Tuesday, December 4, 2018

New biogeographical groups in use at PharmGKB


Recent visitors to the PharmGKB website may have noticed a change in how we report racial and ethnicity information in our variant and clinical annotations. Until July 2018, PharmGKB used the US Office of Management and Budget (OMB) race categories with an additional ethnicity category of Hispanic/Latino. These groups are US-centric, at odds with PharmGKB’s position as an international resource for pharmacogenomic knowledge, and we encountered issues with applying these categories consistently to the global populations described in the pharmacogenomic literature.

To solve these issues, we collaborated with the Bustamante Lab at Stanford University to analyze genetic data from the 1000 Genomes Project and the Human Genome Diversity Project and develop a new grouping system based on biogeographical groups, published in Clinical Pharmacology and Therapeutics. This new system has a total of nine groups; seven geographical groups (American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, Sub-Saharan African) and two groups for African American/Afro-Caribbean and Latino populations which have arisen more recently and are genetically distinct from the seven geographical groups.

The areas covered by the seven geographical groups are shown on the map available in the paper and on this page. Note that these group boundaries are determined by the location of genetic ancestors pre-colonization and pre-Diaspora and do not reflect present-day distribution of people who would belong to each of these groups. The African American and Latino groups exhibit a significant degree of post-colonization and post-Diaspora gene flow between multiple geographical populations and are not shown on the map. 

All nine groups are now being used in PharmGKB curation activities and all existing variant and clinical annotations have been transitioned to this new grouping system. While we encourage pharmacogenomics researchers to consider using this grouping system in their publications in an effort to standardize population reporting across the field of pharmacogenomics research, this system is not intended to be used in place of patient genotypes in the implementation of pharmacogenomics.

You can find more details about our biogeographical grouping system, including detailed descriptions for each group, here. As part of the process of implementing these new groups, we have been reassessing how we tag study populations in curated papers and will be making some more changes in the coming months. All changes will be announced on our blog and our Twitter account @pharmgkb.

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