RESUMEN
While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings.
RESUMEN
Resumen El estudio de las variaciones de las secuencias de ADN y ARN en relación con la respuesta a diferentes fármacos, se ha convertido en un área de estudio particularmente prometedora para la aplicación en genómica clínica y estudios de genomas personalizados. Medicamentos de uso diario en el tratamiento de enfermedades cardiovasculares han demostrado variaciones en la respuesta en función de las variantes genéticas de los individuos. Dos fármacos han concentrado el interés mundial: la warfarina, un anticoagulante oral, y el clopidogrel, un antiagregante plaquetario, los cuales actúan alterando diferentes vías que conforman la cascada de la coagulación, ya sea limitando directamente la producción de trombina o bloqueando otros activadores de la ruta. Los cambios genéticos que se han asociado a la reducción de la actividad enzimática de estos fármacos ocurren en los genes, CYP2C19 para clopidogrel y CYP2C9 y VKORC1 para warfarina. Las variaciones genéticas identificadas para estos genes se relacionan con perfiles genotípicos que determinan la dosis requerida para el paciente. Es allí donde ciencias como la farmacogenómica tienen como fin brindar una ayuda diagnóstica más objetiva al optimizar tiempo y recursos, así como disminuir el riesgo del paciente a sufrir complicaciones que comprometan su vida.
Abstract The study of the variations in DNA and RNA sequencing as regards the response to different drugs has become a particularly promising area for their application in clinical genomics and personalised genome studies. Drugs of daily use in the treatment of cardiovascular diseases have shown variations in the response depending on the genetic variations of the individuals. Two drugs have gathered worldwide interest: warfarin, an oral anticoagulant, and clopidogrel, an antiplatelet drug, which act by altering different pathways that constitute the clotting cascade either by directly limiting the production of thrombin, or by blocking other activators of the pathway. The genetic changes that have been associated with the reduction in the enzyme activity of these drugs occur in the genes, CYP2C19 for clopidogrel, and the genes, CYP2C9 and VKORC1 for warfarin. The genetic variations identified for these genes are associated with genotype profiles that determine the dose required by the patient. It is from there, sciences like pharmacogenomics have as their aim to provide a more objective diagnostic aid in order to optimise time and resources, as well as to reduce the risk of the patient suffering complications that may compromise their life.