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Lewis ACF, Green RC. Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues. Genome Med 2021; 13:14. [PMID: 33509269 PMCID: PMC7844961 DOI: 10.1186/s13073-021-00829-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Clinical use of polygenic risk scores (PRS) will look very different to the more familiar monogenic testing. Here we argue that despite these differences, most of the ethical, legal, and social issues (ELSI) raised in the monogenic setting, such as the relevance of results to family members, the approach to secondary and incidental findings, and the role of expert mediators, continue to be relevant in the polygenic context, albeit in modified form. In addition, PRS will reanimate other old debates. Their use has been proposed both in the practice of clinical medicine and of public health, two contexts with differing norms. In each of these domains, it is unclear what endpoints clinical use of PRS should aim to maximize and under what constraints. Reducing health disparities is a key value for public health, but clinical use of PRS could exacerbate race-based health disparities owing to differences in predictive power across ancestry groups. Finally, PRS will force a reckoning with pre-existing questions concerning biomarkers, namely the relevance of self-reported race, ethnicity and ancestry, and the relationship of risk factors to disease diagnoses. In this Opinion, we argue that despite the parallels to the monogenic setting, new work is urgently needed to gather data, consider normative implications, and develop best practices around this emerging branch of genomics.
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Affiliation(s)
- Anna C F Lewis
- E J Safra Center for Ethics, Harvard University, 124 Mount Auburn, Street, Cambridge, 02138, USA.
| | - Robert C Green
- Brigham and Women's Hospital, 75 Francis St, Boston, MA 02115, USA
- Ariadne Labs, 401 Park Dr 3rd Floor, Boston, MA 02215, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
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Popejoy AB, Ritter DI, Crooks K, Currey E, Fullerton SM, Hindorff LA, Koenig B, Ramos EM, Sorokin EP, Wand H, Wright MW, Zou J, Gignoux CR, Bonham VL, Plon SE, Bustamante CD. The clinical imperative for inclusivity: Race, ethnicity, and ancestry (REA) in genomics. Hum Mutat 2019; 39:1713-1720. [PMID: 30311373 DOI: 10.1002/humu.23644] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/17/2018] [Accepted: 08/30/2018] [Indexed: 12/12/2022]
Abstract
The Clinical Genome Resource (ClinGen) Ancestry and Diversity Working Group highlights the need to develop guidance on race, ethnicity, and ancestry (REA) data collection and use in clinical genomics. We present quantitative and qualitative evidence to characterize: (1) acquisition of REA data via clinical laboratory requisition forms, and (2) information disparity across populations in the Genome Aggregation Database (gnomAD) at clinically relevant sites ascertained from annotations in ClinVar. Our requisition form analysis showed substantial heterogeneity in clinical laboratory ascertainment of REA, as well as marked incongruity among terms used to define REA categories. There was also striking disparity across REA populations in the amount of information available about clinically relevant variants in gnomAD. European ancestral populations constituted the majority of observations (55.8%), allele counts (59.7%), and private alleles (56.1%) in gnomAD at 550 loci with "pathogenic" and "likely pathogenic" expert-reviewed variants in ClinVar. Our findings highlight the importance of implementing and supporting programs to increase diversity in genome sequencing and clinical genomics, as well as measuring uncertainty around population-level datasets that are used in variant interpretation. Finally, we suggest the need for a standardized REA data collection framework to be developed through partnerships and collaborations and adopted across clinical genomics.
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Affiliation(s)
- Alice B Popejoy
- Department of Biomedical Data Science, Stanford University, Standford, California
| | - Deborah I Ritter
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Kristy Crooks
- Department of Pathology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Erin Currey
- Division of Genomics and Society, National Human Genome Research Institute (NHGRI), Bethesda, Maryland
| | | | - Lucia A Hindorff
- Division of Genomics and Society, National Human Genome Research Institute (NHGRI), Bethesda, Maryland
| | - Barbara Koenig
- Department of Anthropology, History, and Social Medicine, University of California, San Francisco
| | - Erin M Ramos
- Division of Genomics and Society, National Human Genome Research Institute (NHGRI), Bethesda, Maryland
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Standford, California
| | - Hannah Wand
- Department of Biomedical Data Science, Stanford University, Standford, California
| | - Mathew W Wright
- Department of Biomedical Data Science, Stanford University, Standford, California
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Standford, California
| | - Christopher R Gignoux
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Vence L Bonham
- Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), Bethesda, Maryland
| | - Sharon E Plon
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Standford, California
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Gomes MB, Gabrielli AB, Santos DC, Pizarro MH, Barros BSV, Negrato CA, Dib SA, Porto LC, Silva DA. Self-reported color-race and genomic ancestry in an admixed population: A contribution of a nationwide survey in patients with type 1 diabetes in Brazil. Diabetes Res Clin Pract 2018; 140:245-252. [PMID: 29574106 DOI: 10.1016/j.diabres.2018.03.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 02/22/2018] [Accepted: 03/09/2018] [Indexed: 12/17/2022]
Abstract
AIMS The development of type 1 diabetes (T1D) and its chronic complications may have a genetic background. The primary objective of our study was to characterize the relationship between self-reported color-race and genomic ancestry (GA) in patients with T1D. As secondary objective, we aimed to characterize GA of patients with T1D from different urban geographical regions of Brazil, compared to healthy Brazilian controls from the same regions. METHODS This was a cross-sectional, nationwide survey conducted in 14 public clinics from 10 Brazilian cities. Global and individual GA were inferred using a panel of 46 ancestry informative markers (AIMs) in 1698 T1D patients. Ancestry percentage was compared with published data of Brazilian healthy controls (n = 936) for the same AIMs. RESULTS A higher median individual European ancestry was observed in T1D patients in comparison to controls 67.8 [31.2] vs. 56.3 [25.7]%, respectively (median [IQR]; p < 0.001). As for self-reported color-race in T1D group, 923 (54.3%) participants reported to be White, 610 (35.9%) Brown, 132 (7.8%) Black, 18 (1.1%) Asian and 15 (0.9%) Indigenous. European GA prevailed in those who self-reported as White (74.6%) and Brown (61.1%) and constituted 39.1% in Black self-reported patients. CONCLUSIONS Our study showed that T1D patients presented a higher percentage of European GA than the healthy population. Additionally, European GA was found in a considerable percentage of T1D patients who self-reported as non-White. Further studies are necessary to establish the influence of GA in the development of T1D as well its related chronic complications in admixed populations.
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Affiliation(s)
- Marília Brito Gomes
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Aline Brazão Gabrielli
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Deborah Conte Santos
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcela Haas Pizarro
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca S V Barros
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Sergio Atala Dib
- Department of Internal Medicine, Diabetes Unit, Federal University of São Paulo, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dayse A Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
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Smart A, Bolnick DA, Tutton R. Health and genetic ancestry testing: time to bridge the gap. BMC Med Genomics 2017; 10:3. [PMID: 28069037 PMCID: PMC5223458 DOI: 10.1186/s12920-016-0240-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 12/21/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health risks associated with particular ancestral lineages. Because some of the proposed associations have received little attention from oversight agencies and professional genetic associations, scientific developments are currently outpacing governance regimes for consumer genetic testing. MAIN TEXT We highlight the recent and unremarked upon emergence of biomedical studies linking markers of genetic ancestry to disease risks, and show that this body of scientific research is becoming part of public discourse connecting ancestry and health. For instance, data on genome-wide ancestry informative markers are being used to assess health risks, and we document over 100 biomedical research articles that propose associations between mitochondrial DNA and Y chromosome markers of genetic ancestry and a wide variety of disease risks. Taking as an example an association between coronary heart disease and British men belonging to Y chromosome haplogroup I, we show how this science was translated into mainstream and online media, and how it circulates among consumers of genetic tests for ancestry. We find wide variations in how the science is interpreted, which suggests the potential for confusion or misunderstanding. CONCLUSION We recommend that stakeholders involved in creating and using estimates of genetic ancestry reconsider their policies for communicating with each other and with the public about the health implications of ancestry information.
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Affiliation(s)
- Andrew Smart
- Department of Sociology, Bath Spa University, Newton Park, Bath, BA2 9BN UK
| | - Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, 2201 Speedway, Stop C3200, Austin, TX 78712-1723 USA
| | - Richard Tutton
- Department of Sociology, Lancaster University, Bowland North, Bailrigg, LA1 4YN UK
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