1
|
Ruíz-Patiño A, Rojas L, Zuluaga J, Arrieta O, Corrales L, Martín C, Franco S, Raez L, Rolfo C, Sánchez N, Cardona AF. Genomic ancestry and cancer among Latin Americans. Clin Transl Oncol 2024; 26:1856-1871. [PMID: 38581481 PMCID: PMC11249489 DOI: 10.1007/s12094-024-03415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/20/2024] [Indexed: 04/08/2024]
Abstract
Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.
Collapse
Affiliation(s)
- Alejandro Ruíz-Patiño
- Clinical Genetics, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Jairo Zuluaga
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Oscar Arrieta
- Instituto Nacional de Cancerología -INCaN, Mexico City, Mexico
| | - Luis Corrales
- Thoracic Oncology Unit, Centro de Investigación y Manejo del Cáncer (CIMCA), San José, Costa Rica
| | - Claudio Martín
- Thoracic Oncology Unit, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Sandra Franco
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Breast Cancer Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Luis Raez
- Oncology Department, Memorial Cancer Institute (MCI), Memorial Healthcare System, Miami, FL, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Sánchez
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Andrés Felipe Cardona
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia.
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Direction of Research and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Cra. 14 #169-49, Bogotá, Colombia.
| |
Collapse
|
2
|
Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
Collapse
Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Acosta-Vega NL, Varela R, Mesa JA, Garai J, Gómez-Gutiérrez A, Serrano-Gómez SJ, Zabaleta J, Sanabria-Salas MC, Combita AL. Genetic ancestry and radical prostatectomy findings in Hispanic/Latino patients. Front Oncol 2024; 14:1338250. [PMID: 38634046 PMCID: PMC11021589 DOI: 10.3389/fonc.2024.1338250] [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: 11/14/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Background African ancestry is a known factor associated with the presentation and aggressiveness of prostate cancer (PC). Hispanic/Latino populations exhibit varying degrees of genetic admixture across Latin American countries, leading to diverse levels of African ancestry. However, it remains unclear whether genetic ancestry plays a role in the aggressiveness of PC in Hispanic/Latino patients. We explored the associations between genetic ancestry and the clinicopathological data in Hispanic/Latino PC patients from Colombia. Patients and methods We estimated the European, Indigenous and African genetic ancestry, of 230 Colombian patients with localized/regionally advanced PC through a validated panel for genotypification of 106 Ancestry Informative Markers. We examined the associations of the genetic ancestry components with the Gleason Grade Groups (GG) and the clinicopathological characteristics. Results No association was observed between the genetic ancestry with the biochemical recurrence or Gleason GG; however, in a two groups comparison, there were statistically significant differences between GG3 and GG4/GG5 for European ancestry, with a higher mean ancestry proportion in GG4/GG5. A lower risk of being diagnosed at an advanced age was observed for patients with high African ancestry than those with low African ancestry patients (OR: 0.96, CI: 0.92-0.99, p=0.03). Conclusion Our findings revealed an increased risk of presentation of PC at an earlier age in patients with higher African ancestry compared to patients with lower African ancestry in our Hispanic/Latino patients.
Collapse
Affiliation(s)
- Natalia L. Acosta-Vega
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
- Programa de doctorado en Ciencias Biológicas, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - Rodolfo Varela
- Departamento de Urología, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
- Departamento de Cirugía, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Jorge Andrés Mesa
- Departamento de Patología Oncológica, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Alberto Gómez-Gutiérrez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - Silvia J. Serrano-Gómez
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - María Carolina Sanabria-Salas
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
| | - Alba L. Combita
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá D.C., Colombia
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| |
Collapse
|
5
|
Busby GB, Kulm S, Bolli A, Kintzle J, Domenico PD, Bottà G. Ancestry-specific polygenic risk scores are risk enhancers for clinical cardiovascular disease assessments. Nat Commun 2023; 14:7105. [PMID: 37925478 PMCID: PMC10625612 DOI: 10.1038/s41467-023-42897-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Clinical implementation of new prediction models requires evaluation of their utility in a broad range of intended use populations. Here we develop and validate ancestry-specific Polygenic Risk Scores (PRSs) for Coronary Artery Disease (CAD) using 29,389 individuals from diverse cohorts and genetic ancestry groups. The CAD PRSs outperform published scores with an average Odds Ratio per Standard Deviation of 1.57 (SD = 0.14) and identify between 12% and 24% of individuals with high genetic risk. Using this risk factor to reclassify borderline or intermediate 10 year Atherosclerotic Cardiovascular Disease (ASCVD) risk improves assessments for both CAD (Net Reclassification Improvement (NRI) = 13.14% (95% CI 9.23-17.06%)) and ASCVD (NRI = 10.70 (95% CI 7.35-14.05)) in an independent cohort of 9,691 individuals. Our analyses demonstrate that using PRSs as Risk Enhancers improves ASCVD risk assessments outlining an approach for guiding ASCVD prevention with genetic information.
Collapse
Affiliation(s)
| | - Scott Kulm
- Allelica Inc, 447 Broadway, New York, NY, 10013, USA
| | | | - Jen Kintzle
- Allelica Inc, 447 Broadway, New York, NY, 10013, USA
| | | | | |
Collapse
|
6
|
Ata F, Rahhal A, Malkawi L, Iqbal P, Khamees I, Alhiyari M, Yousaf Z, Qasim H, Alshurafa A, Sardar S, Javed S, Fernyhough L, Yassin M. Genotypic and Phenotypic Composition of Sickle Cell Disease in the Arab Population - A Systematic Review. Pharmgenomics Pers Med 2023; 16:133-144. [PMID: 36851992 PMCID: PMC9961577 DOI: 10.2147/pgpm.s391394] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Sickle cell disease (SCD) is a genetic disease influenced by ethnicity and regional differences in its clinical course. Recent advances in the management of SCD with newer therapies are being introduced to the Western population. However, many of these treatments are yet to be used in the Arabic SCD population. Understanding the genetic variations of SCD regionally is essential to anticipate the utilization of new treatments. This systematic review's main objective is to pool the available data on the genetic composition of SCD in the Arabic population. Data for 44,034 patients was extracted from 184 studies (11 case reports, 8 case series, 56 retrospectives, 107 prospective observational studies, and 2 clinical trials) using PubMed, Scopus, and Google Scholar. Male (49%) and female (51%) patients were equally reported wherever gender was available (N=13105). Various SCD genotypes were reported in a total of 14,257 patients, including Hb SS (77%) Hb Sβ0 (9.9%), and Hb Sβ+ (7.2%), while the rest of the genotypes, including HbSC, HbSD, HbSE, HbSO Arab, Hb S/α-Thal, Hb Sβ0 + α-Thal, and HBS Oman were individually reported in <4% of the cases. Major SCD complications in the Arab population included pain crises (48.25%) followed by neurological complications (33.46%), hepatobiliary complications (25.53%), musculoskeletal complications (24.73%), and hemolytic anemia (23.57%). The treatments reported for SCD included hydroxyurea (20%), blood transfusion (14.32%), and Deferasirox (3.03%). We did not find the use of stem cell transplantation or newer treatments such as L-Glutamine, Voxelotor, Crizanlizumab, or gene therapy reported in any of the studies included in our review. This review highlights the genetic makeup of SCD in Arab countries and its common phenotypic manifestations and will help direct further research on SCD in this region, especially concerning genetic therapy. Systematic Review Registration The protocol has been registered in the International Prospective Register of Systematic Reviews(PROSPERO):CRD42020218,666. https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=218666.
Collapse
Affiliation(s)
- Fateen Ata
- Department of Endocrinology, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Alaa Rahhal
- Department of Clinical Pharmacy, Hamad Medical Corporation, Doha, Qatar
| | - Lujain Malkawi
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Phool Iqbal
- Department of Internal Medicine, Metropolitan Hospital, New York, NY, USA
| | - Ibrahim Khamees
- Department of Internal Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Mousa Alhiyari
- Department of Internal Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Zohaib Yousaf
- Department of Internal Medicine, Reading Hospital - Tower Health, West Reading, PA, USA
| | - Hana Qasim
- Department of Internal Medicine, UMKC School of medicine, Kansas, MO, USA
| | - Awni Alshurafa
- Department of Medical Oncology /Hematology, National Centre for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sundus Sardar
- Department of Medicine, Division of Nephrology, Pennsylvania State University College of Medicine, Hershey Medical Center, Hershey, PA, USA
| | - Saad Javed
- Department of Internal Medicine, Icahn school of medicine at Mount Sinai/Queens Hospital Center, New York, NY, USA
| | - Liam Fernyhough
- Department of Medical Oncology /Hematology, National Centre for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Department of Medical Education, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Mohamed Yassin
- Department of Medical Oncology /Hematology, National Centre for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| |
Collapse
|
7
|
De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [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: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
Collapse
Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
| |
Collapse
|
8
|
Parada-Márquez JF, Maldonado-Rodriguez ND, Triana-Fonseca P, Contreras-Bravo NC, Calderón-Ospina CA, Restrepo CM, Morel A, Ortega-Recalde OJ, Silgado-Guzmán DF, Angulo-Aguado M, Fonseca-Mendoza DJ. Pharmacogenomic profile of actionable molecular variants related to drugs commonly used in anesthesia: WES analysis reveals new mutations. Front Pharmacol 2023; 14:1047854. [PMID: 37021041 PMCID: PMC10069477 DOI: 10.3389/fphar.2023.1047854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Genetic interindividual variability is associated with adverse drug reactions (ADRs) and affects the response to common drugs used in anesthesia. Despite their importance, these variants remain largely underexplored in Latin-American countries. This study describes rare and common variants found in genes related to metabolism of analgesic and anaesthetic drug in the Colombian population. Methods: We conducted a study that included 625 Colombian healthy individuals. We generated a subset of 14 genes implicated in metabolic pathways of common medications used in anesthesia and assessed them by whole-exome sequencing (WES). Variants were filtered using two pipelines: A) novel or rare (minor allele frequency-MAF <1%) variants including missense, loss-of-function (LoF, e.g., frameshift, nonsense), and splice site variants with potential deleterious effect and B) clinically validated variants described in the PharmGKB (categories 1, 2 and 3) and/or ClinVar databases. For rare and novel missense variants, we applied an optimized prediction framework (OPF) to assess the functional impact of pharmacogenetic variants. Allelic, genotypic frequencies and Hardy-Weinberg equilibrium were calculated. We compare our allelic frequencies with these from populations described in the gnomAD database. Results: Our study identified 148 molecular variants potentially related to variability in the therapeutic response to 14 drugs commonly used in anesthesiology. 83.1% of them correspond to rare and novel missense variants classified as pathogenic according to the pharmacogenetic optimized prediction framework, 5.4% were loss-of-function (LoF), 2.7% led to potential splicing alterations and 8.8% were assigned as actionable or informative pharmacogenetic variants. Novel variants were confirmed by Sanger sequencing. Allelic frequency comparison showed that the Colombian population has a unique pharmacogenomic profile for anesthesia drugs with some allele frequencies different from other populations. Conclusion: Our results demonstrated high allelic heterogeneity among the analyzed sampled, enriched by rare (91.2%) variants in pharmacogenes related to common drugs used in anesthesia. The clinical implications of these results highlight the importance of implementation of next-generation sequencing data into pharmacogenomic approaches and personalized medicine.
Collapse
Affiliation(s)
| | | | - Paula Triana-Fonseca
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Carlos Alberto Calderón-Ospina
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Carlos M. Restrepo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Oscar Javier Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | | | - Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Mariana Angulo-Aguado, ; Dora Janeth Fonseca-Mendoza,
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Mariana Angulo-Aguado, ; Dora Janeth Fonseca-Mendoza,
| |
Collapse
|
9
|
Sleep problems in low income, urban pediatric populations living at different altitudes in Colombia. Sleep Med 2022; 100:64-70. [PMID: 36027664 DOI: 10.1016/j.sleep.2022.07.017] [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: 05/18/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To determine the frequency of sleep problems in low-income, urban pediatric populations in cities at different altitudes in Colombia. METHODS A descriptive, cross-sectional population-based observational study was conducted in children aged between 2 and 12 years in the low income, urban areas of three cities in Colombia (Santa Marta, Bucaramanga, and Bogotá) located at 15, 959, and 2640 m above sea level, respectively. Sociodemographic data were collected, and the Spanish version of the Pediatric Sleep Questionnaire was used. RESULTS 1989 children were surveyed, distributed as follows: Santa Marta (32.0%), Bucaramanga (33.4%), and Bogotá (34.6%). The overall prevalence of sleep problems was 39.0%. Children from Santa Marta had the highest frequency of parasomnias (58.0%); those from Bucaramanga had the highest frequency of attention deficit symptoms (4.0%) and apneic pauses witnessed by parents or caregivers (5.7%). Finally, Bogotá, the only high-altitude location, had the highest frequency of sleep disordered breathing (17.2%). CONCLUSIONS The study found a high frequency of sleep problems in the pediatric population, especially at higher altitudes when compared to lower altitude settings. Sleep disorders warrant early detection and timely therapeutic intervention.
Collapse
|
10
|
Factors associated with meeting the WHO physical activity recommendations in pregnant Colombian women. Sci Rep 2022; 12:19500. [PMID: 36376351 PMCID: PMC9663497 DOI: 10.1038/s41598-022-23947-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
In the absence of medical contraindications, physical activity (PA) can offer health maternal and fetal health outcomes during pregnancy. However, most pregnant women may not consider PA to be feasible, suitable and safe. Hence, it is essential to determine the prevalence of pregnant women who meet the PA recommendations and the possible factors associated with that meeting, since it might be important from the perspective of pregnant women's health. The aim of the present study was to establish the prevalence of meeting the World Health Organization PA recommendations for Colombian pregnant women, as well as possible factors that may be associated with meeting that recommendations. A cross-sectional study including representative data from the National Nutritional Situation Survey (2015) in Colombia was performed. Data were collected in 2015-2016. From an initial sample of 1140 Colombian pregnant women, 702 participants with complete data were included in the final analysis. PA was assessed by self-reported information through the long version of the International Physical Activity Questionnaire. Several potential factors were analysed according to four levels of the socioecological model: the individual, interpersonal, organizational and community levels. The prevalence of Colombian pregnant women who met with the PA recommendations was 7.5%. Indigenous and Mestizo pregnant women showed lower probabilities of meeting the PA recommendations [Indigenous: OR 0.05, 95% CI (0.01-0.18); Mestizo: OR 0.12, 95% CI (0.06-0.22)] than Afro-Colombian participants. Additionally, participants who lived near green and safe spaces for PA were more likely to meet the PA recommendations [OR 2.30, 95% CI (1.06-4.79)] than those who did not live near green areas. In conclusion, a low percentage of Colombian pregnant women met the new PA recommendations. The associations found according to race/ethnicity and living near green and safe areas underline the presence of fundamental disparities associated with meeting PA recommendations.
Collapse
|