Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data [version 2; peer review: 2 approved]

Autor: Ndila, CM, Nyirongo, V, Macharia, AW, Jeffreys, AE, Rowlands, K, Hubbart, C, Busby, GBJ, Band, G, Harding, RM, Rockett, KA, Williams, TN, MalariaGEN Consortium

Publikováno v: Wellcome Open Research, Vol 5 (2021)

Background: The -α 3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::295478e55c3d51a9ae5483f555ecc067
https://wellcomeopenresearch.org/articles/5-287/v2

New insights into malaria susceptibility from the genomes of 17,000 individuals from Africa, Asia, and Oceania

Autor: Kate Rowlands, Timothy M. E. Davis, Salimata Konate, Umberto D'Alessandro, Angeliki Kerasidou, Sodiomon B. Sirima, David J. Conway, Fatoumatta Sisay-Joof, S Ademola, Mahamadou A. Thera, Momodou W. Jallow, Edith C. Bougouma, Alexander J. Mentzer, Alphaxard Manjurano, Chris Drakeley, Carolyne M. Ndila, Giorgio Sirugo, Eleanor Drury, Nguyen Hoan Phu, Moses Laman, Anthony Enimil, Pascal Michon, N T Ngoc Quyen, Terrie E. Taylor, Jennifer Evans, Ogobara K. Doumbo, Anita Ghansah, Malcolm E. Molyneux, Alexander T. Dilthey, Sibiry Sissoko, Olukemi K. Amodu, Kalifa Bojang, Yik Ying Teo, Ousmane Touré, Eleanor M. Riley, Dominic P. Kwiatkowski, Angela Allen, Laurens Manning, D Ansong, Peter Siba, Stephen Allen, Thomas N. Williams, Christina Hubbart, Tobias O. Apinjoh, Cao Quang Thai, Hugh Reyburn, Q S Le, Melanie Bahlo, Geraldine M. Clarke, Spencer Cca., Ivo Mueller, Anna E. Jeffreys, Gil McVean, Valentina D. Mangano, Jj J. Farrar, Victoria Cornelius, Busby Gbj., Kevin Marsh, Jim Stalker, David Modiano, Tran Tinh Hien, Michael T. Wilson, Tsiri Agbenyega, A Hodgson, Sarah J. Dunstan, Harin Karunajeewa, L. Amenga-Etego, Ellen M. Leffler, Katja Kivinen, Eric A. Achidi, Kirk A. Rockett, Kwadwo A. Koram, J Shelton

We conducted a genome-wide association study of host resistance to severePlasmodium falciparummalaria in over 17,000 individuals from 11 malaria-endemic countries, undertaking a wide ranging analysis which identifies five replicable associations with

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2fbf106126518a20ddd4f49ea0df807c
https://doi.org/10.1101/535898

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.

Autor: Ahouidi A; Hopital Le Dantec, Universite Cheikh Anta Diop, Dakar, Senegal., Ali M; Wellcome Sanger Institute, Hinxton, UK., Almagro-Garcia J; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Amambua-Ngwa A; Wellcome Sanger Institute, Hinxton, UK.; Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia., Amaratunga C; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA., Amato R; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Amenga-Etego L; Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana., Andagalu B; United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya., Anderson TJC; Texas Biomedical Research Institute, San Antonio, USA., Andrianaranjaka V; Université d'Antananarivo, Antananarivo, Madagascar., Apinjoh T; University of Buea, Buea, Cameroon., Ariani C; Wellcome Sanger Institute, Hinxton, UK., Ashley EA; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Auburn S; Menzies School of Health Research, Darwin, Australia.; Nuffield Department of Medicine, University of Oxford, Oxford, UK., Awandare GA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.; University of Ghana, Legon, Ghana., Ba H; Institut National de Recherche en Santé Publique, Nouakchott, Mauritania., Baraka V; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania.; Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium., Barry AE; Deakin University, Geelong, Australia.; Burnet Institute, Melbourne, Australia.; Walter and Eliza Hall Institute, Melbourne, Australia., Bejon P; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Bertin GI; Institute of Research for Development (IRD), Paris, France., Boni MF; Nuffield Department of Medicine, University of Oxford, Oxford, UK.; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Borrmann S; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany., Bousema T; London School of Hygiene and Tropical Medicine, London, UK.; Radboud University Medical Center, Nijmegen, The Netherlands., Branch O; NYU School of Medicine Langone Medical Center, New York, USA., Bull PC; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.; Department of Pathology, University of Cambridge, Cambridge, UK., Busby GBJ; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Chookajorn T; Mahidol University, Bangkok, Thailand., Chotivanich K; Mahidol University, Bangkok, Thailand., Claessens A; Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia.; LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France., Conway D; London School of Hygiene and Tropical Medicine, London, UK., Craig A; Liverpool School of Tropical Medicine, Liverpool, UK.; Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi., D'Alessandro U; Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia., Dama S; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Day NP; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Denis B; Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi., Diakite M; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Djimdé A; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Dolecek C; Nuffield Department of Medicine, University of Oxford, Oxford, UK., Dondorp AM; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Drakeley C; London School of Hygiene and Tropical Medicine, London, UK., Drury E; Wellcome Sanger Institute, Hinxton, UK., Duffy P; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA., Echeverry DF; Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia.; Universidad Icesi, Cali, Colombia., Egwang TG; Biotech Laboratories, Kampala, Uganda., Erko B; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia., Fairhurst RM; National Institutes of Health (NIH), Bethesda, USA., Faiz A; Dev Care Foundation, Dhaka, Bangladesh., Fanello CA; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Fukuda MM; Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand., Gamboa D; Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru., Ghansah A; Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana., Golassa L; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia., Goncalves S; Wellcome Sanger Institute, Hinxton, UK., Hamilton WL; Wellcome Sanger Institute, Hinxton, UK.; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK., Harrison GLA; Walter and Eliza Hall Institute, Melbourne, Australia., Hart L; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Henrichs C; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Hien TT; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Hill CA; Department of Entomology, Purdue University, West Lafayette, USA., Hodgson A; Ghana Health Service, Ministry of Health, Accra, Ghana., Hubbart C; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Imwong M; Mahidol University, Bangkok, Thailand., Ishengoma DS; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania.; East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania., Jackson SA; Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA., Jacob CG; Wellcome Sanger Institute, Hinxton, UK., Jeffery B; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Jeffreys AE; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Johnson KJ; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Jyothi D; Wellcome Sanger Institute, Hinxton, UK., Kamaliddin C; Institute of Research for Development (IRD), Paris, France., Kamau E; Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA., Kekre M; Wellcome Sanger Institute, Hinxton, UK., Kluczynski K; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Kochakarn T; Wellcome Sanger Institute, Hinxton, UK.; Mahidol University, Bangkok, Thailand., Konaté A; University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire., Kwiatkowski DP; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK.; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Kyaw MP; The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar.; University of Public Health, Yangon, Myanmar., Lim P; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA.; Medical Care Development International, Maryland, USA., Lon C; Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand., Loua KM; Institut National de Santé Publique, Conakry, Guinea., Maïga-Ascofaré O; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana., Malangone C; Wellcome Sanger Institute, Hinxton, UK., Manske M; Wellcome Sanger Institute, Hinxton, UK., Marfurt J; Menzies School of Health Research, Darwin, Australia., Marsh K; Nuffield Department of Medicine, University of Oxford, Oxford, UK.; African Academy of Sciences, Nairobi, Kenya., Mayxay M; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic.; Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic., Miles A; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Miotto O; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK.; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Mobegi V; School of Medicine, University of Nairobi, Nairobi, Kenya., Mokuolu OA; Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria., Montgomery J; Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia., Mueller I; Walter and Eliza Hall Institute, Melbourne, Australia.; Barcelona Centre for International Health Research, Barcelona, Spain., Newton PN; Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic., Nguyen T; Wellcome Sanger Institute, Hinxton, UK., Nguyen TN; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Noedl H; MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh., Nosten F; Nuffield Department of Medicine, University of Oxford, Oxford, UK.; Shoklo Malaria Research Unit, Bangkok, Thailand., Noviyanti R; Eijkman Institute for Molecular Biology, Jakarta, Indonesia., Nzila A; King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia., Ochola-Oyier LI; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Ocholla H; KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya.; Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya., Oduro A; Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana., Omedo I; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Onyamboko MA; Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic., Ouedraogo JB; Institut de Recherche en Sciences de la Santé, Ouagadougou, Burkina Faso., Oyebola K; Nigerian Institute of Medical Research, Lagos, Nigeria.; Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria., Pearson RD; Wellcome Sanger Institute, Hinxton, UK.; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Peshu N; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Phyo AP; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Shoklo Malaria Research Unit, Bangkok, Thailand., Plowe CV; School of Medicine, University of Maryland, Baltimore, MD, USA., Price RN; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Menzies School of Health Research, Darwin, Australia.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Pukrittayakamee S; Mahidol University, Bangkok, Thailand., Randrianarivelojosia M; Institut Pasteur de Madagascar, Antananarivo, Madagascar.; Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar., Rayner JC; Wellcome Sanger Institute, Hinxton, UK., Ringwald P; World Health Organization (WHO), Geneva, Switzerland., Rockett KA; Wellcome Sanger Institute, Hinxton, UK.; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Rowlands K; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Ruiz L; Universidad Nacional de la Amazonia Peruana, Iquitos, Peru., Saunders D; Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand., Shayo A; Nelson Mandela Institute of Science and Technology, Arusha, Tanzania., Siba P; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea., Simpson VJ; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Stalker J; Wellcome Sanger Institute, Hinxton, UK., Su XZ; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA., Sutherland C; London School of Hygiene and Tropical Medicine, London, UK., Takala-Harrison S; Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA., Tavul L; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea., Thathy V; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.; Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA., Tshefu A; University of Kinshasa, Kinshasa, Congo, Democratic Republic., Verra F; Sapienza University of Rome, Rome, Italy., Vinetz J; Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.; Yale School of Medicine, New Haven, CT, USA., Wellems TE; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA., Wendler J; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., White NJ; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Wright I; MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK., Yavo W; University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire.; Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire., Ye H; Department of Medical Research, Yangon, Myanmar.

Publikováno v: Wellcome open research [Wellcome Open Res] 2021 Jul 13; Vol. 6, pp. 42. Date of Electronic Publication: 2021 Jul 13 (Print Publication: 2021).

Admixture into and within sub-Saharan Africa

Autor: Angeliki Kerasidou, J O'Brien, Aaron Vanderwal, Christina Hubbart, Alistair Miles, Catherine L. Moyes, A Nyika, Abier Elzein, J Shelton, Spencer Cca., Anthony Enimil, A Diss, C Hughes, Lucas Amenga-Etego, E Somaskantharajah, Ogobara K. Doumbo, Jacob Almagro Garcia, Valentina D. Mangano, E Drury, Edith Bougama, Angie Green, Busby Gbj., Geraldine M. Clarke, Dominic P. Kwiatkowski, Jiannis Ragoussis, Alphaxard Manjurano, Bronwyn MacInnis, Tobias O. Apinjoh, D Mead, Gareth Maslen, George B.J. Busby, Kirk A. Rockett, Dushyanth Jyothi, C Potter, C Malangone, Muminatou Jallow, I Ragoussis, Ellen M. Leffler, J Rogers, J Stalker, Quang Si Le, J Rodford, D Barnwell, Alieu Mendy, J deVries, Anna E. Jeffreys, Carolyne M. Ndila, E Hilton, Vysaul Nyirongo

Publikováno v: eLife
eLife, eLife Sciences Publication, 2016, 5, pp.e15266. ⟨10.7554/eLife.15266⟩
Riley, E 2016, ' Admixture into and within sub-Saharan Africa ', eLIFE, vol. 5 . https://doi.org/10.7554/eLife.15266
eLife, Vol 5 (2016)

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,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::abf3967a3144c48294b9e09a091debf7
https://ora.ox.ac.uk/objects/uuid:33f58c0d-85d7-477f-89f2-0413ba356e0d

Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α ^3.7I form of α-thalassaemia using genome-wide microarray data.

Autor: Ndila CM; Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya., Nyirongo V; United Nation Statistics Division, United Nations, New York, New York, 10017, USA., Macharia AW; Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya., Jeffreys AE; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK., Rowlands K; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK., Hubbart C; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK., Busby GBJ; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.; Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, Oxfordshire, OX3 7LF, UK., Band G; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.; Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK., Harding RM; Departments of Zoology and Statistics, University of Oxford, Oxford, Oxfordshire, OX1 3SZ, UK., Rockett KA; Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.; Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK., Williams TN; Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya.; Department of Infectious Diseases, Imperial College Faculty of Medicine, London, W2 1NY, UK.

Publikováno v: Wellcome open research [Wellcome Open Res] 2020 Dec 09; Vol. 5, pp. 287. Date of Electronic Publication: 2020 Dec 09 (Print Publication: 2020).