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Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017; 356:science.aam6393. [PMID: 28522690 DOI: 10.1126/science.aam6393] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/08/2017] [Indexed: 12/29/2022]
Abstract
The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
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Affiliation(s)
- Ellen M Leffler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - George B J Busby
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katja Kivinen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kalifa A Bojang
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - David J Conway
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Muminatou Jallow
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Royal Victoria Teaching Hospital, Independence Drive, Post Office Box 1515, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - Edith C Bougouma
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | | | - David Modiano
- University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Eric Achidi
- Department of Medical Laboratory Sciences, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Kevin Marsh
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, UK
| | - Carolyne M Ndila
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Norbert Peshu
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Thomas N Williams
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Faculty of Medicine, Department of Medicine, Imperial College, Exhibition Road, London SW7 2AZ, UK
| | - Chris Drakeley
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,National Institute for Medical Research, Mwanza Research Centre, Mwanza City, Tanzania
| | - Hugh Reyburn
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Eleanor Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David Kachala
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Malcolm Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Vysaul Nyirongo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Terrie Taylor
- Blantyre Malaria Project, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Nicole Thornton
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Louise Tilley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Shane Grimsley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jim Stalker
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria Cornelius
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. .,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
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Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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