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.
Highlights
MATERIALS AND METHODSGenomic medicine is an emerging medical discipline that entails the use of genomic information about an individual as part of their clinical care – in support of better diagnostic, prognostic, and therapeutic decision-making (Collins and Varmus, 2015; Jameson and Longo, 2015)
We found that disease prevalence and risk are associated with ethnicity, geography, socioeconomics, and genetic ancestry in Colombia, and we discuss the implications of our findings with respect to the development of precision medicine in the country
We focused on the three largest ethnic groups in Colombia: Mestizo, Afro-Colombian, and Indigenous
Summary
MATERIALS AND METHODSGenomic medicine is an emerging medical discipline that entails the use of genomic information about an individual as part of their clinical care – in support of better diagnostic, prognostic, and therapeutic decision-making (Collins and Varmus, 2015; Jameson and Longo, 2015). We have been working to build local capacity in precision medicine via population and clinical genomic studies of diverse Colombian populations over the last decade (Rishishwar et al, 2015a,b; Jordan, 2016; Medina-Rivas et al, 2016; Chande et al, 2017, 2020a,b; Conley et al, 2017; Norris et al, 2018, 2020; Nagar et al, 2019). These studies share the broad aims of (1) characterizing patterns of genetic ancestry and admixture within and between Colombian and other Latin American populations, and (2) exploring the relationship between ancestry and genetic determinants of health and disease in the region
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