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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [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: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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Atilano-Barbosa D, Barrios FA. Brain morphological variability between whites and African Americans: the importance of racial identity in brain imaging research. Front Integr Neurosci 2023; 17:1027382. [PMID: 38192686 PMCID: PMC10773238 DOI: 10.3389/fnint.2023.1027382] [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: 08/24/2022] [Accepted: 04/14/2023] [Indexed: 01/10/2024] Open
Abstract
In a segregated society, marked by a historical background of inequalities, there is a consistent under-representation of ethnic and racial minorities in biomedical research, causing disparities in understanding genetic and acquired diseases as well as in the effectiveness of clinical treatments affecting different groups. The repeated inclusion of small and non-representative samples of the population in neuroimaging research has led to generalization bias in the morphological characterization of the human brain. A few brain morphometric studies between Whites and African Americans have reported differences in orbitofrontal volumetry and insula cortical thickness. Nevertheless, these studies are mostly conducted in small samples and populations with cognitive impairment. For this reason, this study aimed to identify brain morphological variability due to racial identity in representative samples. We hypothesized that, in neurotypical young adults, there are differences in brain morphometry between participants with distinct racial identities. We analyzed the Human Connectome Project (HCP) database to test this hypothesis. Brain volumetry, cortical thickness, and cortical surface area measures of participants identified as Whites (n = 338) or African Americans (n = 56) were analyzed. Non-parametrical permutation analysis of covariance between these racial identity groups adjusting for age, sex, education, and economic income was implemented. Results indicated volumetric differences in choroid plexus, supratentorial, white matter, and subcortical brain structures. Moreover, differences in cortical thickness and surface area in frontal, parietal, temporal, and occipital brain regions were identified between groups. In this regard, the inclusion of sub-representative minorities in neuroimaging research, such as African American persons, is fundamental for the comprehension of human brain morphometric diversity and to design personalized clinical brain treatments for this population.
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Affiliation(s)
| | - Fernando A. Barrios
- Institute of Neurobiology, National Autonomous University of Mexico, Juriquilla, Mexico
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3
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Roach M, Coleman PW, Kittles R. Prostate Cancer, Race, and Health Disparity: What We Know. Cancer J 2023; 29:328-337. [PMID: 37963367 DOI: 10.1097/ppo.0000000000000688] [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: 11/16/2023]
Abstract
ABSTRACT Prostate cancer (PCa) in African American men is one of the most common cancers with a great disparity in outcomes. The higher incidence and tendency to present with more advanced disease have prompted investigators to postulate that this is a problem of innate biology. However, unequal access to health care and poorer quality of care raise questions about the relative importance of genetics versus social/health injustice. Although race is inconsistent with global human genetic diversity, we need to understand the sociocultural reality that race and racism impact biology. Genetic studies reveal enrichment of PCa risk alleles in populations of West African descent and population-level differences in tumor immunology. Structural racism may explain some of the differences previously reported in PCa clinical outcomes; fortunately, there is high-level evidence that when care is comparable, outcomes are comparable.
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Affiliation(s)
- Mack Roach
- From the Particle Therapy Research Program & Outreach, Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Pamela W Coleman
- Department of Surgery/Obstetrics-Gynecology, Howard University College of Medicine, Washington, DC
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4
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Harris AR, Panigrahi G, Liu H, Koparde VN, Bailey-Whyte M, Dorsey TH, Yates CC, Ambs S. Chromatin Accessibility Landscape of Human Triple-negative Breast Cancer Cell Lines Reveals Variation by Patient Donor Ancestry. CANCER RESEARCH COMMUNICATIONS 2023; 3:2014-2029. [PMID: 37732899 PMCID: PMC10552704 DOI: 10.1158/2767-9764.crc-23-0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/01/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
African American (AA) women have an excessive risk of developing triple-negative breast cancer (TNBC). We employed Assay for Transposase-Accessible Chromatin using sequencing to characterize differences in chromatin accessibility between nine commonly used TNBC cell lines derived from patients of European and African ancestry. Principal component and chromosome mapping analyses of accessibility peaks with the most variance revealed separation of chromatin profiles by patient group. Motif enrichment and footprinting analyses of disparate open chromatin regions revealed differences in transcription factor activity, identifying 79 with ancestry-associated binding patterns (FDR < 0.01). AA TNBC cell lines exhibited increased accessibility for 62 transcription factors associated with epithelial-to-mesenchymal transition, cancer stemness/chemotherapeutic resistance, proliferation, and aberrant p53 regulation, as well as KAISO, which has been previously linked to aggressive tumor characteristics in AA patients with cancer. Differential Assay for Transposase-Accessible Chromatin signal analysis identified 1,596 genes located within promoters of differentially open chromatin regions in AA-derived TNBC, identifying DNA methyltransferase 1 as the top upregulated gene associated with African ancestry. Pathway analyses with these genes revealed enrichment in several pathways, including hypoxia. Culturing cells under hypoxia showed ancestry-specific stress responses that led to the identification of a core set of AA-associated transcription factors, which included members of the Kruppel-like factor and Sp subfamilies, as well as KAISO, and identified ZDHHC1, a gene previously implicated in immunity and STING activation, as the top upregulated AA-specific gene under hypoxia. Together, these data reveal a differential chromatin landscape in TNBC associated with donor ancestry. The open chromatin structure of AA TNBC may contribute to a more lethal disease. SIGNIFICANCE We identify an ancestry-associated open chromatin landscape and related transcription factors that may contribute to aggressive TNBC in AA women. Furthermore, this study advocates for the inclusion of diversely sourced cell lines in experimental in vitro studies to advance health equity at all levels of scientific research.
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Affiliation(s)
- Alexandra R. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Gatikrushna Panigrahi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Vishal N. Koparde
- Center for Cancer Research Collaborative Bioinformatics Resource Frederick National Laboratory for Cancer Research, NCI, Frederick, Maryland
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Maeve Bailey-Whyte
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Clayton C. Yates
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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Smith J, Liu C, Beck A, Fei L, Brokamp C, Meryum S, Whaley KG, Minar P, Hellmann J, Denson LA, Margolis P, Dhaliwal J. Racial Disparities in Pediatric Inflammatory Bowel Disease Care: Differences in Outcomes and Health Service Utilization Between Black and White Children. J Pediatr 2023; 260:113522. [PMID: 37244575 PMCID: PMC10894641 DOI: 10.1016/j.jpeds.2023.113522] [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: 09/30/2022] [Revised: 05/08/2023] [Accepted: 05/21/2023] [Indexed: 05/29/2023]
Abstract
OBJECTIVE To describe racial inequities in pediatric inflammatory bowel disease care and explore potential drivers. METHODS We undertook a single-center, comparative cohort study of newly diagnosed Black and non-Hispanic White patients with inflammatory bowel disease, aged <21 years, from January 2013 through 2020. Primary outcome was corticosteroid-free remission (CSFR) at 1 year. Other longitudinal outcomes included sustained CSFR, time to anti-tumor necrosis factor therapy, and evaluation of health service utilization. RESULTS Among 519 children (89% White, 11% Black), 73% presented with Crohn's disease and 27% with ulcerative colitis. Disease phenotype did not differ by race. More patients from Black families had public insurance (58% vs 30%, P < .001). Black patients were less likely to achieve CSFR 1-year post diagnosis (OR: 0.52, 95% CI:0.3-0.9) and less likely to achieve sustained CSFR (OR: 0.48, 95% CI: 0.25-0.92). When adjusted by insurance type, differences by race to 1-year CSFR were no longer significant (aOR: 0.58; 95% CI: 0.33, 1.04; P = .07). Black patients were more likely to transition from remission to a worsened state, and less likely to transition to remission. We found no differences in biologic therapy utilization or surgical outcomes by race. Black patients had fewer gastroenterology clinic visits and 2-fold increased odds for emergency department visits. CONCLUSIONS We observed no differences by race in phenotypic presentation and medication usage. Black patients had half the odds of achieving clinical remission, but a degree of this was mediated by insurance status. Understanding the cause of such differences will require further exploration of social determinants of health.
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Affiliation(s)
- Julia Smith
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Chunyan Liu
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrew Beck
- Division of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Lin Fei
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Cole Brokamp
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Syeda Meryum
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kaitlin G Whaley
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Phillip Minar
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Jennifer Hellmann
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Lee A Denson
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Peter Margolis
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Jasbir Dhaliwal
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati, Cincinnati, OH.
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Wagner JK, Yu JH, Fullwiley D, Moore C, Wilson JF, Bamshad MJ, Royal CD. Guidelines for genetic ancestry inference created through roundtable discussions. HGG ADVANCES 2023; 4:100178. [PMID: 36798092 PMCID: PMC9926022 DOI: 10.1016/j.xhgg.2023.100178] [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: 09/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.
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Affiliation(s)
- Jennifer K. Wagner
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joon-Ho Yu
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
| | - Duana Fullwiley
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
| | | | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Michael J. Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
| | - Charmaine D. Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
| | - Genetic Ancestry Inference Roundtable Participants
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
- The DNA Detectives, Dana Point, CA, USA
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
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Dauda B, Molina SJ, Allen DS, Fuentes A, Ghosh N, Mauro M, Neale BM, Panofsky A, Sohail M, Zhang SR, Lewis ACF. Ancestry: How researchers use it and what they mean by it. Front Genet 2023; 14:1044555. [PMID: 36755575 PMCID: PMC9900027 DOI: 10.3389/fgene.2023.1044555] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Background: Ancestry is often viewed as a more objective and less objectionable population descriptor than race or ethnicity. Perhaps reflecting this, usage of the term "ancestry" is rapidly growing in genetics research, with ancestry groups referenced in many situations. The appropriate usage of population descriptors in genetics research is an ongoing source of debate. Sound normative guidance should rest on an empirical understanding of current usage; in the case of ancestry, questions about how researchers use the concept, and what they mean by it, remain unanswered. Methods: Systematic literature analysis of 205 articles at least tangentially related to human health from diverse disciplines that use the concept of ancestry, and semi-structured interviews with 44 lead authors of some of those articles. Results: Ancestry is relied on to structure research questions and key methodological approaches. Yet researchers struggle to define it, and/or offer diverse definitions. For some ancestry is a genetic concept, but for many-including geneticists-ancestry is only tangentially related to genetics. For some interviewees, ancestry is explicitly equated to ethnicity; for others it is explicitly distanced from it. Ancestry is operationalized using multiple data types (including genetic variation and self-reported identities), though for a large fraction of articles (26%) it is impossible to tell which data types were used. Across the literature and interviews there is no consistent understanding of how ancestry relates to genetic concepts (including genetic ancestry and population structure), nor how these genetic concepts relate to each other. Beyond this conceptual confusion, practices related to summarizing patterns of genetic variation often rest on uninterrogated conventions. Continental labels are by far the most common type of label applied to ancestry groups. We observed many instances of slippage between reference to ancestry groups and racial groups. Conclusion: Ancestry is in practice a highly ambiguous concept, and far from an objective counterpart to race or ethnicity. It is not uniquely a "biological" construct, and it does not represent a "safe haven" for researchers seeking to avoid evoking race or ethnicity in their work. Distinguishing genetic ancestry from ancestry more broadly will be a necessary part of providing conceptual clarity.
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Affiliation(s)
- Bege Dauda
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, United States
| | - Santiago J. Molina
- Department of Sociology, Northwestern University, Evanston, IL, United States
| | - Danielle S. Allen
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Agustin Fuentes
- Department of Anthropology, Princeton University, Princeton, NJ, United States
| | - Nayanika Ghosh
- Department of the History of Science, Harvard University, Cambridge, MA, United States
| | - Madelyn Mauro
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Benjamin M. Neale
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Aaron Panofsky
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Public Policy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Sociology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mashaal Sohail
- Centro de Ciencias Genomicas (CCG), Universidad Nacional Autonoma de Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | - Sarah R. Zhang
- University of California, Berkeley, Berkeley, CA, United States
| | - Anna C. F. Lewis
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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Rey-Vargas L, Bejarano-Rivera LM, Mejia-Henao JC, Sua LF, Bastidas-Andrade JF, Ossa CA, Gutiérrez-Castañeda LD, Fejerman L, Sanabria-Salas MC, Serrano-Gómez SJ. Association of genetic ancestry with HER2, GRB7 AND estrogen receptor expression among Colombian women with breast cancer. Front Oncol 2022; 12:989761. [PMID: 36620598 PMCID: PMC9815522 DOI: 10.3389/fonc.2022.989761] [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: 07/08/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Background Our previous study reported higher mRNA levels of the human epidermal growth factor receptor 2 (HER2)-amplicon genes ERBB2 and GRB7 in estrogen receptor (ER)-positive breast cancer patients with relatively high Indigenous American (IA) ancestry from Colombia. Even though the protein expression of HER2 and GRB7 is highly correlated, they may also express independently, an event that could change the patients' prognosis. In this study, we aimed to explore the differences in ER, HER2 and GRB7 protein expression according to genetic ancestry, to further assess the clinical implications of this association. Methods We estimated genetic ancestry from non-tumoral breast tissue DNA and assessed tumoral protein expression of ER, HER2, and GRB7 by immunohistochemistry in a cohort of Colombian patients from different health institutions. We used binomial and multinomial logistic regression models to test the association between genetic ancestry and protein expression. Kaplan-Meier and log-rank tests were used to evaluate the effect of HER2/GRB7 co-expression on patients' survival. Results Our results show that patients with higher IA ancestry have higher odds of having HER2+/GRB7- breast tumors, compared to the HER2-/GRB7- subtype, and this association seems to be stronger among ER-positive tumors (ER+/HER2+/GRB7-: OR=3.04, 95% CI, 1.47-6.37, p<0.05). However, in the multivariate model this association was attenuated (OR=1.80, 95% CI, 0.72-4.44, p=0.19). On the other hand, it was observed that having a higher European ancestry patients presented lower odds of ER+/HER2+/GRB7- breast tumors, this association remained significant in the multivariate model (OR=0.36, 95% CI, 0.13 - 0.93, p= 0.0395). The survival analysis according to HER2/GRB7 co-expression did not show statistically significant differences in the overall survival and recurrence-free survival. Conclusions Our results suggest that Colombian patients with higher IA ancestry and a lower European fraction have higher odds of ER+/HER2+/GRB7- tumors compared to ER+/HER2-/GRB7- disease. However, this association does not seem to be associated with patients' overall or recurrence-free survival.
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Affiliation(s)
- Laura Rey-Vargas
- Cancer Biology Research Group, National Cancer Institute of Colombia, Bogotá, Colombia,Doctoral Program in Biological Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Juan Carlos Mejia-Henao
- Oncological Pathology Research Group, National Cancer Institute of Colombia, Bogotá, Colombia
| | - Luz F. Sua
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, and Faculty of Health Sciences, Universidad ICESI, Cali, Colombia
| | | | | | - Luz Dary Gutiérrez-Castañeda
- Research Institute, Group of Basic Sciences in Health (CBS), Fundación Universitaria de Ciencias de la Salud (FUCS), Bogotá, Colombia
| | - Laura Fejerman
- Department of Public Health Sciences and Comprehensive Cancer Center, University of California Davis, Davis, CA, United States
| | | | - Silvia J. Serrano-Gómez
- Cancer Biology Research Group, National Cancer Institute of Colombia, Bogotá, Colombia,Research support and follow-up group, National Cancer Institute of Colombia, Bogotá, Colombia,*Correspondence: Silvia J. Serrano-Gómez,
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Thayer Z, Uwizeye G, McKerracher L. Toolkit article: Approaches to measuring social inequities in health in human biology research. Am J Hum Biol 2022; 34:e23804. [PMID: 36173013 DOI: 10.1002/ajhb.23804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 01/25/2023] Open
Abstract
Across populations, human morbidity and mortality risks generally follow clear gradients, with socially-disadvantaged individuals and groups tending to have higher morbidity and mortality at all life stages relative to those more socially advantaged. Anthropologists specialize in understanding the proximate and ultimate factors that shape variation in human biological functioning and health and are therefore well-situated to explore the relationships between social position and health in diverse ecological and cultural contexts. While human biologists have developed sophisticated methods for assessing health using minimally-invasive methods, at a disciplinary level, we have room for conceptual and methodological improvement in how we frame, measure, and analyze the social inequities that might shape health inequities. This toolkit paper elaborates on some steps human biologists should take to enhance the quality of our research on health inequities. Specifically, we address: (1) how to frame unequal health outcomes (i.e., inequalities vs. disparities vs. inequities) and the importance of identifying our conceptual models of how these inequities emerge; (2) how to measure various axes of social inequities across diverse cultural contexts, and (3) approaches to community collaboration and dissemination. We end by discussing (4) future directions in human biology research of health inequities, including understanding the ultimate causes of sensitivity to social inequities and transitioning from research to action.
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Affiliation(s)
- Zaneta Thayer
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, USA
| | - Glorieuse Uwizeye
- Arthur Labatt School of Nursing, University of Western Ontario, London, Ontario, Canada
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10
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Mauro M, Allen DS, Dauda B, Molina SJ, Neale BM, Lewis AC. A scoping review of guidelines for the use of race, ethnicity, and ancestry reveals widespread consensus but also points of ongoing disagreement. Am J Hum Genet 2022; 109:2110-2125. [PMID: 36400022 PMCID: PMC9808506 DOI: 10.1016/j.ajhg.2022.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The use of population descriptors such as race, ethnicity, and ancestry in science, medicine, and public health has a long, complicated, and at times dark history, particularly for genetics, given the field's perceived importance for understanding between-group differences. The historical and potential harms that come with irresponsible use of these categories suggests a clear need for definitive guidance about when and how they can be used appropriately. However, while many prior authors have provided such guidance, no established consensus exists, and the extant literature has not been examined for implied consensus and sources of disagreement. Here, we present the results of a scoping review of published normative recommendations regarding the use of population categories, particularly in genetics research. Following PRISMA guidelines, we extracted recommendations from n = 121 articles matching inclusion criteria. Articles were published consistently throughout the time period examined and in a broad range of journals, demonstrating an ongoing and interdisciplinary perceived need for guidance. Examined recommendations fall under one of eight themes identified during analysis. Seven are characterized by broad agreement across articles; one, "appropriate definitions of population categories and contexts for use," revealed substantial fundamental disagreement among articles. Additionally, while many articles focus on the inappropriate use of race, none fundamentally problematize ancestry. This work can be a resource to researchers looking for normative guidance on the use of population descriptors and can orient authors of future guidelines to this complex field, thereby contributing to the development of more effective future guidelines for genetics research.
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Affiliation(s)
- Madelyn Mauro
- Edmond J. Safra Center for Ethics, Harvard University, Cambridge, MA, USA
| | - Danielle S. Allen
- Edmond J. Safra Center for Ethics, Harvard University, Cambridge, MA, USA
| | - Bege Dauda
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA,Institute of Clinical Bioethics, Saint Joseph’s University, Philadelphia, PA, USA
| | | | - Benjamin M. Neale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna C.F. Lewis
- Edmond J. Safra Center for Ethics, Harvard University, Cambridge, MA, USA,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA,Corresponding author
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11
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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12
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White JA, Kaninjing ET, Adeniji KA, Jibrin P, Obafunwa JO, Ogo CN, Mohammed F, Popoola A, Fatiregun OA, Oluwole OP, Karanam B, Elhussin I, Ambs S, Tang W, Davis M, Polak P, Campbell MJ, Brignole KR, Rotimi SO, Dean-Colomb W, Odedina FT, Martin DN, Yates C. Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry. CANCER RESEARCH COMMUNICATIONS 2022; 2:1005-1016. [PMID: 36922933 PMCID: PMC10010347 DOI: 10.1158/2767-9764.crc-22-0136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022]
Abstract
In this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer tumors and 11 unmatched nontumor tissues to compare genomic mutations with African American (AA) and European American (EA) The Cancer Genome Atlas (TCGA) prostate cancer. NG samples were collected from six sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG nontumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (P ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene-level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T>C), BRCA1 showed an increasing mutation frequency as African ancestry increased. BRCA2_rs11571831 was present only in MAA, and BRCA2_rs766173 was elevated in NG men. A total of 133 somatic variants were present in 26 prostate cancer-associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies >10%. Compared with TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥0.734) with Catalogue of Somatic Mutations in Cancer signatures 5 and 6, and mutated genes showed significant (q < 0.001) gene ontology (GO) and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that mutations in DNA damage response genes were higher in NG prostate cancer samples and that a portion of those mutations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG prostate cancer exome to date and highlight the need to increase diversity of study populations. Significance MAA have higher rates of prostate cancer incidence and mortality, however, are severely underrepresented in genomic studies. This is the first study utilizing whole-exome sequencing in NG men to identify West African ancestry-linked variant patterns that impact DNA damage repair pathways.
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Affiliation(s)
- Jason A White
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
| | | | | | | | - John O Obafunwa
- Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | | | | | | | | | | | - Isra Elhussin
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Melissa Davis
- Department of Surgery, New York Presbyterian - Weill Cornell Medicine, New York, New York
| | | | - Moray J Campbell
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | | | | | - Windy Dean-Colomb
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama.,Piedmont Medical Oncology - Newnan, Newnan, Georgia
| | - Folake T Odedina
- Center for Health Equity and Community Engagement Research, Mayo Clinic, Jacksonville, Florida
| | - Damali N Martin
- Division of Cancer Control and Population Sciences, NCI, Rockville, Maryland
| | - Clayton Yates
- Tuskegee University, Center for Cancer Research, Tuskegee, Alabama
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13
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Relative impact of genetic ancestry and neighborhood socioeconomic status on all-cause mortality in self-identified African Americans. PLoS One 2022; 17:e0273735. [PMID: 36037186 PMCID: PMC9423617 DOI: 10.1371/journal.pone.0273735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Self-identified race/ethnicity is a correlate of both genetic ancestry and socioeconomic factors, both of which may contribute to racial disparities in mortality. Investigators often hold a priori assumptions, rarely made explicit, regarding the relative importance of these factors. We studied 2,239 self-identified African Americans (SIAA) from the Prostate, Lung, Colorectal and Ovarian screening trial enrolled from 1993–1998 and followed prospectively until 2019 or until death, whichever came first. Percent African genetic ancestry was estimated using the GRAF-Pop distance-based method. A neighborhood socioeconomic status (nSES) index was estimated using census tract measures of income, housing, and employment and linked to participant residence in 2012. We used Directed Acyclic Graphs (DAGs) to represent causal models favoring (1) biomedical and (2) social causes of mortality. Hazard ratios were estimated using Cox models adjusted for sociodemographic, behavioral, and neighborhood covariates guided by each DAG. 901 deaths occurred over 40,767 person-years of follow-up. In unadjusted (biomedical) models, a 10% increase in percent African ancestry was associated with a 7% higher rate of all-cause mortality (HR: 1.07, 95% CI: 1.02, 1.12). This effect was attenuated in covariate adjusted (social) models (aHR: 1.01, 95% CI: 0.96, 1.06). Mortality was lower comparing participants in the highest to lowest nSES quintile following adjustment for covariates and ancestry (aHR: 0.74, 95% CI: 0.57, 0.98, Ptrend = 0.017). Higher African ancestry and lower nSES were associated with higher mortality, but African ancestry was not associated with mortality following covariate adjustment. Socioeconomic factors may be more important drivers of mortality in African Americans.
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14
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Ahmad S, Ashktorab H, Brim H, Housseau F. Inflammation, microbiome and colorectal cancer disparity in African-Americans: Are there bugs in the genetics? World J Gastroenterol 2022; 28:2782-2801. [PMID: 35978869 PMCID: PMC9280725 DOI: 10.3748/wjg.v28.i25.2782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/27/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Dysregulated interactions between host inflammation and gut microbiota over the course of life increase the risk of colorectal cancer (CRC). While environmental factors and socio-economic realities of race remain predominant contributors to CRC disparities in African-Americans (AAs), this review focuses on the biological mediators of CRC disparity, namely the under-appreciated influence of inherited ancestral genetic regulation on mucosal innate immunity and its interaction with the microbiome. There remains a poor understanding of mechanisms linking immune-related genetic polymorphisms and microbiome diversity that could influence chronic inflammation and exacerbate CRC disparities in AAs. A better understanding of the relationship between host genetics, bacteria, and CRC pathogenesis will improve the prediction of cancer risk across race/ethnicity groups overall.
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Affiliation(s)
- Sami Ahmad
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, DC 20060, United States
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC 20060, United States
| | - Franck Housseau
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
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15
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Rujchanarong D, Scott D, Park Y, Brown S, Mehta AS, Drake R, Sandusky GE, Nakshatri H, Angel PM. Metabolic Links to Socioeconomic Stresses Uniquely Affecting Ancestry in Normal Breast Tissue at Risk for Breast Cancer. Front Oncol 2022; 12:876651. [PMID: 35832545 PMCID: PMC9273232 DOI: 10.3389/fonc.2022.876651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
A primary difference between black women (BW) and white women (WW) diagnosed with breast cancer is aggressiveness of the tumor. Black women have higher mortalities with similar incidence of breast cancer compared to other race/ethnicities, and they are diagnosed at a younger age with more advanced tumors with double the rate of lethal, triple negative breast cancers. One hypothesis is that chronic social and economic stressors result in ancestry-dependent molecular responses that create a tumor permissive tissue microenvironment in normal breast tissue. Altered regulation of N-glycosylation of proteins, a glucose metabolism-linked post-translational modification attached to an asparagine (N) residue, has been associated with two strong independent risk factors for breast cancer: increased breast density and body mass index (BMI). Interestingly, high body mass index (BMI) levels have been reported to associate with increases of cancer-associated N-glycan signatures. In this study, we used matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) to investigate molecular pattern changes of N-glycosylation in ancestry defined normal breast tissue from BW and WW with significant 5-year risk of breast cancer by Gail score. N-glycosylation was tested against social stressors including marital status, single, education, economic status (income), personal reproductive history, the risk factors BMI and age. Normal breast tissue microarrays from the Susan G. Komen tissue bank (BW=43; WW= 43) were used to evaluate glycosylation against socioeconomic stress and risk factors. One specific N-glycan (2158 m/z) appeared dependent on ancestry with high sensitivity and specificity (AUC 0.77, Brown/Wilson p-value<0.0001). Application of a linear regression model with ancestry as group variable and socioeconomic covariates as predictors identified a specific N-glycan signature associated with different socioeconomic stresses. For WW, household income was strongly associated to certain N-glycans, while for BW, marital status (married and single) was strongly associated with the same N-glycan signature. Current work focuses on understanding if combined N-glycan biosignatures can further help understand normal breast tissue at risk. This study lays the foundation for understanding the complexities linking socioeconomic stresses and molecular factors to their role in ancestry dependent breast cancer risk.
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Affiliation(s)
- Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Danielle Scott
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sean Brown
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Richard Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - George E. Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
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16
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Marzinke MA, Greene DN, Bossuyt PM, Chambliss AB, Cirrincione LR, McCudden CR, Melanson SEF, Noguez JH, Patel K, Radix AE, Takwoingi Y, Winston-McPherson G, Young BA, Hoenig MP. Limited Evidence for Use of a Black Race Modifier in eGFR Calculations: A Systematic Review. Clin Chem 2021; 68:521-533. [DOI: 10.1093/clinchem/hvab279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Commonly used estimated glomerular filtration rate (eGFR) equations include a Black race modifier (BRM) that was incorporated during equation derivation. Race is a social construct, and a poorly characterized variable that is applied inconsistently in clinical settings. The BRM results in higher eGFR for any creatinine concentration, implying fundamental differences in creatinine production or excretion in Black individuals compared to other populations. Equations without inclusion of the BRM have the potential to detect kidney disease earlier in patients at the greatest risk of chronic kidney disease (CKD), but also has the potential to over-diagnose CKD or impact downstream clinical interventions. The purpose of this study was to use an evidence- based approach to systematically evaluate the literature relevant to the performance of the eGFR equations with and without the BRM and to examine the clinical impact of the use or removal.
Content
PubMed and Embase databases were searched for studies comparing measured GFR to eGFR in racially diverse adult populations using the Modification of Diet in Renal Disease or the 2009-Chronic Kidney Disease Epidemiology Collaboration-creatinine equations based on standardized creatinine measurements. Additionally, we searched for studies comparing clinical use of eGFR calculated with and without the BRM. 8,632 unique publications were identified; an additional 3 studies were added post-hoc. In total, 96 studies were subjected to further analysis and 44 studies were used to make a final assessment.
Summary
There is limited published evidence to support the use of a BRM in eGFR equations.
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Affiliation(s)
- Mark A Marzinke
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dina N Greene
- Department of Laboratory Medicine and Pathology; University of Washington, Seattle, WA; Kaiser Permanente, Renton, WA
| | - Patrick M Bossuyt
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | | | - Christopher R McCudden
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital; University of Ottawa; Eastern Ontario Regional Laboratory Association, Ottawa, Ontario, Canada
| | - Stacy E F Melanson
- Department of Pathology; Brigham and Women’s Hospital; Harvard Medical School, Boston, MA
| | - Jaime H Noguez
- Department of Pathology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Khushbu Patel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Asa E Radix
- Callen-Lorde Community Health Center, New York, NY
| | - Yemisi Takwoingi
- Institute of Applied Health Research,University of Birmingham and NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, United Kingdom
| | | | - Bessie A Young
- Office of Healthcare Equity, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
| | - Melanie P Hoenig
- Renal Division, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA
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17
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Barroso I. The importance of increasing population diversity in genetic studies of type 2 diabetes and related glycaemic traits. Diabetologia 2021; 64:2653-2664. [PMID: 34595549 PMCID: PMC8563561 DOI: 10.1007/s00125-021-05575-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/07/2021] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes has a global prevalence, with epidemiological data suggesting that some populations have a higher risk of developing this disease. However, to date, most genetic studies of type 2 diabetes and related glycaemic traits have been performed in individuals of European ancestry. The same is true for most other complex diseases, largely due to use of 'convenience samples'. Rapid genotyping of large population cohorts and case-control studies from existing collections was performed when the genome-wide association study (GWAS) 'revolution' began, back in 2005. Although global representation has increased in the intervening 15 years, further expansion and inclusion of diverse populations in genetic and genomic studies is still needed. In this review, I discuss the progress made in incorporating multi-ancestry participants in genetic analyses of type 2 diabetes and related glycaemic traits, and associated opportunities and challenges. I also discuss how increased representation of global diversity in genetic and genomic studies is required to fulfil the promise of precision medicine for all.
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Affiliation(s)
- Inês Barroso
- Exeter Centre of Excellence for Diabetes research (EXCEED), University of Exeter Medical School, Exeter, UK.
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18
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Johnson JR, Kittles RA. Genetic ancestry and racial differences in prostate tumours. Nat Rev Urol 2021; 19:133-134. [PMID: 34815564 DOI: 10.1038/s41585-021-00544-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jabril R Johnson
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Rick A Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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19
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Johnson JR, Woods-Burnham L, Hooker SE, Batai K, Kittles RA. Genetic Contributions to Prostate Cancer Disparities in Men of West African Descent. Front Oncol 2021; 11:770500. [PMID: 34820334 PMCID: PMC8606679 DOI: 10.3389/fonc.2021.770500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) is the second most frequently diagnosed malignancy and the second leading cause of death in men worldwide, after adjusting for age. According to the International Agency for Research on Cancer, continents such as North America and Europe report higher incidence of PCa; however, mortality rates are highest among men of African ancestry in the western, southern, and central regions of Africa and the Caribbean. The American Cancer Society reports, African Americans (AAs), in the United States, have a 1.7 increased incidence and 2.4 times higher mortality rate, compared to European American's (EAs). Hence, early population history in west Africa and the subsequent African Diaspora may play an important role in understanding the global disproportionate burden of PCa shared among Africans and other men of African descent. Nonetheless, disparities involved in diagnosis, treatment, and survival of PCa patients has also been correlated to socioeconomic status, education and access to healthcare. Although recent studies suggest equal PCa treatments yield equal outcomes among patients, data illuminates an unsettling reality of disparities in treatment and care in both, developed and developing countries, especially for men of African descent. Yet, even after adjusting for the effects of the aforementioned factors; racial disparities in mortality rates remain significant. This suggests that molecular and genomic factors may account for much of PCa disparities.
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Affiliation(s)
- Jabril R. Johnson
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Leanne Woods-Burnham
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Stanley E. Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Ken Batai
- Department of Urology, University of Arizona, Tucson, AZ, United States
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
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20
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McKenna B, Mekawi Y, Katrinli S, Carter S, Stevens JS, Powers A, Smith AK, Michopoulos V. When Anger Remains Unspoken: Anger and Accelerated Epigenetic Aging Among Stress-Exposed Black Americans. Psychosom Med 2021; 83:949-958. [PMID: 34747582 PMCID: PMC8580214 DOI: 10.1097/psy.0000000000001007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Race-related lifetime stress exposure (LSE) including racial discrimination, trauma, and stressful life events have been shown to contribute to racial health disparities. However, little is known about associations between race-related stressors and premature biological aging that confer the risk of adverse health outcomes. Even less is known about the mechanisms through which race-related stressors may be associated with accelerated aging. Early evidence suggests psychological processes such as anger, and particularly the internalization of anger, may play a role. METHODS In a community sample of predominantly low-income Black adults (n = 219; age = 45.91 [12.33] years; 64% female), the present study examined the association of race-related LSE (as defined by exposure to racial discrimination, trauma, and stressful life events) and epigenetic age acceleration through anger expression. RESULTS Internalized and externalized anger expression were each significantly associated with LSE and age acceleration. Although LSE was not directly associated with age acceleration (ΔR2 = 0.001, p = .64), we found that greater LSE was indirectly associated with age acceleration through increases in internalized, but not externalized, anger (indirect effect: β = 0.03, standard error = 0.02, 95% confidence interval = 0.003 to 0.08; total effect: β = 0.02, 95% confidence interval = -0.25 to 0.31). CONCLUSIONS These results suggest race-related LSE may elicit the internalization of anger, which, along with the externalization of anger, may initiate detrimental epigenetic alterations that confer the risk of adverse health outcomes. These findings lay the groundwork for longitudinal studies of the association between race-related stress and racial health disparities.
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Affiliation(s)
| | - Yara Mekawi
- Department of Psychiatry and Behavioral Sciences, Emory School of Medicine, Atlanta, GA
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA
| | - Sierra Carter
- Department of Psychology, Georgia State University, Atlanta, GA
| | - Jennifer S. Stevens
- Department of Psychiatry and Behavioral Sciences, Emory School of Medicine, Atlanta, GA
| | - Abigail Powers
- Department of Psychiatry and Behavioral Sciences, Emory School of Medicine, Atlanta, GA
| | - Alicia K. Smith
- Department of Psychiatry and Behavioral Sciences, Emory School of Medicine, Atlanta, GA
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory School of Medicine, Atlanta, GA
- Yerkes National Primate Research Center, Atlanta, GA
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21
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Kaufman JS, Merckx J, Cooper RS. Use of Racial and Ethnic Categories in Medical Testing and Diagnosis: Primum Non Nocere. Clin Chem 2021; 67:1456-1465. [PMID: 34557889 DOI: 10.1093/clinchem/hvab164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Use of race and ethnicity is common in medical tests and procedures, even though these categories are defined by sociological, historical, and political processes, and vary considerably in their definitions over time and place. Because all societies organize themselves around these constructs in some way, they are undeniable facets of the human experience, with myriad health consequences. In the biomedical literature, they are also commonly interpreted as representing biological heterogeneity that is relevant for health and disease. CONTENT We review the use of race and ethnicity in medical practice, especially in the USA, and provide 2 specific examples to represent a large number of similar instances. We then critique these uses along a number of different dimensions, including limitations in measurement, within- versus between-group variance, and implications for informativeness of risk markers for individuals, generalization from arbitrary or nonrepresentative samples, perpetuation of myths and stereotypes, instability in time and place, crowding out of more relevant risk markers, stigmatization, and the tainting of medicine with the history of oppression. We conclude with recommendations to improve practice that are technical, ethical, and pragmatic. SUMMARY Medicine has evolved from a mystical healing art to a mature science of human health through a rigorous process of quantification, experimentation, and evaluation. Folkloric traditions, such as race- and ethnic-specific medicine will fade from use as we become increasingly critical of outdated and irrational clinical practices and replace these with personalized, evidenced-based tests, algorithms, and procedures that privilege patients' individual humanity over obsolete and misleading labels.
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Font-Porterias N, Giménez A, Carballo-Mesa A, Calafell F, Comas D. Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants. Front Genet 2021; 12:683880. [PMID: 34220960 PMCID: PMC8244592 DOI: 10.3389/fgene.2021.683880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/13/2021] [Indexed: 01/04/2023] Open
Abstract
Genetic patterns of inter-population variation are a result of different demographic and adaptive histories, which gradually shape the frequency distribution of the variants. However, the study of clinically relevant mutations has a Eurocentric bias. The Romani, the largest transnational minority ethnic group in Europe, originated in South Asia and received extensive gene flow from West Eurasia. Most medical genetic studies have only explored founder mutations related to Mendelian disorders in this population. Here we analyze exome sequences and genome-wide array data of 89 healthy Spanish Roma individuals to study complex traits and disease. We apply a different framework and focus on variants with both increased and decreased allele frequencies, taking into account their local ancestry. We report several OMIM traits enriched for genes with deleterious variants showing increased frequencies in Roma or in non-Roma (e.g., obesity is enriched in Roma, with an associated variant linked to South Asian ancestry; while non-insulin dependent diabetes is enriched in non-Roma Europeans). In addition, previously reported pathogenic variants also show differences among populations, where some variants segregating at low frequency in non-Roma are virtually absent in the Roma. Lastly, we describe frequency changes in drug-response variation, where many of the variants increased in Roma are clinically associated with metabolic and cardiovascular-related drugs. These results suggest that clinically relevant variation in Roma cannot only be characterized in terms of founder mutations. Instead, we observe frequency differences compared to non-Roma: some variants are absent, while other have drifted to higher frequencies. As a result of the admixture events, these clinically damaging variants can be traced back to both European and South Asian-related ancestries. This can be attributed to a different prevalence of some genetic disorders or to the fact that genetic susceptibility variants are mostly studied in populations of European descent, and can differ in individuals with different ancestries.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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Batai K, Hooker S, Kittles RA. Leveraging genetic ancestry to study health disparities. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:363-375. [PMID: 32935870 PMCID: PMC8246846 DOI: 10.1002/ajpa.24144] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/22/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
Research to understand human genomic variation and its implications in health has great potential to contribute in the reduction of health disparities. Biological anthropology can play important roles in genomics and health disparities research using a biocultural approach. This paper argues that racial/ethnic categories should not be used as a surrogate for sociocultural factors or global genomic clusters in biomedical research or clinical settings, because of the high genetic heterogeneity that exists within traditional racial/ethnic groups. Genetic ancestry is used to show variation in ancestral genomic contributions to recently admixed populations in the United States, such as African Americans and Hispanic/Latino Americans. Genetic ancestry estimates are also used to examine the relationship between ancestry-related biological and sociocultural factors affecting health disparities. To localize areas of genomes that contribute to health disparities, admixture mapping and genome-wide association studies (GWAS) are often used. Recent GWAS have identified many genetic variants that are highly differentiated among human populations that are associated with disease risk. Some of these are population-specific variants. Many of these variants may impact disease risk and help explain a portion of the difference in disease burden among racial/ethnic groups. Genetic ancestry is also of particular interest in precision medicine and disparities in drug efficacy and outcomes. By using genetic ancestry, we can learn about potential biological differences that may contribute to the heterogeneity observed across self-reported racial groups.
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Affiliation(s)
- Ken Batai
- Department of UrologyUniversity of ArizonaTucsonArizonaUSA
| | - Stanley Hooker
- Division of Health Equities, Department of Population SciencesCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Rick A. Kittles
- Division of Health Equities, Department of Population SciencesCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
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24
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Pobiner B. HUMAN EVOLUTION, THEN AND NOW. Evolution 2021; 75:1587-1590. [PMID: 37139929 DOI: 10.1111/evo.14236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Briana Pobiner
- Department of Anthropology Smithsonian Institution 10th Street & Constitution Avenue, NW, MRC 112 Washington DC 20013
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25
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Winston-McPherson GN, Mathias PC, Lockwood CM, Greene DN. Evaluation of Patient Demographics in Clinical Cancer Genomic Testing. J Appl Lab Med 2021; 6:119-124. [PMID: 33398333 DOI: 10.1093/jalm/jfaa219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/20/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Inequitable use of next-generation sequencing (NGS) testing for cancer risk and treatment can contribute to heath disparity. Consequently, it is important to assess the population receiving this testing. In this article, we characterize the population receiving both germline and somatic NGS testing for cancer predisposition and precision oncology at the Genetics and Solid Tumors Laboratory of the University of Washington Medical Center. METHODS The general demographics, including ancestry, of patients receiving somatic testing to identify genes related to cancer treatment or prognosis, diagnosis, or germline testing for heritable cancer risk from January 2015 to July 2017 were characterized. Ancestry was determined using single nucleotide variant data and documented pedigree. The demographics of the patient population receiving testing were compared with a reference population comprising patients receiving care from the University of Washington Medical Center with a diagnosis of malignant neoplasm of breast, ovary, colon, rectum, or prostate between January 2015 and May 2018. RESULTS A total of 2210 unique patients were included in this study. Women composed 66% of our total tested population. Patients of European ancestry composed 78% of the tested cohort. The percentages of American Indian/Alaskan Native and Native Hawaiian/Other Pacific Islander in the cohort receiving NGS testing were significantly different than their respective distributions in the reference cohort. CONCLUSIONS Characterizing the demographics of patients receiving NGS testing for cancer predisposition and precision oncology using single nucleotide variant data and documented pedigree may help identify potential health disparities.
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Affiliation(s)
| | - Patrick C Mathias
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Dina N Greene
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
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Woods-Burnham L, Johnson JR, Hooker SE, Bedell FW, Dorff TB, Kittles RA. The Role of Diverse Populations in US Clinical Trials. MED 2021; 2:21-24. [DOI: 10.1016/j.medj.2020.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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