ABSTRACT
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.
ABSTRACT
el diagnóstico y tamizaje prenatal, así como el diagnóstico y seguimiento de enfermedades en diversos campos de la medicina, se hace, en la actualidad, de manera más sencilla gracias al ADN libre en plasma. Este ADN representa una pequeña parte de la información genética de un tejido en particular o, en el caso de las mujeres en embarazo, una proporción del ADN fetal. En la oncología, por ejemplo, dada la heterogeneidad del cáncer, la aplicación del ADN libre en plasma ha sido difícil de implementar ya que solo existen algunos biomarcadores tumorales específicos para su uso en investigación. Metodologías como la reacción en cadena de la polimerasa (PCR) en tiempo real muestran una gran sensibilidad para detectar mutaciones que permitan establecer un correcto dignóstico y tratamiento de algunas enfermedades como las fetales o las tumorales, al mismo tiempo que disminuye costos. Lo anterior, no deja de ser una gran oportunidad para continuar los procesos de investigación y desarrollo de pruebas que permitan, en un futuro cercano, implementar el uso del ADN libre de células en el área clínica, con resultados confiables en el diagnóstico y tratamiento de enfermedades sin poner en riesgo la integridad del paciente
The prenatal diagnosis and screening, as well as the diagnosis and monitoring of diseases in various medicine fields, is now made more easily thanks to the cell free DNA present in plasma. This DNA represents a small part of the genetic information of a particular tissue or, in the case of pregnant women, a proportion of the fetal DNA. In oncology, for example, given the heterogeneity of cancer, the application of cell free DNA has been difficult to implement since there are only some specific tumoral biomarkers for research use. Methodologies such as real-time polymerase chain reaction (PCR) show a high sensitivity to detect mutations that allow a correct diagnosis and treatment of fetal or tumoral diseases, at the same time reducing costs. This represents a great opportunity to continue the research and developmental processes of tests that allow its implementation in the clinical area in the near future, with reliable results in diagnosis and treatment of diseases without compromising the patient's integrity
