Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Alexander Macharia
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Sophie Uyoga
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Gavin Band
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
Carolyne M Ndila
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Ewen M Harrison
Centre for Medical Infomatics, Usher Insitute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and Dentistry, University of Bamako, Bamako, Mali
Abdoulaye K Kone
Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and Dentistry, University of Bamako, Bamako, Mali
Dapa A Diallo
Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and Dentistry, University of Bamako, Bamako, Mali
Ogobara K Doumbo
Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and Dentistry, University of Bamako, Bamako, Mali
Kirsten E Lyke
Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, United States
Christopher V Plowe
Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, United States
Joann M Moulds
Lifeshare Blood Centers, Shreveport, United States
Mohammed Shebbe
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Neema Mturi
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Norbert Peshu
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
Kathryn Maitland
Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Medicine, Imperial College, London, United Kingdom
Ahmed Raza
Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Dominic P Kwiatkowski
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom
Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Malaria has been a major driving force in the evolution of the human genome. In sub-Saharan African populations, two neighbouring polymorphisms in the Complement Receptor One (CR1) gene, named Sl2 and McCb, occur at high frequencies, consistent with selection by malaria. Previous studies have been inconclusive. Using a large case-control study of severe malaria in Kenyan children and statistical models adjusted for confounders, we estimate the relationship between Sl2 and McCb and malaria phenotypes, and find they have opposing associations. The Sl2 polymorphism is associated with markedly reduced odds of cerebral malaria and death, while the McCb polymorphism is associated with increased odds of cerebral malaria. We also identify an apparent interaction between Sl2 and α+thalassaemia, with the protective association of Sl2 greatest in children with normal α-globin. The complex relationship between these three mutations may explain previous conflicting findings, highlighting the importance of considering genetic interactions in disease-association studies.