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Wu S, Powell V, Chintoh A, Alarabi M, Agarwal SM, Remington G. Safety of BEN guidelines in clozapine treatment: A Canadian perspective. Schizophr Res 2024; 264:451-456. [PMID: 38262312 DOI: 10.1016/j.schres.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/29/2023] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
OBJECTIVE Unidentified benign ethnic neutropenia (BEN) has been recognized as a factor contributing to clozapine underutilization and discontinuation. Guidelines were implemented to accommodate BEN in Canada, and our main objective was to evaluate clozapine's safety in a sample of Canadian psychiatric patients with BEN. METHOD A retrospective chart review was conducted at the Centre for Addiction and Mental Health, Toronto, Canada. Through the clozapine clinic registry, participants were identified who (i) received clozapine using the approved BEN guidelines for hematological monitoring, and (ii) had at least one complete blood count pre- and post-clozapine initiation. RESULTS Our sample population was comprised of 41 BEN patients who were African-Caribbean (49 %), African (34 %), African-North American (12 %), Middle Eastern (2 %), and Indian-Caribbean (2 %). There was a significant reduction in hematological alerts for these patients while monitored under BEN guidelines (p < 0.001). The mean within-patient ANC value was not significantly different one year after clozapine initiation compared to the pre-clozapine baseline (p = 0.069). None of the patients discontinued clozapine for hematological reasons. CONCLUSIONS Findings demonstrated that patients monitored under the modified hematological guidelines for BEN can be safely treated with clozapine. These findings have important clinical ramifications as increased implementation of BEN guidelines may allow for broader use of clozapine.
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Affiliation(s)
- Sally Wu
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Temerty Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Canada
| | - Valerie Powell
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
| | - Araba Chintoh
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Mohammed Alarabi
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Department of Psychiatry, King Saud University, Riyadh, Saudi Arabia
| | - Sri Mahavir Agarwal
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Temerty Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Gary Remington
- Schizophrenia Division, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Temerty Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Department of Psychological Clinical Science, University of Toronto Scarborough, Toronto, ON, Canada.
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Schurz H, Naranbhai V, Yates TA, Gilchrist JJ, Parks T, Dodd PJ, Möller M, Hoal EG, Morris AP, Hill AVS. Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture. eLife 2024; 13:e84394. [PMID: 38224499 PMCID: PMC10789494 DOI: 10.7554/elife.84394] [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: 10/23/2022] [Accepted: 11/23/2023] [Indexed: 01/17/2024] Open
Abstract
The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.
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Affiliation(s)
- Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Massachusetts General HospitalBostonUnited States
- Dana-Farber Cancer InstituteBostonUnited States
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Harvard Medical SchoolBostonUnited States
| | - Tom A Yates
- Division of Infection and Immunity, Faculty of Medical Sciences, University College LondonLondonUnited Kingdom
| | - James J Gilchrist
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases Imperial College LondonLondonUnited Kingdom
| | - Peter J Dodd
- School of Health and Related Research, University of SheffieldSheffieldUnited Kingdom
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of ManchesterManchesterUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Jenner Institute, University of OxfordOxfordUnited Kingdom
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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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4
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Le T, Rojas PS, Fakunle M, Huang FW. Racial disparity in the genomics of precision oncology of prostate cancer. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1867. [PMID: 37565547 PMCID: PMC10440844 DOI: 10.1002/cnr2.1867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Significant racial disparities in prostate cancer incidence and mortality have been reported between African American Men (AAM), who are at increased risk for prostate cancer, and European American Men (EAM). In most of the studies carried out on prostate cancer, this population is underrepresented. With the advancement of genome-wide association studies, several genetic predictor models of prostate cancer risk have been elaborated, as well as numerous studies that identify both germline and somatic mutations with clinical utility. RECENT FINDINGS Despite significant advances, the AAM population continues to be underrepresented in genomic studies, which can limit generalizability and potentially widen disparities. Here we outline racial disparities in currently available genomic applications that are used to estimate the risk of individuals developing prostate cancer and to identify personalized oncology treatment strategies. While the incidence and mortality of prostate cancer are different between AAM and EAM, samples from AAM remain to be unrepresented in different studies. CONCLUSION This disparity impacts the available genomic data on prostate cancer. As a result, the disparity can limit the predictive utility of the genomic applications and may lead to the widening of the existing disparities. More studies with substantially higher recruitment and engagement of African American patients are necessary to overcome this disparity.
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Affiliation(s)
- Tu Le
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
| | - Pilar Soto Rojas
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of OncologyHospital Universitario Virgen MacarenaSevilleSpain
| | - Mary Fakunle
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Franklin W. Huang
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Chan Zuckerberg BiohubSan FranciscoCaliforniaUSA
- Institute for Human GeneticsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Bakar Computational Health Sciences InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Initiative for Prostate Cancer ResearchUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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5
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Tripathi S, Gabriel K, Dheer S, Parajuli A, Augustin AI, Elahi A, Awan O, Dako F. Understanding Biases and Disparities in Radiology AI Datasets: A Review. J Am Coll Radiol 2023; 20:836-841. [PMID: 37454752 DOI: 10.1016/j.jacr.2023.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Artificial intelligence (AI) continues to show great potential in disease detection and diagnosis on medical imaging with increasingly high accuracy. An important component of AI model creation is dataset development for training, validation, and testing. Diverse and high-quality datasets are critical to ensure robust and unbiased AI models that maintain validity, especially in traditionally underserved populations globally. Yet publicly available datasets demonstrate problems with quality and inclusivity. In this literature review, the authors evaluate publicly available medical imaging datasets for demographic, geographic, genetic, and disease representation or lack thereof and call for an increase emphasis on dataset development to maximize the impact of AI models.
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Affiliation(s)
- Satvik Tripathi
- Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania.
| | - Kyla Gabriel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Suhani Dheer
- Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Aastha Parajuli
- Department of Radiology, Kathmandu University of School of Medical Sciences, Dhulikhel, Nepal
| | | | - Ameena Elahi
- Department of Information Services, University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Omar Awan
- Department of Radiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Farouk Dako
- Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
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Adam Y, Sadeeq S, Kumuthini J, Ajayi O, Wells G, Solomon R, Ogunlana O, Adetiba E, Iweala E, Brors B, Adebiyi E. Polygenic Risk Score in African populations: progress and challenges. F1000Res 2023; 11:175. [PMID: 37273966 PMCID: PMC10233318 DOI: 10.12688/f1000research.76218.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 06/06/2023] Open
Abstract
Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects single nucleotide polymorphisms (SNPs) that contribute to the disease with low effect size making it more precise at individual level risk prediction. PRS analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with low effect size but play an indispensable role to the observed phenotypic/trait variance. PRS analysis has applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies show that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that lack of sufficient GWAS data and tools is the limiting factor of applying PRS analysis to sub-Saharan populations. We recommend developing Africa-specific PRS methods and tools for estimating and analyzing African population data for clinical evaluation of PRSs of interest and predicting rare diseases.
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Affiliation(s)
- Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Suraju Sadeeq
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Judit Kumuthini
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Olabode Ajayi
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Gordon Wells
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Rotimi Solomon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Olubanke Ogunlana
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Emmanuel Adetiba
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Electrical & Information Engineering (EIE), Covenant University, Ota, Ogun State, 112212, Nigeria
- HRA, Institute for Systems Science, Durban University of Technology, Durban, South Africa
| | - Emeka Iweala
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Benedikt Brors
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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Adam Y, Sadeeq S, Kumuthini J, Ajayi O, Wells G, Solomon R, Ogunlana O, Adetiba E, Iweala E, Brors B, Adebiyi E. Polygenic Risk Score in African populations: progress and challenges. F1000Res 2023; 11:175. [PMID: 37273966 PMCID: PMC10233318 DOI: 10.12688/f1000research.76218.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2023] [Indexed: 11/23/2023] Open
Abstract
Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects single nucleotide polymorphisms (SNPs) that contribute to the disease with low effect size making it more precise at individual level risk prediction. PRS analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with low effect size but play an indispensable role to the observed phenotypic/trait variance. PRS analysis has applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies show that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that lack of sufficient GWAS data and tools is the limiting factor of applying PRS analysis to sub-Saharan populations. We recommend developing Africa-specific PRS methods and tools for estimating and analyzing African population data for clinical evaluation of PRSs of interest and predicting rare diseases.
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Affiliation(s)
- Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Suraju Sadeeq
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Judit Kumuthini
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Olabode Ajayi
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Gordon Wells
- South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town, South Africa
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Rotimi Solomon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Olubanke Ogunlana
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Emmanuel Adetiba
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Electrical & Information Engineering (EIE), Covenant University, Ota, Ogun State, 112212, Nigeria
- HRA, Institute for Systems Science, Durban University of Technology, Durban, South Africa
| | - Emeka Iweala
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept of Biochemistry, Covenant University, Ota, Ogun State, 112212, Nigeria
| | - Benedikt Brors
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 112212, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, 112212, Nigeria
- Dept Computer & Information Sciences, Covenant University, Ota, Ogun State, 112212, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil. Funct Integr Genomics 2023; 23:74. [PMID: 36867305 PMCID: PMC9982798 DOI: 10.1007/s10142-023-00999-0] [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: 12/27/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Brazilian quilombos are communities formed by enslaved Africans and their descendants all over the country during slavery and shortly after its abolition. Quilombos harbor a great fraction of the largely unknown genetic diversity of the African diaspora in Brazil. Thus, genetic studies in quilombos have the potential to provide important insights not only into the African roots of the Brazilian population but also into the genetic bases of complex traits and human adaptation to diverse environments. This review summarizes the main results of genetic studies performed on quilombos so far. Here, we analyzed the patterns of African, Amerindian, European, and subcontinental ancestry (within Africa) of quilombos from the five different geographic regions of Brazil. In addition, uniparental markers (from the mtDNA and the Y chromosome) studies are analyzed together to reveal demographic processes and sex-biased admixture that occurred during the formation of these unique populations. Lastly, the prevalence of known malaria-adaptive African mutations and other African-specific variants discovered in quilombos, as well as the genetic bases of health-related traits, are discussed here, together with their implication for the health of populations of African descent.
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Soremekun C, Machipisa T, Soremekun O, Pirie F, Oyekanmi N, Motala AA, Chikowore T, Fatumo S. Multivariate GWAS analysis reveals loci associated with liver functions in continental African populations. PLoS One 2023; 18:e0280344. [PMID: 36809439 PMCID: PMC9942994 DOI: 10.1371/journal.pone.0280344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/27/2022] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Liver disease is any condition that causes liver damage and inflammation and may likely affect the function of the liver. Vital biochemical screening tools that can be used to evaluate the health of the liver and help diagnose, prevent, monitor, and control the development of liver disease are known as liver function tests (LFT). LFTs are performed to estimate the level of liver biomarkers in the blood. Several factors are associated with differences in concentration levels of LFTs in individuals, such as genetic and environmental factors. The aim of our study was to identify genetic loci associated with liver biomarker levels with a shared genetic basis in continental Africans, using a multivariate genome-wide association study (GWAS) approach. METHODS We used two distinct African populations, the Ugandan Genome Resource (UGR = 6,407) and South African Zulu cohort (SZC = 2,598). The six LFTs used in our analysis were: aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), gamma-glutamyl transferase (GGT), total bilirubin, and albumin. A multivariate GWAS of LFTs was conducted using the exact linear mixed model (mvLMM) approach implemented in GEMMA and the resulting P-values were presented in Manhattan and quantile-quantile (QQ) plots. First, we attempted to replicate the findings of the UGR cohort in SZC. Secondly, given that the genetic architecture of UGR is different from that of SZC, we further undertook similar analysis in the SZC and discussed the results separately. RESULTS A total of 59 SNPs reached genome-wide significance (P = 5x10-8) in the UGR cohort and with 13 SNPs successfully replicated in SZC. These included a novel lead SNP near the RHPN1 locus (lead SNP rs374279268, P-value = 4.79x10-9, Effect Allele Frequency (EAF) = 0.989) and a lead SNP at the RGS11 locus (lead SNP rs148110594, P-value = 2.34x10-8, EAF = 0.928). 17 SNPs were significant in the SZC, while all the SNPs fall within a signal on chromosome 2, rs1976391 mapped to UGT1A was identified as the lead SNP within this region. CONCLUSIONS Using multivariate GWAS method improves the power to detect novel genotype-phenotype associations for liver functions not found with the standard univariate GWAS in the same dataset.
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Affiliation(s)
- Chisom Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
- Department of Immunology and Molecular Biology, College of Health Science, Makerere University, Kampala, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tafadzwa Machipisa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Hatter Institute for Cardiovascular Diseases Research in Africa and Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Michael G. DeGroote School of Medicine, Hamilton, Ontario, Canada
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Nashiru Oyekanmi
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Ayesha A. Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Pediatrics, MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Yang G, Alarcon C, Friedman P, Gong L, Klein T, O’Brien T, Nutescu EA, Tuck M, Meltzer D, Perera MA. The Role of Global and Local Ancestry on Clopidogrel Response in African Americans. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2023; 28:221-232. [PMID: 36540979 PMCID: PMC9782753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pharmacogenomics has long lacked dedicated studies in African Americans, resulting in a lack of indepth data in this populations. The ACCOuNT consortium has collected a cohort of 167 African American patients on steady state clopidogrel with the goal of discovering population specific variation that may contribute to the response of this anti-platelet agent. Here we analyze the role of both global and local ancestry on the clinical phenotypes of P2Y12 reaction units (PRU) and high on-treatment platelet reactivity (HTPR) in this cohort. We found that local ancestry at the TSS of three genes, IRS-1, ABCB1 and KDR were nominally associated with PRU, and local ancestry-adjusted SNP association identified variants in ITGA2 associated to increased PRU. These finding help to explain the variability in drug response seen in African Americans, especially as few studies on genes outside of CYP2C19 has been conducted in this population.
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Affiliation(s)
- Guang Yang
- Department of Pharmacology, Center for Pharmacogenomics, Feinherg School of Medicine, Northwestern University, Chicago, IL
| | - Cristina Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Feinherg School of Medicine, Northwestern University, Chicago, IL
| | - Paula Friedman
- Department of Pharmacology, Center for Pharmacogenomics, Feinherg School of Medicine, Northwestern University, Chicago, IL
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Teri Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Travis O’Brien
- Department of Pharmacology and Physiology, The George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Edith A. Nutescu
- Department of Pharmacy Practice and Center for Pharmacoepidemiology and Pharmacoeconomic Research, University of Illinois Chicago, College of Pharmacy, Chicago, IL
| | - Matthew Tuck
- Washington DC VA Medical Center, Washington, DC and The George Washington University, Washington, DC
| | - David Meltzer
- Section of Hospital Medicine, Department of Medicine, University of Chicago, Chicago, IL
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinherg School of Medicine, Northwestern University, Chicago, IL
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11
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Betulinic acid and its ionic derivatives impaired growth of prostate cancer cells without induction of GRP78 and CHOP. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2022. [DOI: 10.2478/cipms-2022-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
Prostate cancer (PCa) is the most common invasive malignancy for men in the USA. The incidence and mortality rates of PCa are significantly higher among African American men, as compared to those in Caucasian men. Betulinic acid (BA) is a penta-cyclic triterpenoid that is often found in the bark of several species of plants. It possesses a variety of biological activities, including anti-cancer activities. We examined the cytotoxic effects and endoplasmic reticulum (ER) stress induced by BA and its ionic derivatives with PCa cells derived from African Americans and Caucasian men. The viability of all PCa cells was reduced by the BA compounds, and the cytotoxicity of these BA compounds was independent of ethnicity and androgen dependency. The BA compounds induced modest effects on ER stress proteins when compared with ER stress inducers, tunicamycin and thapsigargin. The induction of glucose regulated protein 78 (GRP78) was largely correlated with the expression of C/EBP homologous protein (CHOP) and cleaved poly [ADP-ribose] polymerase (PARP)/caspase-3 in the PCa cells. In summary, our data demonstrated that BA compounds impaired the growth of PCa cells regardless of ethnicity – through GRP78- and CHOP-independent pathways.
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12
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Onu JU, Olatayo TI, Okorie AC, Ohaeri JU. Family, twin and adoption studies of severe mental disorders in sub-Saharan Africa: a scoping review. Soc Psychiatry Psychiatr Epidemiol 2022; 58:685-692. [PMID: 36542114 DOI: 10.1007/s00127-022-02407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE The traditional genetic epidemiological studies are necessary to improve accurate risk communication to service users and their families. This scoping review aimed to describe the volume and scope of existing research evidence on family, twin and adoption studies of severe mental disorders (SMDs) in SSA. This is with a view to identifying gaps in the literature and the adequacy of data for a systematic review and meta-analysis. METHODS Literature search was done for all original peer-reviewed research articles on the topic in SSA using PubMed and MEDLINE. Publications included were peer-reviewed original articles, irrespective of their quality, carried out in the region from the 1970s till 9th March, 2022, which were available in English or translated to English. Case reports, abstracts, and studies among populations living outside the region were excluded. RESULTS A total of five studies that met the inclusion criteria across the 46 countries in the region were identified. Of the three thematic areas of focus, only family studies on SMDs had research work in SSA. These studies provided evidence of familial clustering of SMDs in SSA. There were no twin and adoption studies on SMDs in the region. However, the review noted the establishment of two twin registries in Guinea-Bissau and Nigeria. A huge gap exists in the area of twin and adoption studies on SMDs in SSA. CONCLUSION The volume of research evidence on traditional family genetic studies of SMDs is grossly inadequate to consider a systematic review in SSA. We have suggested studies to remedy the situation.
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Affiliation(s)
- Justus U Onu
- Department of Mental Health, Nnamdi Azikiwe University, Nnewi Campus, Awka, Anambra State, Nigeria.
| | - Temitope I Olatayo
- Department of Clinical Services, Federal Neuropsychiatric Hospital, Enugu, Enugu State, Nigeria
| | | | - Jude U Ohaeri
- Department of Psychological Medicine, University of Nigeria, Enugu Campus, Nsukka, Nigeria
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13
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Omotoso OE, Teibo JO, Atiba FA, Oladimeji T, Adebesin AO, Babalghith AO. Bridging the genomic data gap in Africa: implications for global disease burdens. Global Health 2022; 18:103. [PMID: 36494695 PMCID: PMC9733397 DOI: 10.1186/s12992-022-00898-2] [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: 08/01/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
This paper highlights the gap in the use of genomic data of Africans for global research efforts for disease cures. Genomic data represents an important tool used in disease research for understanding how diseases affect several populations and how these differences can be harnessed for the development of effective cures especially vaccines that have an impact at the genetic level e.g., RNA vaccines.This paper then provides a review of global genomic data status where three continents are reported to be the major contributor of genomic data to repositories used for disease research and the development of vaccines and medicines around the world.We reviewed the most recently published information about genetic data inclusiveness of populations, explaining how genomic data of Africans is lacking in global research efforts that cater towards the eradication of pandemics via the development of vaccines and other cures. We also discuss the implication of this non-inclusiveness for global disease burdens and indicate where changes need to be made in the last part of the paper.Lastly, the entire centers on some general policy recommendations to fully include African genomic data in such global genetic repositories. These recommendations can be implemented in African countries to improve genetic data collection, storage, and usage policies.
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Affiliation(s)
| | - John Oluwafemi Teibo
- Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Festus Adebayo Atiba
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Ahmad O. Babalghith
- Medical Genetics Department, College of Medicine, Umm al-qura University, Makkah, Saudi Arabia
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Cuevas AG, Mann FD, Krueger RF. The weight of childhood adversity: evidence that childhood adversity moderates the impact of genetic risk on waist circumference in adulthood. Int J Obes (Lond) 2022; 46:1875-1882. [PMID: 35931810 DOI: 10.1038/s41366-022-01191-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The present study tested the interactive effects of childhood adversity and polygenic risk scores for waist circumference (PRS-WC) on waist circumference (WC). Consistent with a diathesis-stress model, we hypothesize that the relationship between PRS-WC and WC will be magnified by increasing levels of childhood adversity. METHODS Observational study of 7976 adults (6347 European Americans and 1629 African Americans) in the Health and Retirement Study with genotyped data. PRS-WC were calculated by the HRS administrative core using the weighted sum of risk alleles based on a genome-wide association study conducted by the Genetic Investigation of Anthropometric Traits (GIANT) consortium. Childhood adversity was operationalized using a sum score of three traumatic events that occurred before the age of 18 years. RESULTS There was a statistically significant interaction between PRS-WC and childhood adversity for European Americans, whereby the magnitude of PRS-WC predicting WC increased as the number of adverse events increased. CONCLUSIONS This study supports the idea of the interactive effects of genetic risks and childhood adversity on obesity. More epidemiological studies, particularly with understudied populations, are needed to better understand the roles that genetics and childhood adversity play on the development and progression of obesity.
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Affiliation(s)
- Adolfo G Cuevas
- Department of Social and Behavioral Sciences, School of Global Public Health, New York University, New York, NY, USA.
| | - Frank D Mann
- Program in Public Health, Department of Family, Population, and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Robert F Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
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Kwan SY, Sabotta CM, Joon A, Wei P, Petty LE, Below JE, Wu X, Zhang J, Jenq RR, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. mSystems 2022; 7:e0003322. [PMID: 35477306 PMCID: PMC9238400 DOI: 10.1128/msystems.00033-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/02/2022] [Indexed: 02/08/2023] Open
Abstract
Mexican Americans have a high prevalence of diabetes and burden of diabetes-related complications, highlighting the need for novel preventive strategies and noninvasive predictors of diabetes risk tailored to this population. Changes in the gut microbiome have the potential to predict diabetes. Here, we aimed to identify alterations in the gut microbiome associated with diabetes in the high-risk population of Mexican Americans in South Texas. Stool samples were collected from 216 subjects from the population-based Cameron County Hispanic Cohort. Among them, 75 had type 2 diabetes. Taxonomic and functional profiling of the stool samples were assessed by 16S and shotgun metagenomic sequencing, and the influence of genetic factors was explored. The gut microbiome of subjects with diabetes was enriched with proinflammatory Proteobacteria members (Enterobacteriaceae, Escherichia-Shigella) and depleted of butyrate-producing Clostridiales members (Faecalibacterium prausnitzii, Peptostreptococcaceae, and Clostridium sensu stricto 1). The accompanying metagenomic changes in subjects with diabetes suggested dysregulated amino acid metabolism, reduced galacturonate and glucuronate catabolism (correlating with Faecalibacterium prausnitzii abundance), and enriched heme biosynthesis (correlating with Enterobacteriaceae abundance). Polymorphism rs7129790 near MMP27 was strongly associated with high Proteobacteria abundance and was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. In conclusion, Mexican Americans in South Texas with diabetes display distinct gut microbiome and metagenomic signatures. These signatures may have utility in risk modeling and disease prevention in this high-risk population. IMPORTANCE The gut microbiome composition varies across ethnicities and geographical locations, yet studies on diabetes-associated microbiome changes specific to high-risk Mexican Americans are lacking. Here, we aimed to identify specific alterations associated with diabetes in this population, as well as host genetic factors that may explain increased disease susceptibility in this ethnic group. Using samples from a population-based cohort of Mexican Americans with a high prevalence of obesity and diabetes, we confirmed findings from studies on other ethnicities that suggested promotion of a chronic proinflammatory environment, loss of butyrate production, and compromised intestinal barrier integrity. High abundance of proinflammatory Proteobacteria was associated with a polymorphism that was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. Validation of microbiome-based risk models for diabetes should be evaluated in prospective cohort studies.
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Affiliation(s)
- Suet-Ying Kwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Caroline M. Sabotta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Aron Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lauren E. Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer E. Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ernest T. Hawk
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joseph B. McCormick
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Susan P. Fisher-Hoch
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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16
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Prostate cancer risk in men of differing genetic ancestry and approaches to disease screening and management in these groups. Br J Cancer 2022; 126:1366-1373. [PMID: 34923574 PMCID: PMC9090767 DOI: 10.1038/s41416-021-01669-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/02/2021] [Accepted: 12/03/2021] [Indexed: 01/12/2023] Open
Abstract
Prostate cancer is the second most common solid tumour in men worldwide and it is also the most common cancer affecting men of African descent. Prostate cancer incidence and mortality vary across regions and populations. Some of this is explained by a large heritable component of this disease. It has been established that men of African and African Caribbean ethnicity are predisposed to prostate cancer (PrCa) that can have an earlier onset and a more aggressive course, thereby leading to poorer outcomes for patients in this group. Literature searches were carried out using the PubMed, EMBASE and Cochrane Library databases to identify studies associated with PrCa risk and its association with ancestry, screening and management of PrCa. In order to be included, studies were required to be published in English in full-text form. An attractive approach is to identify high-risk groups and develop a targeted screening programme for them as the benefits of population-wide screening in PrCa using prostate-specific antigen (PSA) testing in general population screening have shown evidence of benefit; however, the harms are considered to weigh heavier because screening using PSA testing can lead to over-diagnosis and over-treatment. The aim of targeted screening of higher-risk groups identified by genetic risk stratification is to reduce over-diagnosis and treat those who are most likely to benefit.
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17
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Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, Daniel CR, Wu X, Zhang J, Jenq RR, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease. Hepatology 2022; 75:955-967. [PMID: 34633706 PMCID: PMC8930512 DOI: 10.1002/hep.32197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Hispanics are disproportionately affected by NAFLD, liver fibrosis, cirrhosis, and HCC. Preventive strategies and noninvasive means to identify those in this population at high risk for liver fibrosis, are urgently needed. We aimed to characterize the gut microbiome signatures and related biological functions associated with liver fibrosis in Hispanics and identify environmental and genetic factors affecting them. APPROACH AND RESULTS Subjects of the population-based Cameron County Hispanic Cohort (CCHC; n = 217) were screened by vibration-controlled transient elastography (FibroScan). Among them, 144 (66.7%) had steatosis and 28 (13.0%) had liver fibrosis. The gut microbiome of subjects with liver fibrosis was enriched with immunogenic commensals (e.g., Prevotella copri, Holdemanella, Clostridiaceae 1) and depleted of Bacteroides caccae, Parabacteroides distasonis, Enterobacter, and Marinifilaceae. The liver fibrosis-associated metagenome was characterized by changes in the urea cycle, L-citrulline biosynthesis and creatinine degradation pathways, and altered synthesis of B vitamins and lipoic acid. These metagenomic changes strongly correlated with the depletion of Parabacteroides distasonis and enrichment of Prevotella and Holdemanella. Liver fibrosis was also associated with depletion of bacterial pathways related to L-fucose biosynthesis. Alcohol consumption, even moderate, was associated with high Prevotella abundance. The single-nucleotide polymorphisms rs3769502 and rs7573751 in the NCK adaptor protein 2 (NCK2) gene positively associated with high Prevotella abundance. CONCLUSION Hispanics with liver fibrosis display microbiome profiles and associated functional changes that may promote oxidative stress and a proinflammatory environment. These microbiome signatures, together with NCK2 polymorphisms, may have utility in risk modeling and disease prevention in this high-risk population.
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Affiliation(s)
- Suet-Ying Kwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jingjing Jiao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aron Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren E. Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer E. Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carrie R. Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ernest T. Hawk
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph B. McCormick
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas
| | - Susan P. Fisher-Hoch
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville Regional Campus, Brownsville, Texas
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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18
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Ahamad N, Gupta S, Parashar D. Using Omics to Study Leprosy, Tuberculosis, and Other Mycobacterial Diseases. Front Cell Infect Microbiol 2022; 12:792617. [PMID: 35281437 PMCID: PMC8908319 DOI: 10.3389/fcimb.2022.792617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Mycobacteria are members of the Actinomycetales order, and they are classified into one family, Mycobacteriaceae. More than 20 mycobacterial species cause disease in humans. The Mycobacterium group, called the Mycobacterium tuberculosis complex (MTBC), has nine closely related species that cause tuberculosis in animals and humans. TB can be detected worldwide and one-fourth of the world's population is contaminated with tuberculosis. According to the WHO, about two million dies from it, and more than nine million people are newly infected with TB each year. Mycobacterium tuberculosis (M. tuberculosis) is the most potential causative agent of tuberculosis and prompts enormous mortality and morbidity worldwide due to the incompletely understood pathogenesis of human tuberculosis. Moreover, modern diagnostic approaches for human tuberculosis are inefficient and have many lacks, while MTBC species can modulate host immune response and escape host immune attacks to sustain in the human body. "Multi-omics" strategies such as genomics, transcriptomics, proteomics, metabolomics, and deep sequencing technologies could be a comprehensive strategy to investigate the pathogenesis of mycobacterial species in humans and offer significant discovery to find out biomarkers at the early stage of disease in the host. Thus, in this review, we attempt to understand an overview of the mission of "omics" approaches in mycobacterial pathogenesis, including tuberculosis, leprosy, and other mycobacterial diseases.
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Affiliation(s)
- Naseem Ahamad
- Department of Oral and Maxillofacial Diagnostic Sciences, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, India
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, United States
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Jang HM, Hwang MY, Kim BJ, Kim YJ. Validation and genetic heritability estimation of known type 2 diabetes related variants in the Korean population. Genomics Inform 2022; 19:e37. [PMID: 35012284 PMCID: PMC8752982 DOI: 10.5808/gi.21071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies (GWASs) facilitated the discovery of countless disease-associated variants. However, GWASs have mostly been conducted in European ancestry samples. Recent studies have reported that these European-based association results may reduce disease prediction accuracy when applied in non-Europeans. Therefore, previously reported variants should be validated in non-European populations to establish reliable scientific evidence for precision medicine. In this study, we validated known associations with type 2 diabetes (T2D) and related metabolic traits in 125,850 samples from a Korean population genotyped by the Korea Biobank Array (KBA). At the end of December 2020, there were 8,823 variants associated with glycemic traits, lipids, liver enzymes, and T2D in the GWAS catalog. Considering the availability of imputed datasets in the KBA genome data, publicly available East-Asian T2D summary statistics, and the linkage disequilibrium among the variants (r2 < 0.2), 2,900 independent variants were selected for further analysis. Among these, 1,837 variants (63.3%) were statistically significant (p ≤ 0.05). Most of the non-replicated variants (n = 1,063) showed insufficient statistical power and decreased minor allele frequencies compared with the replicated variants. Moreover, most of known variants showed <10% genetic heritability. These results could provide valuable scientific evidence for future study designs, the current power of GWASs, and future applications in precision medicine in the Korean population.
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Affiliation(s)
- Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju 28159, Korea
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju 28159, Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju 28159, Korea
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju 28159, Korea
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Armstrong ND, Srinivasasainagendra V, Patki A, Tanner RM, Hidalgo BA, Tiwari HK, Limdi NA, Lange EM, Lange LA, Arnett DK, Irvin MR. Genetic Contributors of Incident Stroke in 10,700 African Americans With Hypertension: A Meta-Analysis From the Genetics of Hypertension Associated Treatments and Reasons for Geographic and Racial Differences in Stroke Studies. Front Genet 2022; 12:781451. [PMID: 34992631 PMCID: PMC8724550 DOI: 10.3389/fgene.2021.781451] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals. Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS AAs aiming to evaluate cross-ethnic performance. Results: We identified 10 statistically significant (p < 5.00E-08) and 90 additional suggestive (p < 1.00E-06) variants associated with incident stroke in the meta-analysis. Six of the top 10 variants were located in an intergenic region on chromosome 18 (LINC01443-LOC644669). Additional variants of interest were located in or near the COL12A1, SNTG1, PCDH7, TMTC1, and NTM genes. Replication was conducted in the Warfarin Pharmacogenomics Cohort (WPC), and while none of the variants were directly validated, seven intronic variants of NTM proximal to our target variants, had a p-value <5.00E-04 in the WPC. The inclusion of the PRS did not improve the prediction accuracy compared to a reference model adjusting for age, sex, and genetic ancestry in either study and had lower predictive accuracy compared to models accounting for established stroke risk factors. These results demonstrate the necessity for PRS derivation in AAs, particularly for diseases that affect AAs disproportionately. Conclusion: This study highlights biologically plausible genetic determinants for incident stroke in hypertensive AAs. Ultimately, a better understanding of genetic risk factors for stroke in AAs may give new insight into stroke burden and potential clinical tools for those among the highest at risk.
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Affiliation(s)
- Nicole D Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Rikki M Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bertha A Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ethan M Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, United States
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
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21
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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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22
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Bree KK, Hensley PJ, Pettaway CA. Germline Mutations in African American Men With Prostate Cancer: Incidence, Implications and Diagnostic Disparities. Urology 2021; 163:148-155. [PMID: 34453957 DOI: 10.1016/j.urology.2021.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022]
Abstract
Recent data suggests that African American men (AAM) with prostate cancer (PCa) exhibit genetic alterations in highly penetrant germline genes, as well as low penetrant single nucleotide polymorphisms. The importance of germline variants of uncertain significance (VUS) remain poorly elucidated and given the elevated rates of VUS in AAM compared to Caucasians with PCa, further studies are needed to facilitate potential reclassification of VUS. Ongoing efforts to include AAM in genomics research is of paramount importance in order to ensure applicability of discoveries across diverse populations and potentially reduce PCa disparities as we embark on the era of precision medicine.
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Affiliation(s)
- Kelly K Bree
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick J Hensley
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Curtis A Pettaway
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX.
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23
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Peprah E, Armstrong-Hough M, Cook SH, Mukasa B, Taylor JY, Xu H, Chang L, Gyamfi J, Ryan N, Ojo T, Snyder A, Iwelunmor J, Ezechi O, Iyegbe C, O’Reilly P, Pascal Kengne A. An Emerging Syndemic of Smoking and Cardiopulmonary Diseases in People Living with HIV in Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3111. [PMID: 33803504 PMCID: PMC8003038 DOI: 10.3390/ijerph18063111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/11/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND African countries have the highest number of people living with HIV (PWH). The continent is home to 12% of the global population, but accounts for 71% of PWH globally. Antiretroviral therapy has played an important role in the reduction of the morbidity and mortality rates for HIV, which necessitates increased surveillance of the threats from pernicious risks to which PWH who live longer remain exposed. This includes cardiopulmonary comorbidities, which pose significant public health and economic challenges. A significant contributor to the cardiopulmonary comorbidities is tobacco smoking. Indeed, globally, PWH have a 2-4-fold higher utilization of tobacco compared to the general population, leading to endothelial dysfunction and atherogenesis that result in cardiopulmonary diseases, such as chronic obstructive pulmonary disease and coronary artery disease. In the context of PWH, we discuss (1) the current trends in cigarette smoking and (2) the lack of geographically relevant data on the cardiopulmonary conditions associated with smoking; we then review (3) the current evidence on chronic inflammation induced by smoking and the potential pathways for cardiopulmonary disease and (4) the multifactorial nature of the syndemic of smoking, HIV, and cardiopulmonary diseases. This commentary calls for a major, multi-setting cohort study using a syndemics framework to assess cardiopulmonary disease outcomes among PWH who smoke. CONCLUSION We call for a parallel program of implementation research to promote the adoption of evidence-based interventions, which could improve health outcomes for PWH with cardiopulmonary diseases and address the health inequities experienced by PWH in African countries.
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Affiliation(s)
- Emmanuel Peprah
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Mari Armstrong-Hough
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Stephanie H. Cook
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | | | | | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Linda Chang
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Joyce Gyamfi
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Nessa Ryan
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Temitope Ojo
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Anya Snyder
- School of Global Public Health, New York University, New York, NY 10012, USA; (M.A.-H.); (S.H.C.); (J.G.); (N.R.); (T.O.); (A.S.)
| | - Juliet Iwelunmor
- College for Public Health and Social Justice, Saint Louis University, St. Louis, MO 63103, USA;
| | - Oliver Ezechi
- Nigerian Institute of Medical Research, Lagos, Nigeria;
| | - Conrad Iyegbe
- Icahn School of Medicine at Mount Sinai, Mount Sinai Hospital, New York, NY 10029, USA; (C.I.); (P.O.); (A.P.K.)
| | - Paul O’Reilly
- Icahn School of Medicine at Mount Sinai, Mount Sinai Hospital, New York, NY 10029, USA; (C.I.); (P.O.); (A.P.K.)
| | - Andre Pascal Kengne
- Icahn School of Medicine at Mount Sinai, Mount Sinai Hospital, New York, NY 10029, USA; (C.I.); (P.O.); (A.P.K.)
- South African Medical Research Council, Cape Town, South Africa
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24
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Vallender EJ, Ladner ME, Akinhanmi MO, Caples FV, Frye MA, Balls-Berry JE. Motivating and Discouraging Factors for Bipolar Patient Participation in Genomic Research. Public Health Genomics 2021; 24:89-98. [PMID: 33657561 DOI: 10.1159/000513723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
AIMS The goal of this project was to better understand the motivating and discouraging factors toward genetic research and biobank programs in patients with bipolar disorder, particularly across gender and racial identities. METHODS A survey (n = 63) of adults diagnosed with bipolar disorder was conducted at the general psychiatric inpatient unit and outpatient clinic at the University of Mississippi Medical Center. Participants were asked to rate on a Likert scale their attitudes toward medical research generally, mental health research specifically, and willingness to participate in a bipolar DNA biobank. Last, they were asked to endorse motivating factors or concerns for their attitude toward participation. RESULTS Neither attitudes toward research nor willingness to participate in a bipolar biobank differed across gender, age, or education level, but Black/African American participants were statistically significantly less likely to endorse a willingness to participate in a biobank compared to White participants. As observed in previous work, Black/African American participants were significantly more likely to endorse concerns regarding violations of trust, privacy, or autonomy. However, while there were no significant differences in discouraging factors among individuals who indicated an opposition to participating in a biobank compared to those who indicated support, there was a significant decrease in support of motivating factors, including increasing knowledge, personal benefit, and duty to community, for those not interested in participating. CONCLUSIONS Black/African American participants with bipolar disorder were more likely to express concerns about DNA and biobank research. But while race was a contributing factor to support or opposition to biobanking for bipolar disorder research, more salient was insufficient positive motivation. These results highlight the need to emphasize contemporary safeguards on DNA research and biobanking as an ethical duty and to identify the need for community-based educational interventions to promote a greater understanding of the positive benefits to motivate increased research participation.
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Affiliation(s)
- Eric J Vallender
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, USA,
| | - Mark E Ladner
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Margaret O Akinhanmi
- Satcher Health Leadership Institute, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Felicia V Caples
- Department of Behavioral and Environmental Health, Jackson State University, Jackson, Mississippi, USA
| | - Mark A Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joyce E Balls-Berry
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Neurology, Washington University, St. Louis, Missouri, USA
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25
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Cole BS, Gudiseva HV, Pistilli M, Salowe R, McHugh CP, Zody MC, Chavali VRM, Ying GS, Moore JH, O'Brien JM. The Role of Genetic Ancestry as a Risk Factor for Primary Open-angle Glaucoma in African Americans. Invest Ophthalmol Vis Sci 2021; 62:28. [PMID: 33605984 PMCID: PMC7900887 DOI: 10.1167/iovs.62.2.28] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/27/2021] [Indexed: 01/01/2023] Open
Abstract
Purpose POAG is the leading cause of irreversible blindness in African Americans. In this study, we quantitatively assess the association of autosomal ancestry with POAG risk in a large cohort of self-identified African Americans. Methods Subjects recruited to the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study were classified as glaucoma cases or controls by fellowship-trained glaucoma specialists. POAAGG subjects were genotyped using the MEGA Ex array (discovery cohort, n = 3830; replication cohort, n = 2135). Population structure was interrogated using principal component analysis in the context of the 1000 Genomes Project superpopulations. Results The majority of POAAGG samples lie on an axis between African and European superpopulations, with great variation in admixture. Cases had a significantly lower mean value of the ancestral component q0 than controls for both cohorts (P = 6.14-4; P = 3-6), consistent with higher degree of African ancestry. Among POAG cases, higher African ancestry was also associated with thinner central corneal thickness (P = 2-4). Admixture mapping showed that local genetic ancestry was not a significant risk factor for POAG. A polygenic risk score, comprised of 23 glaucoma-associated single nucleotide polymorphisms from the NHGRI-EBI genome-wide association study catalog, was significant in both cohorts (P < 0.001), suggesting that both known POAG single nucleotide polymorphisms and an omnigenic ancestry effect influence POAG risk. Conclusions In sum, the POAAGG study population is very admixed, with a higher degree of African ancestry associated with an increased POAG risk. Further analyses should consider social and environmental factors as possible confounding factors for disease predisposition.
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Affiliation(s)
- Brian S. Cole
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Harini V. Gudiseva
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Maxwell Pistilli
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Rebecca Salowe
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | | | - Michael C. Zody
- New York Genome Center, New York City, New York, United States
| | - Venkata R. M. Chavali
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Gui Shuang Ying
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Jason H. Moore
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joan M. O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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26
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Hassan R, Allali I, Agamah FE, Elsheikh SSM, Thomford NE, Dandara C, Chimusa ER. Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine. Brief Bioinform 2020; 22:6012864. [PMID: 33253350 DOI: 10.1093/bib/bbaa292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/19/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.
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Affiliation(s)
- Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | | | - Nicholas E Thomford
- Lecturers at the Department of Medical Biochemistry School of Medical Sciences, University of Cape Coast, Ghana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town
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27
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Katongole P, Sande OJ, Yusuf M, Joloba M, Reynolds SJ, Niyonzima N. Clinical characteristics and primary management of patients diagnosed with prostate cancer between 2015 and 2019 at the Uganda Cancer Institute. PLoS One 2020; 15:e0236458. [PMID: 33125383 PMCID: PMC7598473 DOI: 10.1371/journal.pone.0236458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/18/2020] [Indexed: 12/24/2022] Open
Abstract
Background Prostate cancer is the second most common cancer among men in Uganda, with over 2086 incident cases in 2018. This study’s objective was to report the clinical characteristics and primary management of men diagnosed with prostate cancer at the Uganda Cancer Institute from 1st January 2015 to 31st December 2019. Methods Records from all men diagnosed with Prostate cancer at the Uganda Cancer Institute from 1st January 2015 to 31st December 2019 were reviewed. Clinical characteristics and primary treatment were recorded. Risk categorization was done using the European Society for Medical Oncology prostate cancer risk group classification. Results A total of 874 medical records for men diagnosed with prostate cancer was retrieved. The median age was 70 years (interquartile range 64–77). In this study, 501 (57.32%) patients had localized disease. Among patients with localized disease, 2 (0.23%) were classified as low-risk, 5 (0.53%) as intermediate-risk, and 494 (56.52%) as high-risk. Three hundred seventy-three (373) patients had metastatic disease at diagnosis. Among patients with distant metastases, the most common site of metastases was bone 143 (16.36%), followed by spinal cord 54 (6.18%), abdomen 22 (2.52%), and lungs 14 (1.60%). Regarding the primary treatment options majority of the patients were on chemotherapy 384(43.94%) followed by hormonal therapy 336 (38.44%) and radiotherapy 127 (14.53%). Conclusion The majority of the patients diagnosed with prostate cancer at the Uganda Cancer Institute presented with advanced disease. The primary treatments were mostly chemotherapy, hormonal therapy, and radiotherapy. There is a need to improve prostate cancer screening in regional health care facilities and the communities to enhance early detection and management of prostate cancer.
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Affiliation(s)
- Paul Katongole
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Department of Medical Biochemistry, College of Health Sciences Makerere University, Kampala, Uganda
- * E-mail:
| | - Obondo J. Sande
- Department of Immunology and Molecular Biology, College of Health Sciences Makerere University, Kampala, Uganda
| | | | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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28
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Theusch E, Chen YDI, Rotter JI, Krauss RM, Medina MW. Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines. BMC Genomics 2020; 21:555. [PMID: 32787775 PMCID: PMC7430882 DOI: 10.1186/s12864-020-06966-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/03/2020] [Indexed: 01/10/2023] Open
Abstract
Background Statins are widely prescribed to lower plasma low-density lipoprotein cholesterol levels. Though statins reduce cardiovascular disease risk overall, statin efficacy varies, and some people experience adverse side effects while on statin treatment. Statins also have pleiotropic effects not directly related to their cholesterol-lowering properties, but the mechanisms are not well understood. To identify potential genetic modulators of clinical statin response, we looked for genetic variants associated with statin-induced changes in gene expression (differential eQTLs or deQTLs) in lymphoblastoid cell lines (LCLs) derived from participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial. We exposed CAP LCLs to 2 μM simvastatin or control buffer for 24 h and performed polyA-selected, strand-specific RNA-seq. Statin-induced changes in gene expression from 259 European ancestry or 153 African American ancestry LCLs were adjusted for potential confounders prior to association with genotyped and imputed genetic variants within 1 Mb of each gene’s transcription start site. Results From the deQTL meta-analysis of the two ancestral populations, we identified significant cis-deQTLs for 15 genes (TBC1D4, MDGA1, CHI3L2, OAS1, GATM, ASNSD1, GLUL, TDRD12, PPIP5K2, OAS3, SERPINB1, ANKDD1A, DTD1, CYFIP2, and GSDME), eight of which were significant in at least one of the ancestry subsets alone. We also conducted eQTL analyses of the endogenous (control-treated), statin-treated, and average of endogenous and statin-treated LCL gene expression levels. We identified eQTLs for approximately 6000 genes in each of the three (endogenous, statin-treated, and average) eQTL meta-analyses, with smaller numbers identified in the ancestral subsets alone. Conclusions Several of the genes in which we identified deQTLs have functions in human health and disease, such as defense from viruses, glucose regulation, and response to chemotherapy drugs. This suggests that DNA variation may play a role in statin effects on various health outcomes. These findings could prove useful to future studies aiming to assess benefit versus risk of statin treatment using individual genetic profiles.
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Affiliation(s)
- Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Yii-Der I Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald M Krauss
- Departments of Pediatrics and Medicine, University of California San Francisco, Oakland, CA, USA
| | - Marisa W Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA.
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29
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Piccini G, Montomoli E. Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development. Hum Vaccin Immunother 2020; 16:2056-2071. [PMID: 32692622 PMCID: PMC7553687 DOI: 10.1080/21645515.2020.1785791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Invasive non-typhoidal Salmonella (iNTS) infections are a leading cause of bacteremia in Sub-Saharan Africa (sSA), thereby representing a major public health threat. Salmonella Typhimurium clade ST313 and Salmonella Enteriditis lineages associated with Western and Central/Eastern Africa are among the iNTS serovars which are of the greatest concern due to their case-fatality rate, especially in children and in the immunocompromised population. Identification of pathogen-associated features and host susceptibility factors that increase the risk for invasive non-typhoidal salmonellosis would be instrumental for the design of targeted prevention strategies, which are urgently needed given the increasing spread of multidrug-resistant iNTS in Africa. This review summarizes current knowledge of bacterial traits and host immune responses associated with iNTS infections in sSA, then discusses how this knowledge can guide vaccine development while providing a summary of vaccine candidates in preclinical and early clinical development.
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Affiliation(s)
| | - Emanuele Montomoli
- VisMederi srl , Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena , Siena, Italy
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30
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Gingras SN, Tang D, Tuff J, McLaren PJ. Minding the gap in HIV host genetics: opportunities and challenges. Hum Genet 2020; 139:865-875. [PMID: 32409920 PMCID: PMC7272494 DOI: 10.1007/s00439-020-02177-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in identifying and confirming novel genetic variants that are associated with diverse HIV phenotypes. However, these studies have predominantly focused on European cohorts. HLA molecules have been consistently associated with HIV outcomes, some of which have been found to be population specific, underscoring the need for diversity in GWAS. Recently, there has been a concerted effort to address this gap that leads to health care (disease prevention, diagnosis, treatment) disparities with marginal improvement. As precision medicine becomes more utilized, non-European individuals will be more and more disadvantaged, as the genetic variants identified in genomic research based on European populations may not accurately reflect that of non-European individuals. Leveraging pre-existing, large, multiethnic cohorts, such as the UK Biobank, 23andMe, and the National Institute of Health's All of Us Research Program, can contribute in raising genomic research in non-European populations and ultimately lead to better health outcomes.
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Affiliation(s)
- Shanelle N. Gingras
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - David Tang
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeffrey Tuff
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Paul J. McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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31
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Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Cell 2020; 179:984-1002.e36. [PMID: 31675503 DOI: 10.1016/j.cell.2019.10.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/03/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.
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Affiliation(s)
- Deepti Gurdasani
- William Harvey Research Institute, Queen Mary's University of London, London, UK
| | | | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI)/National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | | | | | | | - Marc Haber
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Tachmazidou
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY, UK
| | - Iain Mathieson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Ekoru
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris Finan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Li Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Alex J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles L Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Dermot Maher
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Stephen B Montgomery
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew P Morris
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Biostatistics, University of Liverpool, Liverpool, UK
| | | | | | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA.
| | - Pontiano Kaleebu
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda.
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK.
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Manry J, Vincent QB, Johnson C, Chrabieh M, Lorenzo L, Theodorou I, Ardant MF, Marion E, Chauty A, Marsollier L, Abel L, Alcaïs A. Genome-wide association study of Buruli ulcer in rural Benin highlights role of two LncRNAs and the autophagy pathway. Commun Biol 2020; 3:177. [PMID: 32313116 PMCID: PMC7171125 DOI: 10.1038/s42003-020-0920-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/24/2020] [Indexed: 02/07/2023] Open
Abstract
Buruli ulcer, caused by Mycobacterium ulcerans and characterized by devastating necrotizing skin lesions, is the third mycobacterial disease worldwide. The role of host genetics in susceptibility to Buruli ulcer has long been suggested. We conduct the first genome-wide association study of Buruli ulcer on a sample of 1524 well characterized patients and controls from rural Benin. Two-stage analyses identify two variants located within LncRNA genes: rs9814705 in ENSG00000240095.1 (P = 2.85 × 10−7; odds ratio = 1.80 [1.43–2.27]), and rs76647377 in LINC01622 (P = 9.85 × 10−8; hazard ratio = 0.41 [0.28–0.60]). Furthermore, we replicate the protective effect of allele G of a missense variant located in ATG16L1, previously shown to decrease bacterial autophagy (rs2241880, P = 0.003; odds ratio = 0.31 [0.14–0.68]). Our results suggest LncRNAs and the autophagy pathway as critical factors in the development of Buruli ulcer. Jeremy Manry, Quentin Vincent et al. report a genome-wide association study for susceptibility to Buruli ulcer in a rural population from the West African country of Benin. They identify two independently associated variants within LncRNA genes and confirm the protective effect of a missense variant in the bacterial autophagy gene ATG16L1.
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Affiliation(s)
- Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France. .,Université de Paris, Imagine Institute, Paris, France.
| | - Quentin B Vincent
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Christian Johnson
- Fondation Raoul Follereau, Paris, France.,Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable. Université d'Abomey, Calavi, Benin
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France
| | - Ioannis Theodorou
- Center for Immunology and Infectious Diseases, INSERM UMR S 1135, Pierre and Marie Curie University, and AP-HP Laboratoire d'Immunologie et Histocompatibilité Hôpital Saint-Louis, Paris, France
| | - Marie-Françoise Ardant
- Fondation Raoul Follereau, Paris, France.,Centre de Dépistage et de Traitement de la Lèpre et de l'Ulcère de Buruli (CDTLUB), Pobè, Benin
| | - Estelle Marion
- INSERM UMR-U892 and CNRS U6299, team 7, Angers University, Angers University Hospital, Angers, France
| | - Annick Chauty
- Fondation Raoul Follereau, Paris, France.,Centre de Dépistage et de Traitement de la Lèpre et de l'Ulcère de Buruli (CDTLUB), Pobè, Benin
| | - Laurent Marsollier
- INSERM UMR-U892 and CNRS U6299, team 7, Angers University, Angers University Hospital, Angers, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France.,Université de Paris, Imagine Institute, Paris, France.,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Paris, France. .,Université de Paris, Imagine Institute, Paris, France.
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Zhong Y, De T, Alarcon C, Park CS, Lec B, Perera MA. Discovery of novel hepatocyte eQTLs in African Americans. PLoS Genet 2020; 16:e1008662. [PMID: 32310939 PMCID: PMC7192504 DOI: 10.1371/journal.pgen.1008662] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 04/30/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL. These AA-specific eQTLs are less correlated to GTEx eQTLs. in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs). We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci. Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes. Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.
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Affiliation(s)
- Yizhen Zhong
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tanima De
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Cristina Alarcon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - C. Sehwan Park
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bianca Lec
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Minoli A. Perera
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- * E-mail:
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Abstract
BACKGROUND Age at menarche and age at natural menopause occur significantly earlier in African American women than in other ethnic groups. African American women also have twice the prevalence of cardiometabolic disorders related to the timing of these reproductive traits. OBJECTIVES The objectives of this integrative review were to (a) summarize the genome-wide association studies of reproductive traits in African American women, (b) identify genes that overlap with reproductive traits and cardiometabolic risk factors in African American women, and (c) propose biological mechanisms explaining the link between reproductive traits and cardiometabolic risk factors. METHODS PubMed was searched for genome-wide association studies of genes associated with reproductive traits in African American women. After extracting and summarizing the primary genes, we examined whether any of the associations with reproductive traits had also been identified with cardiometabolic risk factors in African American women. RESULTS Seven studies met the inclusion criteria. Associations with both reproductive and cardiometabolic traits were reported in or near the following genes: FTO, SEC16B, TMEM18, APOE, PHACTR1, KCNQ1, LDLR, PIK3R1, and RORA. Biological pathways implicated include body weight regulation, vascular homeostasis, and lipid metabolism. DISCUSSION A better understanding of the genetic basis of reproductive traits in African American women may provide insight into the biological mechanisms linking variation in these traits with increased risk for cardiometabolic disorders in this population.
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Lule SA, Mentzer AJ, Namara B, Muwenzi AG, Nassanga B, kizito D, Akurut H, Lubyayi L, Tumusiime J, Zziwa C, Akello F, Gurdasani D, Sandhu M, Smeeth L, Elliott AM, Webb EL. A genome-wide association and replication study of blood pressure in Ugandan early adolescents. Mol Genet Genomic Med 2019; 7:e00950. [PMID: 31469255 PMCID: PMC6785527 DOI: 10.1002/mgg3.950] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genetic association studies of blood pressure (BP) have mostly been conducted in non-African populations. Using the Entebbe Mother and Baby Study (EMaBS), we aimed to identify genetic variants associated with BP among Ugandan adolescents. METHODS Systolic and diastolic BP were measured among 10- and 11-year olds. Whole-genome genotype data were generated using Illumina omni 2.5M arrays and untyped variants were imputed. Genome-wide association study (GWAS) was conducted using linear mixed model regression to account for population structure. Linear regression analysis was used to assess whether variants previously associated with BP (p < 5.0 × 10-8 ) in published BP GWASs were replicated in our study. RESULTS Of the 14 million variants analyzed among 815 adolescents, none reached genome-wide significance (p < 5.0×10-8 ) for association with systolic or diastolic BP. The most strongly associated variants were rs181430167 (p = 6.8 × 10-7 ) for systolic BP and rs12991132 (p = 4.0 × 10-7 ) for diastolic BP. Thirty-three (17 single nucleotide polymorphisms (SNPs) for systolic BP, 15 SNPs for diastolic BP and one SNP for both) of 330 variants previously identified as associated with BP were replicated in this study, but none remained significant after accounting for multiple testing. CONCLUSION Variants showing suggestive associations are worthy of future investigation. Replication results suggest that variants influencing adolescent BP may overlap somewhat with those already established in previous studies, largely based on adults in Western settings.
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Affiliation(s)
- Swaib A. Lule
- London School of Hygiene and Tropical MedicineLondonUK
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | - Alexander J. Mentzer
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
- Big Data Institute, Li Ka Shing Centre for Health Information and DiscoveryUniversity of OxfordOxfordUK
| | | | | | | | | | - Helen Akurut
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | | | | | | | | | - Deept Gurdasani
- Wellcome Trust Sanger InstituteCambridgeUK
- University of CambridgeCambridgeUK
| | - Manjinder Sandhu
- Wellcome Trust Sanger InstituteCambridgeUK
- University of CambridgeCambridgeUK
| | - Liam Smeeth
- London School of Hygiene and Tropical MedicineLondonUK
| | - Alison M. Elliott
- London School of Hygiene and Tropical MedicineLondonUK
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | - Emily L. Webb
- London School of Hygiene and Tropical MedicineLondonUK
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Freedman D, Zaami S. Neuroscience and mental state issues in forensic assessment. INTERNATIONAL JOURNAL OF LAW AND PSYCHIATRY 2019; 65:101437. [PMID: 30952490 DOI: 10.1016/j.ijlp.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Neuroscience has already changed how the law understands an individual's cognitive processes, how those processes shape behavior, and how bio-psychosocial history and neurodevelopmental approaches provide information, which is critical to understanding mental states underlying behavior, including criminal behavior. In this paper, we briefly review the state of forensic assessment of mental conditions in the relative culpability of criminal defendants, focused primarily on the weaknesses of current approaches. We then turn to focus on neuroscience approaches and how they have the potential to improve assessment, but with significant risks and limitations.
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Affiliation(s)
- David Freedman
- International Academy of Law and Mental Health, PO Box 205, New York, NY 10276, United States of America.
| | - Simona Zaami
- Forensic Medicine, Sapienza University of Rome, Rome, Italy
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Fatumo S, Carstensen T, Nashiru O, Gurdasani D, Sandhu M, Kaleebu P. Complimentary Methods for Multivariate Genome-Wide Association Study Identify New Susceptibility Genes for Blood Cell Traits. Front Genet 2019; 10:334. [PMID: 31080455 PMCID: PMC6497788 DOI: 10.3389/fgene.2019.00334] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/28/2019] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have found hundreds of novel loci associated with full blood count (FBC) phenotypes. However, most of these studies were performed in a single phenotype framework without putting into consideration the clinical relatedness among traits. In this work, in addition to the standard univariate GWAS, we also use two different multivariate methods to perform the first multiple traits GWAS of FBC traits in ∼7000 individuals from the Ugandan General Population Cohort (GPC). We started by performing the standard univariate GWAS approach. We then performed our first multivariate method, in this approach, we tested for marker associations with 15 FBC traits simultaneously in a multivariate mixed model implemented in GEMMA while accounting for the relatedness of individuals and pedigree structures, as well as population substructure. In this analysis, we provide a framework for the combination of multiple phenotypes in multivariate GWAS analysis and show evidence of multi-collinearity whenever the correlation between traits exceeds the correlation coefficient threshold of r 2 >=0.75. This approach identifies two known and one novel loci. In the second multivariate method, we applied principal component analysis (PCA) to the same 15 correlated FBC traits. We then tested for marker associations with each PC in univariate linear mixed models implemented in GEMMA. We show that the FBC composite phenotype as assessed by each PC expresses information that is not completely encapsulated by the individual FBC traits, as this approach identifies three known and five novel loci that were not identified using both the standard univariate and multivariate GWAS methods. Across both multivariate methods, we identified six novel loci. As a proof of concept, both multivariate methods also identified known loci, HBB and ITFG3. The two multivariate methods show that multivariate genotype-phenotype methods increase power and identify novel genotype-phenotype associations not found with the standard univariate GWAS in the same dataset.
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Affiliation(s)
- Segun Fatumo
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda,London School of Hygiene and Tropical Medicine, London, United Kingdom,H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria,*Correspondence: Segun Fatumo, ;
| | - Tommy Carstensen
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Deepti Gurdasani
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Manjinder Sandhu
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom,Division of Computational Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pontiano Kaleebu
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda,London School of Hygiene and Tropical Medicine, London, United Kingdom
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38
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Mweemba O, Musuku J, Mayosi BM, Parker M, Rutakumwa R, Seeley J, Tindana P, De Vries J. Use of broad consent and related procedures in genomics research: Perspectives from research participants in the Genetics of Rheumatic Heart Disease (RHDGen) study in a University Teaching Hospital in Zambia. Glob Bioeth 2019; 31:184-199. [PMID: 33343192 PMCID: PMC7734073 DOI: 10.1080/11287462.2019.1592868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The use of broad consent for genomics research raises important ethical questions for the conduct of genomics research, including relating to its acceptability to research participants and comprehension of difficult scientific concepts. To explore these and other challenges, we conducted a study using qualitative methods with participants enrolled in an H3Africa Rheumatic Heart Disease genomics study (the RHDGen network) in Zambia to explore their views on broad consent, sample and data sharing and secondary use. In-depth interviews were conducted with RHDGen participants (n = 18), study staff (n = 5) and with individuals who refused to participate (n = 3). In general, broad consent was seen to be reasonable if reasons for storing the samples for future research use were disclosed. Some felt that broad consent should be restricted by specifying planned future studies and that secondary research should ideally relate to original disease for which samples were collected. A few participants felt that broad consent would delay the return of research results to participants. This study echoes findings in other similar studies in other parts of the continent that suggested that broad consent could be an acceptable consent model in Africa if careful thought is given to restrictions on re-use.
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Affiliation(s)
- Oliver Mweemba
- Department of Health Promotion and Education, University of Zambia, Lusaka, Zambia
| | - John Musuku
- Children Hospital, University Teaching Hospitals, Lusaka, Zambia
| | - Bongani M Mayosi
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Michael Parker
- Wellcome Centre for Ethics and Humanities (Ethox), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rwamahe Rutakumwa
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda.,Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, UK
| | - Paulina Tindana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Jantina De Vries
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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Palk AC, Dalvie S, de Vries J, Martin AR, Stein DJ. Potential use of clinical polygenic risk scores in psychiatry - ethical implications and communicating high polygenic risk. Philos Ethics Humanit Med 2019; 14:4. [PMID: 30813945 PMCID: PMC6391805 DOI: 10.1186/s13010-019-0073-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/14/2019] [Indexed: 06/09/2023] Open
Abstract
Psychiatric disorders present distinct clinical challenges which are partly attributable to their multifactorial aetiology and the absence of laboratory tests that can be used to confirm diagnosis or predict risk. Psychiatric disorders are highly heritable, but also polygenic, with genetic risk conferred by interactions between thousands of variants of small effect that can be summarized in a polygenic risk score. We discuss four areas in which the use of polygenic risk scores in psychiatric research and clinical contexts could have ethical implications. First, there is concern that clinical use of polygenic risk scores may exacerbate existing health inequities. Second, research findings regarding polygenic risk could be misinterpreted in stigmatising or discriminatory ways. Third, there are concerns associated with testing minors as well as eugenics concerns elicited by prenatal polygenic risk testing. Fourth, potential challenges that could arise with the feedback and interpretation of high polygenic risk for a psychiatric disorder would require consideration. While there would be extensive overlap with the challenges of feeding back genetic findings in general, the potential clinical use of polygenic risk scoring warrants discussion in its own right, given the recency of this possibility. To this end, we discuss how lay interpretations of risk and genetic information could intersect. Consideration of these factors would be necessary for ensuring effective and constructive communication and interpretation of polygenic risk information which, in turn, could have implications for the uptake of any therapeutic recommendations. Recent advances in polygenic risk scoring have major implications for its clinical potential, however, care should be taken to ensure that communication of polygenic risk does not feed into problematic assumptions regarding mental disorders or support reductive interpretations.
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Affiliation(s)
- A. C. Palk
- Department of Psychiatry, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925 South Africa
| | - S. Dalvie
- Department of Psychiatry and SA MRC Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925 South Africa
| | - J. de Vries
- Department of Medicine, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925 South Africa
| | - A. R. Martin
- Analytic & Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
- Stanley Center for Psychiatric Research & Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - D. J. Stein
- Department of Psychiatry and SA MRC Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925 South Africa
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40
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Modeling Heterogeneity in the Genetic Architecture of Ethnically Diverse Groups Using Random Effect Interaction Models. Genetics 2019; 211:1395-1407. [PMID: 30796011 PMCID: PMC6456318 DOI: 10.1534/genetics.119.301909] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
In humans, most genome-wide association studies have been conducted using data from Caucasians and many of the reported findings have not replicated in other populations. This lack of replication may be due to statistical issues (small sample sizes or confounding) or perhaps more fundamentally to differences in the genetic architecture of traits between ethnically diverse subpopulations. What aspects of the genetic architecture of traits vary between subpopulations and how can this be quantified? We consider studying effect heterogeneity using Bayesian random effect interaction models. The proposed methodology can be applied using shrinkage and variable selection methods, and produces useful information about effect heterogeneity in the form of whole-genome summaries (e.g., the proportions of variance of a complex trait explained by a set of SNPs and the average correlation of effects) as well as SNP-specific attributes. Using simulations, we show that the proposed methodology yields (nearly) unbiased estimates when the sample size is not too small relative to the number of SNPs used. Subsequently, we used the methodology for the analyses of four complex human traits (standing height, high-density lipoprotein, low-density lipoprotein, and serum urate levels) in European-Americans (EAs) and African-Americans (AAs). The estimated correlations of effects between the two subpopulations were well below unity for all the traits, ranging from 0.73 to 0.50. The extent of effect heterogeneity varied between traits and SNP sets. Height showed less differences in SNP effects between AAs and EAs whereas HDL, a trait highly influenced by lifestyle, exhibited a greater extent of effect heterogeneity. For all the traits, we observed substantial variability in effect heterogeneity across SNPs, suggesting that effect heterogeneity varies between regions of the genome.
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Closing the Disparity in Pancreatic Cancer Outcomes: A Closer Look at Nonmodifiable Factors and Their Potential Use in Treatment. Pancreas 2019; 48:242-249. [PMID: 30629027 DOI: 10.1097/mpa.0000000000001238] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES African Americans (AAs) have disproportionately higher incidence and lower survival rates from pancreatic cancer compared with whites. Historically, this disparity has been attributed to modifiable risk factors. Recent studies suggest that nonmodifiable aspects may also play an important role. We review these new contributions as potential targets for closing the disparity. METHODS A PubMed search was conducted to review studies of nonmodifiable elements contributing to pancreatic cancer disparities in AAs. RESULTS Several nonmodifiable risks are associated with the racial disparity in pancreatic cancer. SSTR5 P335L, Kaiso, and KDM4/JMJD2A demonstrate differential racial expression, increasing their potential as therapeutic targets. Many social determinants of health and their associations with diabetes, obesity, and the microbiome are partially modifiable risk factors that significantly contribute to outcomes in minorities. Barriers to progress include the low minority inclusion in research studies. CONCLUSIONS Genomics, epigenetics, the microbiome, and social determinants of health are components that contribute to the pancreatic cancer disparity in AAs. These factors can be researched, targeted, and modified to improve mortality rates. Closing the disparity in pancreatic cancer will require an integrated approach of personalized medicine, increased minority recruitment to studies, and advanced health care/education access.
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Suarez-Kurtz G, Aklillu E, Saito Y, Somogyi AA. Conference report: pharmacogenomics in special populations at WCP2018. Br J Clin Pharmacol 2019; 85:467-475. [PMID: 30537134 DOI: 10.1111/bcp.13828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
The 18th World Congress of Basic and Clinical Pharmacology (WCP2018), coordinated by IUPHAR and hosted by the Japanese Pharmacological Society and the Japanese Society of Clinical Pharmacology and Therapeutics, was held in July 2018 at the Kyoto International Conference Center, in Kyoto, Japan. Having as its main theme 'Pharmacology for the Future: Science, Drug Development and Therapeutics', WCP2018 was attended by over 4500 delegates, representing 78 countries. The present report is an overview of a symposium at WCP2018, entitled Pharmacogenomics in Special Populations, organized by IUPHAR´s Pharmacogenetics/Genomics (PGx) section. The PGx section congregates distinguished scientists from different continents, covering expertise from basic research, to clinical implementation and ethical aspects of PGx, and one of its major activities is the coordination of symposia and workshops to foster exchange of PGx knowledge (https://iuphar.org/sections-subcoms/pharmacogenetics-genomics/). The symposium attracted a large audience to listen to presentations covering various areas of research and clinical adoption of PGx in Oceania, Africa, Latin America and Asia.
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Affiliation(s)
| | - Eleni Aklillu
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yoshiro Saito
- Division of Medical Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, Australia
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Awany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER. Host and Microbiome Genome-Wide Association Studies: Current State and Challenges. Front Genet 2019; 9:637. [PMID: 30723493 PMCID: PMC6349833 DOI: 10.3389/fgene.2018.00637] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
The involvement of the microbiome in health and disease is well established. Microbiome genome-wide association studies (mGWAS) are used to elucidate the interaction of host genetic variation with the microbiome. The emergence of this relatively new field has been facilitated by the advent of next generation sequencing technologies that enable the investigation of the complex interaction between host genetics and microbial communities. In this paper, we review recent studies investigating host-microbiome interactions using mGWAS. Additionally, we highlight the marked disparity in the sampling population of mGWAS carried out to date and draw attention to the critical need for inclusion of diverse populations.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Sian Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kilaza S Mwaikono
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andres Gomez
- Department of Animal Science, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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An KR, Tam DY, Fremes SE. Commentary: The association of race with coronary artery bypass grafting mortality: A complex issue. J Thorac Cardiovasc Surg 2018; 157:2226-2227. [PMID: 30678879 DOI: 10.1016/j.jtcvs.2018.12.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Kevin R An
- From the Schulich Heart Centre, Division of Cardiac Surgery, Department of Surgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Derrick Y Tam
- From the Schulich Heart Centre, Division of Cardiac Surgery, Department of Surgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephen E Fremes
- From the Schulich Heart Centre, Division of Cardiac Surgery, Department of Surgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada.
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Hayes VM, Bornman MSR. Prostate Cancer in Southern Africa: Does Africa Hold Untapped Potential to Add Value to the Current Understanding of a Common Disease? J Glob Oncol 2018; 4:1-7. [PMID: 30241160 PMCID: PMC6223485 DOI: 10.1200/jgo.2016.008862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Vanessa M Hayes
- Vanessa M. Hayes, University of Sydney, University of New South Wales, and Garvan Institute of Medical Research, Sydney, Australia; and University of Limpopo, Limpopo, South Africa and; Vanessa M. Hayes and M.S. Riana Bornman, University of Pretoria, Pretoria South Africa
| | - M S Riana Bornman
- Vanessa M. Hayes, University of Sydney, University of New South Wales, and Garvan Institute of Medical Research, Sydney, Australia; and University of Limpopo, Limpopo, South Africa and; Vanessa M. Hayes and M.S. Riana Bornman, University of Pretoria, Pretoria South Africa
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46
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Awany D, Allali I, Chimusa ER. Tantalizing dilemma in risk prediction from disease scoring statistics. Brief Funct Genomics 2018; 18:211-219. [PMID: 30605512 PMCID: PMC6609536 DOI: 10.1093/bfgp/ely040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 08/17/2018] [Accepted: 11/29/2018] [Indexed: 02/01/2023] Open
Abstract
Over the past decade, human host genome-wide association studies (GWASs) have contributed greatly to our understanding of the impact of host genetics on phenotypes. Recently, the microbiome has been recognized as a complex trait in host genetic variation, leading to microbiome GWAS (mGWASs). For these, many different statistical methods and software tools have been developed for association mapping. Applications of these methods and tools have revealed several important findings; however, the establishment of causal factors and the direction of causality in the interactive role between human genetic polymorphisms, the microbiome and the host phenotypes are still a huge challenge. Here, we review disease scoring approaches in host and mGWAS and their underlying statistical methods and tools. We highlight the challenges in pinpointing the genetic-associated causal factors in host and mGWAS and discuss the role of multi-omic approach in disease scoring statistics that may provide a better understanding of human phenotypic variation by enabling further system biological experiment to establish causality.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
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47
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Xu H, Dorn GW, Shetty A, Parihar A, Dave T, Robinson SW, Gottlieb SS, Donahue MP, Tomaselli GF, Kraus WE, Mitchell BD, Liggett SB. A Genome-Wide Association Study of Idiopathic Dilated Cardiomyopathy in African Americans. J Pers Med 2018; 8:E11. [PMID: 29495422 PMCID: PMC5872085 DOI: 10.3390/jpm8010011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 01/03/2023] Open
Abstract
Idiopathic dilated cardiomyopathy (IDC) is the most common form of non-ischemic chronic heart failure. Despite the higher prevalence of IDC in African Americans, the genetics of IDC have been relatively understudied in this ethnic group. We performed a genome-wide association study to identify susceptibility genes for IDC in African Americans recruited from five sites in the U.S. (662 unrelated cases and 1167 controls). The heritability of IDC was calculated to be 33% (95% confidence interval: 19-47%; p = 6.4 × 10-7). We detected association of a variant in a novel intronic locus in the CACNB4 gene meeting genome-wide levels of significance (p = 4.1 × 10-8). The CACNB4 gene encodes a calcium channel subunit expressed in the heart that is important for cardiac muscle contraction. This variant has not previously been associated with IDC in any racial group. Pathway analysis, based on the 1000 genes most strongly associated with IDC, showed an enrichment for genes related to calcium signaling, growth factor signaling, neuronal/neuromuscular signaling, and various types of cellular level signaling, including gap junction and cAMP signaling. Our results suggest a novel locus for IDC in African Americans and provide additional insights into the genetic architecture and etiology.
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Affiliation(s)
- Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Gerald W Dorn
- Center for Pharmacogenomics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Ankita Parihar
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Tushar Dave
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Shawn W Robinson
- Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Stephen S Gottlieb
- Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mark P Donahue
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27708, USA.
| | - Gordon F Tomaselli
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - William E Kraus
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27708, USA.
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA.
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA.
| | - Stephen B Liggett
- Department of Internal Medicine and Molecular Pharmacology and Physiology, and the Center for Personalized Medicine and Genomics, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA.
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Sallah N, Carstensen T, Wakeham K, Bagni R, Labo N, Pollard MO, Gurdasani D, Ekoru K, Pomilla C, Young EH, Fatumo S, Asiki G, Kamali A, Sandhu M, Kellam P, Whitby D, Barroso I, Newton R. Whole-genome association study of antibody response to Epstein-Barr virus in an African population: a pilot. Glob Health Epidemiol Genom 2017; 2:e18. [PMID: 29868224 PMCID: PMC5870407 DOI: 10.1017/gheg.2017.16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 02/02/2023] Open
Abstract
Epstein Barr virus (EBV) infects 95% of the global population and is associated with up to 2% of cancers globally. Immunoglobulin G (IgG) antibody levels to EBV have been shown to be heritable and associated with developing malignancies. We, therefore, performed a pilot genome-wide association analysis of anti-EBV IgG traits in an African population, using a combined approach including array genotyping, whole-genome sequencing and imputation to a panel with African sequence data. In 1562 Ugandans, we identify a variant in human leukocyte antigen (HLA)-DQA1, rs9272371 (p = 2.6 × 10-17) associated with anti-EBV nuclear antigen-1 responses. Trans-ancestry meta-analysis and fine-mapping with European-ancestry individuals suggest the presence of distinct HLA class II variants driving associations in Uganda. In addition, we identify four putative, novel, very rare African-specific loci with preliminary evidence for association with anti-viral capsid antigen IgG responses which will require replication for validation. These findings reinforce the need for the expansion of such studies in African populations with relevant datasets to capture genetic diversity.
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Affiliation(s)
- N. Sallah
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - T. Carstensen
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - K. Wakeham
- MRC/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - R. Bagni
- Protein Expression Lab, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - N. Labo
- Viral Oncology Section, Aids and Cancer Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - M. O. Pollard
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - D. Gurdasani
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - K. Ekoru
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C. Pomilla
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - E. H. Young
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - S. Fatumo
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria
| | - G. Asiki
- MRC/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - A. Kamali
- MRC/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - M. Sandhu
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - P. Kellam
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - D. Whitby
- Viral Oncology Section, Aids and Cancer Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - I. Barroso
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - R. Newton
- MRC/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
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49
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Petros Z, Lee MTM, Takahashi A, Zhang Y, Yimer G, Habtewold A, Schuppe-Koistinen I, Mushiroda T, Makonnen E, Kubo M, Aklillu E. Genome-Wide Association and Replication Study of Hepatotoxicity Induced by Antiretrovirals Alone or with Concomitant Anti-Tuberculosis Drugs. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:207-216. [PMID: 28388302 DOI: 10.1089/omi.2017.0019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients. Treatment-naïve newly diagnosed HIV patients (n = 719) with or without tuberculosis (TB) co-infection were enrolled prospectively and received efavirenz-based ARV therapy with or without rifampicin-based short course ATD, respectively. Whole-genome genotyping was performed by using the Illumina Omni Express Exome Bead Chip genotyping array with 951,117 single nucleotide polymorphisms (SNPs) on a total of 41 cases of DIH, and 452 people without DIH (treatment tolerants). The replication study was carried out for 100 SNPs with the lowest p-values (top SNPs) by using an independent cohort consisting of 18 DIH cases and 208 treatment tolerants. We identified a missense SNP rs199650082 (2756G→A, R919Q, p = 1.4 × 10-6, odds ratio [OR] = 18.2, 95% confidence interval [CI] = 7.1-46.9) in an endoplasmic reticulum to the nucleus signaling-1 (ERN1) gene on chromosome 17 to be associated with DIH in the ARV-only cohort. In the ARV-ATD co-treatment groups, rs4842407, a long intergenic noncoding RNAs (lincRNAs) transcript variant on chromosome 12, was associated with DIH (p = 5.3 × 10-7, OR = 5.4, 95% CI = 2.8-10.3). These genetic variants that are putatively associated with DIH due to ARV drugs alone and ARV-ATD co-treatment establish a foundation for future personalized medicine in people with HIV and TB and call for larger studies in independent populations.
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Affiliation(s)
- Zelalem Petros
- 1 Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan .,2 Department of Pharmacology, School of Medicine, College of Health Sciences, Addis Ababa University , Addis Ababa, Ethiopia
| | - Ming Ta Michael Lee
- 1 Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan
| | - Atsushi Takahashi
- 3 Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan
| | - Yanfei Zhang
- 1 Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan
| | - Getnet Yimer
- 2 Department of Pharmacology, School of Medicine, College of Health Sciences, Addis Ababa University , Addis Ababa, Ethiopia
| | - Abiy Habtewold
- 2 Department of Pharmacology, School of Medicine, College of Health Sciences, Addis Ababa University , Addis Ababa, Ethiopia
| | - Ina Schuppe-Koistinen
- 4 Department of Physiology and Pharmacology, Science for Life Laboratory, Karolinska Institutet , Stockholm, Sweden
| | - Taisei Mushiroda
- 5 Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan
| | - Eyasu Makonnen
- 2 Department of Pharmacology, School of Medicine, College of Health Sciences, Addis Ababa University , Addis Ababa, Ethiopia
| | - Michiaki Kubo
- 6 Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences , Yokohama, Japan
| | - Eleni Aklillu
- 7 Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge C1:68 , KarolinskaInstitutet, Stockholm, Sweden
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Salowe R, O’Keefe L, Merriam S, Lee R, Khachatryan N, Sankar P, Miller-Ellis E, Lehman A, Addis V, Murphy W, Henderer J, Maguire M, O’Brien J. Cost and yield considerations when expanding recruitment for genetic studies: the primary open-angle African American glaucoma genetics study. BMC Med Res Methodol 2017; 17:101. [PMID: 28705151 PMCID: PMC5512952 DOI: 10.1186/s12874-017-0374-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/26/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND African Americans have been historically under-represented in genetic studies. More research is needed on effective recruitment strategies for this population, especially on approaches that supplement traditional clinic enrollment. This study evaluates the cost and efficacy of four supplemental recruitment methods employed by the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study. METHODS After enrolling 2304 patients from University of Pennsylvania ophthalmology clinics, the POAAGG study implemented four new recruitment methods to supplement clinic enrollment. These methods included: 1) outreach in the local community, 2) in-house screening of community members ("in-reach"), 3) expansion to two external sites, and 4) sampling of the Penn Medicine Biobank. The cost per subject was calculated for each method and enrollment among cases, controls, and suspects was reported. RESULTS The biobank offered the lowest cost ($5/subject) and highest enrollment yield (n = 2073) of the four methods, but provided very few glaucoma cases (n = 31). External sites provided 88% of cases recruited from the four methods (n = 388; $85/subject), but case enrollment at these sites declined over the next 9 months as the pool of eligible subjects was depleted. Outreach and in-reach screenings of community members were very high cost for low return on enrollment ($569/subject for 102 subjects and $606/subject for 45 subjects, respectively). CONCLUSIONS The biobank offered the most cost-effective method for control enrollment, while expansion to external sites was necessary to recruit richly phenotyped cases. These recruitment methods helped the POAAGG study to exceed enrollment of the discovery cohort (n = 5500) 6 months in advance of the predicated deadline and could be adopted by other large genetic studies seeking to supplement clinic enrollment.
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Affiliation(s)
- Rebecca Salowe
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Laura O’Keefe
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Sayaka Merriam
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Roy Lee
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Naira Khachatryan
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Prithvi Sankar
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | | | - Amanda Lehman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Victoria Addis
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | | | - Jeffrey Henderer
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA USA
| | - Maureen Maguire
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Joan O’Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA USA
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