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Standardized biogeographic grouping system for annotating populations in pharmacogenetic research

By Rachel Huddart, Alison E Fohner, Michelle Whirl-Carrillo, Genevieve L. Wojcik, Christopher R. Gignoux, Alice B Popejoy, Carlos D. Bustamante, Russ B. Altman, Teri E. Klein

Posted 03 Aug 2018
bioRxiv DOI: 10.1101/384016 (published DOI: 10.1002/cpt.1322)

The frequencies of pharmacogenetic alleles vary considerably between populations which has important implications for the impact of these alleles in different populations. However, current population grouping methods to communicate these patterns are insufficient as they are inconsistent and fail to reflect the distribution of genetic variability around the world. To facilitate and standardize the reporting of global variability in pharmacogenetic allele frequencies, we present nine broad biogeographical groups, defined by global autosomal genetic structure. These groups are based on data from large-scale initiatives, including the 1000 Genomes Project and the Human Genome Diversity Project, and reflect population genetic history, genetic distances between populations, and geographical proximity, with borders falling predominantly along national boundaries to simplify application of the grouping system. The geographically-defined groups are American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, and Sub-Saharan African. Because of their distinct genetic patterns and frequent inclusion in published data, we also present two admixed groups: African American/Afro-Caribbean and Latino. Here, we characterize this population grouping system in the context of broad genomic data and present its utility for annotating pharmacogenetic studies and alleles. We recognize that broadly grouping global populations is an oversimplification of human diversity, does not capture complex social and cultural identity, and uses arbitrary geographic borders. However, this grouping method is consistent with robust population genetic patterns and meets a need of the pharmacogenetics field by enabling consistent communication of the scale of variability in global allele frequencies.

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