Design of a custom genotyping chip for African populations

Liudmila Mainzer, University of Illinois at Urbana-Champaign

Usage Details

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. While existing genotyping chip designs have included African populations in the first trial set, European populations have dominated development of these arrays, and African populations in current reference panels are not representative of more differentiated population groups within Africa. The goal of this Blue Waters allocation is to aid in the design of an efficient and cost-effective genotyping chip that would capture the genetic diversity of populations of African origin, including African-Americans. The chip design will be done as a collaborative project as part of the H3Africa Custom Chip design task force led by Zane Lombard (Wits) and Debo Adeyemo (NHGRI). This allocation involves Blue Waters in an international collaboration including the Wellcome Trust Sanger Institute, the Human Heredity and Health in Africa initiative funded by NIH and the Wellcome Trust, and Baylor College of Medicine. This work will enable the identification of genetic variation specific to African populations, which will help better understand the links between genotype and disease in people of African origin, and thus extend the principles of personalized medicine to these underserved populations. It will permit deeper study of African genetic diversity, which will bring important insights into the history and evolution of humans in general. It will also demonstrate, in a production-grade project, the capability of Blue Waters to conduct high-throughput analysis of human genomes.