10585473 DOI: 10.1016/j.xhgg.2023.100243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Responding to calls for human genomics to shift away from the use of race, genomic investigators are coalescing around the possibility of using genetic ancestry. This shift has renewed questions about the use of social and genetic concepts of difference in precision medicine research (PMR). Drawing from qualitative data on five PMR projects, we illustrate negotiations within and between research teams as genomic investigators deliberate on the relevance of race and genetic ancestry for different analyses and contexts. We highlight how concepts of both social and genetic difference are embedded within and travel through research practices, and identify multiple points across the research life course at which conceptual slippage and conflation between race and genetic ancestry occur. We argue that moving beyond race will require PMR investigators to confront the entrenched ways in which race is built into research practices and biomedical infrastructures.
Collapse
Affiliation(s)
- Michael Bentz
- Division of Ethics, Department of Medical Humanities and Ethics, Vagelos College of Physicians & Surgeons, Columbia University, 630 West 168th Street, PH 1525, New York, NY 10032, USA.
| | - Aliya Saperstein
- Department of Sociology, Stanford University, 450 Jane Stanford Way, Building 120, Room 160, Stanford, CA 94305-2047, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Box 357120, Seattle, WA 98195-7120, USA
| | - Janet K Shim
- Department of Social & Behavioral Sciences, University of California, San Francisco, 490 Illinois Street, Floor 12, Box 0612, San Francisco, CA 94143-0612, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Vagelos College of Physicians & Surgeons, Columbia University, 630 West 168th Street, PH 1525, New York, NY 10032, USA.
| |
Collapse
|
16
|
Toivonen J, Allara E, Castrén J, di Angelantonio E, Arvas M. The value of genetic data from 665,460 individuals in managing iron deficiency anaemia and suitability to donate blood. Vox Sang 2024; 119:34-42. [PMID: 38018286 DOI: 10.1111/vox.13564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/15/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND OBJECTIVES Although the genetic determinants of haemoglobin and ferritin have been widely studied, those of the clinically and globally relevant iron deficiency anaemia (IDA) and deferral due to hypohaemoglobinemia (Hb-deferral) are unclear. In this investigation, we aimed to quantify the value of genetic information in predicting IDA and Hb-deferral. MATERIALS AND METHODS We analysed genetic data from up to 665,460 participants of the FinnGen, Blood Service Biobank and UK Biobank, and used INTERVAL (N = 39,979) for validation. We performed genome-wide association studies (GWASs) of IDA and Hb-deferral and utilized publicly available genetic associations to compute polygenic scores for IDA, ferritin and Hb. We fitted models to estimate the effect sizes of these polygenic risk scores (PRSs) on IDA and Hb-deferral risk while accounting for the individual's age, sex, weight, height, smoking status and blood donation history. RESULTS Significant variants in GWASs of IDA and Hb-deferral appear to be a small subset of variants associated with ferritin and Hb. Effect sizes of genetic predictors of IDA and Hb-deferral are similar to those of age and weight which are typically used in blood donor management. A total genetic score for Hb-deferral was estimated for each individual. The odds ratio estimate between first decile against that at ninth decile of total genetic score distribution ranged from 1.4 to 2.2. CONCLUSION The value of genetic data in predicting IDA or suitability to donate blood appears to be on a practically useful level.
Collapse
Affiliation(s)
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | | | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Health Data Science Research Centre, Human Technopole, Milan, Italy
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| |
Collapse
|
17
|
Tokutomi T, Yoshida A, Fukushima A, Nagami F, Minoura Y, Sasaki M. Stakeholder Perception of the Implementation of Genetic Risk Testing for Twelve Multifactorial Diseases. Genes (Basel) 2023; 15:49. [PMID: 38254940 PMCID: PMC10815213 DOI: 10.3390/genes15010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-wide association studies have been employed to develop numerous risk prediction models using polygenic risk scores (PRSs) for multifactorial diseases. However, healthcare providers lack confidence in their understanding of PRS risk stratification for multifactorial diseases, which underscores the need to assess the readiness of PRSs for clinical use. To address this issue, we surveyed the perceptions of healthcare providers as stakeholders in the clinical implementation of genetic-based risk prediction for multifactorial diseases. We conducted a web-based study on the need for risk prediction based on genetic information and the appropriate timing of testing for 12 multifactorial diseases. Responses were obtained from 506 stakeholders. Positive perceptions of genetic risk testing were found for adult-onset chronic diseases. As per participant opinion, testing for adult-onset diseases should be performed after the age of 20 years, whereas testing for psychiatric and allergic disorders that manifest during childhood should be performed from birth to 19 years of age. The stakeholders recognized the need for genetic risk testing for diseases that develop in adulthood, believing that the appropriate testing time is after maturity. This study contributes to the discussion on the clinical implementation of the PRS for genetic risk prediction of multifactorial diseases.
Collapse
Affiliation(s)
- Tomoharu Tokutomi
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Iwate 020-8505, Japan
| | - Akiko Yoshida
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Iwate 020-8505, Japan
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Iwate 020-8505, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-0872, Japan
| | - Yuko Minoura
- Departments of Medical Genetics and Genomics, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
| |
Collapse
|
18
|
Fox BM, Martschenko DO. Placing Publics in Public Health Genomics. Public Health Genomics 2023; 27:23-29. [PMID: 38128495 PMCID: PMC11007191 DOI: 10.1159/000535942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Brandy M. Fox
- Center for Biomedical Ethics, Department of Pediatrics, Stanford Medicine, Stanford, CA
| | | |
Collapse
|
19
|
Zhang K, Loong SSE, Yuen LZH, Venketasubramanian N, Chin HL, Lai PS, Tan BYQ. Genetics in Ischemic Stroke: Current Perspectives and Future Directions. J Cardiovasc Dev Dis 2023; 10:495. [PMID: 38132662 PMCID: PMC10743455 DOI: 10.3390/jcdd10120495] [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: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Ischemic stroke is a heterogeneous condition influenced by a combination of genetic and environmental factors. Recent advancements have explored genetics in relation to various aspects of ischemic stroke, including the alteration of individual stroke occurrence risk, modulation of treatment response, and effectiveness of post-stroke functional recovery. This article aims to review the recent findings from genetic studies related to various clinical and molecular aspects of ischemic stroke. The potential clinical applications of these genetic insights in stratifying stroke risk, guiding personalized therapy, and identifying new therapeutic targets are discussed herein.
Collapse
Affiliation(s)
- Ka Zhang
- Division of Neurology, Department of Medicine, National University Hospital, Singapore 119074, Singapore;
| | - Shaun S. E. Loong
- Cardiovascular-Metabolic Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Linus Z. H. Yuen
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | | | - Hui-Lin Chin
- Khoo Teck Puat National University Children’s Medical Institute, National University Hospital, Singapore 119074, Singapore;
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Benjamin Y. Q. Tan
- Division of Neurology, Department of Medicine, National University Hospital, Singapore 119074, Singapore;
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| |
Collapse
|
20
|
Austin CA, Sanderson K, Crona D, Kistler C. Pharmacogenetics: Using science to reduce racial bias in pain management? J Am Geriatr Soc 2023; 71:3973-3976. [PMID: 37529936 PMCID: PMC10834849 DOI: 10.1111/jgs.18524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/12/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023]
Affiliation(s)
- C. Adrian Austin
- Division of Geriatric Medicine and Center on Aging, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Pulmonary and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Keia Sanderson
- Davison of Nephrology and Hypertension, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel Crona
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
- Department of Pharmacy, UNC Hospitals and Clinics, Chapel Hill, North Carolina, USA
| | - Christine Kistler
- Division of Geriatric Medicine and Center on Aging, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Family Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- The Cecil G. Sheps Center for Health Services Research, University of North Carolina, Chapel Hill, North Carolina, USA
| |
Collapse
|
21
|
Riddle L, Joseph G, Caruncho M, Koenig BA, James JE. The role of polygenic risk scores in breast cancer risk perception and decision-making. J Community Genet 2023; 14:489-501. [PMID: 37311883 PMCID: PMC10576692 DOI: 10.1007/s12687-023-00655-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Polygenic risk scores (PRS) have the potential to improve the accuracy of clinical risk assessments, yet questions about their clinical validity and readiness for clinical implementation persist. Understanding how individuals integrate and act on the information provided by PRS is critical for their effective integration into routine clinical care, yet few studies have examined how individuals respond to the receipt of polygenic risk information. We conducted an embedded Ethical, Legal, and Social Implications (ELSI) study to examine if and how unaffected participants in a US population breast cancer screening trial understood and utilized PRS, as part of a multifactorial risk score combining traditional risk factors with a genetic risk assessment, to make screening and risk-reduction decisions. Semi-structured qualitative interviews were conducted with 24 trial participants who were designated at elevated risk for breast cancer due to their combined risk score. Interviews were analyzed using a grounded theory approach. Participants understood PRS conceptually and accepted it as one of many risk factors to consider, yet the value and meaning they ascribed to this risk estimate varied. Most participants reported financial and insurance barriers to enhanced screening with MRI and were not interested in taking risk-reducing medications. These findings contribute to our understanding of how PRS may be best translated from research to clinical care. Furthermore, they illuminate ethical concerns about identifying risk and making recommendations based on polygenic risk in a population screening context where many may have trouble accessing appropriate care.
Collapse
Affiliation(s)
- Leslie Riddle
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mikaella Caruncho
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Barbara Ann Koenig
- Department of Humanities and Social Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer Elyse James
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
22
|
Chapman CR. Ethical, legal, and social implications of genetic risk prediction for multifactorial disease: a narrative review identifying concerns about interpretation and use of polygenic scores. J Community Genet 2023; 14:441-452. [PMID: 36529843 PMCID: PMC10576696 DOI: 10.1007/s12687-022-00625-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022] Open
Abstract
Advances in genomics have enabled the development of polygenic scores (PGS), sometimes called polygenic risk scores, in the context of multifactorial diseases and disorders such as cancer, cardiovascular disease, and schizophrenia. PGS estimate an individual's genetic predisposition, as compared to other members of a population, for conditions which are influenced by both genetic and environmental factors. There is significant interest in using genetic risk prediction afforded through PGS in public health, clinical care, and research settings, yet many acknowledge the need to thoughtfully consider and address ethical, legal, and social implications (ELSI). To contribute to this effort, this paper reports on a narrative review of the literature, with the aim of identifying and categorizing ELSI relating to genetic risk prediction in the context of multifactorial disease, which have been raised by scholars in the field. Ninety-two articles, spanning from 1977 to 2021, met the inclusion criteria for this study. Identified ELSI included potential benefits, challenges and risks that focused on concerns about interpretation and use, and ethical obligations to maximize benefits, minimize risks, promote justice, and support autonomy. This research will support geneticists, clinicians, genetic counselors, patients, patient advocates, and policymakers in recognizing and addressing ethical concerns associated with PGS; it will also guide future empirical and normative research.
Collapse
Affiliation(s)
- Carolyn Riley Chapman
- Department of Population Health (Division of Medical Ethics), NYU Grossman School of Medicine, New York, NY, USA.
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, Science Building, 435 E. 30th St, 8th Floor, New York, NY, 10016, USA.
| |
Collapse
|
23
|
Wand H, Martschenko DO, Smitherman A, Michelson S, Pun T, Witte JS, Scott SA, Cho MK, Ashley EA. Re-envisioning community genetics: community empowerment in preventive genomics. J Community Genet 2023; 14:459-469. [PMID: 36765027 PMCID: PMC9918397 DOI: 10.1007/s12687-023-00638-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
As genomic technologies rapidly develop, polygenic scores (PGS) are entering into a growing conversation on how to improve precision in public health and prevent chronic disease. While the integration of PGS into public health and clinical services raises potential benefits, it also introduces potential harms. In particular, there is a high level of uncertainty about how to incorporate PGS into clinical settings in a manner that is equitable, just, and aligned with the long-term goals of many healthcare systems to support person-centered and value-based care. This paper argues that any conversation about whether and how to design and implement PGS clinical services requires dynamic engagement with local communities, patients, and families. These parties often face the consequences, both positive and negative, of such uncertainties and should therefore drive clinical translation. As a collaborative effort between hospital stakeholders, community partners, and researchers, this paper describes a community-empowered co-design process for addressing uncertainty and making programmatic decisions about the implementation of PGS into clinical services. We provide a framework for others interested in designing clinical programs that are responsive to, and inclusive and respectful of, local communities.
Collapse
Affiliation(s)
- Hannah Wand
- Department of Cardiology, Stanford Medicine, Stanford, CA, USA.
- Center for Inherited Cardiovascular Disease, Stanford Health Care, Palo Alto, CA, USA.
- Biomedical Data Science and Genetics (By Courtesy), Stanford Medicine, Stanford, CA, USA.
| | | | | | - Sheryl Michelson
- Patient and Family Partner Program, Stanford Health Care, Palo Alto, CA, USA
| | - Ting Pun
- Patient and Family Partner Program, Stanford Health Care, Palo Alto, CA, USA
| | - John S Witte
- Biomedical Data Science and Genetics (By Courtesy), Stanford Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford Medicine, Stanford, CA, USA
- Stanford Medicine, Stanford Cancer Institute, Stanford, CA, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, CA, USA
- Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, Stanford Medicine, Stanford, CA, USA
| | - Euan A Ashley
- Department of Cardiology, Stanford Medicine, Stanford, CA, USA
- Center for Inherited Cardiovascular Disease, Stanford Health Care, Palo Alto, CA, USA
- Biomedical Data Science and Genetics (By Courtesy), Stanford Medicine, Stanford, CA, USA
| |
Collapse
|
24
|
Davoudi F, Moradi A, Becker TM, Lock JG, Abbey B, Fontanarosa D, Haworth A, Clements J, Ecker RC, Batra J. Genomic and Phenotypic Biomarkers for Precision Medicine Guidance in Advanced Prostate Cancer. Curr Treat Options Oncol 2023; 24:1451-1471. [PMID: 37561382 PMCID: PMC10547634 DOI: 10.1007/s11864-023-01121-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 08/11/2023]
Abstract
OPINION STATEMENT Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen.
Collapse
Affiliation(s)
- Fatemeh Davoudi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Moradi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Therese M. Becker
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
| | - John G. Lock
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, 2052 Australia
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Sciences, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC Australia
| | - Davide Fontanarosa
- School of Clinical Sciences, Queensland University of Technology, Gardens Point Campus, 2 George St, Brisbane, QLD 4000 Australia
- Centre for Biomedical Technologies (CBT), Queensland University of Technology, Brisbane, QLD 4000 Australia
| | - Annette Haworth
- Institute of Medical Physics, School of Physics, University of Sydney, Camperdown, NSW 2006 Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
- TissueGnostics GmbH, EU 1020 Vienna, Austria
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| |
Collapse
|
25
|
Moorthy T, Nguyen H, Chen Y, Austin J, Smoller JW, Hercher L, Sabatello M. How do experts in psychiatric genetics view the clinical utility of polygenic risk scores for schizophrenia? Am J Med Genet B Neuropsychiatr Genet 2023; 192:161-170. [PMID: 37158703 PMCID: PMC10524148 DOI: 10.1002/ajmg.b.32939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 03/02/2023] [Accepted: 04/15/2023] [Indexed: 05/10/2023]
Abstract
Polygenic risk scores (PRS) are promising for identifying common variant-related inheritance for psychiatric conditions but their integration into clinical practice depends on their clinical utility and psychiatrists' understanding of PRS. Our online survey explored these issues with 276 professionals working in psychiatric genetics (RR: 19%). Overall, participants demonstrated knowledge of how to interpret PRS results. Their performance on knowledge-based questions was positively correlated with participants' self-reported familiarity with PRS (r = 0.21, p = 0.0006) although differences were not statistically significant (Wald Chi-square = 3.29, df = 1, p = 0.07). However, only 48.9% of all participants answered all knowledge questions correctly. Many participants (56.5%), especially researchers (42%), indicated having at least occasional conversations about the role of genetics in psychiatric conditions with patients and/or family members. Most participants (62.7%) indicated that PRS are not yet sufficiently robust for assessment of susceptibility to schizophrenia; most significant obstacles were low predictive power and lack of population diversity in available PRS (selected, respectively, by 53.6% and 29.3% of participants). Nevertheless, 89.8% of participants were optimistic about the use of PRS in the next 10 years, suggesting a belief that current shortcomings could be addressed. Our findings inform about the perceptions of psychiatric professionals regarding PRS and the application of PRS in psychiatry.
Collapse
Affiliation(s)
- Tiahna Moorthy
- NYC Health + Hospitals/Jacobi Medical Center, Bronx, NY, USA
| | | | - Ying Chen
- New York State Psychiatric Institute, New York City, NY, USA
| | - Jehannine Austin
- Psychiatry and Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jordan W Smoller
- Psychiatry, Harvard Medical School, Boston, MA, USA
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Precision Psychiatry and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura Hercher
- Sarah Lawrence College Joan H. Marks Graduate Program in Human Genetics, Bronxville, NY, USA
| | - Maya Sabatello
- Medical Sciences (in Medicine), Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York City, NY, USA
- Medical Sciences (in Medical Humanities and Ethics), Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York City, NY, USA
- Precision Medicine: Ethics, Politics and Culture Project, Columbia University, New York City, NY, USA
| |
Collapse
|
26
|
Chen T, Zhang H, Mazumder R, Lin X. Ensembled best subset selection using summary statistics for polygenic risk prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559307. [PMID: 37886515 PMCID: PMC10602024 DOI: 10.1101/2023.09.25.559307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Polygenic risk scores (PRS) enhance population risk stratification and advance personalized medicine, yet existing methods face a tradeoff between predictive power and computational efficiency. We introduce ALL-Sum, a fast and scalable PRS method that combines an efficient summary statistic-based L 0 L 2 penalized regression algorithm with an ensembling step that aggregates estimates from different tuning parameters for improved prediction performance. In extensive large-scale simulations across a wide range of polygenicity and genome-wide association studies (GWAS) sample sizes, ALL-Sum consistently outperforms popular alternative methods in terms of prediction accuracy, runtime, and memory usage. We analyze 27 published GWAS summary statistics for 11 complex traits from 9 reputable data sources, including the Global Lipids Genetics Consortium, Breast Cancer Association Consortium, and FinnGen, evaluated using individual-level UKBB data. ALL-Sum achieves the highest accuracy for most traits, particularly for GWAS with large sample sizes. We provide ALL-Sum as a user-friendly command-line software with pre-computed reference data for streamlined user-end analysis.
Collapse
|
27
|
Monti R, Ohler U. Toward Identification of Functional Sequences and Variants in Noncoding DNA. Annu Rev Biomed Data Sci 2023; 6:191-210. [PMID: 37262323 DOI: 10.1146/annurev-biodatasci-122120-110102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the noncoding part of the genome, which encodes gene regulation, is necessary to identify genetic mechanisms of disease and translate findings from genome-wide association studies into actionable results for treatments and personalized care. Here we provide an overview of the computational analysis of noncoding regions, starting from gene-regulatory mechanisms and their representation in data. Deep learning methods, when applied to these data, highlight important regulatory sequence elements and predict the functional effects of genetic variants. These and other algorithms are used to predict damaging sequence variants. Finally, we introduce rare-variant association tests that incorporate functional annotations and predictions in order to increase interpretability and statistical power.
Collapse
Affiliation(s)
- Remo Monti
- Max Delbrück Center for Molecular Medicine (MDC), Helmholtz Association of German Research Centers, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany;
- Digital Health-Machine Learning, Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine (MDC), Helmholtz Association of German Research Centers, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany;
| |
Collapse
|
28
|
Lo Faro V, Johansson T, Höglund J, Hadizadeh F, Johansson Å. Polygenic risk scores and risk stratification in deep vein thrombosis. Thromb Res 2023; 228:151-162. [PMID: 37331118 DOI: 10.1016/j.thromres.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/18/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
INTRODUCTION Deep vein thrombosis (DVT) is a complex disease, where 60 % of risk is due to genetic factors, such as the Factor V Leiden (FVL) variant. DVT is either asymptomatic or manifests with unspecific symptoms and, if left untreated, DVT leads to severe complications. The impact is dramatic and currently, there is still a research gap in DVT prevention. We characterized the genetic contribution and stratified individuals based on genetic makeup to evaluate if it favorably impacts risk prediction. METHODS In the UK Biobank (UKB), we performed gene-based association tests using exome sequencing data, as well as a genome-wide association study. We also constructed polygenic risk scores (PRS) in a subset of the cohort (Number of cases = 8231; Number of controls = 276,360) and calculated the impact on the prediction capacity of the PRS in a non-overlapping part of the cohort (Number of cases = 4342; Number of controls = 142,822). We generated additional PRSs that excluded the known causative variants. RESULTS We discovered and replicated a novel common variant (rs11604583) near the region where are located the TRIM51 and LRRC55 genes and identified a novel rare variant (rs187725533) located near the CREB3L1 gene, associated with 2.5-fold higher risk of DVT. In one of the PRS models constructed, the top decile of risk is associated with 3.4-fold increased risk, an effect that is 2.3-fold when excluding FVL carriers. In the top PRS decile, the cumulative risk of DVT at the age of 80 years is 10 % for FVL carriers, contraposed to 5 % for non-carriers. The population attributable fractions of having a high polygenic risk on the rate of DVT was estimated to be around 20 % in our cohort. CONCLUSION Individuals with a high polygenic risk of DVT, and not only carriers of well-studied variants such as FVL, may benefit from prevention strategies.
Collapse
Affiliation(s)
- Valeria Lo Faro
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Therese Johansson
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Centre for Women's Mental Health during the Reproductive Lifespan - Womher, Uppsala University, Uppsala, Sweden
| | - Julia Höglund
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fatemeh Hadizadeh
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
29
|
Raben TG, Lello L, Widen E, Hsu SDH. Biobank-scale methods and projections for sparse polygenic prediction from machine learning. Sci Rep 2023; 13:11662. [PMID: 37468507 PMCID: PMC10356957 DOI: 10.1038/s41598-023-37580-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.
Collapse
Affiliation(s)
- Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, Michigan, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| |
Collapse
|
30
|
Smith JL, Schaid DJ, Kullo IJ. Implementing Reporting Standards for Polygenic Risk Scores for Atherosclerotic Cardiovascular Disease. Curr Atheroscler Rep 2023; 25:323-330. [PMID: 37223852 PMCID: PMC10495216 DOI: 10.1007/s11883-023-01104-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE OF REVIEW There is considerable interest in using polygenic risk scores (PRSs) for assessing risk of atherosclerotic cardiovascular disease (ASCVD). A barrier to the clinical use of PRSs is heterogeneity in how PRS studies are reported. In this review, we summarize approaches to establish a uniform reporting framework for PRSs for coronary heart disease (CHD), the most common form of ASCVD. RECENT FINDINGS Reporting standards for PRSs need to be contextualized for disease specific applications. In addition to metrics of predictive performance, reporting standards for PRSs for CHD should include how cases/control were ascertained, degree of adjustment for conventional CHD risk factors, portability to diverse genetic ancestry groups and admixed individuals, and quality control measures for clinical deployment. Such a framework will enable PRSs to be optimized and benchmarked for clinical use.
Collapse
Affiliation(s)
- Johanna L Smith
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
- Gonda Vascular Center, Rochester, MN, USA.
| |
Collapse
|
31
|
Sun L, Wang Z, Lu T, Manolio TA, Paterson AD. eXclusionarY: 10 years later, where are the sex chromosomes in GWASs? Am J Hum Genet 2023; 110:903-912. [PMID: 37267899 DOI: 10.1016/j.ajhg.2023.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
10 years ago, a detailed analysis showed that only 33% of genome-wide association study (GWAS) results included the X chromosome. Multiple recommendations were made to combat such exclusion. Here, we re-surveyed the research landscape to determine whether these earlier recommendations had been translated. Unfortunately, among the genome-wide summary statistics reported in 2021 in the NHGRI-EBI GWAS Catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the exclusion phenomenon not only persists but has also expanded into an exclusionary problem. Normalizing by physical length of the chromosome, the average number of studies published through November 2022 with genome-wide-significant findings on the X chromosome is ∼1 study/Mb. By contrast, it ranges from ∼6 to ∼16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ∼0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ∼0.012 studies/Mb/year. Among the studies that reported significant associations on the X chromosome, we noted extreme heterogeneities in data analysis and reporting of results, suggesting the need for clear guidelines. Unsurprisingly, among the 430 scores sampled from the PolyGenic Score Catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWASs, we propose such studies would more properly be referred to as "AWASs," meaning "autosome-wide scans."
Collapse
Affiliation(s)
- Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Tianyuan Lu
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
| |
Collapse
|
32
|
Raz A, Minari J. AI-driven risk scores: should social scoring and polygenic scores based on ethnicity be equally prohibited? Front Genet 2023; 14:1169580. [PMID: 37323663 PMCID: PMC10267818 DOI: 10.3389/fgene.2023.1169580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Aviad Raz
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beer-Sheba, Israel
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| |
Collapse
|
33
|
de Hemptinne MC, Posthuma D. Addressing the ethical and societal challenges posed by genome-wide association studies of behavioral and brain-related traits. Nat Neurosci 2023:10.1038/s41593-023-01333-4. [PMID: 37217727 DOI: 10.1038/s41593-023-01333-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
Genome-wide association studies have led to the identification of robust statistical associations of genetic variants with numerous brain-related traits, including neurological and psychiatric conditions, and psychological and behavioral measures. These results may provide insight into the biology underlying these traits and may facilitate clinically useful predictions. However, these results also carry the risk of harm, including possible negative effects of inaccurate predictions, violations of privacy, stigma and genomic discrimination, raising serious ethical and legal implications. Here, we discuss ethical concerns surrounding the results of genome-wide association studies for individuals, society and researchers. Given the success of genome-wide association studies and the increasing availability of nonclinical genomic prediction technologies, better laws and guidelines are urgently needed to regulate the storage, processing and responsible use of genetic data. Also, researchers should be aware of possible misuse of their results, and we provide guidance to help avoid such negative impacts on individuals and society.
Collapse
Affiliation(s)
- Matthieu C de Hemptinne
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
34
|
Reddi HV, Wand H, Funke B, Zimmermann MT, Lebo MS, Qian E, Shirts BH, Zou YS, Zhang BM, Rose NC, Abu-El-Haija A. Laboratory perspectives in the development of polygenic risk scores for disease: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100804. [PMID: 36971772 DOI: 10.1016/j.gim.2023.100804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Hannah Wand
- Division of Cardiovascular Medicine, Department of Medicine, Stanford Medicine, Stanford, CA
| | | | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, CT
| | - Brian H Shirts
- Department of Laboratory Medicine & Pathology, UW Medicine, University of Washington, Seattle, WA
| | - Ying S Zou
- Department of Genomic Medicine and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Nancy C Rose
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, UT
| | - Aya Abu-El-Haija
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| |
Collapse
|
35
|
Ahern J, Thompson W, Fan CC, Loughnan R. Comparing Pruning and Thresholding with Continuous Shrinkage Polygenic Score Methods in a Large Sample of Ancestrally Diverse Adolescents from the ABCD Study ®. Behav Genet 2023; 53:292-309. [PMID: 37017779 PMCID: PMC10655749 DOI: 10.1007/s10519-023-10139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023]
Abstract
Using individuals' genetic data researchers can generate Polygenic Scores (PS) that are able to predict risk for diseases, variability in different behaviors as well as anthropomorphic measures. This is achieved by leveraging models learned from previously published large Genome-Wide Association Studies (GWASs) associating locations in the genome with a phenotype of interest. Previous GWASs have predominantly been performed in European ancestry individuals. This is of concern as PS generated in samples with a different ancestry to the original training GWAS have been shown to have lower performance and limited portability, and many efforts are now underway to collect genetic databases on individuals of diverse ancestries. In this study, we compare multiple methods of generating PS, including pruning and thresholding and Bayesian continuous shrinkage models, to determine which of them is best able to overcome these limitations. To do this we use the ABCD Study, a longitudinal cohort with deep phenotyping on individuals of diverse ancestry. We generate PS for anthropometric and psychiatric phenotypes using previously published GWAS summary statistics and examine their performance in three subsamples of ABCD: African ancestry individuals (n = 811), European ancestry Individuals (n = 6703), and admixed ancestry individuals (n = 3664). We find that the single ancestry continuous shrinkage method, PRScs (CS), and the multi ancestry meta method, PRScsx Meta (CSx Meta), show the best performance across ancestries and phenotypes.
Collapse
Affiliation(s)
- Jonathan Ahern
- Department of Cognitive Science, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92161, USA.
| | - Wesley Thompson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92161, USA
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74103, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74103, USA
- Department of Radiology, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Robert Loughnan
- Department of Cognitive Science, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92161, USA
| |
Collapse
|
36
|
Park JK, Lu CY. Polygenic Scores in the Direct-to-Consumer Setting: Challenges and Opportunities for a New Era in Consumer Genetic Testing. J Pers Med 2023; 13:jpm13040573. [PMID: 37108959 PMCID: PMC10144199 DOI: 10.3390/jpm13040573] [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: 02/21/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Direct-to-consumer (DTC) genetic tests have generated considerable scholarly attention and public intrigue. Although the current consumer genetic testing regime relies on the reporting of individual variants of interest to consumers, there has recently been interest in the possibility of integrating polygenic scores (PGS), which aggregate genetic liability for disease across the entire genome. While PGS have thus far been extensively explored as clinical and public health tools, the use of PGS in consumer genetic testing has not yet received systematic attention, even though they are already in use for some consumer genetic tests. In this narrative review, we highlight the ethical, legal, and social implications of the use of PGS in DTC genetic tests and synthesize existing solutions to these concerns. We organize these concerns into three domains: (1) industry variation; (2) privacy and commercialization; and (3) patient safety and risk. While previously expressed concerns in these domains will remain relevant, the emergence of PGS-based DTC genetic tests raises challenges that will require novel approaches.
Collapse
Affiliation(s)
- Jin K Park
- Harvard Medical School, Boston, MA 02115, USA
| | - Christine Y Lu
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02115, USA
- Kolling Institute, Faculty of Medicine and Health, The University of Sydney and the Northern Sydney Local Health District, Sydney, NSW 2077, Australia
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
37
|
Ayoub A, Lapointe J, Nabi H, Pashayan N. Risk-Stratified Breast Cancer Screening Incorporating a Polygenic Risk Score: A Survey of UK General Practitioners’ Knowledge and Attitudes. Genes (Basel) 2023; 14:genes14030732. [PMID: 36981003 PMCID: PMC10048009 DOI: 10.3390/genes14030732] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
A polygenic risk score (PRS) quantifies the aggregated effects of common genetic variants in an individual. A ‘personalised breast cancer risk assessment’ combines PRS with other genetic and nongenetic risk factors to offer risk-stratified screening and interventions. Large-scale studies are evaluating the clinical utility and feasibility of implementing risk-stratified screening; however, General Practitioners’ (GPs) views remain largely unknown. This study aimed to explore GPs’: (i) knowledge of risk-stratified screening; (ii) attitudes towards risk-stratified screening; and (iii) preferences for continuing professional development. A cross-sectional online survey of UK GPs was conducted between July–August 2022. The survey was distributed by the Royal College of General Practitioners and via other mailing lists and social media. In total, 109 GPs completed the survey; 49% were not familiar with the concept of PRS. Regarding risk-stratified screening pathways, 75% agreed with earlier and more frequent screening for women at high risk, 43% neither agreed nor disagreed with later and less screening for women at lower-than-average risk, and 55% disagreed with completely removing screening for women at much lower risk. In total, 81% felt positive about the potential impact of risk-stratified screening towards patients and 62% felt positive about the potential impact on their practice. GPs selected training of healthcare professionals as the priority for future risk-stratified screening implementation, preferring online formats for learning. The results suggest limited knowledge of PRS and risk-stratified screening amongst GPs. Training—preferably using online learning formats—was identified as the top priority for future implementation. GPs felt positive about the potential impact of risk-stratified screening; however, there was hesitance and disagreement towards a low-risk screening pathway.
Collapse
Affiliation(s)
- Aya Ayoub
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
- Correspondence:
| | - Julie Lapointe
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, QC G1R 3S3, Canada
| | - Hermann Nabi
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec City, QC G1R 3S3, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Nora Pashayan
- Department of Applied Health Research, University College London (UCL), London WC1E 7HB, UK
| |
Collapse
|
38
|
Bowman-Smart H, Gyngell C, Mand C, Amor DJ, Delatycki MB, Savulescu J. Non-Invasive Prenatal Testing for "Non-Medical" Traits: Ensuring Consistency in Ethical Decision-Making. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:3-20. [PMID: 34846986 PMCID: PMC7614328 DOI: 10.1080/15265161.2021.1996659] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The scope of noninvasive prenatal testing (NIPT) could expand in the future to include detailed analysis of the fetal genome. This will allow for the testing for virtually any trait with a genetic contribution, including "non-medical" traits. Here we discuss the potential use of NIPT for these traits. We outline a scenario which highlights possible inconsistencies with ethical decision-making. We then discuss the case against permitting these uses. The objections include practical problems; increasing inequities; increasing the burden of choice; negative impacts on the child, family, and society; and issues with implementation. We then outline the case for permitting the use of NIPT for these traits. These include arguments for reproductive liberty and autonomy; questioning the labeling of traits as "non-medical"; and the principle of procreative beneficence. This summary of the case for and against can serve as a basis for the development of a consistent and coherent ethical framework.
Collapse
Affiliation(s)
- Hilary Bowman-Smart
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
- Corresponding author: Hilary Bowman-Smart Murdoch Children’s Research Institute, 50 Flemington Rd, Parkville Victoria Australia 3052, , (03) 8341 6200
| | - Christopher Gyngell
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Cara Mand
- Murdoch Children’s Research Institute, Parkville, Australia
| | - David J. Amor
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
- Victorian Clinical Genetics Services, Parkville, Australia
| | - Martin B. Delatycki
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
- Victorian Clinical Genetics Services, Parkville, Australia
| | - Julian Savulescu
- Murdoch Children’s Research Institute, Parkville, Australia
- Uehiro Centre for Practical Ethics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
39
|
The necessity of incorporating non-genetic risk factors into polygenic risk score models. Sci Rep 2023; 13:1351. [PMID: 36807592 PMCID: PMC9941118 DOI: 10.1038/s41598-023-27637-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/05/2023] [Indexed: 02/22/2023] Open
Abstract
The growing public interest in genetic risk scores for various health conditions can be harnessed to inspire preventive health action. However, current commercially available genetic risk scores can be deceiving as they do not consider other, easily attainable risk factors, such as sex, BMI, age, smoking habits, parental disease status and physical activity. Recent scientific literature shows that adding these factors can improve PGS based predictions significantly. However, implementation of existing PGS based models that also consider these factors requires reference data based on a specific genotyping chip, which is not always available. In this paper, we offer a method naïve to the genotyping chip used. We train these models using the UK Biobank data and test these externally in the Lifelines cohort. We show improved performance at identifying the 10% most at-risk individuals for type 2 diabetes (T2D) and coronary artery disease (CAD) by including common risk factors. Incidence in the highest risk group increases from 3.0- and 4.0-fold to 5.8 for T2D, when comparing the genetics-based model, common risk factor-based model and combined model, respectively. Similarly, we observe an increase from 2.4- and 3.0-fold to 4.7-fold risk for CAD. As such, we conclude that it is paramount that these additional variables are considered when reporting risk, unlike current practice with current available genetic tests.
Collapse
|
40
|
Young MA, Yanes T, Cust AE, Dunlop K, Limb S, Newson AJ, Purvis R, Thiyagarajan L, Scott RJ, Verma K, James PA, Steinberg J. Human Genetics Society of Australasia Position Statement: Use of Polygenic Scores in Clinical Practice and Population Health. Twin Res Hum Genet 2023; 26:40-48. [PMID: 36950972 DOI: 10.1017/thg.2023.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Considerable progress continues to be made with regards to the value and use of disease associated polygenic scores (PGS). PGS aim to capture a person's genetic liability to a condition, disease, or a trait, combining information across many risk variants and incorporating their effect sizes. They are already available for clinicians and consumers to order in Australasia. However, debate is ongoing over the readiness of this information for integration into clinical practice and population health. This position statement provides the viewpoint of the Human Genetics Society of Australasia (HGSA) regarding the clinical application of disease-associated PGS in both individual patients and population health. The statement details how PGS are calculated, highlights their breadth of possible application, and examines their current challenges and limitations. We consider fundamental lessons from Mendelian genetics and their continuing relevance to PGS, while also acknowledging the distinct elements of PGS. Use of PGS in practice should be evidence based, and the evidence for the associated benefit, while rapidly emerging, remains limited. Given that clinicians and consumers can already order PGS, their current limitations and key issues warrant consideration. PGS can be developed for most complex conditions and traits and can be used across multiple clinical settings and for population health. The HGSA's view is that further evaluation, including regulatory, implementation and health system evaluation are required before PGS can be routinely implemented in the Australasian healthcare system.
Collapse
Affiliation(s)
- Mary-Anne Young
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia
| | - Tatiane Yanes
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne E Cust
- The Melanoma Institute Australia, The University of Sydney, NSW, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Kate Dunlop
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Sharne Limb
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospitals, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Ainsley J Newson
- The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics. Sydney, New South Wales, Australia
| | - Rebecca Purvis
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospitals, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Lavvina Thiyagarajan
- The University of New South Wales, Sydney, New South Wales, Australia
- Sydney Children's Hospital Network, Sydney, New South Wales, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health and Wellbeing, University of Newcastle, New South Wales, Australia
- Division of Molecular Medicine, NSW Health Pathology North, New Lambton, Newcastle, New South Wales, Australia
| | - Kunal Verma
- Monash Genetics, Monash Health, Melbourn, Victoria, Australia
- Monash Heart, Monash Health, Victoria, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospitals, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Julia Steinberg
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| |
Collapse
|
41
|
Fritzsche MC, Akyüz K, Cano Abadía M, McLennan S, Marttinen P, Mayrhofer MT, Buyx AM. Ethical layering in AI-driven polygenic risk scores-New complexities, new challenges. Front Genet 2023; 14:1098439. [PMID: 36816027 PMCID: PMC9933509 DOI: 10.3389/fgene.2023.1098439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Researchers aim to develop polygenic risk scores as a tool to prevent and more effectively treat serious diseases, disorders and conditions such as breast cancer, type 2 diabetes mellitus and coronary heart disease. Recently, machine learning techniques, in particular deep neural networks, have been increasingly developed to create polygenic risk scores using electronic health records as well as genomic and other health data. While the use of artificial intelligence for polygenic risk scores may enable greater accuracy, performance and prediction, it also presents a range of increasingly complex ethical challenges. The ethical and social issues of many polygenic risk score applications in medicine have been widely discussed. However, in the literature and in practice, the ethical implications of their confluence with the use of artificial intelligence have not yet been sufficiently considered. Based on a comprehensive review of the existing literature, we argue that this stands in need of urgent consideration for research and subsequent translation into the clinical setting. Considering the many ethical layers involved, we will first give a brief overview of the development of artificial intelligence-driven polygenic risk scores, associated ethical and social implications, challenges in artificial intelligence ethics, and finally, explore potential complexities of polygenic risk scores driven by artificial intelligence. We point out emerging complexity regarding fairness, challenges in building trust, explaining and understanding artificial intelligence and polygenic risk scores as well as regulatory uncertainties and further challenges. We strongly advocate taking a proactive approach to embedding ethics in research and implementation processes for polygenic risk scores driven by artificial intelligence.
Collapse
Affiliation(s)
- Marie-Christine Fritzsche
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany,Department of Science, Technology and Society (STS), School of Social Sciences and Technology, Technical University of Munich, Munich, Germany,*Correspondence: Marie-Christine Fritzsche,
| | - Kaya Akyüz
- Biobanking and Biomolecular Resources Research Infrastructure Consortium - European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria,Department of Science and Technology Studies, University of Vienna, Vienna, Austria
| | - Mónica Cano Abadía
- Biobanking and Biomolecular Resources Research Infrastructure Consortium - European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Stuart McLennan
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany,Department of Science, Technology and Society (STS), School of Social Sciences and Technology, Technical University of Munich, Munich, Germany
| | - Pekka Marttinen
- Helsinki Institute for Information Technology HIIT, Aalto University, Helsinki, Finland
| | - Michaela Th. Mayrhofer
- Biobanking and Biomolecular Resources Research Infrastructure Consortium - European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Alena M. Buyx
- Institute of History and Ethics in Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany,Department of Science, Technology and Society (STS), School of Social Sciences and Technology, Technical University of Munich, Munich, Germany
| |
Collapse
|
42
|
Udine E, Jain A, van Blitterswijk M. Advances in sequencing technologies for amyotrophic lateral sclerosis research. Mol Neurodegener 2023; 18:4. [PMID: 36635726 PMCID: PMC9838075 DOI: 10.1186/s13024-022-00593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is caused by upper and lower motor neuron loss and has a fairly rapid disease progression, leading to fatality in an average of 2-5 years after symptom onset. Numerous genes have been implicated in this disease; however, many cases remain unexplained. Several technologies are being used to identify regions of interest and investigate candidate genes. Initial approaches to detect ALS genes include, among others, linkage analysis, Sanger sequencing, and genome-wide association studies. More recently, next-generation sequencing methods, such as whole-exome and whole-genome sequencing, have been introduced. While those methods have been particularly useful in discovering new ALS-linked genes, methodological advances are becoming increasingly important, especially given the complex genetics of ALS. Novel sequencing technologies, like long-read sequencing, are beginning to be used to uncover the contribution of repeat expansions and other types of structural variation, which may help explain missing heritability in ALS. In this review, we discuss how popular and/or upcoming methods are being used to discover ALS genes, highlighting emerging long-read sequencing platforms and their role in aiding our understanding of this challenging disease.
Collapse
Affiliation(s)
- Evan Udine
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Angita Jain
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road S, Jacksonville, FL 32224 USA ,grid.417467.70000 0004 0443 9942Center for Clinical and Translational Sciences, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224 USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL, 32224, USA.
| |
Collapse
|
43
|
Lello L, Hsu M, Widen E, Raben TG. Sibling variation in polygenic traits and DNA recombination mapping with UK Biobank and IVF family data. Sci Rep 2023; 13:376. [PMID: 36611071 PMCID: PMC9825593 DOI: 10.1038/s41598-023-27561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
We use UK Biobank and a unique IVF family dataset (including genotyped embryos) to investigate sibling variation in both phenotype and genotype. We compare phenotype (disease status, height, blood biomarkers) and genotype (polygenic scores, polygenic health index) distributions among siblings to those in the general population. As expected, the between-siblings standard deviation in polygenic scores is [Formula: see text] times smaller than in the general population, but variation is still significant. As previously demonstrated, this allows for substantial benefit from polygenic screening in IVF. Differences in sibling genotypes result from distinct recombination patterns in sexual reproduction. We develop a novel sibling-pair method for detection of recombination breaks via statistical discontinuities. The new method is used to construct a dataset of 1.44 million recombination events which may be useful in further study of meiosis.
Collapse
Affiliation(s)
- Louis Lello
- Genomic Prediction, Inc., North Brunswick, NJ, USA.
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA.
| | - Maximus Hsu
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Genomic Prediction, Inc., North Brunswick, NJ, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
| | - Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
| |
Collapse
|
44
|
Maj C, Staerk C, Borisov O, Klinkhammer H, Wai Yeung M, Krawitz P, Mayr A. Statistical learning for sparser fine-mapped polygenic models: The prediction of LDL-cholesterol. Genet Epidemiol 2022; 46:589-603. [PMID: 35938382 DOI: 10.1002/gepi.22495] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
Polygenic risk scores quantify the individual genetic predisposition regarding a particular trait. We propose and illustrate the application of existing statistical learning methods to derive sparser models for genome-wide data with a polygenic signal. Our approach is based on three consecutive steps. First, potentially informative loci are identified by a marginal screening approach. Then, fine-mapping is independently applied for blocks of variants in linkage disequilibrium, where informative variants are retrieved by using variable selection methods including boosting with probing and stochastic searches with the Adaptive Subspace method. Finally, joint prediction models with the selected variants are derived using statistical boosting. In contrast to alternative approaches relying on univariate summary statistics from genome-wide association studies, our three-step approach enables to select and fit multivariable regression models on large-scale genotype data. Based on UK Biobank data, we develop prediction models for LDL-cholesterol as a continuous trait. Additionally, we consider a recent scalable algorithm for the Lasso. Results show that statistical learning approaches based on fine-mapping of genetic signals result in a competitive prediction performance compared to classical polygenic risk approaches, while yielding sparser risk models.
Collapse
Affiliation(s)
- Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Christian Staerk
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Ming Wai Yeung
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Department of Cardiology, University of Groningen, Groningen, The Netherlands
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| |
Collapse
|
45
|
Smith HS, Sanchez CE, Maag R, Buentello A, Murdock DR, Metcalf GA, Hadley TD, Riconda DL, Boerwinkle E, Wehrens XH, Ballantyne CM, Gibbs RA, McGuire AL, Pereira S. Patient and Clinician Perceptions of Precision Cardiology Care: Findings From the HeartCare Study. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003605. [PMID: 36282588 PMCID: PMC10163837 DOI: 10.1161/circgen.121.003605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 08/04/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Routine genome-wide screening for cardiovascular disease risk may inform clinical decision-making. However, little is known about whether clinicians and patients would find such testing useful or acceptable within the context of a genomics-enabled learning health system. METHODS We conducted surveys with patients and their clinicians who were participating in the HeartCare Study, a precision cardiology care project that returned results from a next-generation sequencing panel of 158 genes associated with cardiovascular disease risk. Six weeks after return of results, we assessed patients' and clinicians' perceived utility and disutility of HeartCare, the effect of the test on clinical recommendations, and patients' attitudes toward integration of research and clinical care. RESULTS Among 666 HeartCare patients with a result returned during the survey study period, 42.0% completed a full or partial survey. Patient-participants who completed a full survey (n=224) generally had positive perceptions of HeartCare independent of whether they received a positive or negative result. Most patient-participants considered genetic testing for cardiovascular disease risk to have more benefit than risk (88.3%) and agreed that it provided information that they wanted to know (81.2%), while most disagreed that the test caused them to feel confused (77.7%) or overwhelmed (78.0%). For 122 of their patients with positive results, clinicians (n=13) reported making changes in clinical care for 66.4% of patients, recommending changes in health behaviors for 36.9% of patients, and recommending to 33.6% of patients that their family members have clinical testing. CONCLUSIONS Both patients and clinicians thought the HeartCare panel screen for cardiovascular disease risk provided information that was useful in terms of personal or health benefits to the patient and that informed clinical care without causing patients to be confused or overwhelmed. Further research is needed to assess perceptions of genome-wide screening among the US cardiology clinic population.
Collapse
Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Clarissa E. Sanchez
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Ronald Maag
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Alexandria Buentello
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - David R. Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Ginger A. Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Trevor D. Hadley
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Daniel L. Riconda
- Dept of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- School of Health Professions, Baylor College of Medicine, Houston, TX
| | - Eric Boerwinkle
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Xander H.T. Wehrens
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX
- Dept of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX
| | - Christie M. Ballantyne
- Dept of Medicine, Section of Cardiology & Cardiovascular Research, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Amy L. McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| | - Stacey Pereira
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX
| |
Collapse
|
46
|
Attitudes among Parents towards Return of Disease-Related Polygenic Risk Scores (PRS) for Their Children. J Pers Med 2022; 12:jpm12121945. [PMID: 36556166 PMCID: PMC9786589 DOI: 10.3390/jpm12121945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/28/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
The electronic MEdical Records and GEnomics (eMERGE) consortium will return risk reports pertaining to specific diseases, a key component of which will be polygenic risk scores (PRS), to 25,000 participants, including 5000 children. Understanding comprehension and the perceived value of these PRS-based reports among parents will be critical for effective return of results in children. To address this issue, we conducted semi-structured interviews with 40 African American and Hispanic parents at The Children's Hospital of Philadelphia and Boston Children's Hospital. Each participant received a hypothetical risk report identifying their child as high risk for either type 2 diabetes or asthma. Participants were assessed on their comprehension of absolute versus relative risk framing, likelihood of following risk-reduction recommendations, perceived value of the information, psychosocial impact, education/support needed, and suggestions to improve the PRS-based report to make it more accessible. Results demonstrated high perceived value in receiving PRS-based reports but also draws attention to important shortfalls in comprehension due to factors including the health of the child, family history, and how the risk was framed. This study provides an insight into implementing the return of genomic risk scores in a pediatric setting.
Collapse
|
47
|
Fuh-Ngwa V, Zhou Y, Melton PE, van der Mei I, Charlesworth JC, Lin X, Zarghami A, Broadley SA, Ponsonby AL, Simpson-Yap S, Lechner-Scott J, Taylor BV. Ensemble machine learning identifies genetic loci associated with future worsening of disability in people with multiple sclerosis. Sci Rep 2022; 12:19291. [PMID: 36369345 PMCID: PMC9652373 DOI: 10.1038/s41598-022-23685-w] [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: 04/29/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Limited studies have been conducted to identify and validate multiple sclerosis (MS) genetic loci associated with disability progression. We aimed to identify MS genetic loci associated with worsening of disability over time, and to develop and validate ensemble genetic learning model(s) to identify people with MS (PwMS) at risk of future worsening. We examined associations of 208 previously established MS genetic loci with the risk of worsening of disability; we learned ensemble genetic decision rules and validated the predictions in an external dataset. We found 7 genetic loci (rs7731626: HR 0.92, P = 2.4 × 10-5; rs12211604: HR 1.16, P = 3.2 × 10-7; rs55858457: HR 0.93, P = 3.7 × 10-7; rs10271373: HR 0.90, P = 1.1 × 10-7; rs11256593: HR 1.13, P = 5.1 × 10-57; rs12588969: HR = 1.10, P = 2.1 × 10-10; rs1465697: HR 1.09, P = 1.7 × 10-128) associated with risk worsening of disability; most of which were located near or tagged to 13 genomic regions enriched in peptide hormones and steroids biosynthesis pathways by positional and eQTL mapping. The derived ensembles produced a set of genetic decision rules that can be translated to provide additional prognostic values to existing clinical predictions, with the additional benefit of incorporating relevant genetic information into clinical decision making for PwMS. The present study extends our knowledge of MS progression genetics and provides the basis of future studies regarding the functional significance of the identified loci.
Collapse
Affiliation(s)
- Valery Fuh-Ngwa
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Yuan Zhou
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Phillip E. Melton
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Ingrid van der Mei
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Jac C. Charlesworth
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Xin Lin
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Amin Zarghami
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| | - Simon A. Broadley
- grid.1022.10000 0004 0437 5432Menzies Health Institute Queensland and School of Medicine, Griffith University Gold Coast, G40 Griffith Health Centre, QLD 4222, Australia
| | - Anne-Louise Ponsonby
- grid.1058.c0000 0000 9442 535XDeveloping Brain Division, The Florey Institute for Neuroscience and Mental Health, Royal Children’s Hospital, University of Melbourne Murdoch Children’s Research Institute, Parkville, VIC 3052 Australia
| | - Steve Simpson-Yap
- grid.1008.90000 0001 2179 088XNeuroepidemiology Unit, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, VIC 3053 Australia
| | - Jeannette Lechner-Scott
- grid.266842.c0000 0000 8831 109XDepartment of Neurology, Hunter Medical Research Institute, Hunter New England Health, University of Newcastle, Callaghan, NSW 2310 Australia
| | - Bruce V. Taylor
- grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000 Australia
| |
Collapse
|
48
|
Kulkarni A, Wafik M. Genomics makes prostate cancer personal. TRENDS IN UROLOGY & MEN'S HEALTH 2022. [DOI: 10.1002/tre.883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
49
|
Widen E, Lello L, Raben TG, Tellier LCAM, Hsu SDH. Polygenic Health Index, General Health, and Pleiotropy: Sibling Analysis and Disease Risk Reduction. Sci Rep 2022; 12:18173. [PMID: 36307513 PMCID: PMC9616929 DOI: 10.1038/s41598-022-22637-8] [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: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
We construct a polygenic health index as a weighted sum of polygenic risk scores for 20 major disease conditions, including, e.g., coronary artery disease, type 1 and 2 diabetes, schizophrenia, etc. Individual weights are determined by population-level estimates of impact on life expectancy. We validate this index in odds ratios and selection experiments using unrelated individuals and siblings (pairs and trios) from the UK Biobank. Individuals with higher index scores have decreased disease risk across almost all 20 diseases (no significant risk increases), and longer calculated life expectancy. When estimated Disability Adjusted Life Years (DALYs) are used as the performance metric, the gain from selection among ten individuals (highest index score vs average) is found to be roughly 4 DALYs. We find no statistical evidence for antagonistic trade-offs in risk reduction across these diseases. Correlations between genetic disease risks are found to be mostly positive and generally mild. These results have important implications for public health and also for fundamental issues such as pleiotropy and genetic architecture of human disease conditions.
Collapse
Affiliation(s)
- Erik Widen
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA. .,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA. .,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA.
| | - Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA
| | - Laurent C A M Tellier
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Genomic Prediction, Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| |
Collapse
|
50
|
Educational considerations based on medical student use of polygenic risk information and apparent race in a simulated consultation. Genet Med 2022; 24:2389-2398. [PMID: 36053286 DOI: 10.1016/j.gim.2022.08.004] [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: 02/23/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/21/2022] Open
Abstract
PURPOSE To craft evidence-based educational approaches related to polygenic risk score (PRS) implementation, it is crucial to forecast issues and biases that may arise when PRS are introduced in clinical care. METHODS Medical students (N = 84) were randomized to a simulated primary care encounter with a Black or White virtual reality-based patient and received either a direct-to-consumer-style PRS report for 5 common complex conditions or control information. The virtual patient inquired about 2 health concerns and her genetic report in the encounter. Data sources included participants' verbalizations in the simulation, care plan recommendations, and self-report outcomes. RESULTS When medical students received PRSs, they rated the patient as less healthy and requiring more strict advice. Patterns suggest that PRSs influenced specific medical recommendations related to the patient's concerns, despite student reports that participants did not use it for that purpose. We observed complex patterns regarding the effect of patient race on recommendations and behaviors. CONCLUSION Educational approaches should consider potential unintentional influences of PRSs on decision-making and evaluate ways that they may be applied inconsistently across patients from different racial groups.
Collapse
|