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Baynam G, Baker S, Steward C, Summar M, Halley M, Pariser A. Increasing Diversity, Equity, Inclusion, and Accessibility in Rare Disease Clinical Trials. Pharmaceut Med 2024:10.1007/s40290-024-00529-8. [PMID: 38977611 DOI: 10.1007/s40290-024-00529-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Diversity, equity, inclusion, and accessibility (DEIA) are foundational principles for clinical trials and medical research. In rare diseases clinical research, where numbers of participants are already challenged by rarity itself, maximizing inclusion is of particular importance to clinical trial success, as well as ensuring the generalizability and relevance of the trial results to the people affected by these diseases. In this article, we review the medical and gray literature and cite case examples to provide insights into how DEIA can be proactively integrated into rare diseases clinical research. Here, we particularly focus on genetic diversity. While the rare diseases DEIA literature is nascent, it is accelerating as many patient advocacy groups, professional societies, training and educational organizations, researcher groups, and funders are setting intentional strategies to attain DEIA goals moving forward, and to establish metrics to ensure continued improvement. Successful examples in underserved and underrepresented populations are available that can serve as case studies upon which rare diseases clinical research programs can be built. Rare diseases have historically been innovation drivers in basic, translational, and clinical research, and ultimately, all populations benefit from data diversity in rare diseases populations that deliver novel insights and approaches to how clinical research can be performed.
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Affiliation(s)
- Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, Perth, WA, Australia
| | - Simeón Baker
- Genomics England, London, UK
- HealthWeb Solutions, London, UK
- School of Health Studies, University of Western Ontario, London, ON, Canada
| | | | | | - Meghan Halley
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
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Wu M, Davis JD, Zhao C, Daley T, Oliver KE. Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment. J Clin Transl Endocrinol 2024; 36:100344. [PMID: 38765466 PMCID: PMC11099334 DOI: 10.1016/j.jcte.2024.100344] [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: 12/14/2023] [Revised: 02/21/2024] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Cystic fibrosis (CF) has been traditionally viewed as a disease that affects White individuals. However, CF occurs among all races, ethnicities, and geographic ancestries. The disorder results from mutations in the CF transmembrane conductance regulator (CFTR). Varying incidence of CF is reported among Black, Indigenous, and People of Color (BIPOC), who typically exhibit worse clinical outcomes. These populations are more likely to carry rare CFTR variants omitted from newborn screening panels, leading to disparities in care such as delayed diagnosis and treatment. In this study, we present a case-in-point describing an individual of Gambian descent identified with CF. Patient genotype includes a premature termination codon (PTC) (c.2353C>T) and previously undescribed single nucleotide deletion (c.1970delG), arguing against effectiveness of currently available CFTR modulator-based interventions. Strategies for overcoming these two variants will likely include combinations of PTC suppressors, nonsense mediated decay inhibitors, and/or alternative approaches (e.g. gene therapy). Investigations such as the present study establish a foundation from which therapeutic treatments may be developed. Importantly, c.2353C>T and c.1970delG were not detected in the patient by traditional CFTR screening panels, which include an implicit racial and ethnic diagnostic bias as these tests are comprised of mutations largely observed in people of European ancestry. We suggest that next-generation sequencing of CFTR should be utilized to confirm or exclude a CF diagnosis, in order to equitably serve BIPOC individuals. Additional epidemiologic data, basic science investigations, and translational work are imperative for improving understanding of disease prevalence and progression, CFTR variant frequency, genotype-phenotype correlation, pharmacologic responsiveness, and personalized medicine approaches for patients with African ancestry and other historically understudied geographic lineages.
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Affiliation(s)
- Malinda Wu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Jacob D. Davis
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Conan Zhao
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tanicia Daley
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Pediatric Institute, Children’s Healthcare of Atlanta, Atlanta, GA, USA
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3
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Ideozu JE, Liu M, Riley-Gillis BM, Paladugu SR, Rahimov F, Krishnan P, Tripathi R, Dorr P, Levy H, Singh A, Waring JF, Vasanthakumar A. Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences. Genome Med 2024; 16:43. [PMID: 38515211 PMCID: PMC10956269 DOI: 10.1186/s13073-024-01316-5] [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: 08/11/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF. METHODS We analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes. RESULTS We detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05]. CONCLUSIONS We leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.
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Affiliation(s)
- Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA.
| | - Mengzhen Liu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | - Sri R Paladugu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | - Fedik Rahimov
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | | | | | - Hara Levy
- Department of Pediatrics, Division of Pulmonology and Sleep Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Jeffrey F Waring
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
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El Makhzen N, Daimi H, Bouguenouch L, Abriel H. The burden of cystic fibrosis in North Africa. Front Genet 2024; 14:1295008. [PMID: 38269366 PMCID: PMC10806102 DOI: 10.3389/fgene.2023.1295008] [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: 09/15/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Background: Over 200 pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are associated with cystic fibrosis (CF)-the most prevalent autosomal recessive disease globally, the p.Phe508del variant being the most commonly observed. Main text: Recent epidemiological studies suggest a higher global prevalence of CF than previously thought. Nevertheless, comprehensive CF data remains extremely scarce among African populations, contributing to a significant information gap within the African healthcare system. Consequently, the underestimation of CF among children from African populations is likely. The goal of this article is to review the pathogenesis of CF and its prevalence in the countries of North Africa. Conclusion: The prevalence of CF in North African countries is likely underestimated due to the complexity of the disease and the lack of a timely, proper clinical and genetic investigation that allows the early identification of CF patients and thus facilitates therapeutic recommendations. Therefore, specific genetic and epidemiological studies on African individuals showing CF symptoms should be conducted to enhance the diagnostic yield of CF in Africa.
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Affiliation(s)
- Nada El Makhzen
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Houria Daimi
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Department of Biology, Faculty of Sciences, University of Gabes, Gabès, Tunisia
| | - Laila Bouguenouch
- Laboratory of Medical Genetics and Oncogenetics, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hugues Abriel
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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Joynt AT, Kavanagh EW, Newby GA, Mitchell S, Eastman AC, Paul KC, Bowling AD, Osorio DL, Merlo CA, Patel SU, Raraigh KS, Liu DR, Sharma N, Cutting GR. Protospacer modification improves base editing of a canonical splice site variant and recovery of CFTR function in human airway epithelial cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:335-350. [PMID: 37547293 PMCID: PMC10400809 DOI: 10.1016/j.omtn.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 06/26/2023] [Indexed: 08/08/2023]
Abstract
Canonical splice site variants affecting the 5' GT and 3' AG nucleotides of introns result in severe missplicing and account for about 10% of disease-causing genomic alterations. Treatment of such variants has proven challenging due to the unstable mRNA or protein isoforms that typically result from disruption of these sites. Here, we investigate CRISPR-Cas9-mediated adenine base editing for such variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We validate a CFTR expression minigene (EMG) system for testing base editing designs for two different targets. We then use the EMG system to test non-standard single-guide RNAs with either shortened or lengthened protospacers to correct the most common cystic fibrosis-causing variant in individuals of African descent (c.2988+1G>A). Varying the spacer region length allowed placement of the editing window in a more efficient context and enabled use of alternate protospacer adjacent motifs. Using these modifications, we restored clinically significant levels of CFTR function to human airway epithelial cells from two donors bearing the c.2988+1G>A variant.
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Affiliation(s)
- Anya T. Joynt
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Erin W. Kavanagh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Shakela Mitchell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Alice C. Eastman
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Kathleen C. Paul
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Alyssa D. Bowling
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Derek L. Osorio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Karen S. Raraigh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Neeraj Sharma
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Garry R. Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
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6
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Zampoli M, Morrow BM, Paul G. Real-world disparities and ethical considerations with access to CFTR modulator drugs: Mind the gap! Front Pharmacol 2023; 14:1163391. [PMID: 37050905 PMCID: PMC10083423 DOI: 10.3389/fphar.2023.1163391] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The third Sustainable Development Goal (SDG), to ensure healthy lives and promote well-being for all at all ages, has particular relevance and implementation challenges amongst people living with rare diseases such as cystic fibrosis (CF). Although the treatment and projected outcome of CF has significantly improved with the advent of CF transmembrane conductance regulator protein modulator (CFTRm) therapy, there remains significant global inequality with regards to access to these life-saving and life-altering drugs. Elexacaftor, tezacaftor, and ivacaftor (ETI) triple combination therapy, first licensed in the United States in 2019, has rapidly become the standard of care for children aged 6 years and older in most high-income countries for individuals with CFTR variants responsive to ETI. Negotiated agreements for access to ETI are currently in place in North America,Europe, Israel ,Australia and New Zealand. However, less priority has been given to negotiate agreements for access to CFTRm in low-middle income countries(LMIC) with significant CF populations such as Central and South America, India, the Middle East, and Southern Africa. These countries and individuals living with CF are therefore effectively being left behind, in direct conflict with the stated principle of the 2030 SDGs. In this review, we highlight the current global inequity in access to CFTRm drugs and its impact on widening disparities between high-income countries and LMIC in CF outcomes and survival. We further discuss the reasons for this inequity and explore the ethical- and human rights-based principles and dilemmas that clinicians, families, governments, and healthcare funders must consider when prioritizing fair and affordable access to expensive CFTRm drugs. Lastly, we propose possible solutions to overcoming the barriers to accessing affordable CFTRm drugs in LMIC and illustrate with examples how access to drug therapies for other conditions have been successfully negotiated in LMIC through innovative partnerships between governments and pharmaceutical industries.
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Affiliation(s)
- M. Zampoli
- Department of Paediatrics and Child Health and Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa
- *Correspondence: M. Zampoli,
| | - B. M Morrow
- Department of Paediatrics and Child Health and Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa
| | - G Paul
- Division of Pulmonary Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
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de Azevedo LVF, Cruz FCRM, Martins JP, Marson FAL. Cystic Fibrosis: A Descriptive Analysis of Deaths in a Two-Decade Period in Brazil According to Age, Race, and Sex. Diagnostics (Basel) 2023; 13:diagnostics13040763. [PMID: 36832251 PMCID: PMC9954801 DOI: 10.3390/diagnostics13040763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/24/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
The diagnosis of cystic fibrosis has improved in the last few years due to greater access to diagnostic tools and the evolution of molecular biology; the knowledge obtained has contributed to the understanding of its death profile. In this context, an epidemiological study was developed focusing on deaths from cystic fibrosis in Brazil from 1996 to 2019. The data were collected from the Data-SUS (Unified National Health System Information Technology Department from Brazil). The epidemiological analysis included patients' age groups, racial groups, and sex. In our data, between 1996 and 2019, Σ3050 deaths were recorded, totaling a ≅330% increase in the number of deaths resulting from cystic fibrosis. This fact might be related to a better diagnosis of the disease, mainly in patients from racial groups that are not commonly associated with cystic fibrosis, such as Black individuals, Hispanic or Latino (mixed individuals/Pardos) individuals, and American Indians (Indigenous peoples from Brazil). Regarding of race, the Σ of deaths was: nine (0.3%) in the American Indian group, 12 (0.4%) in the Asian group, 99 (3.6%) in the Black or African American group, 787 (28.6%) in the Hispanic or Latino group, and 1843 (67.0%) in the White group. The White group showed the highest prevalence of deaths, and the increase in mortality was ≅150 times in this group, while, in the Hispanic or Latino group, it was ≅75 times. Regarding sex, the numbers and percentage of deaths of both male (N = 1492; 48.9%) and female (N = 1557; 51.1%) patients were seen to be relatively close. As for age groups, the >60-year-old group presented the most significant results, with an increase of ≅60 times in the registered deaths. In conclusion, in Brazil, despite the number of deaths from cystic fibrosis being prevalent in the White group, it increased in all racial groups (Hispanic or Latino, Black or African American, American Indian, or Asian individuals) and was associated with older age.
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Zacarias S, Batista MSP, Ramalho SS, Victor BL, Farinha CM. Rescue of Rare CFTR Trafficking Mutants Highlights a Structural Location-Dependent Pattern for Correction. Int J Mol Sci 2023; 24:ijms24043211. [PMID: 36834620 PMCID: PMC9961391 DOI: 10.3390/ijms24043211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) channel. Currently, more than 2100 variants have been identified in the gene, with a large number being very rare. The approval of modulators that act on mutant CFTR protein, correcting its molecular defect and thus alleviating the burden of the disease, revolutionized the field of CF. However, these drugs do not apply to all patients with CF, especially those with rare mutations-for which there is a lack of knowledge on the molecular mechanisms of the disease and the response to modulators. In this work, we evaluated the impact of several rare putative class II mutations on the expression, processing, and response of CFTR to modulators. Novel cell models consisting of bronchial epithelial cell lines expressing CFTR with 14 rare variants were created. The variants studied are localized at Transmembrane Domain 1 (TMD1) or very close to the signature motif of Nucleotide Binding Domain 1 (NBD1). Our data show that all mutations analyzed significantly decrease CFTR processing and while TMD1 mutations respond to modulators, those localized in NBD1 do not. Molecular modeling calculations confirm that the mutations in NBD1 induce greater destabilization of CFTR structure than those in TMD1. Furthermore, the structural proximity of TMD1 mutants to the reported binding site of CFTR modulators such as VX-809 and VX-661, make them more efficient in stabilizing the CFTR mutants analyzed. Overall, our data suggest a pattern for mutation location and impact in response to modulators that correlates with the global effect of the mutations on CFTR structure.
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9
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Gombault C, Grenet G, Segurel L, Duret L, Gueyffier F, Cathébras P, Pontier D, Mainbourg S, Sanchez-Mazas A, Lega JC. Population designations in biomedical research: Limitations and perspectives. HLA 2023; 101:3-15. [PMID: 36258305 PMCID: PMC10099491 DOI: 10.1111/tan.14852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Abstract
In biomedical research, population differences are of central interest. Variations in the frequency and severity of diseases and in treatment effects among human subpopulation groups are common in many medical conditions. Unfortunately, the practices in terms of subpopulation labeling do not exhibit the level of rigor one would expect in biomedical research, especially when studying multifactorial diseases such as cancer or atherosclerosis. The reporting of population differences in clinical research is characterized by large disparities in practices, and fraught with methodological issues and inconsistencies. The actual designations such as "Black" or "Asian" refer to broad and heterogeneous groups, with a great discrepancy among countries. Moreover, the use of obsolete concepts such as "Caucasian" is unfortunate and imprecise. The use of adequate labeling to reflect the scientific hypothesis needs to be promoted. Furthermore, the use of "race/ethnicity" as a unique cause of human heterogeneity may distract from investigating other factors related to a medical condition, particularly if this label is employed as a proxy for cultural habits, diet, or environmental exposure. In addition, the wide range of opinions among researchers does not facilitate the attempts made for resolving this heterogeneity in labeling. "Race," "ethnicity," "ancestry," "geographical origin," and other similar concepts are saturated with meanings. Even if the feasibility of a global consensus on labeling seems difficult, geneticists, sociologists, anthropologists, and ethicists should help develop policies and practices for the biomedical field.
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Affiliation(s)
- Caroline Gombault
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Guillaume Grenet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Pole de Santé Publique, Hospices Civils de Lyon, Service Hospitalo-Universitaire de PharmacoToxicologie, Lyon, France
| | - Laure Segurel
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - François Gueyffier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Pôle de Santé Publique, Hospices Civils De Lyon, Lyon, France
| | - Pascal Cathébras
- Service de Médecine Interne, Hôpital Nord, CHU de Saint-Etienne, Saint-Etienne, France
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Sabine Mainbourg
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Service de Médecine Interne et Pathologie Vasculaire, Hôpital Lyon Sud, Hospices Civils De Lyon, Lyon, France
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Jean-Christophe Lega
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Service de Médecine Interne et Pathologie Vasculaire, Hôpital Lyon Sud, Hospices Civils De Lyon, Lyon, France
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Gau J, Nwora C, Eldakar‐Hein ST, Goel MS, Lahey T, Repp AB. Things We Do for No Reason™: Routine inclusion of race in the history of present illness. J Hosp Med 2022; 17:123-126. [PMCID: PMC9291165 DOI: 10.12788/jhm.3650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/25/2021] [Accepted: 05/04/2021] [Indexed: 08/13/2023]
Affiliation(s)
- Jonathan Gau
- Internal Medicine Residency ProgramUC Irvine School of MedicineOrangeCalifornia
| | - Christle Nwora
- Pediatrics Urban Health Residency ProgramJohns HopkinsBaltimoreMaryland
| | - Shaden T. Eldakar‐Hein
- Lewis Katz School of Medicine at Temple University/St. Luke's University Health NetworkPhiladelphiaPennsylvania
| | - Mita Sanghavi Goel
- Division of General Internal Medicine & Geriatrics, Feinberg School of MedicineNorthwestern UniversityChicagoIllinois
| | - Tim Lahey
- University of Vermont Medical Center and the Larner College of Medicine at the University of VermontBurlingtonVermont
| | - Allen B. Repp
- University of Vermont Medical Center and the Larner College of Medicine at the University of VermontBurlingtonVermont
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11
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Zurca AD, Suttle ML, October TW. An Antiracism Approach to Conducting, Reporting, and Evaluating Pediatric Critical Care Research. Pediatr Crit Care Med 2022; 23:129-132. [PMID: 35119430 DOI: 10.1097/pcc.0000000000002869] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Reporting race and ethnicity without consideration for the complexity of these variables is unfortunately common in research. This practice exacerbates the systemic racism present in healthcare and research, of which pediatric critical care is not immune. Scientifically, this approach lacks rigor, as people are grouped into socially derived categories that are often not scientifically justified, and the field is denied the opportunity to examine closely the true associations between race/ethnicity and clinical outcomes. In this Special Article for Pediatric Critical Care Medicine, we introduce an antiracism approach to conducting, reporting, and evaluating pediatric critical care research. We propose four recommendations: 1) race and ethnicity are social constructs that should be evaluated as such, with researchers considering the context and relevance of related social determinants of health; 2) race and ethnicity data should be collected with sufficient detail to allow detection of meaningful results and minimize the risk of overgeneralizing findings; 3) as health equity research evolves, the pediatric critical care research field must adapt and proactively strive for inclusivity; and 4) the research community, including investigators, authors, research ethics committees, funding organizations, professional organizations, and journal editorial boards, are all accountable for rigorously conducting and reporting race/ethnicity in research. Taking an antiracism approach to research requires the field to ask the difficult question of why racial/ethnic differences exist to eliminate healthcare disparities and optimize healthcare outcomes for all children.
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Affiliation(s)
- Adrian D Zurca
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA
| | - Markita L Suttle
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH
| | - Tessie W October
- Division of Critical Care Medicine, Children's National Hospital, Washington, DC
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12
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Shahian DM, Badhwar V, O'Brien SM, Habib RH, Han J, McDonald DE, Antman MS, Higgins RSD, Preventza O, Estrera AL, Calhoon JH, Grondin SC, Cooke DT. Social Risk Factors in Society of Thoracic Surgeons Risk Models Part 1: Concepts, Indicator Variables, and Controversies. Ann Thorac Surg 2022; 113:1703-1717. [PMID: 34998732 DOI: 10.1016/j.athoracsur.2021.11.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/01/2022]
Affiliation(s)
- David M Shahian
- Division of Cardiac Surgery, Department of Surgery, and Center for Quality and Safety, Massachusetts General Hospital and Harvard Medical School, Boston, MA.
| | - Vinay Badhwar
- Department of Cardiovascular and Thoracic Surgery, West Virginia University, Morgantown WV
| | | | | | - Jane Han
- Society of Thoracic Surgeons, Chicago, IL
| | | | | | - Robert S D Higgins
- Johns Hopkins University School of Medicine and Johns Hopkins Hospital, Baltimore, MD
| | - Ourania Preventza
- Baylor College of Medicine, Texas Heart Institute, Baylor St. Luke's Medical Center, Houston, TX
| | - Anthony L Estrera
- McGovern Medical School at UTHealth; Memorial Hermann Heart and Vascular Institute; Houston, TX
| | - John H Calhoon
- Department of Cardiothoracic Surgery, University of Texas Health Science Center at San Antonio
| | - Sean C Grondin
- Cumming School of Medicine, University of Calgary, and Foothills Medical Centre, Calgary, Alberta, Canada
| | - David T Cooke
- Division of General Thoracic Surgery, UC Davis Health, Sacramento, CA
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Zahir FR. The Need for Precision Therapies as Determined by Genetic Signature for Cystic Fibrosis. J Pers Med 2021; 11:jpm11121353. [PMID: 34945826 PMCID: PMC8708496 DOI: 10.3390/jpm11121353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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Olawoye O, Chuka-Okosa C, Akpa O, Realini T, Hauser M, Ashaye A. Eyes of Africa: The Genetics of Blindness: Study Design and Methodology. BMC Ophthalmol 2021; 21:272. [PMID: 34243759 PMCID: PMC8267233 DOI: 10.1186/s12886-021-02029-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This report describes the design and methodology of the "Eyes of Africa: The Genetics of Blindness," a collaborative study funded through the Human Heredity and Health in Africa (H3Africa) program of the National Institute of Health. METHODS This is a case control study that is collecting a large well phenotyped data set among glaucoma patients and controls for a genome wide association study. (GWAS). Multiplex families segregating Mendelian forms of early-onset glaucoma will also be collected for exome sequencing. DISCUSSION A total of 4500 cases/controls have been recruited into the study at the end of the 3rd funded year of the study. All these participants have been appropriately phenotyped and blood samples have been received from these participants. Recent GWAS of POAG in African individuals demonstrated genome-wide significant association with the APBB2 locus which is an association that is unique to individuals of African ancestry. This study will add to the existing knowledge and understanding of POAG in the African population.
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Affiliation(s)
- Olusola Olawoye
- Department of Ophthalmology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Chimdi Chuka-Okosa
- Department of Ophthalmology, College of Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Onoja Akpa
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tony Realini
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, USA
| | - Michael Hauser
- Department of Medicine, Duke University, NC Durham, USA
- Department of Ophthalmology, Duke University, NC Durham, USA
| | - Adeyinka Ashaye
- Department of Ophthalmology, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Abstract
Disease classification, or nosology, was historically driven by careful examination of clinical features of patients. As technologies to measure and understand human phenotypes advanced, so too did classifications of disease, and the advent of genetic data has led to a surge in genetic subtyping in the past decades. Although the fundamental process of refining disease definitions and subtypes is shared across diverse fields, each field is driven by its own goals and technological expertise, leading to inconsistent and conflicting definitions of disease subtypes. Here, we review several classical and recent subtypes and subtyping approaches and provide concrete definitions to delineate subtypes. In particular, we focus on subtypes with distinct causal disease biology, which are of primary interest to scientists, and subtypes with pragmatic medical benefits, which are of primary interest to physicians. We propose genetic heterogeneity as a gold standard for establishing biologically distinct subtypes of complex polygenic disease. We focus especially on methods to find and validate genetic subtypes, emphasizing common pitfalls and how to avoid them.
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Affiliation(s)
- Andy Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA; .,Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
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16
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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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Cystic fibrosis in low and middle-income countries (LMIC): A view from four different regions of the world. Paediatr Respir Rev 2021; 38:37-44. [PMID: 32826173 DOI: 10.1016/j.prrv.2020.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/23/2023]
Abstract
Cystic fibrosis (CF) has been shown to affect people all over the world. While life expectancy for people with CF has increased substantially, CF is still associated with death in infants and young children in many regions, particularly in low and middle-income countries (LMIC). These countries face significant challenges to promote CF diagnosis and improvements to CF care due to financial constraints and a significant burden of other diseases. In this review, we describe the status of CF diagnosis and care in different LMIC settings, from four different parts of the world (Brazil, South Africa, Israel and India). We highlight challenges and opportunities for CF practitioners in LMIC to improve CF care and outcomes. While early CF diagnosis is the key to optimising outcomes, newborn screening may not be feasible for countries with lower CF incidence and higher birth rates, such as India or South Africa. CF therapies and care in LMIC need to be adapted to available resources of these countries. Collaboration initiatives of the global CF community with LMIC may improve CF care in these countries. Most individuals with CF in LMIC are not benefiting from CFTR modulator treatments due to the prohibitive cost of these drugs.
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18
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Phenotypic Presentations of Cystic Fibrosis in Children of African Descent. Genes (Basel) 2021; 12:genes12030458. [PMID: 33807078 PMCID: PMC8004676 DOI: 10.3390/genes12030458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
The Robert Debre Pediatric Cystic Fibrosis (CF) centre, located in the North East of Paris, a multicultural area, is in charge of a cohort of around a hundred and sixty children diagnosed with CF. Between 2000 and 2019, the proportion of children of African descent in this centre increased from 2% to 10%. We report the clinical features of 17 children of African descent diagnosed with CF: 4 (23%) were diagnosed after a meconium ileus, 14 (83%) had exocrine pancreatic insufficiency, and 7 (41%) had early Pseudomonas aeruginosa infection before the age of two. Even though the majority of patients were diagnosed through NBS, the twenty-nine-mutation testing kit proved less effective in non-Caucasian populations, with a false negative rate of 25% in this series. CF is definitely not solely a Caucasian disease and the literature reveals similar phenotypes in Caucasian and African people provided that they present the same CFTR mutations. Clinicians have to keep in mind that the diagnosis of CF in patients of African descent must be evoked in the case of symptoms and a sweat test must be performed, despite a negative result for NBS.
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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20
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Walker JM, Garcet S, Aleman JO, Mason CE, Danko D, Butler D, Zuffa S, Swann JR, Krueger J, Breslow JL, Holt PR. Obesity and ethnicity alter gene expression in skin. Sci Rep 2020; 10:14079. [PMID: 32826922 PMCID: PMC7442822 DOI: 10.1038/s41598-020-70244-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022] Open
Abstract
Obesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and ethnicity. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from European Americans with a trend to increased epidermal thickening. In obese African Americans, compared to obese European Americans, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.
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Affiliation(s)
- Jeanne M Walker
- The Rockefeller University Hospital, New York, NY, 10065, USA.
| | - Sandra Garcet
- Laboratory of Investigational Dermatology, The Rockefeller University, New York, NY, 10065, USA
| | - Jose O Aleman
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY, 10065, USA
- Laboratory of Translational Obesity Research, New York University Langone Health, New York, NY, 10016, USA
| | | | - David Danko
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Daniel Butler
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Simone Zuffa
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Jonathan R Swann
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James Krueger
- Laboratory of Investigational Dermatology, The Rockefeller University, New York, NY, 10065, USA
| | - Jan L Breslow
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY, 10065, USA
| | - Peter R Holt
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY, 10065, USA.
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21
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Abstract
The majority of studies of genetic association with disease have been performed in Europeans. This European bias has important implications for risk prediction of diseases across global populations. In this commentary, we justify the need to study more diverse populations using both empirical examples and theoretical reasoning.
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Affiliation(s)
- Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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22
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Zeiger AM, McGarry ME, Mak ACY, Medina V, Salazar S, Eng C, Liu AK, Oh SS, Nuckton TJ, Jain D, Blackwell TW, Kang HM, Abecasis G, Oñate LC, Seibold MA, Burchard EG, Rodriguez-Santana J. Identification of CFTR variants in Latino patients with cystic fibrosis from the Dominican Republic and Puerto Rico. Pediatr Pulmonol 2020; 55:533-540. [PMID: 31665830 PMCID: PMC7571374 DOI: 10.1002/ppul.24549] [Citation(s) in RCA: 5] [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] [Received: 08/02/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022]
Abstract
BACKGROUND In cystic fibrosis (CF), the spectrum and frequency of CFTR variants differ by geography and race/ethnicity. CFTR variants in White patients are well-described compared with Latino patients. No studies of CFTR variants have been done in patients with CF in the Dominican Republic or Puerto Rico. METHODS CFTR was sequenced in 61 Dominican Republican patients and 21 Puerto Rican patients with CF and greater than 60 mmol/L sweat chloride. The spectrum of CFTR variants was identified and the proportion of patients with 0, 1, or 2 CFTR variants identified was determined. The functional effects of identified CFTR variants were investigated using clinical annotation databases and computational prediction tools. RESULTS Our study found 10% of Dominican patients had two CFTR variants identified compared with 81% of Puerto Rican patients. No CFTR variants were identified in 69% of Dominican patients and 10% of Puerto Rican patients. In Dominican patients, there were 19 identified CFTR variants, accounting for 25 out of 122 disease alleles (20%). In Puerto Rican patients, there were 16 identified CFTR variants, accounting for 36 out of 42 disease alleles (86%) in Puerto Rican patients. Thirty CFTR variants were identified overall. The most frequent variants for Dominican patients were p.Phe508del and p.Ala559Thr and for Puerto Rican patients were p.Phe508del, p.Arg1066Cys, p.Arg334Trp, and p.I507del. CONCLUSIONS In this first description of the CFTR variants in patients with CF from the Dominican Republic and Puerto Rico, there was a low detection rate of two CFTR variants after full sequencing with the majority of patients from the Dominican Republic without identified variants.
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Affiliation(s)
- Andrew M. Zeiger
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Meghan E. McGarry
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Angel C. Y. Mak
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Vivian Medina
- Department of Pediatrics, Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Sandra Salazar
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Amy K. Liu
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sam S. Oh
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Thomas J. Nuckton
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Thomas W. Blackwell
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Hyun Min Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Goncalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Leandra Cordero Oñate
- Department of Pediatrics, Neumología Pediátrica del Hospital Infantil Dr. Robert Reid Cabral, Santo Domingo, República Dominicana
| | - Max A. Seibold
- Department of Pediatrics, National Jewish Health, Denver, Colorado
| | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET RESPIRATORY MEDICINE 2020; 8:65-124. [DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
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Martins RDS, Campos Junior M, Dos Santos Moreira A, Marques Zembrzuski V, da Fonseca ACP, Abreu GDM, Cabello PH, de Cabello GMK. Identification of a novel large deletion and other copy number variations in the CFTR gene in patients with Cystic Fibrosis from a multiethnic population. Mol Genet Genomic Med 2019; 7:e00645. [PMID: 31199594 PMCID: PMC6625342 DOI: 10.1002/mgg3.645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/30/2022] Open
Abstract
Background Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). There are over 2000 different pathogenic and non‐pathogenic variants described in association with a broad clinical heterogeneity. The most common types of mutations in this gene are single nucleotide substitutions or small deletions and insertions. However, large rearrangements, such as large duplications or deletions, are also a possible cause of CF; these variations are rarely tested in routine screenings, and much of them remain unidentified in some populations, especially those with high ethnic heterogeneity. Methods The present study utilized the Multiplex Ligation‐dependent Probe Amplification (MLPA) technique for the detection of duplications and deletions in 165 CF patients from the Rio de Janeiro State (Brazil), which after extensive mutational screening, still exhibited one or two unidentified CF alleles. Results Five patients with alterations in MLPA signals were detected. After validation, we identified three copy number variations, one large duplication (CFTRdup2‐3) and two large deletions (CFTRdel25‐26 and CFTRdel25‐27‐CTTNBP2). Two detected deletions were not validated. They were false positives caused by a small deletion of 18 base pairs (232del18) and a point mutation (S168L) in the probe binding site. Conclusion Our results highlight the importance of screening for large rearrangements in CF cases with no or only one CFTR mutation defined.
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Affiliation(s)
- Raisa da Silva Martins
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Molecular and Cellular Biology Graduate Program (PPGBMC), Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Mario Campos Junior
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Aline Dos Santos Moreira
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | - Pedro Hernan Cabello
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Genetics Laboratory, Grande Rio University (UNIGRANRIO), Rio de Janeiro, Brazil
| | - Giselda Maria Kalil de Cabello
- Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Molecular and Cellular Biology Graduate Program (PPGBMC), Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
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26
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Hoch H, Sontag MK, Scarbro S, Juarez-Colunga E, McLean C, Kempe A, Sagel SD. Clinical outcomes in U.S. infants with cystic fibrosis from 2001 to 2012. Pediatr Pulmonol 2018; 53:1492-1497. [PMID: 30259702 DOI: 10.1002/ppul.24165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND All 50 United States implemented newborn screening (NBS) for cystic fibrosis (CF) by 2010. The purpose of this study was to evaluate trends over the decade when NBS became universal to determine current rates of malnutrition, stunting, and infection rates in U.S. infants with CF. METHODS Annual data were obtained on infants with CF up to 24 months of age diagnosed between 2001 and 2010 in the CF Foundation Patient Registry (CFFPR), in both the years of and after diagnosis, including method of diagnosis, demographics, and growth parameters and microbiology. RESULTS Data were obtained on 8178 infants diagnosed with CF. The percentage of infants diagnosed by NBS increased from 15% in 2001-83% in 2012 (P < 0.001). Mean weight, length, and weight-for-length z-scores in the year of diagnosis increased from 2001 to 2012 (Wt z-score 2001: -1.32 (SD 1.41), 2012: -0.72 (SD 1.12); Ht z-score 2001: -1.32 (SD 1.57), 2012 -0.60 (SD 1.21); Wt/Ht Z score 2001: -0.54 (SD 1.18), 2012: 0.06 (SD 1.05); P < 0.001 for each). The proportion of infants on pancreatic enzymes decreased from 94% in 2001-83% in 2012 (P < 0.0001). Pseudomonas aeruginosa culture positivity in the diagnosis year decreased significantly (27% in 2001, 15% in 2012, P < 0.001). CONCLUSIONS Nationwide implementation of CF NBS is temporally associated with significant improvements in growth outcomes and reductions in P. aeruginosa infections. Current rates of malnutrition, stunting, and airway infection present a target for early intervention and quality improvement efforts.
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Affiliation(s)
- Heather Hoch
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado
| | - Marci K Sontag
- Department of Epidemiology, University of Colorado School of Public Health, Aurora, Colorado
| | - Sharon Scarbro
- Adult and Child Consortium for Outcomes Research and Delivery Science, University of Colorado School of Medicine, Aurora, Colorado
| | - Elizabeth Juarez-Colunga
- Adult and Child Consortium for Outcomes Research and Delivery Science, University of Colorado School of Medicine, Aurora, Colorado
| | - Cindie McLean
- Department of Epidemiology, University of Colorado School of Public Health, Aurora, Colorado
| | - Allison Kempe
- Adult and Child Consortium for Outcomes Research and Delivery Science, University of Colorado School of Medicine, Aurora, Colorado
| | - Scott D Sagel
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado
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