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Yin L, Pettengill JB. Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases. BMC Res Notes 2024; 17:191. [PMID: 38982485 PMCID: PMC11232179 DOI: 10.1186/s13104-024-06847-z] [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: 09/20/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
OBJECTIVES Much has been written about the utility of genomic databases to public health. Within food safety these databases contain data from two types of isolates-those from patients (i.e., clinical) and those from non-clinical sources (e.g., a food manufacturing environment). A genetic match between isolates from these sources represents a signal of interest. We investigate the match rate within three large genomic databases (Listeria monocytogenes, Escherichia coli, and Salmonella) and the smaller Cronobacter database; the databases are part of the Pathogen Detection project at NCBI (National Center for Biotechnology Information). RESULTS Currently, the match rate of clinical isolates to non-clinical isolates is 33% for L. monocytogenes, 46% for Salmonella, and 7% for E. coli. These match rates are associated with several database features including the diversity of the organism, the database size, and the proportion of non-clinical BioSamples. Modeling match rate via logistic regression showed relatively good performance. Our prediction model illustrates the importance of populating databases with non-clinical isolates to better identify a match for clinical samples. Such information should help public health officials prioritize surveillance strategies and show the critical need to populate fledgling databases (e.g., Cronobacter sakazakii).
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Affiliation(s)
- Lanlan Yin
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MA, USA
| | - James B Pettengill
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MA, USA.
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2
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Cahoon JL, Rui X, Tang E, Simons C, Langie J, Chen M, Lo YC, Chiang CWK. Imputation accuracy across global human populations. Am J Hum Genet 2024; 111:979-989. [PMID: 38604166 PMCID: PMC11080279 DOI: 10.1016/j.ajhg.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of references from non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative improved the imputation of admixed African-ancestry and Hispanic/Latino samples, but imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we imputed the genotypes of over 43,000 individuals across 123 populations around the world and identified numerous populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for variants with minor allele frequencies between 1% and 5% in Saudi Arabians (n = 1,061), Vietnamese (n = 1,264), Thai (n = 2,435), and Papua New Guineans (n = 776) were 0.79, 0.78, 0.76, and 0.62, respectively, compared to 0.90-0.93 for comparable European populations matched in sample size and SNP array content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European-ancestry reference increased, as predicted. Using sequencing data as ground truth, we also showed that Rsq may over-estimate imputation accuracy for non-European populations more than European populations, suggesting further disparity in accuracy between populations. Using 1,496 sequenced individuals from Taiwan Biobank as a second reference panel to TOPMed, we also assessed a strategy to improve imputation for non-European populations with meta-imputation, but this design did not improve accuracy across frequency spectra. Taken together, our analyses suggest that we must ultimately strive to increase diversity and size to promote equity within genetics research.
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Affiliation(s)
- Jordan L Cahoon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Christopher Simons
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA.
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3
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Greene BL, Rosenberg AR, Marron JM. A Communication and Decision-Making Framework for Pediatric Precision Medicine. Pediatrics 2024; 153:e2023062850. [PMID: 38505927 PMCID: PMC10979296 DOI: 10.1542/peds.2023-062850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 03/21/2024] Open
Abstract
Advances in genomic testing have been pivotal in moving childhood cancer care forward, with genomic testing now a standard diagnostic tool for many children, adolescents, and young adults with cancer. Beyond oncology, the role of genomic testing in pediatric research and clinical care is growing, including for children with developmental differences, cardiac abnormalities, and epilepsy. Despite more standard use in their patients, pediatricians have limited guidance on how to communicate this complex information or how to engage parents in decisions related to precision medicine. Drawing from empirical work in pediatric informed consent and existing models of shared decision-making, we use pediatric precision cancer medicine as a case study to propose a conceptual framework to approach communication and decision-making about genomic testing in pediatrics. The framework relies on identifying the type of genomic testing, its intended role, and its anticipated implications to inform the scope of information delivered and the parents' role in decision-making (leading to shared decision-making along a continuum from clinician-guided to parent-guided). This type of framework rests on practices known to be standard in other complex decision-making but also integrates unique features of genomic testing and precision medicine. With the increasing prominence of genomics and precision medicine in pediatrics, with our communication and decision-making framework, we aim to guide clinicians to better support their pediatric patients and their parents in making informed, goal-concordant decisions throughout their care trajectory.
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Affiliation(s)
- Brittany L. Greene
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Abby R. Rosenberg
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Dana-Farber Cancer Institute, Department of Psychosocial Oncology and Palliative Care, Boston, Massachusetts
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jonathan M. Marron
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts
- Center for Bioethics, Harvard Medical School, Boston, Massachusetts
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4
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Ma A, O'Shea R, Wedd L, Wong C, Jamieson RV, Rankin N. What is the power of a genomic multidisciplinary team approach? A systematic review of implementation and sustainability. Eur J Hum Genet 2024; 32:381-391. [PMID: 38378794 PMCID: PMC10999446 DOI: 10.1038/s41431-024-01555-5] [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: 06/13/2023] [Revised: 12/07/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024] Open
Abstract
Due to the increasing complexity of genomic data interpretation, and need for close collaboration with clinical, laboratory, and research expertise, genomics often requires a multidisciplinary team (MDT) approach. This systematic review aims to establish the evidence for effectiveness of the genomic multidisciplinary team, and the implementation components of this model that can inform precision care. MEDLINE, Embase and PsycINFO databases were searched in 2022 and 2023. We included qualitative and quantitative studies of the genomic MDT, including observational and cohort studies, for diagnosis and management, and implementation outcomes of effectiveness, adoption, efficiency, safety, and acceptability. A narrative synthesis was mapped against the Genomic Medicine Integrative Research framework. 1530 studies were screened, and 17 papers met selection criteria. All studies pointed towards the effectiveness of the genomic MDT approach, with 10-78% diagnostic yield depending on clinical context, and an increased yield of 6-25% attributed to the MDT. The genomic MDT was found to be highly efficient in interpretation of variants of uncertain significance, timeliness for a rapid result, made a significant impact on management, and was acceptable for adoption by a wide variety of subspecialists. Only one study utilized an implementation science based approach. The genomic MDT approach appears to be highly effective and efficient, facilitating higher diagnostic rates and improved patient management. However, key gaps remain in health systems readiness for this collaborative model, and there is a lack of implementation science based research especially addressing the cost, sustainability, scale up, and equity of access.
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Affiliation(s)
- Alan Ma
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia.
- Department of Clinical Genetics, Children's Hospital at Westmead, The Sydney Children's Hospitals Network, Sydney, NSW, Australia.
- Eye Genetics Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.
| | - Rosie O'Shea
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Laura Wedd
- Department of Clinical Genetics, Children's Hospital at Westmead, The Sydney Children's Hospitals Network, Sydney, NSW, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - Claire Wong
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia
- Department of Clinical Genetics, Children's Hospital at Westmead, The Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Robyn V Jamieson
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia
- Department of Clinical Genetics, Children's Hospital at Westmead, The Sydney Children's Hospitals Network, Sydney, NSW, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - Nicole Rankin
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
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5
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Dordunoo D, Limoges J, Chiu P, Puddester R, Carlsson L, Pike A. Genomics-informed nursing strategies and health equity: A scoping review protocol. PLoS One 2023; 18:e0295914. [PMID: 38100433 PMCID: PMC10723661 DOI: 10.1371/journal.pone.0295914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
OBJECTIVE The objective of this scoping review is to map the available evidence on strategies that nurses can use to facilitate genomics-informed healthcare to address health disparities. INTRODUCTION Advancements in genomics over the last two decades have led to an increase in the delivery of genomics-informed health care. Although the integration of genomics into health care services continues to enhance patient outcomes, access to genomic technologies is not equitable, exacerbating existing health disparities amongst certain populations. As the largest portion of the health workforce, nurses play a critical role in the delivery of equitable genomics-informed care. However, little is known about how nurses can help address health disparities within the context of genomics-informed health care. A review of the literature will provide the necessary foundation to identify promising practices, policy, and knowledge gaps for further areas of inquiry. INCLUSION CRITERIA We will include papers that explore strategies that nurses can undertake to facilitate genomics-informed care to address health disparities. METHODS This review will be conducted using JBI methodology for scoping reviews. We will search electronic databases including MEDLINE (OVID), EMBASE, Cochrane Library, PsychInfo, and CINAHL for quantitative and qualitative studies, systematic reviews and grey literature. Theses, books, and unavailable full-text papers will be excluded. The search will be limited to papers from 2013 and beyond. Two reviewers will screen titles and abstracts followed by full-text and disagreements will be resolved by a third reviewer. We will use a data extraction tool using Microsoft Excel and analyse data using descriptive statistics and conventional content analysis. Findings will be presented in the form of evidence tables and a narrative summary. We will report findings using the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). DISCUSSION Genomics will continue to transform all aspects of health care across the wellness continuum from prevention, assessment, diagnosis, management, treatment, and palliative care. The identification of nursing strategies to address health disparities will build the foundation for policy and practice to ensure that the integration of genomic technologies benefits everyone.
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Affiliation(s)
- Dzifa Dordunoo
- University of Victoria, School of Nursing, Director, Centre for Evidence informed Nursing and Health Care: JBI Centre of Excellence, Victoria, Canada
| | - Jacqueline Limoges
- Athabasca University, Chair, Ontario Cancer Research Ethics Board, Toronto, Canada
| | | | - Rebecca Puddester
- Memorial University of Newfoundland, Faculty of Nursing, St. John’s, Canada
| | | | - April Pike
- Memorial University of Newfoundland, Faculty of Nursing, St. John’s, Canada
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George SHL, Medina-Rivera A, Idaghdour Y, Lappalainen T, Gallego Romero I. Increasing diversity of functional genetics studies to advance biological discovery and human health. Am J Hum Genet 2023; 110:1996-2002. [PMID: 37995684 PMCID: PMC10716434 DOI: 10.1016/j.ajhg.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.
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Affiliation(s)
- Sophia H L George
- Department of Obstetrics, Gynecology and Reproductive Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miami, FL, USA.
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre El Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE; Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; New York Genome Center, New York, NY, USA.
| | - Irene Gallego Romero
- Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, VIC, Australia; Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
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7
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Puddester R, Limoges J, Dewell S, Maddigan J, Carlsson L, Pike A. The Canadian Landscape of Genetics and Genomics in Nursing: A Policy Document Analysis. Can J Nurs Res 2023; 55:494-509. [PMID: 36850071 PMCID: PMC10619171 DOI: 10.1177/08445621231159164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Genetics and genomics (GG) are transforming approaches to healthcare in Canada and around the globe. Canadian nurses must be prepared to integrate GG in their practice, but modest research in this area suggests that Canadian nurses have limited GG competency. Countries that have integrated GG across nursing provided guidance to nurses about the practice implications of GG through regional nursing policy documents. These documents propelled action to integrate GG across nursing. Little is known about the GG content in the nursing policy document infrastructure in Canada. PURPOSE This study aimed to examine the guidance for GG-informed nursing practice as provided by Canadian nursing organizations in official professional documents. METHODS Qualitative document analysis was used. A hybrid inductive/deductive analysis approach was used to analyze findings within the diffusion of innovation theory framework. RESULTS There is an overall lack of depth and breadth of Canadian nursing documents that include content related to GG. Of the (n = 37) documents analyzed, four themes were generated including (a) GG guidance in nursing education; (b) regulators' requirements for foundational GG knowledge, (c) Canadian Nurses Association (CNA) as an early catalyst to GG integration; and (d) early adopters in speciality practice. CONCLUSION There are opportunities to enhance the guidance available to Canadian nurses for the application of GG, through documents of nursing professional associations, nursing education accreditation organizations, and regulatory bodies. Findings suggest oncology and perinatal nurses are the early adopters which is an important consideration in future strategies to implement GG into Canadian nursing.
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Affiliation(s)
- Rebecca Puddester
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jacqueline Limoges
- Faculty of Health Disciplines, Athabasca University, Athabasca, AB, Canada
| | - Sarah Dewell
- School of Nursing, University of Northern British Columbia, Prince George, BC, Canada
| | - Joy Maddigan
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lindsay Carlsson
- Drug Development Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - April Pike
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
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Shahrier S, Gaydarska H, Takashima K, Yoshizawa G, Minari J. A conceptual analysis of public opinion regarding genome research in Japan. Front Genet 2023; 14:1170794. [PMID: 38098474 PMCID: PMC10720899 DOI: 10.3389/fgene.2023.1170794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
In the 20 years since the completion of the Human Genome Project, the gap between scientific development and public understanding of genome research has been widening. While genome research has been increasingly utilized for social and clinical purposes in a multifaceted manner, this has resulted in an increase in the potential risks associated with genomic data. In this context, our study aims to consider the nature of public perceptions of genome research, primarily by using as a case study the results of previous public surveys relevant to donations for social benefits in Japan. We explored certain types of awareness, attitude, and intention (A-A-I) in such surveys and discussed the resultant key findings through the cultural transmission framework. Reframing the public's response toward genome research based on A-A-I analysis and behavioral science may contribute to developing more systematic communication approaches with the public. With a view to establishing such approaches, our perspective suggests some new insights to discuss the science-society gap in genome research internationally.
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Affiliation(s)
- Shibly Shahrier
- Teesside University International Business School, Teesside University, Tees Valley, United Kingdom
| | - Hristina Gaydarska
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto, Japan
| | - Kayo Takashima
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto, Japan
| | - Go Yoshizawa
- Innovation System Research Center, Kwansei Gakuin University, Nishinomiya, Hyogo, Japan
| | - Jusaku Minari
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto, Japan
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Ayday E, Vaidya J, Jiang X, Telenti A. Ensuring Trust in Genomics Research. ... IEEE INTERNATIONAL CONFERENCE ON TRUST, PRIVACY AND SECURITY IN INTELLIGENT SYSTEMS AND APPLICATIONS : (TPS-ISA ...). IEEE INTERNATIONAL CONFERENCE ON TRUST, PRIVACY AND SECURITY IN INTELLIGENT SYSTEMS AND APPLICATIONS 2023; 2023:1-12. [PMID: 38562180 PMCID: PMC10981793 DOI: 10.1109/tps-isa58951.2023.00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Reproducibility, transparency, representation, and privacy underpin the trust on genomics research in general and genome-wide association studies (GWAS) in particular. Concerns about these issues can be mitigated by technologies that address privacy protection, quality control, and verifiability of GWAS. However, many of the existing technological solutions have been developed in isolation and may address one aspect of reproducibility, transparency, representation, and privacy of GWAS while unknowingly impacting other aspects. As a consequence, the current patchwork of technological tools only partially and in an overlapping manner address issues with GWAS, sometimes even creating more problems. This paper addresses the progress in a field that creates technological solutions that augment the acceptance and security of population genetic analyses. The text identifies areas that are falling behind in technical implementation or where there is insufficient research. We make the case that a full understanding of the different GWAS settings, technological tools and new research directions can holistically address the requirements for the acceptance of GWAS.
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Affiliation(s)
- Erman Ayday
- Department of Computer and Data Sciences Case Western Reserve University Cleveland, OH
| | - Jaideep Vaidya
- Management Science and Information Systems Department Rutgers University Newark, NJ
| | - Xiaoqian Jiang
- Department of Data Science and Artificial Intelligence University of Texas - Health Houston, TX
| | - Amalio Telenti
- Dept. of Integrative Structural and Computational Biology Scripps Institute La Jolla, CA
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10
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Cahoon JL, Rui X, Tang E, Simons C, Langie J, Chen M, Lo YC, Chiang CWK. Imputation Accuracy Across Global Human Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541241. [PMID: 37292811 PMCID: PMC10245797 DOI: 10.1101/2023.05.22.541241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of populations with non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative contains a substantial number of admixed African-ancestry and Hispanic/Latino samples to impute these populations with nearly the same accuracy as European-ancestry cohorts. However, imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we curated genome-wide array data from 23 publications published between 2008 to 2021. In total, we imputed over 43k individuals across 123 populations around the world. We identified a number of populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for 1-5% alleles in Saudi Arabians (N=1061), Vietnamese (N=1264), Thai (N=2435), and Papua New Guineans (N=776) were 0.79, 0.78, 0.76, and 0.62, respectively. In contrast, the mean Rsq ranged from 0.90 to 0.93 for comparable European populations matched in sample size and SNP content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European reference increased, as predicted. Further analysis using sequencing data as ground truth suggested that imputation software may over-estimate imputation accuracy for non-European populations than European populations, suggesting further disparity between populations. Using 1496 whole genome sequenced individuals from Taiwan Biobank as a reference, we also assessed a strategy to improve imputation for non-European populations with meta-imputation, which can combine results from TOPMed with smaller population-specific reference panels. We found that meta-imputation in this design did not improve Rsq genome-wide. Taken together, our analysis suggests that with the current size of alternative reference panels, meta-imputation alone cannot improve imputation efficacy for underrepresented cohorts and we must ultimately strive to increase diversity and size to promote equity within genetics research.
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Affiliation(s)
- Jordan L. Cahoon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Christopher Simons
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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11
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Skantharajah N, Baichoo S, Boughtwood TF, Casas-Silva E, Chandrasekharan S, Dave SM, Fakhro KA, Falcon de Vargas AB, Gayle SS, Gupta VK, Hendricks-Sturrup R, Hobb AE, Li S, Llamas B, Lopez-Correa C, Machirori M, Melendez-Zajgla J, Millner MA, Page AJ, Paglione LD, Raven-Adams MC, Smith L, Thomas EM, Kumuthini J, Corpas M. Equity, diversity, and inclusion at the Global Alliance for Genomics and Health. CELL GENOMICS 2023; 3:100386. [PMID: 37868041 PMCID: PMC10589617 DOI: 10.1016/j.xgen.2023.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.
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Affiliation(s)
- Neerjah Skantharajah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | | | - Sanjay M. Dave
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Khalid A. Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Aida B. Falcon de Vargas
- Hospital Vargas de Caracas, Vargas Medical School, Universidad Central de Venezuela, Caracas, Venezuela
- Hospital de Clínicas Caracas, Caracas, Venezuela
| | | | - Vivek K. Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Stephanie Li
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
| | | | - Mavis Machirori
- Ada Lovelace Institute, London, UK
- PEALS, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Mareike A. Millner
- Maastricht University, Health Law and Governance Group, Maastricht, the Netherlands
| | - Angela J.H. Page
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Laura D. Paglione
- Spherical Cow Group, New York, NY, USA
- Laura Paglione LLC, New York, NY, USA
| | - Maili C. Raven-Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | - Lindsay Smith
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Ericka M. Thomas
- The All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Judit Kumuthini
- South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | - Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
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12
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Paik KE, Hicklen R, Kaggwa F, Puyat CV, Nakayama LF, Ong BA, Shropshire JNI, Villanueva C. Digital Determinants of Health: Health data poverty amplifies existing health disparities-A scoping review. PLOS DIGITAL HEALTH 2023; 2:e0000313. [PMID: 37824445 PMCID: PMC10569513 DOI: 10.1371/journal.pdig.0000313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/02/2023] [Indexed: 10/14/2023]
Abstract
Artificial intelligence (AI) and machine learning (ML) have an immense potential to transform healthcare as already demonstrated in various medical specialties. This scoping review focuses on the factors that influence health data poverty, by conducting a literature review, analysis, and appraisal of results. Health data poverty is often an unseen factor which leads to perpetuating or exacerbating health disparities. Improvements or failures in addressing health data poverty will directly impact the effectiveness of AI/ML systems. The potential causes are complex and may enter anywhere along the development process. The initial results highlighted studies with common themes of health disparities (72%), AL/ML bias (28%) and biases in input data (18%). To properly evaluate disparities that exist we recommend a strengthened effort to generate unbiased equitable data, improved understanding of the limitations of AI/ML tools, and rigorous regulation with continuous monitoring of the clinical outcomes of deployed tools.
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Affiliation(s)
- Kenneth Eugene Paik
- MIT Critical Data, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Laboratory for Computational Physiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rachel Hicklen
- Research Medical Library, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Fred Kaggwa
- Department of Computer Science, Mbarara University of Science & Technology, Mbarara, Uganda
| | | | - Luis Filipe Nakayama
- MIT Critical Data, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Ophthalmology, São Paulo Federal University, São Paulo, Brazil
| | - Bradley Ashley Ong
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | | | - Cleva Villanueva
- Instituto Politécnico Nacional, Escuela Superior de Medicina, Mexico City, Mexico
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13
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Natri HM, Chapman CR, Heraty S, Dwyer P, Walker N, Kapp SK, Dron HA, Martinez-Agosto JA, Mikkola L, Doherty M. Ethical challenges in autism genomics: Recommendations for researchers. Eur J Med Genet 2023; 66:104810. [PMID: 37478903 DOI: 10.1016/j.ejmg.2023.104810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
Equitable and just genetic research and clinical translation require an examination of the ethical questions pertaining to vulnerable and marginalized communities. Autism research and advocate communities have expressed concerns over current practices of genetics research, urging the field to shift towards paradigms and practices that ensure benefits and avoid harm to research participants and the wider autistic community. Building upon a framework of bioethical principles, we provide the background for the concerns and present recommendations for ethically sustainable and justice-oriented genetic and genomic autism research. With the primary goal of enhancing the health, well-being, and autonomy of autistic persons, we make recommendations to guide priority setting, responsible research conduct, and informed consent practices. Further, we discuss the ethical challenges particularly pertaining to research involving highly vulnerable individuals and groups, such as those with impaired cognitive or communication ability. Finally, we consider the clinical translation of autism genetics studies, including the use of genetic testing. These guidelines, developed by an interdisciplinary working group comprising autistic and non-autistic individuals, will aid in leveraging the potential of genetics research to enhance the quality of life of autistic individuals and are widely applicable across stigmatized traits and vulnerable communities.
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Affiliation(s)
- Heini M Natri
- Translational Genomics Research Institute (TGen), Phoenix, AZ, 85004, USA.
| | - Carolyn R Chapman
- Department of Population Health (Division of Medical Ethics), NYU Grossman School of Medicine, New York, NY, 10016, USA; Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Síofra Heraty
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, University of London, Birkbeck, London, WC1E 7HX, UK
| | - Patrick Dwyer
- Center for Mind and Brain, UC Davis, Davis, CA, 95618, USA; Department of Psychology, UC Davis, Davis, CA, 95618, USA; MIND Institute, UC Davis Health, Sacramento, CA, 95817, USA
| | - Nick Walker
- California Institute of Integral Studies, San Francisco, CA, 94103, USA
| | - Steven K Kapp
- Department of Psychology, University of Portsmouth, Portsmouth, Hampshire, PO1 2UP, UK
| | - Heather A Dron
- Sterilization and Social Justice Lab, UCLA Institute for Genetics and Society, Los Angeles, CA, 90095, USA
| | | | - Lea Mikkola
- Turku Bioscience Center, InFLAMES Research Flagship Center, University of Turku, Turku, 20520, Finland
| | - Mary Doherty
- Department of Neuroscience, Brighton and Sussex Medical School, Brighton, BN1 9PX, UK
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Adsit-Morris C, Collins RN, Goering S, Karabin J, Lee SSJ, Reardon J. Unbounding ELSI: The Ongoing Work of Centering Equity and Justice. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:103-105. [PMID: 37339305 PMCID: PMC11034805 DOI: 10.1080/15265161.2023.2214055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
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15
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Jackson F, Clinton C, Caldwell J. Core issues, case studies, and the need for expanded Legacy African American genomics. Front Genet 2023; 14:843209. [PMID: 37359364 PMCID: PMC10287052 DOI: 10.3389/fgene.2023.843209] [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: 12/25/2021] [Accepted: 04/18/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Genomic studies of Legacy African Americans have a tangled and convoluted history in western science. In this review paper, core issues affecting African American genomic studies are addressed and two case studies, the New York African Burial Ground and the Gullah Geechee peoples, are presented to highlight the current status of genomic research among Africa Americans. Methods: To investigate our target population's core issues, a metadatabase derived from 22 publicly accessible databases were reviewed, evaluated, and synthesized to identify the core bioethical issues prevalent during the centuries of the African American presence in North America. The sequence of metadatabase development included 5 steps: identification of information, record screening and retention of topic relevant information, identification of eligibility via synthesis for concept identifications, and inclusion of studies used for conceptual summaries and studies used for genetic and genomic summaries. To these data we added our emic perspectives and specific insights from our case studies. Results: Overall, there is a paucity of existing research on underrepresent African American genomic diversity. In every category of genomic testing (i.e., diagnostic, clinical predictive, pharmacogenomic, direct-to-consumer, and tumor testing), African Americans are disproportionately underrepresented compared to European Americans. The first of our case studies is from the New York African Burial Ground Project where genomic studies of grave soil derived aDNA yields insights into the causes of death of 17th and 18th Century African Americans. In the second of our case studies, research among the Gullah Geechee people of the Carolina Lowcountry reveals a connection between genomic studies and health disparities. Discussion: African Americans have historically borne the brunt of the earliest biomedical studies used to generate and refine primitive concepts in genetics. As exploited victims these investigations, African American men, women, and children were subjected to an ethics-free western science. Now that bioethical safeguards have been added, underrepresented and marginalized people who were once the convenient targets of western science, are now excluded from its health-related benefits. Recommendations to enhance the inclusion of African Americans in global genomic databases and clinical trials should include the following: emphasis on the connection of inclusion to advances in precision medicine, emphasis on the relevance of inclusion to fundamental questions in human evolutionary biology, emphasis on the historical relevance of inclusion for Legacy African Americans, emphasis on the ability of inclusion to foster expanded scientific expertise in the target population, ethical engagement with their descendants, and increase the number of science researchers from these communities.
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Affiliation(s)
- Fatimah Jackson
- Department of Biology, Howard University, Washington, DC, United States
| | - Carter Clinton
- Department of Biology, North Carolina State University, Raleigh, NC, United States
| | - Jennifer Caldwell
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
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Abstract
This report is the product of a major year-long initiative to acknowledge and reckon with past injustice, as well as progress toward justice, within the American Society of Human Genetics (ASHG) and the broader field of human genetics. Approved by the ASHG Board of Directors and launched in 2021, the initiative was sparked by the social and racial reckonings in 2020. The ASHG Bboard of Directors asked ASHG to acknowledge and provide examples of how human genetics theories and knowledge "have been used to feed and justify racism, eugenics, and other systemic forms of injustice, and to focus specifically on examples of ASHG's role in fostering or failing to rebuke harms and on steps the Society could take to address findings." The initiative was undertaken with support and input from an expert panel of human geneticists, historians, clinician-scientists, equity scholars, and social scientists and included a research and environmental scan, four expert panel meetings, and a community dialogue as its main activities.
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Affiliation(s)
| | - Daria Turner
- Ripple Effect Communications, Rockville, MD, USA
| | - Maya June
- American Society of Human Genetics, Rockville, MD, USA
| | - Mona V Miller
- American Society of Human Genetics, Rockville, MD, USA
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17
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Aguilera-Cobos L, García-Sanz P, Rosario-Lozano MP, Claros MG, Blasco-Amaro JA. An innovative framework to determine the implementation level of personalized medicine: A systematic review. Front Public Health 2023; 11:1039688. [PMID: 36817923 PMCID: PMC9936069 DOI: 10.3389/fpubh.2023.1039688] [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: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background Personalized medicine (PM) is now the new frontier in patient care. The application of this new paradigm extends to various pathologies and different patient care phases, such as diagnosis and treatment. Translating biotechnological advances to clinical routine means adapting health services at all levels is necessary. Purpose This article aims to identify the elements for devising a framework that will allow the level of PM implementation in the country under study to be quantitatively and qualitatively assessed and that can be used as a guideline for future implementation plans. Methods A systematic review was conducted per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The research question was: What are the domains for determining the level of implementation of PM at the national level? The domains for assessing the degree of PM implementation, which would form the framework, were established. Results 19 full-text studies that met the inclusion criteria were peer-selected in the systematic review. From all the studies that were included, 37 elements-encompassed in 11 domains-were extracted for determining the degree of PM implementation. These domains and their constituent elements comprise the qualitative and quantitative assessment framework presented herein. Each of the elements can be assessed individually. On the other hand, the domains were standardized to all have the same weight in an overall assessment. Conclusions A framework has been developed that takes a multi-factorial approach to determine the degree of implementation of PM at the national level. This framework could also be used to rank countries and their implementation strategies according to the score they receive in the application of the latter. It could also be used as a guide for developing future national PM implementation strategies. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022338611, Identifier: CRD42022338611.
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Affiliation(s)
- Lorena Aguilera-Cobos
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain,Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain,*Correspondence: Lorena Aguilera-Cobos ✉
| | - Patricia García-Sanz
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain,Patricia García-Sanz ✉
| | - María Piedad Rosario-Lozano
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain,Institute of Biomedical Research in Málaga (IBIMA), Málaga, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Málaga, Spain,Institute for Mediterranean and Subtropical Horticulture “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Juan Antonio Blasco-Amaro
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
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Horn R, Merchant J, Bale M, Chneiweiss H, Hallowell N, Kerasidou A, Lucassen A, Montgomery J, Parker M, Patch C, Winkler E. Managing expectations, rights, and duties in large-scale genomics initiatives: a European comparison. Eur J Hum Genet 2023; 31:142-147. [PMID: 36471117 PMCID: PMC9734861 DOI: 10.1038/s41431-022-01247-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ruth Horn
- The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford, Oxford, UK. .,Ethics of Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.
| | - Jennifer Merchant
- CNRS Law & Humanities/CERSA UMR-7109, University Paris-Panthéon-Assas, Paris, France.,Institut Universitaire de France, Paris, France
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Alvarellos M, Sheppard HE, Knarston I, Davison C, Raine N, Seeger T, Prieto Barja P, Chatzou Dunford M. Democratizing clinical-genomic data: How federated platforms can promote benefits sharing in genomics. Front Genet 2023; 13:1045450. [PMID: 36704354 PMCID: PMC9871385 DOI: 10.3389/fgene.2022.1045450] [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: 09/15/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Since the first sequencing of the human genome, associated sequencing costs have dramatically lowered, leading to an explosion of genomic data. This valuable data should in theory be of huge benefit to the global community, although unfortunately the benefits of these advances have not been widely distributed. Much of today's clinical-genomic data is siloed and inaccessible in adherence with strict governance and privacy policies, with more than 97% of hospital data going unused, according to one reference. Despite these challenges, there are promising efforts to make clinical-genomic data accessible and useful without compromising security. Specifically, federated data platforms are emerging as key resources to facilitate secure data sharing without having to physically move the data from outside of its organizational or jurisdictional boundaries. In this perspective, we summarize the overarching progress in establishing federated data platforms, and highlight critical considerations on how they should be managed to ensure patient and public trust. These platforms are enabling global collaboration and improving representation of underrepresented groups, since sequencing efforts have not prioritized diverse population representation until recently. Federated data platforms, when combined with advances in no-code technology, can be accessible to the diverse end-users that make up the genomics workforce, and we discuss potential strategies to develop sustainable business models so that the platforms can continue to enable research long term. Although these platforms must be carefully managed to ensure appropriate and ethical use, they are democratizing access and insights to clinical-genomic data that will progress research and enable impactful therapeutic findings.
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Giudicelli GC, De Souza CMB, Veronese FV, Pereira LV, Hünemeier T, Vianna FSL. Precision medicine implementation challenges for APOL1 testing in chronic kidney disease in admixed populations. Front Genet 2022; 13:1016341. [PMID: 36588788 PMCID: PMC9797503 DOI: 10.3389/fgene.2022.1016341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic Kidney Disease (CKD) is a public health problem that presents genetic and environmental risk factors. Two alleles in the Apolipoprotein L1 (APOL1) gene were associated with chronic kidney disease; these alleles are common in individuals of African ancestry but rare in European descendants. Genomic studies on Afro-Americans have indicated a higher prevalence and severity of chronic kidney disease in people of African ancestry when compared to other ethnic groups. However, estimates in low- and middle-income countries are still limited. Precision medicine approaches could improve clinical outcomes in carriers of risk alleles in the Apolipoprotein L1 gene through early diagnosis and specific therapies. Nevertheless, to enhance the definition of studies on these variants, it would be necessary to include individuals with different ancestry profiles in the sample, such as Latinos, African Americans, and Indigenous peoples. There is evidence that measuring genetic ancestry improves clinical care for admixed people. For chronic kidney disease, this knowledge could help establish public health strategies for monitoring patients and understanding the impact of the Apolipoprotein L1 genetic variants in admixed populations. Therefore, researchers need to develop resources, methodologies, and incentives for vulnerable and disadvantaged communities, to develop and implement precision medicine strategies and contribute to consolidating diversity in science and precision medicine in clinical practice.
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Affiliation(s)
- Giovanna Câmara Giudicelli
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil
| | - Celia Mariana Barbosa De Souza
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francisco Veríssimo Veronese
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lygia V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain
| | - Fernanda Sales Luiz Vianna
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil,Programa de Medicina Personalizada Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,*Correspondence: Fernanda Sales Luiz Vianna,
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21
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Mwaka ES, Bagenda G, Sebatta DE, Nabukenya S, Munabi I. Benefit sharing in genomic and biobanking research in Uganda: Perceptions of researchers and research ethics committee members. Front Genet 2022; 13:1037401. [DOI: 10.3389/fgene.2022.1037401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Genomic and biobanking research has increased in Africa over the past few years. This has raised pertinent ethical, legal, and societal concerns for stakeholders such as sample or data ownership, commercialization, and benefit sharing. There is limited awareness of the concept of benefit sharing by stakeholders in sub-Saharan Africa.Objective: This study aimed to explore the perceptions of researchers and research ethics committee members on benefit sharing in international collaborative genomic and biobanking research.Methods: Qualitative in-depth interviews were conducted with 15 researchers and 19 research ethics committee members. A thematic approach was used to interpret the results.Results: Six themes emerged from the data and these included perceptions on the benefits of genomic and biobanking research; discussion of benefit sharing with participants during the informed consent process; legal implications of benefit sharing and the role of material transfer agreements; equity and fairness in sharing the benefits of genomic research; perceived barriers to fair benefit sharing; and recommendations for fostering fair and equitable benefit sharing in genomic and biobanking research. Most respondents clearly understood the various forms of benefits of genomic and biobanking research and opined that such benefits should be fairly and equitably shared with low and middle-income country researchers and their institutions, and research communities. The perceived barriers to the fair benefit sharing unfavorable include power disparities, weak research regulatory frameworks, and lack of scientific integrity.Conclusion: Overall, respondents believed that the distribution of the advantages of genomic and biobanking research in North-South collaborative research was not equitable nor fair, and that the playing field was not leveled. Therefore, we advocate the following for fair and equitable benefit sharing: Building the capacities and empowering research scientists in developing nations; strengthening regulatory frameworks and extending the purview of the research ethics committee in the development and implementation of material transfer agreements; and meaningfully involving local research communities in benefit sharing negotiations.
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Equitable partnerships and the path to inclusive, innovative and impactful human microbiome research. Nat Rev Gastroenterol Hepatol 2022; 19:683-684. [PMID: 36171273 DOI: 10.1038/s41575-022-00689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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23
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No person left behind: Mapping the health policy landscape for genomics research in the Caribbean. LANCET REGIONAL HEALTH. AMERICAS 2022; 15:100367. [PMID: 36778076 PMCID: PMC9904062 DOI: 10.1016/j.lana.2022.100367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Caribbean has long been an under-represented geographical region in the field of genomics research. Such under-representation may result in Caribbean people being underserved by precision medicine and other public health benefits of genomics. A collaboration among regional and international researchers aims to address this issue through the H3ECaribbean project (Human Heredity, Environment, and Health in the Caribbean), which builds on the lessons and success of H3Africa. The Caribbean project aims to target issues of social justice by encouraging the inclusion of diverse Caribbean communities in genomics research. This paper explores a framework for the ethical and socially acceptable conduct of genomics research in the Caribbean, taking account of the cultural peculiarities of the region. This is done in part by exploring research ethics issues identified in indigenous communities in North America, Small Island Developing States, and similar endeavours from the African continent. The framework provides guidance for interacting with local community leaders, as well as detailing steps for obtaining informed consent of all participants. Specifically, the authors outline the methods to ensure effective interaction and enforce full transparency with study participants to combat historical neglect when working with under-represented communities in the Caribbean.
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Lemke AA, Esplin ED, Goldenberg AJ, Gonzaga-Jauregui C, Hanchard NA, Harris-Wai J, Ideozu JE, Isasi R, Landstrom AP, Prince AER, Turbitt E, Sabatello M, Schrier Vergano SA, Taylor MRG, Yu JH, Brothers KB, Garrison NA. Addressing underrepresentation in genomics research through community engagement. Am J Hum Genet 2022; 109:1563-1571. [PMID: 36055208 PMCID: PMC9502069 DOI: 10.1016/j.ajhg.2022.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vision of the American Society of Human Genetics (ASHG) is that people everywhere will realize the benefits of human genetics and genomics. Implicit in that vision is the importance of ensuring that the benefits of human genetics and genomics research are realized in ways that minimize harms and maximize benefits, a goal that can only be achieved through focused efforts to address health inequities and increase the representation of underrepresented communities in genetics and genomics research. This guidance is intended to advance community engagement as an approach that can be used across the research lifecycle. Community engagement uniquely offers researchers in human genetics and genomics an opportunity to pursue that vision successfully, including by addressing underrepresentation in genomics research.
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Affiliation(s)
- Amy A Lemke
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Norton Children's Research Institute, affiliated with the University of Louisville School of Medicine, Louisville, KY, USA.
| | - Edward D Esplin
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Invitae, San Francisco, CA, USA
| | - Aaron J Goldenberg
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland OH, USA
| | - Claudia Gonzaga-Jauregui
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | - Neil A Hanchard
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Childhood Complex Disease Genomics Section, Center for Precision Health Research, National Human Genomics Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julie Harris-Wai
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; University of California at San Francisco, Department of Social and Behavioral Sciences, Program on Bioethics, Institute for Health and Aging, San Francisco CA, USA
| | - Justin E Ideozu
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Genomic Medicine, Genetic Research Center, AbbVie, Chicago, IL, USA
| | - Rosario Isasi
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Dr. J. T. Macdonald Foundation Department of Human Genetics, University of Miami Leonard M. Miller School of Medicine, Miami FL, USA; John P. Hussman Institute for Human Genomics, University of Miami Leonard M. Miller School of Medicine, Miami FL, USA
| | - Andrew P Landstrom
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Department of Pediatrics, Division of Pediatric Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Anya E R Prince
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; University of Iowa College of Law, Iowa City IA, USA
| | - Erin Turbitt
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Discipline of Genetic Counselling, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - Maya Sabatello
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; 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
| | - Samantha A Schrier Vergano
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Matthew R G Taylor
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Adult Medical Genetics Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joon-Ho Yu
- Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Division of Genetic Medicine, Department of Pediatrics , University of Washington School of Medicine, Seattle, WA, USA; Division of Bioethics and Palliative Care, Department of Pediatrics , University of Washington School of Medicine, Seattle, WA, USA; Institute for Public Health Genetics, School of Public Health, University of Washington, Seattle, WA, USA; Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA, USA
| | - Kyle B Brothers
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Norton Children's Research Institute, affiliated with the University of Louisville School of Medicine, Louisville, KY, USA
| | - Nanibaa' A Garrison
- Professional Practice and Social Implications Committee, American Society of Human Genetics, Rockville MD, USA; Professional Practice and Social Implications Community Engagement Guidance Writing Group, American Society of Human Genetics, Rockville, MD, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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25
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Atkinson EG, Bianchi SB, Ye GY, Martínez-Magaña JJ, Tietz GE, Montalvo-Ortiz JL, Giusti-Rodriguez P, Palmer AA, Sanchez-Roige S. Cross-ancestry genomic research: time to close the gap. Neuropsychopharmacology 2022; 47:1737-1738. [PMID: 35739257 PMCID: PMC9372026 DOI: 10.1038/s41386-022-01365-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Gordon Y Ye
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Grace E Tietz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
- US Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, Clinical Neurosciences Division, West Haven, CT, USA
| | - Paola Giusti-Rodriguez
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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26
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Hanchard NA, Chahrour M, de Vries J. Tailored community engagement to address the genetics diversity gap. MED 2022; 3:369-370. [PMID: 35690058 PMCID: PMC10612127 DOI: 10.1016/j.medj.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Neil A Hanchard
- Childhood Complex Disease Genomics Section, Center for Personalized Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Maria Chahrour
- Eugene McDermott Center for Human Growth and Development, Departments of Neuroscience and Psychiatry, Center for the Genetics of Host Defense, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jantina de Vries
- UCT Neuroscience Institute and Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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