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Lewis AGC, Hernandez DM, Garcés-Palacio IC, Soliman AS. Impact of the universal health insurance benefits on cervical cancer mortality in Colombia. BMC Health Serv Res 2024; 24:693. [PMID: 38822370 PMCID: PMC11143589 DOI: 10.1186/s12913-024-10979-0] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Cervical cancer patients in Colombia have a lower likelihood of survival compared to breast cancer patients. In 1993, Colombia enrolled citizens in one of two health insurance regimes (contributory-private insurance and subsidized- public insurance) with fewer benefits in the subsidized regime. In 2008, the Constitutional Court required the Colombian government to unify services of both regimes by 2012. This study evaluated the impact of this insurance change on cervical cancer mortality before and after 2012. METHODS We accessed 24,491 cervical cancer mortality records for 2006-2020 from the vital statistics of Colombia's National Administrative Department of Statistics (DANE). We calculated crude mortality rates by health insurance type and departments (geopolitical division). Changes by department were analyzed by rate differences between 2006 and 2012 and 2013-2020, for each health insurance type. We analyzed trends using join-point regressions by health insurance and the two time-periods. RESULTS The contributory regime (private insurance) exhibited a significant decline in cervical cancer mortality from 2006 to 2012, characterized by a noteworthy average annual percentage change (AAPC) of -3.27% (P = 0.02; 95% CI [-5.81, -0.65]), followed by a marginal non-significant increase from 2013 to 2020 (AAPC 0.08%; P = 0.92; 95% CI [-1.63, 1.82]). In the subsidized regime (public insurance), there is a non-significant decrease in mortality between 2006 and 2012 (AAPC - 0.29%; P = 0.76; 95% CI [-2.17, 1.62]), followed by a significant increase from 2013 to 2020 (AAPC of 2.28%; P < 0.001; 95% CI [1.21, 3.36]). Examining departments from 2013 to 2020 versus 2006 to 2012, the subsidized regime showed fewer cervical cancer-related deaths in 5 out of 32 departments, while 6 departments had higher mortality. In 21 departments, mortality rates remained similar between both regimes. CONCLUSION Improvement of health benefits of the subsidized regime did not show a positive impact on cervical cancer mortality in women enrolled in this health insurance scheme, possibly due to unresolved administrative and socioeconomic barriers that hinder access to quality cancer screening and treatment.
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Affiliation(s)
- Almira G C Lewis
- Department of Global Health, Boston University School of Public Health, Boston University, Boston, MA, USA
| | - Diana M Hernandez
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Isabel C Garcés-Palacio
- Epidemiology group, School of Public Health, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Amr S Soliman
- Department of Community Health and Social Science, City University of New York School of Medicine, New York, NY, USA
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Jordan IK, Sharma S, Mariño-Ramírez L. Population Pharmacogenomics for Health Equity. Genes (Basel) 2023; 14:1840. [PMID: 37895188 PMCID: PMC10606908 DOI: 10.3390/genes14101840] [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: 07/28/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Health equity means the opportunity for all people and populations to attain optimal health, and it requires intentional efforts to promote fairness in patient treatments and outcomes. Pharmacogenomic variants are genetic differences associated with how patients respond to medications, and their presence can inform treatment decisions. In this perspective, we contend that the study of pharmacogenomic variation within and between human populations-population pharmacogenomics-can and should be leveraged in support of health equity. The key observation in support of this contention is that racial and ethnic groups exhibit pronounced differences in the frequencies of numerous pharmacogenomic variants, with direct implications for clinical practice. The use of race and ethnicity to stratify pharmacogenomic risk provides a means to avoid potential harm caused by biases introduced when treatment regimens do not consider genetic differences between population groups, particularly when majority group genetic profiles are assumed to hold for minority groups. We focus on the mitigation of adverse drug reactions as an area where population pharmacogenomics can have a direct and immediate impact on public health.
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Affiliation(s)
- I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Shivam Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA;
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3
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Nega MH, Berhe DF, Ribeiro V. Pharmacogenetic analysis of inter-ethnic variability in the uptake transporter SLCO1B1 gene in Colombian, Mozambican, and Portuguese populations. BMC Med Genomics 2023; 16:207. [PMID: 37658350 PMCID: PMC10474731 DOI: 10.1186/s12920-023-01642-4] [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: 02/08/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Statin-induced myopathy is reported to be associated with the solute carrier organic anion transporter family member 1B1 gene single nucleotide polymorphism, c.521 T > C. There is no epidemiologic data on this gene polymorphism in several countries. Therefore, this study aimed at assessing the genotype and allele frequencies of the gene variant in three countries. METHODS This study involved healthy individuals from Colombia, Mozambique, and Portugal. Genomic DNA was isolated from blood samples using the Qiamp DNA Extraction Kit (Qiagen). The isolated DNA was genotyped using novel Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. Microstat and GraphPad QuickCal software were used for the Chi-square test and the evaluation of Hardy-Weinberg equilibrium respectively. RESULTS A total of 181 individuals' blood samples were analyzed. Overall, the TT (74.0%) genotype was the highest and the CC (7.8%) was the lowest. Country wise genotypic frequencies were Colombia 47(70.2%) TT, 12(17.9%) TC and 8(11.9%) CC; Mozambique 47(88.7%) TT, 5(9.4%) TC, and 1(1.9%) CC; and Portugal 40(65.6%) TT, 16(26.2%) TC, and 5(8.2%) CC. The reference (T) allele was highest among Mozambicans (93.4%) compared to Colombians (79.1%) and Portuguese (78.7%). Mozambicans showed statistically significant genotypic and allelic frequency differences compared to Colombians (p < 0.01) and Portuguese (p < 0.01). CONCLUSIONS Overall and country-wise, CC genotype was less frequent and it is relatively high for Colombians and Portuguese populations. This finding may imply statins risk-benefit variability associated with CC genotype among these populations that needs further understanding.
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Affiliation(s)
- Mulata Haile Nega
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Mekelle University, Mekelle, Ethiopia.
- Laboratory of Pharmacogenomics and Molecular Toxicology, Center for Molecular and Structural Biomedicine (CBME/CCMAR), University of Algarve, Faro, Algarve, Portugal.
| | - Derbew Fikadu Berhe
- University of Global Health Equity, Kigali, Rwanda
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Vera Ribeiro
- Laboratory of Pharmacogenomics and Molecular Toxicology, Center for Molecular and Structural Biomedicine (CBME/CCMAR), University of Algarve, Faro, Algarve, Portugal
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4
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Nguyen AH, Sukasem C, Nguyen QN, Pham HT. The pharmacogenomics of carbamazepine-induced cutaneous adverse drug reaction in the South of Vietnam. Front Pharmacol 2023; 14:1217516. [PMID: 37521485 PMCID: PMC10374328 DOI: 10.3389/fphar.2023.1217516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Background: The relationship between HLA-B*15:02 and Severe Cutaneous Adverse Reactions was rigorously examined in Japanese, Han Chinese, Thais, and Caucasians. However, the number of studies about this topic in Vietnamese population is still limited and mostly focuses on the North of Vietnam. Objective: This study aims to clarify the genetic culprit of SCARs in Vietnamese population, particularly in the South of Vietnam, and to validate our result by a meta-analysis about this topic in Vietnamese. Method: A retrospective case-control study with 37 patients treated with carbamazepine monotherapy. Statistical calculation and meta-analysis were performed by R software. Result: HLA-B*15:02 increases the risk of SJS 12.5 times higher in CBZ-treated patients (p-value = 0.017). However, this allele has no impact on MCARs (Mild Cutaneous Adverse Reactions) of CBZ. The number needed to test and the number needed to genotype is two and nine patients respectively. Conclusion: This study recommends more investigations about the cost-effectiveness of this test to accelerate the protection of Southern Vietnamese from SCARs.
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Affiliation(s)
- Ai-Hoc Nguyen
- Department of Pathology, Division of Pharmacogenomics and Personalized Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Department of Pharmacy, Nhan Dan Gia Dinh Hospital, Ho ChiMinh City, Vietnam
| | - Chonlaphat Sukasem
- Department of Pathology, Division of Pharmacogenomics and Personalized Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Pharmacogenomics and Precision Medicine Clinic, Bumrungrad International Hospital, Bangkok, Thailand
- Bumrungrad Genomic Medicine Institute (BGMI), Bumrungrad International Hospital, Bangkok, Thailand
| | - Quy Ngoc Nguyen
- Department of Pharmacy, Nguyen Tat Thanh University, Ho ChiMinh City, Vietnam
| | - Hong Tham Pham
- Department of Pharmacy, Nhan Dan Gia Dinh Hospital, Ho ChiMinh City, Vietnam
- Department of Pharmacy, Nguyen Tat Thanh University, Ho ChiMinh City, Vietnam
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Sharma S, Mariño-Ramírez L, Jordan IK. Race, Ethnicity, and Pharmacogenomic Variation in the United States and the United Kingdom. Pharmaceutics 2023; 15:1923. [PMID: 37514109 PMCID: PMC10383154 DOI: 10.3390/pharmaceutics15071923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The relevance of race and ethnicity to genetics and medicine has long been a matter of debate. An emerging consensus holds that race and ethnicity are social constructs and thus poor proxies for genetic diversity. The goal of this study was to evaluate the relationship between race, ethnicity, and clinically relevant pharmacogenomic variation in cosmopolitan populations. We studied racially and ethnically diverse cohorts of 65,120 participants from the United States All of Us Research Program (All of Us) and 31,396 participants from the United Kingdom Biobank (UKB). Genome-wide patterns of pharmacogenomic variation-6311 drug response-associated variants for All of Us and 5966 variants for UKB-were analyzed with machine learning classifiers to predict participants' self-identified race and ethnicity. Pharmacogenomic variation predicts race/ethnicity with averages of 92.1% accuracy for All of Us and 94.3% accuracy for UKB. Group-specific prediction accuracies range from 99.0% for the White group in UKB to 92.9% for the Hispanic group in All of Us. Prediction accuracies are substantially lower for individuals who identified with more than one group in All of Us (16.7%) or as Mixed in UKB (70.7%). There are numerous individual pharmacogenomic variants with large allele frequency differences between race/ethnicity groups in both cohorts. Frequency differences for toxicity-associated variants predict hundreds of adverse drug reactions per 1000 treated participants for minority groups in All of Us. Our results indicate that race and ethnicity can be used to stratify pharmacogenomic risk in the US and UK populations and should not be discounted when making treatment decisions. We resolve the contradiction between the results reported here and the orthodoxy of race and ethnicity as non-genetic, social constructs by emphasizing the distinction between global and local patterns of human genetic diversity, and we stress the current and future limitations of race and ethnicity as proxies for pharmacogenomic variation.
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Affiliation(s)
- Shivam Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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6
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Shaaban S, Ji Y. Pharmacogenomics and health disparities, are we helping? Front Genet 2023; 14:1099541. [PMID: 36755573 PMCID: PMC9900000 DOI: 10.3389/fgene.2023.1099541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Pharmacogenomics has been at the forefront of precision medicine during the last few decades. Precision medicine carries the potential of improving health outcomes at both the individual as well as population levels. To harness the benefits of its initiatives, careful dissection of existing health disparities as they relate to precision medicine is of paramount importance. Attempting to address the existing disparities at the early stages of design and implementation of these efforts is the only guarantee of a successful just outcome. In this review, we glance at a few determinants of existing health disparities as they intersect with pharmacogenomics research and implementation. In our opinion, highlighting these disparities is imperative for the purpose of researching meaningful solutions. Failing to identify, and hence address, these disparities in the context of the current and future precision medicine initiatives would leave an already strained health system, even more inundated with inequality.
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Affiliation(s)
- Sherin Shaaban
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States,*Correspondence: Sherin Shaaban,
| | - Yuan Ji
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States,ARUP Laboratories, Salt Lake City, Utah, United States
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7
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Silva-Alarcon S, Valencia C, Newball L, Saldarriaga W, Castillo A. Molecular Variants in Genes related to the Response to Ocular Hypotensive Drugs in an Afro-Colombian Population. Open Ophthalmol J 2022. [DOI: 10.2174/18743641-v16-e2205250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aims:
This study aimed to conduct an exploratory analysis of the pharmacogenomic variants involved in ocular hypotensive drugs to understand the individual differential response in an Afro-descendant population.
Background:
Glaucoma is the leading cause of irreversible blindness worldwide. The pharmacologic treatment available consists of lowering intraocular pressure by administering topical drugs. In Asian and Caucasian people, pharmacogenomic variants associated with the efficacy of these treatments have been identified. However, in Afro-descendant populations, there is a profound gap in this knowledge.
Objective:
This study identified the pharmacogenomic variants related to ocular hypotensive efficacy treatment in Afro-descendant individuals from the Archipelago of San Andres and Providence, Colombia.
Methods:
An analysis of whole-exome sequencings (WES), functional annotation, and clinical significance was performed for pharmacogenomic variants reported in PharmGKB databases; in turn, an in silico available prediction analysis was carried out for the novel variants.
Results:
We identified six out of 18 non-synonymous variants with a clinical annotation in PharmGKB. Five were classified as level three evidence for the hypotensive drugs; rs1801252 and rs1801253 in the ADRB1 gene and rs1042714 in the ADRB2 gene. These pharmacogenomic variants have been involved in a lack of efficacy of topical beta-blockers and higher systolic and diastolic pressure under treatment with ophthalmic timolol drug. The rs1045642 in the ABCB1 gene was associated with greater efficacy of treatments with latanoprost drug. Also, we found the haplotypes *17 for CYP2D6 and *10 for CYP2C19; both related to reducing the enzyme activity to timolol drug metabolization. In addition, we observed 50 novel potentially actionable variants; 36 synonymous, two insertion variants that caused frameshift mutations, and 12 non-synonymous, where five were predicted to be pathogenic based on several pathogenicity predictions.
Conclusion:
Our results suggested that the pharmacogenomic variants were found to decrease the ocular hypotensive efficacy treatment in a Colombian Afro-descendant population and revealed a significant proportion of novel variants with a potential to influence drug response.
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Agudelo Motta ML, Osorio Ortega DF, Rubio Roa AC, Beltrán Casas OI. Privacidad y confidencialidad de los datos genéticos y genómicos de uso diagnóstico en Colombia. REVISTA LATINOAMERICANA DE BIOÉTICA 2022. [DOI: 10.18359/rlbi.5196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
La información genética y genómica requiere regulaciones estrictas para su manejo adecuado con el fin de evitar la divulgación inapropiada y la discriminación secundaria, pues tiene una relación directa con los derechos fundamentales y los principios bioéticos. De ahí la necesidad de evaluar la regulación colombiana existente, por lo que se realizó una revisión sistemática de la literatura en bases de datos del 2000 al 2020, sitios web del Congreso de la República de Colombia, la Comisión de Reforma de la Ley Australiana y la Corte Constitucional de Colombia, para identificar las falencias y los aciertos en la jurisprudencia actual del manejo, el control y la accesibilidad de la población colombiana a las pruebas e información genética. Se toma como referente Australia para comprender y plantear mejoras. Se encontró que en Colombia la información genética se cataloga como sensible (Sentencia C-334-10) con regulaciones inespecíficas sin norma legislativa. En contraste, Australia dispone de directrices bioéticas específicas, penalización y protocolos que abarcan las implicaciones individuales y colectivas descritas en el Privacy Legislation Amendment Act del 2006. Es necesario que en Colombia se cree una regulación jurídica específica para la información genética y genómica con énfasis en pautas de uso sobre la privacidad, la divulgación y la no discriminación.
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Ángela María JU, Mario CF, Mauricio HC, Ana Gisset GP, Jorge Alirio HR, Guillermo PP, Alejandro BC. A cross-sectional study of the socio-demographic and epidemiological factors associated with childhood cancer in Cali, Colombia. Heliyon 2022; 8:e09410. [PMID: 35620634 PMCID: PMC9126933 DOI: 10.1016/j.heliyon.2022.e09410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/09/2022] [Accepted: 05/06/2022] [Indexed: 11/27/2022] Open
Abstract
This study investigates the occurrence of childhood cancer between the years 2015 and 2016 in the city of Cali, Colombia, with respect to: a) sociodemographic characteristics, b) type of cancer, c) epidemiological weeks of cancer and d) comparative survival according to health system affiliation by consolidating the records notified to the municipal health secretariat. Statistically significant differences were found between the groups analysed in relation to the variables related to the type of cancer (p = 0.006). With respect to the proportion of cancer mortality between the years 2015–2016 there was no significant change, even though survival increased in the year 2016. The implications for collective health and public policies in Latin America are discussed.
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10
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Pharmacogenomic analysis of a genetically distinct Indigenous population. THE PHARMACOGENOMICS JOURNAL 2022; 22:100-108. [PMID: 34824386 DOI: 10.1038/s41397-021-00262-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022]
Abstract
Indigenous Australians face a disproportionately severe burden of chronic disease relative to other Australians, with elevated rates of morbidity and mortality. While genomics technologies are slowly gaining momentum in personalised treatments for many, a lack of pharmacogenomic research in Indigenous peoples could delay adoption. Appropriately implementing pharmacogenomics in clinical care necessitates an understanding of the frequencies of pharmacologically relevant genetic variants within Indigenous populations. We analysed whole-genome sequence data from 187 individuals from the Tiwi Islands and characterised the pharmacogenomic landscape of this population. Specifically, we compared variant profiles and allelic distributions of previously described pharmacologically significant genes and variants with other population groups. We identified 22 translationally relevant pharmacogenomic variants and 18 clinically actionable guidelines with implications for drug dosing and treatment of conditions including heart disease, diabetes and cancer. We specifically observed increased poor and intermediate metabolizer phenotypes in the CYP2C9 (PM:19%, IM:44%) and CYP2C19 (PM:18%, IM:44%) genes.
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Charnaud S, Munro JE, Semenec L, Mazhari R, Brewster J, Bourke C, Ruybal-Pesántez S, James R, Lautu-Gumal D, Karunajeewa H, Mueller I, Bahlo M. PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus. Commun Biol 2022; 5:168. [PMID: 35217695 PMCID: PMC8881578 DOI: 10.1038/s42003-022-03102-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/01/2022] [Indexed: 01/31/2023] Open
Abstract
The CYP2D6 enzyme is estimated to metabolize 25% of commonly used pharmaceuticals and is of intense pharmacogenetic interest due to the polymorphic nature of the CYP2D6 gene. Accurate allele typing of CYP2D6 has proved challenging due to frequent copy number variants (CNVs) and paralogous pseudogenes. SNP-arrays, qPCR and short-read sequencing have been employed to interrogate CYP2D6, however these technologies are unable to capture longer range information. Long-read sequencing using the PacBio Single Molecule Real Time (SMRT) sequencing platform has yielded promising results for CYP2D6 allele typing. However, previous studies have been limited in scale and have employed nascent data processing pipelines. We present a robust data processing pipeline "PLASTER" for accurate allele typing of SMRT sequenced amplicons. We demonstrate the pipeline by typing CYP2D6 alleles in a large cohort of 377 Solomon Islanders. This pharmacogenetic method will improve drug safety and efficacy through screening prior to drug administration.
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Affiliation(s)
- Sarah Charnaud
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Jacob E. Munro
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Lucie Semenec
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia ,grid.1004.50000 0001 2158 5405ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW Australia
| | - Ramin Mazhari
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Jessica Brewster
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Caitlin Bourke
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Shazia Ruybal-Pesántez
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia ,grid.1056.20000 0001 2224 8486Burnet Institute, Melbourne, VIC Australia
| | - Robert James
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Dulcie Lautu-Gumal
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Harin Karunajeewa
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Ivo Mueller
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
| | - Melanie Bahlo
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Melbourne, VIC Australia
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Jordan IK, Sharma S, Nagar SD, Valderrama-Aguirre A, Mariño-Ramírez L. Genetic Ancestry Inference for Pharmacogenomics. Methods Mol Biol 2022; 2547:595-609. [PMID: 36068478 PMCID: PMC9486757 DOI: 10.1007/978-1-0716-2573-6_21] [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] [Indexed: 06/15/2023]
Abstract
Genetic ancestry inference can be used to stratify patient cohorts and to model pharmacogenomic variation within and between populations. We provide a detailed guide to genetic ancestry inference using genome-wide genetic variant datasets, with an emphasis on two widely used techniques: principal components analysis (PCA) and ADMIXTURE analysis. PCA can be used for patient stratification and categorical ancestry inference, whereas ADMIXTURE is used to characterize genetic ancestry as a continuous variable. Visualization methods are critical for the interpretation of genetic ancestry inference methods, and we provide instructions for how the results of PCA and ADMIXTURE can be effectively visualized.
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Affiliation(s)
- I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Shivam Sharma
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA.
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13
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Bharti N, Banerjee R, Achalere A, Kasibhatla SM, Joshi R. Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations. PeerJ 2021; 9:e12294. [PMID: 34824904 PMCID: PMC8590392 DOI: 10.7717/peerj.12294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 01/09/2023] Open
Abstract
Objectives Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. Methods Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. Results Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’. Conclusions Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.
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Affiliation(s)
- Neeraj Bharti
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Ruma Banerjee
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Archana Achalere
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Sunitha Manjari Kasibhatla
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Rajendra Joshi
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
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14
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Favela-Mendoza AF, Rodríguez-Rodríguez BG, Rojas-Prado E, Chávez-Arreguin M, Aguilar-Velázquez JA, Martínez-Cortés G, Rangel-Villalobos H. Prevalence of protective haplotypes of the SLCO1B1 gene for statin transport in Mexican populations. Per Med 2021; 18:533-540. [PMID: 34674552 DOI: 10.2217/pme-2020-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To evaluate the genetic distribution of the rs4149056 and rs2306283 variants in the SLCO1B1 gene in Mexican Mestizo (admixed) and Native American groups. Materials & methods: We recruited 360 volunteers who were qPCR-genotyped with TaqMan probes. Results: Allele and genotype frequencies are reported. Among the expected rs4149056-rs2306283 haplotypes, T-A (42.35-58.47%) was the most prevalent which relates to the normal activity of the OATP1B1 transporter. This was followed by the T-G haplotype associated with further statin transport and cholesterol reduction (32.49-43.76%). Conclusion: Based on these SLCO1B1 gene variants, we confirmed that a minimum fraction of the Mexican study populations would be at risk from decreasing simvastatin transport and the development of statin-induced myopathy.
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Affiliation(s)
- Alma Faviola Favela-Mendoza
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Brenda Guadalupe Rodríguez-Rodríguez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Eduardo Rojas-Prado
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Mariana Chávez-Arreguin
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - José Alonso Aguilar-Velázquez
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Gabriela Martínez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México
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15
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Chande AT, Nagar SD, Rishishwar L, Mariño-Ramírez L, Medina-Rivas MA, Valderrama-Aguirre AE, Jordan IK, Gallo JE. The Impact of Ethnicity and Genetic Ancestry on Disease Prevalence and Risk in Colombia. Front Genet 2021; 12:690366. [PMID: 34650589 PMCID: PMC8507149 DOI: 10.3389/fgene.2021.690366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Currently, the vast majority of genomic research cohorts are made up of participants with European ancestry. Genomic medicine will only reach its full potential when genomic studies become more broadly representative of global populations. We are working to support the establishment of genomic medicine in developing countries in Latin America via studies of ethnically and ancestrally diverse Colombian populations. The goal of this study was to analyze the effect of ethnicity and genetic ancestry on observed disease prevalence and predicted disease risk in Colombia. Population distributions of Colombia's three major ethnic groups - Mestizo, Afro-Colombian, and Indigenous - were compared to disease prevalence and socioeconomic indicators. Indigenous and Mestizo ethnicity show the highest correlations with disease prevalence, whereas the effect of Afro-Colombian ethnicity is substantially lower. Mestizo ethnicity is mostly negatively correlated with six high-impact health conditions and positively correlated with seven of eight common cancers; Indigenous ethnicity shows the opposite effect. Malaria prevalence in particular is strongly correlated with ethnicity. Disease prevalence co-varies across geographic regions, consistent with the regional distribution of ethnic groups. Ethnicity is also correlated with regional variation in human development, partially explaining the observed differences in disease prevalence. Patterns of genetic ancestry and admixture for a cohort of 624 individuals from Medellín were compared to disease risk inferred via polygenic risk scores (PRS). African genetic ancestry is most strongly correlated with predicted disease risk, whereas European and Native American ancestry show weaker effects. African ancestry is mostly positively correlated with disease risk, and European ancestry is mostly negatively correlated. The relationships between ethnicity and disease prevalence do not show an overall correspondence with the relationships between ancestry and disease risk. We discuss possible reasons for the divergent health effects of ethnicity and ancestry as well as the implication of our results for the development of precision medicine in Colombia.
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Affiliation(s)
- Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Colombia.,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, United States
| | - Miguel A Medina-Rivas
- Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - Augusto E Valderrama-Aguirre
- Biomedical Research Institute (COL0082529), Cali, Colombia.,Department of Biomedical Sciences, Universidad Santiago de Cali, Cali, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
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16
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Jacob CG, Thuy-Nhien N, Mayxay M, Maude RJ, Quang HH, Hongvanthong B, Vanisaveth V, Ngo Duc T, Rekol H, van der Pluijm R, von Seidlein L, Fairhurst R, Nosten F, Hossain MA, Park N, Goodwin S, Ringwald P, Chindavongsa K, Newton P, Ashley E, Phalivong S, Maude R, Leang R, Huch C, Dong LT, Nguyen KT, Nhat TM, Hien TT, Nguyen H, Zdrojewski N, Canavati S, Sayeed AA, Uddin D, Buckee C, Fanello CI, Onyamboko M, Peto T, Tripura R, Amaratunga C, Myint Thu A, Delmas G, Landier J, Parker DM, Chau NH, Lek D, Suon S, Callery J, Jittamala P, Hanboonkunupakarn B, Pukrittayakamee S, Phyo AP, Smithuis F, Lin K, Thant M, Hlaing TM, Satpathi P, Satpathi S, Behera PK, Tripura A, Baidya S, Valecha N, Anvikar AR, Ul Islam A, Faiz A, Kunasol C, Drury E, Kekre M, Ali M, Love K, Rajatileka S, Jeffreys AE, Rowlands K, Hubbart CS, Dhorda M, Vongpromek R, Kotanan N, Wongnak P, Almagro Garcia J, Pearson RD, Ariani CV, Chookajorn T, Malangone C, Nguyen T, Stalker J, Jeffery B, Keatley J, Johnson KJ, Muddyman D, Chan XHS, Sillitoe J, Amato R, Simpson V, Gonçalves S, Rockett K, Day NP, Dondorp AM, Kwiatkowski DP, Miotto O. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination. eLife 2021; 10:e62997. [PMID: 34372970 PMCID: PMC8354633 DOI: 10.7554/elife.62997] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/30/2021] [Indexed: 02/04/2023] Open
Abstract
Background National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures. Methods Samples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs. Results GenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs. Conclusions GenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community. Funding The GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
| | | | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of HealthVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Richard J Maude
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Huynh Hong Quang
- Institute of Malariology, Parasitology and Entomology (IMPE-QN)Quy NhonViet Nam
| | - Bouasy Hongvanthong
- Centre of Malariology, Parasitology, and EntomologyVientianeLao People's Democratic Republic
| | - Viengxay Vanisaveth
- Centre of Malariology, Parasitology, and EntomologyVientianeLao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE)HanoiViet Nam
| | - Huy Rekol
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Rob van der Pluijm
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Lorenz von Seidlein
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Rick Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - François Nosten
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | - Paul Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Elizabeth Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Sonexay Phalivong
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
| | - Rapeephan Maude
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Faculty of Medicine, Ramathibodi Hospital, Mahidol UniversityBangkokThailand
| | - Rithea Leang
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Cheah Huch
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Le Thanh Dong
- Institute of Malariology, Parasitology and Entomology (IMPEHCM)Ho Chi Minh CityViet Nam
| | - Kim-Tuyen Nguyen
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tran Minh Nhat
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tran Tinh Hien
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | | | | | | | | | - Didar Uddin
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Caroline Buckee
- Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Caterina I Fanello
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Marie Onyamboko
- Kinshasa School of Public Health, University of KinshasaKinshasaDemocratic Republic of the Congo
| | - Thomas Peto
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Rupam Tripura
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Aung Myint Thu
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | - Gilles Delmas
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | - Jordi Landier
- Shoklo Malaria Research UnitMae SotThailand
- Aix-Marseille Université, INSERM, IRD, SESSTIM, Aix Marseille Institute of Public Health, ISSPAMMarseilleFrance
| | - Daniel M Parker
- Shoklo Malaria Research UnitMae SotThailand
- Susan and Henry Samueli College of Health Sciences, University of California, IrvineIrvineUnited States
| | | | - Dysoley Lek
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - James Callery
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | | | - Sasithon Pukrittayakamee
- Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- The Royal Society of ThailandBangkokThailand
| | - Aung Pyae Phyo
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Myanmar-Oxford Clinical Research UnitYangonMyanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Myanmar-Oxford Clinical Research UnitYangonMyanmar
| | - Khin Lin
- Department of Medical ResearchPyin Oo LwinMyanmar
| | - Myo Thant
- Defence Services Medical Research CentreYangonMyanmar
| | | | | | | | | | | | | | - Neena Valecha
- National Institute of Malaria Research, Indian Council of Medical ResearchNew DelhiIndia
| | - Anupkumar R Anvikar
- National Institute of Malaria Research, Indian Council of Medical ResearchNew DelhiIndia
| | | | - Abul Faiz
- Malaria Research Group and Dev Care FoundationDhakaBangladesh
| | - Chanon Kunasol
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | - Mihir Kekre
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Mozam Ali
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Katie Love
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Christina S Hubbart
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Mehul Dhorda
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Worldwide Antimalarial Resistance Network (WWARN), Asia Regional CentreBangkokThailand
| | - Ranitha Vongpromek
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Worldwide Antimalarial Resistance Network (WWARN), Asia Regional CentreBangkokThailand
| | - Namfon Kotanan
- Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Phrutsamon Wongnak
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Jacob Almagro Garcia
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | - Richard D Pearson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | | | | | - T Nguyen
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Jim Stalker
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Kimberly J Johnson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Xin Hui S Chan
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | | | - Victoria Simpson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Kirk Rockett
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Nicholas P Day
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Arjen M Dondorp
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Dominic P Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | - Olivo Miotto
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
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Chande AT, Rishishwar L, Ban D, Nagar SD, Conley AB, Rowell J, Valderrama-Aguirre AE, Medina-Rivas MA, Jordan IK. The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia. Genome Biol Evol 2021; 12:1516-1527. [PMID: 32681795 PMCID: PMC7513793 DOI: 10.1093/gbe/evaa154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).
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Affiliation(s)
- Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Dongjo Ban
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Shashwat D Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Jessica Rowell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Augusto E Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Biomedical Research Institute (COL0082529), Cali, Colombia.,Universidad Santiago de Cali, Colombia
| | - Miguel A Medina-Rivas
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
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18
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Zhou DT, Mudhluli TE, Madhombiro M, Nyamhunga A, Matekaire-Chirimo R, Mudzviti T, Manasa J, Ma Q, Maponga CC, Morse GD. Emerging role for pharmacogenomics in HIV research in Africa. Future Virol 2021. [DOI: 10.2217/fvl-2020-0388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tweetable abstract Pharmacogenomics (Pgx); the study of how genes affect drug response may optimize treatment by improving effectiveness and safety of medications. To apply current guidelines for African HIV-infected patients Pgx research is key.
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Affiliation(s)
- Danai Tavonga Zhou
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Medical Laboratory Sciences Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Taona Emmah Mudhluli
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Munyaradzi Madhombiro
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Primary Health Care, Psychiatry Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Albert Nyamhunga
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Oncology, Radiology Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Ratidzo Matekaire-Chirimo
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Primary Health Care, Paediatrics Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Tinashe Mudzviti
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Box A 178, Avondale, Harare, Zimbabwe
| | - Justen Manasa
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Microbiology Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Qing Ma
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
| | - Charles Chiedza Maponga
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Box A 178, Avondale, Harare, Zimbabwe
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
| | - Gene D Morse
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
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19
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Wenning L, Pillai GC, Knepper TC, Ilic K, Ali AM, Hibma JE. Clinical Pharmacology Worldwide: A Global Health Perspective. Clin Pharmacol Ther 2021; 110:946-951. [PMID: 33893656 DOI: 10.1002/cpt.2274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/07/2021] [Indexed: 11/06/2022]
Abstract
Low- and middle-income countries (LMICs) have the highest rates of mortality and morbidity globally, but lag behind high-income countries in the number of clinical trials and trained researchers, as well as research data pertaining to their populations. Lack of local clinical pharmacology and pharmacometrics expertise, limited training opportunities, and lack of local genomic data may contribute to health inequalities and limit the application of precision medicine. Continuing to develop health care infrastructure, including well-designed clinical pharmacology training and data collection in LMICs, can help address these challenges. International collaboration aimed at improving training and infrastructure and encouraging locally driven research and clinical trials will be of benefit. This review describes several examples where clinical pharmacology expertise could be leveraged, including opportunities for pharmacogenomic expertise that could drive improved recommendations for clinical guidelines. Also described are clinical pharmacology and pharmacometrics training programs in Africa, and the personal experience of a Tanzanian researcher currently on a training sabbatical in the United States, as illustrative examples of how training in clinical pharmacology can be effectively implemented in LMICs. These training efforts will benefit from advocacy for employment opportunities and career development pathways for clinical pharmacologists that are gradually being recognized and developed in LMICs. Clinical pharmacologists have a key role to play in global health, and development of training and research infrastructure to advance this expertise in LMICs will be of tremendous benefit.
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Affiliation(s)
| | - Goonaseelan Colin Pillai
- Division of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa.,Pharmacometrics Africa, Cape Town, South Africa.,CP+ Associates GmbH, Basel, Switzerland
| | | | - Katarina Ilic
- Shire, a Takeda Company, Lexington, Massachusetts, USA
| | - Ali Mohamed Ali
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, California, USA
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20
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Mufwambi W, Stingl J, Masimirembwa C, Manasa J, Nhachi C, Stadler N, Mwila C, Kalungia AC, Mukosha M, Mutiti CS, Kamoto A, Kaonga P, Godman B, Munkombwe D. Healthcare Professionals' Knowledge of Pharmacogenetics and Attitudes Towards Antimicrobial Utilization in Zambia: Implications for a Precision Medicine Approach to Reducing Antimicrobial Resistance. Front Pharmacol 2021; 11:551522. [PMID: 33510634 PMCID: PMC7835886 DOI: 10.3389/fphar.2020.551522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction: Sub-Saharan Africa and other low- and middle-income countries (LMICs) have the highest rates of antimicrobial resistance (AMR) driven by high rates of antimicrobial utilization. This is a concern as AMR appreciably increases morbidity, mortality and costs. Pharmacogenetics (PGx) and precision medicine are emerging approaches to combat AMR. Consequently, as a first step there is a need to assess AMR knowledge and attitudes, and knowledge of PGx, among healthcare professionals and use the findings to guide future interventions. Methodology: We conducted a cross-sectional study involving 304 healthcare professionals at tertiary hospitals in Lusaka, Zambia. Structural Equation Modeling (SEM) was used to analyze relationships among latent variables. Results: Overall correctness of answers concerning AMR among healthcare professionals was 60.4% (7/11). Knowledge of pharmacogenetics was low (38%). SEM showed that high AMR knowledge score correlated with a positive attitude toward combating AMR (p < 0.001). Pharmacists had relatively higher AMR knowledge scores (mean = 7.67, SD = 1.1), whereas nurses had lower scores (mean = 5.57, SD = 1.9). A minority of respondents [31.5% (n = 95)] indicated that poor access to local antibiogram data promoted AMR, with the majority [56.5% (n = 190)] responding that poor adherence to prescribed antimicrobials can lead to AMR. Pharmacists had the highest scores for attitude (mean = 5.60, SD = 1.6) whereas nurses had the lowest scores (mean = 4.02, SD = 1.4). Conclusion: AMR knowledge and attitudes, as well as knowledge on PGx among healthcare professionals in Zambia, is sub-optimal and has the potential to affect the uptake of precision medicine approaches to reduce AMR rates. Educational and positive behavioral change interventions are required to address this and in future, we will be seeking to introduce these to improve the use of antimicrobials.
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Affiliation(s)
- Webrod Mufwambi
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
- University of Zimbabwe, College of Health Sciences, Harare, Zimbabwe
| | - Julia Stingl
- RWTH University Hospital Aachen, Aachen, Germany
| | | | - Justen Manasa
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
- University of Zimbabwe, College of Health Sciences, Harare, Zimbabwe
| | - Charles Nhachi
- University of Zimbabwe, College of Health Sciences, Harare, Zimbabwe
| | - Nadina Stadler
- Research Division, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Chiluba Mwila
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | - Moses Mukosha
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Chenai S. Mutiti
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
- University of Zimbabwe, College of Health Sciences, Harare, Zimbabwe
| | - Alfred Kamoto
- African Institute of Biomedical Science and Technology, Harare, Zimbabwe
- University of Zimbabwe, College of Health Sciences, Harare, Zimbabwe
| | - Patrick Kaonga
- Department of Epidemiology and Biostatistics, School of Public Health, University of Zambia, Lusaka, Zambia
- Tropical Gastroenterology and Nutrition Group, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Brian Godman
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Rankuwa, South Africa
- Division of Clinical Pharmacology, Karolinska Institute, Stockholm, Sweden
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Derick Munkombwe
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
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21
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Mario-Vásquez JE, Naranjo-González CA, Montiel J, Zuluaga LM, Vásquez AM, Tobón-Castaño A, Bedoya G, Segura C. Association of variants in IL1B, TLR9, TREM1, IL10RA, and CD3G and Native American ancestry on malaria susceptibility in Colombian populations. INFECTION GENETICS AND EVOLUTION 2020; 87:104675. [PMID: 33316430 DOI: 10.1016/j.meegid.2020.104675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/19/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Host genetics is an influencing factor in the manifestation of infectious diseases. In this study, the association of mild malaria with 28 variants in 16 genes previously reported in other populations and/or close to ancestry-informative markers (AIMs) selected was evaluated in an admixed 736 Colombian population sample. Additionally, the effect of genetic ancestry on phenotype expression was explored. For this purpose, the ancestral genetic composition of Turbo and El Bagre was determined. A higher Native American ancestry trend was found in the population with lower malaria susceptibility [odds ratio (OR) = 0.416, 95% confidence interval (95% CI) = 0.234-0.740, P = 0.003]. Three AIMs presented significant associations with the disease phenotype (MID1752, MID921, and MID1586). The first two were associated with greater malaria susceptibility (D/D, OR = 2.23, 95% CI = 1.06-4.69, P = 0.032 and I/D-I/I, OR = 2.14, 95% CI = 1.18-3.87, P = 0.011, respectively), and the latter has a protective effect on the appearance of malaria (I/I, OR = 0.18, 95% CI = 0.08-0.40, P < 0.0001). After adjustment by age, sex, municipality, and genetic ancestry, genotype association analysis showed evidence of association with malaria susceptibility for variants in or near IL1B, TLR9, TREM1, IL10RA, and CD3G genes: rs1143629-IL1B (G/A-A/A, OR = 0.41, 95% CI = 0.21-0.78, P = 0.0051), rs352139-TLR9 (T/T, OR = 0.28, 95% CI = 0.11-0.72, P = 0.0053), rs352140-TLR9 (C/C, OR = 0.41, 95% CI = 0.20-0.87, P = 0.019), rs2234237-TREM1 (T/A-A/A, OR = 0.43, 95% CI = 0.23-0.79, P = 0.0056), rs4252246-IL10RA (C/A-A/A, OR = 2.11, 95% CI = 1.18-3.75, P = 0.01), and rs1561966-CD3G (A/A, OR = 0.20, 95% CI = 0.06-0.69, P = 0.0058). The results showed the participation of genes involved in immunological processes and suggested an effect of ancestral genetic composition over the traits analyzed. Compared to the paisa population (Antioquia), Turbo and El Bagre showed a strong decrease in European ancestry and an increase in African and Native American ancestries. Also, a novel association of two single nucleotide polymorphisms with malaria susceptibility was identified in this study.
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Affiliation(s)
- Jorge Eliécer Mario-Vásquez
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | | | - Jehidys Montiel
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Lina M Zuluaga
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Ana M Vásquez
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Alberto Tobón-Castaño
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia
| | - Gabriel Bedoya
- Grupo Genética Molecular (GENMOL), Universidad de Antioquia, Carrera 53 No. 61-30, Lab 430. Medellín, Colombia
| | - Cesar Segura
- Grupo Malaria-Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Lab 610, Medellín, Colombia.
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22
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Nagar SD, Conley AB, Jordan IK. Population structure and pharmacogenomic risk stratification in the United States. BMC Biol 2020; 18:140. [PMID: 33050895 PMCID: PMC7557099 DOI: 10.1186/s12915-020-00875-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black (African-American), and Hispanic (Latino). Our approach to the question of PGx risk stratification entailed the integration of two distinct methodologies: population genetics and evidence-based medicine. This integrated approach allowed us to consider the clinical implications for the observed patterns of PGx variation found within and between population groups. RESULTS Whole genome genotypes were used to characterize individuals' continental ancestry fractions-European, African, and Native American-and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals' SIRE with > 96% accuracy, and accordingly, GA provides only a marginal increase in resolution for PGx risk stratification. In light of the concordance between SIRE and GA, taken together with the fact that information on SIRE is readily available to clinicians, we evaluated PGx variation between SIRE groups to explore the potential clinical utility of race and ethnicity. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. The vast majority of PGx variation is found within rather than between groups, a well-established fact for almost all genetic variants, which is often taken to argue against the clinical utility of population stratification. Nevertheless, analysis of highly differentiated PGx variants illustrates how SIRE partitions PGx variation based on groups' characteristic ancestry patterns. These cases underscore the extent to which SIRE carries clinically valuable information for stratifying PGx risk among populations, albeit with less utility for predicting individual-level PGx alleles (genotypes), supporting the concept of population pharmacogenomics. CONCLUSIONS Perhaps most interestingly, we show that individuals who identify as Black or Hispanic stand to gain far more from the consideration of race/ethnicity in treatment decisions than individuals from the majority White population.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Andrew B. Conley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, 950 Atlantic Drive, Atlanta, GA 30332 USA
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, 950 Atlantic Drive, Atlanta, GA 30332 USA
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23
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Pot M, Brehme M, El-Heliebi A, Gschmeidler B, Hofer P, Kroneis T, Schirmer M, Schumann S, Prainsack B. Personalized medicine in Austria: expectations and limitations. Per Med 2020; 17:423-428. [PMID: 33026295 DOI: 10.2217/pme-2020-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Mirjam Pot
- Department of Political Science, University of Vienna, Vienna 1010, Austria
| | | | - Amin El-Heliebi
- Medical University of Graz, Gottfried Schatz Research Center, Division of Cell Biology, Histology and Embryology, Graz 8036, Austria.,Center for Biomarker Research in Medicine, Graz 8010, Austria
| | | | - Philipp Hofer
- Medical University of Vienna, Department of Pathology, Vienna 1090, Austria
| | - Thomas Kroneis
- Medical University of Graz, Gottfried Schatz Research Center, Division of Cell Biology, Histology and Embryology, Graz 8036, Austria.,Center for Biomarker Research in Medicine, Graz 8010, Austria
| | - Michael Schirmer
- Department of Internal Medicine, Medical University of Innsbruck, Clinic II, Innsbruck 6020, Austria
| | - Simone Schumann
- Open Science - Life Sciences in Dialogue, Vienna 1030, Austria
| | - Barbara Prainsack
- Department of Political Science, University of Vienna, Vienna 1010, Austria.,Department of Global Health & Social Medicine, King's College London, Strand, London WC2R 2LS, United Kingdom
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24
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Abstract
OBJECTIVES This scoping review synthesizes the recent literature on precision public health and the influence of predictive models on health equity with the intent to highlight central concepts for each topic and identify research opportunities for the biomedical informatics community. METHODS Searches were conducted using PubMed for publications between 2017-01-01 and 2019-12-31. RESULTS Precision public health is defined as the use of data and evidence to tailor interventions to the characteristics of a single population. It differs from precision medicine in terms of its focus on populations and the limited role of human genomics. High-resolution spatial analysis in a global health context and application of genomics to infectious organisms are areas of progress. Opportunities for informatics research include (i) the development of frameworks for measuring non-clinical concepts, such as social position, (ii) the development of methods for learning from similar populations, and (iii) the evaluation of precision public health implementations. Just as the effects of interventions can differ across populations, predictive models can perform systematically differently across subpopulations due to information bias, sampling bias, random error, and the choice of the output. Algorithm developers, professional societies, and governments can take steps to prevent and mitigate these biases. However, even if the steps to avoid bias are clear in theory, they can be very challenging to accomplish in practice. CONCLUSIONS Both precision public health and predictive modelling require careful consideration in how subpopulations are defined and access to data on subpopulations can be challenging. While the theory for both topics has advanced considerably, there is much work to be done in understanding how to implement and evaluate these approaches in practice.
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25
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Abstract
PURPOSE OF REVIEW Precision medicine could help to improve diagnosis and treatment of asthma; however, in the tropics there are special conditions to be considered for applying this strategy. In this review, we analyze recent advances of precision allergology in tropical regions, highlighting its limitations and needs in high-admixed populations living under environments with high exposure to house dust mites and helminth infections. RECENT FINDINGS Advances have been made regarding the genetic characterization of the great diversity of populations living in the tropics. Genes involved in shared biological pathways between immune responses to nematodes and the allergic responses suggested new mechanisms of predisposition. Genome wide association studies of asthma are progressively focusing on some highly replicated genes such as those in chromosome 17q31-13, which have been also replicated in African ancestry populations. Some diagnostic difficulties, because of the endemicity of helminth infections, are now more evident in the context of phenotype definition. SUMMARY The clinical impact of the advances in precision medicine for asthma in the tropics is still limited and mainly related to component resolved diagnosis. More basic and clinical research is needed to identify genetic, epigenetic, or other biologic markers that allow and accurate definition of phenotypes and endotypes of this heterogeneous disease. This will substantially improve the selection of personalized treatments.
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26
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Sariola S, Gilbert SF. Toward a Symbiotic Perspective on Public Health: Recognizing the Ambivalence of Microbes in the Anthropocene. Microorganisms 2020; 8:E746. [PMID: 32429344 PMCID: PMC7285259 DOI: 10.3390/microorganisms8050746] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Microbes evolve in complex environments that are often fashioned, in part, by human desires. In a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. The germ theory of disease cast microbes as enemies of the body and the body politic. Antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. Public health perspectives such as "Precision Public Health" and "One Health" have recently been proposed to further manage microbial populations. However, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. We propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. This perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the "One Health" model with the genomic methodologies utilized in the "Precision Public Health" model. In the Anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions.
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Affiliation(s)
- Salla Sariola
- Faculty of Social Sciences, Sociology, University of Helsinki, 00014 Helsinki, Finland;
| | - Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
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27
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Ahsan T, Urmi NJ, Sajib AA. Heterogeneity in the distribution of 159 drug-response related SNPs in world populations and their genetic relatedness. PLoS One 2020; 15:e0228000. [PMID: 31971968 PMCID: PMC6977754 DOI: 10.1371/journal.pone.0228000] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/03/2020] [Indexed: 12/25/2022] Open
Abstract
Interethnic variability in drug response arises from genetic differences associated with drug metabolism, action and transport. These genetic variations can affect drug efficacy as well as cause adverse drug reactions (ADRs). We retrieved drug-response related single nucleotide polymorphism (SNP) associated data from databases and analyzed to elucidate population specific distribution of 159 drug-response related SNPs in twenty six populations belonging to five super-populations (African, Admixed Americans, East Asian, European and South Asian). Significant interpopulation differences exist in the minor (variant) allele frequencies (MAFs), linkage disequilibrium (LD) and haplotype distributions among these populations. 65 of the drug-response related alleles, which are considered as minor (variant) in global population, are present as the major alleles (frequency ≥0.5) in at least one or more populations. Populations that belong to the same super-population have similar distribution pattern for majority of the variant alleles. These drug response related variant allele frequencies and their pairwise LD measure (r2) can clearly distinguish the populations in a way that correspond to the known evolutionary history of human and current geographic distributions, while D' cannot. The data presented here may aid in identifying drugs that are more appropriate and/or require pharmacogenetic testing in these populations. Our findings emphasize on the importance of distinct, ethnicity-specific clinical guidelines, especially for the African populations, to avoid ADRs and ensure effective drug treatment.
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Affiliation(s)
- Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | | | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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