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1. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 2; peer review: 2 approved]

Author

MalariaGEN, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Roberto Amato, Lucas Amenga-Etego, Ben Andagalu, Tim J. C. Anderson, Voahangy Andrianaranjaka, Tobias Apinjoh, Cristina Ariani, Elizabeth A Ashley, Sarah Auburn, Gordon A. Awandare, Hampate Ba, Vito Baraka, Alyssa E. Barry, Philip Bejon, Gwladys I. Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C. Bull, George B. J. Busby, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David Conway, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas PJ Day, Brigitte Denis, Mahamadou Diakite, Abdoulaye Djimdé, Christiane Dolecek, Arjen M Dondorp, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, William L. Hamilton, G. L. Abby Harrison, Lee Hart, Christa Henrichs, Tran Tinh Hien, Catherine A. Hill, Abraham Hodgson, Christina Hubbart, Mallika Imwong, Deus S. Ishengoma, Scott A. Jackson, Chris G. Jacob, Ben Jeffery, Anna E. Jeffreys, Kimberly J. Johnson, Dushyanth Jyothi, Claire Kamaliddin, Edwin Kamau, Mihir Kekre, Krzysztof Kluczynski, Theerarat Kochakarn, Abibatou Konaté, Dominic P. Kwiatkowski, Myat Phone Kyaw, Pharath Lim, Chanthap Lon, Kovana M. Loua, Oumou Maïga-Ascofaré, Cinzia Malangone, Magnus Manske, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Alistair Miles, Olivo Miotto, Victor Mobegi, Olugbenga A. Mokuolu, Jacqui Montgomery, Ivo Mueller, Paul N. Newton, Thuy Nguyen, Thuy-Nhien Nguyen, Harald Noedl, Francois Nosten, Rintis Noviyanti, Alexis Nzila, Lynette I. Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A. Onyamboko, Jean-Bosco Ouedraogo, Kolapo Oyebola, Richard D. Pearson, Norbert Peshu, Aung Pyae Phyo, Chris V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Kirk A. Rockett, Katherine Rowlands, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Jim Stalker, Xin-zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Livingstone Tavul, Vandana Thathy, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E. Wellems, Jason Wendler, Nicholas J. White, Ian Wright, William Yavo, and Htut Ye

Subjects
Medicine, Science
Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Published
2021
Full Text
View/download PDF

2. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 1; peer review: 2 approved]

Author

MalariaGEN, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Roberto Amato, Lucas Amenga-Etego, Ben Andagalu, Tim J. C. Anderson, Voahangy Andrianaranjaka, Tobias Apinjoh, Cristina Ariani, Elizabeth A. Ashley, Sarah Auburn, Gordon Awandare, Hampate Ba, Vito Baraka, Alyssa E. Barry, Philip Bejon, Gwladys I. Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C. Bull, George B. J. Busby, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David Conway, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas PJ Day, Brigitte Denis, Mahamadou Diakite, Abdoulaye Djimdé, Christiane Dolecek, Arjen M Dondorp, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, William L. Hamilton, G. L. Abby Harrison, Lee Hart, Christa Henrichs, Tran Tinh Hien, Catherine A. Hill, Abraham Hodgson, Christina Hubbart, Mallika Imwong, Deus S. Ishengoma, Scott A. Jackson, Chris G. Jacob, Ben Jeffery, Anna E. Jeffreys, Kimberly J. Johnson, Dushyanth Jyothi, Claire Kamaliddin, Edwin Kamau, Mihir Kekre, Krzysztof Kluczynski, Theerarat Kochakarn, Abibatou Konaté, Dominic P. Kwiatkowski, Myat Phone Kyaw, Pharath Lim, Chanthap Lon, Kovana M. Loua, Oumou Maïga-Ascofaré, Cinzia Malangone, Magnus Manske, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Alistair Miles, Olivo Miotto, Victor Mobegi, Olugbenga A. Mokuolu, Jacqui Montgomery, Ivo Mueller, Paul N. Newton, Thuy Nguyen, Thuy-Nhien Nguyen, Harald Noedl, Francois Nosten, Rintis Noviyanti, Alexis Nzila, Lynette I. Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A. Onyamboko, Jean-Bosco Ouedraogo, Kolapo Oyebola, Richard D. Pearson, Norbert Peshu, Aung Pyae Phyo, Chris V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Kirk A. Rockett, Katherine Rowlands, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Jim Stalker, Xin-zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Livingstone Tavul, Vandana Thathy, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E. Wellems, Jason Wendler, Nicholas J. White, Ian Wright, William Yavo, and Htut Ye

Subjects
Medicine, Science
Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Published
2021
Full Text
View/download PDF

3. An open dataset of

Author

Ambroise, Ahouidi, Mozam, Ali, Jacob, Almagro-Garcia, Alfred, Amambua-Ngwa, Chanaki, Amaratunga, Roberto, Amato, Lucas, Amenga-Etego, Ben, Andagalu, Tim J C, Anderson, Voahangy, Andrianaranjaka, Tobias, Apinjoh, Cristina, Ariani, Elizabeth A, Ashley, Sarah, Auburn, Gordon A, Awandare, Hampate, Ba, Vito, Baraka, Alyssa E, Barry, Philip, Bejon, Gwladys I, Bertin, Maciej F, Boni, Steffen, Borrmann, Teun, Bousema, Oralee, Branch, Peter C, Bull, George B J, Busby, Thanat, Chookajorn, Kesinee, Chotivanich, Antoine, Claessens, David, Conway, Alister, Craig, Umberto, D'Alessandro, Souleymane, Dama, Nicholas Pj, Day, Brigitte, Denis, Mahamadou, Diakite, Abdoulaye, Djimdé, Christiane, Dolecek, Arjen M, Dondorp, Chris, Drakeley, Eleanor, Drury, Patrick, Duffy, Diego F, Echeverry, Thomas G, Egwang, Berhanu, Erko, Rick M, Fairhurst, Abdul, Faiz, Caterina A, Fanello, Mark M, Fukuda, Dionicia, Gamboa, Anita, Ghansah, Lemu, Golassa, Sonia, Goncalves, William L, Hamilton, G L Abby, Harrison, Lee, Hart, Christa, Henrichs, Tran Tinh, Hien, Catherine A, Hill, Abraham, Hodgson, Christina, Hubbart, Mallika, Imwong, Deus S, Ishengoma, Scott A, Jackson, Chris G, Jacob, Ben, Jeffery, Anna E, Jeffreys, Kimberly J, Johnson, Dushyanth, Jyothi, Claire, Kamaliddin, Edwin, Kamau, Mihir, Kekre, Krzysztof, Kluczynski, Theerarat, Kochakarn, Abibatou, Konaté, Dominic P, Kwiatkowski, Myat Phone, Kyaw, Pharath, Lim, Chanthap, Lon, Kovana M, Loua, Oumou, Maïga-Ascofaré, Cinzia, Malangone, Magnus, Manske, Jutta, Marfurt, Kevin, Marsh, Mayfong, Mayxay, Alistair, Miles, Olivo, Miotto, Victor, Mobegi, Olugbenga A, Mokuolu, Jacqui, Montgomery, Ivo, Mueller, Paul N, Newton, Thuy, Nguyen, Thuy-Nhien, Nguyen, Harald, Noedl, Francois, Nosten, Rintis, Noviyanti, Alexis, Nzila, Lynette I, Ochola-Oyier, Harold, Ocholla, Abraham, Oduro, Irene, Omedo, Marie A, Onyamboko, Jean-Bosco, Ouedraogo, Kolapo, Oyebola, Richard D, Pearson, Norbert, Peshu, Aung Pyae, Phyo, Chris V, Plowe, Ric N, Price, Sasithon, Pukrittayakamee, Milijaona, Randrianarivelojosia, Julian C, Rayner, Pascal, Ringwald, Kirk A, Rockett, Katherine, Rowlands, Lastenia, Ruiz, David, Saunders, Alex, Shayo, Peter, Siba, Victoria J, Simpson, Jim, Stalker, Xin-Zhuan, Su, Colin, Sutherland, Shannon, Takala-Harrison, Livingstone, Tavul, Vandana, Thathy, Antoinette, Tshefu, Federica, Verra, Joseph, Vinetz, Thomas E, Wellems, Jason, Wendler, Nicholas J, White, Ian, Wright, William, Yavo, and Htut, Ye

Subjects
data resource, drug resistance, plasmodium falciparum, parasitic diseases, evolution, malaria, genomics, rapid diagnostic test failure, population genetics, Articles, genomic epidemiology, Research Article
Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Published
2021

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

Author

Gordon A. Awandare, Alistair Miles, Alister Craig, Nicholas J. White, Thanat Chookajorn, Colin J. Sutherland, Sarah Auburn, David J. Conway, Peter Siba, Xin-zhuan Su, Krzysztof Kluczynski, Kevin Marsh, Victoria Simpson, Mayfong Mayxay, Thuy-Nhien Nguyen, Thomas G. Egwang, Paul N. Newton, Lynette Isabella Ochola-Oyier, Lee Hart, Ambroise D. Ahouidi, Mallika Imwong, Alyssa E. Barry, Joseph M. Vinetz, Jacob Almagro-Garcia, Steffen Borrmann, Vito Baraka, MalariaGEN, Abraham Hodgson, Eleanor Drury, Aung Pyae Phyo, Marie A. Onyamboko, Jutta Marfurt, Jim Stalker, Christopher G Jacob, Ben Andagalu, Pascal Ringwald, Maciej F. Boni, Richard D. Pearson, Magnus Manske, Anita Ghansah, Rintis Noviyanti, Lastenia Ruiz, Umberto D'Alessandro, William L Hamilton, Sasithon Pukrittayakamee, Cinzia Malangone, Caterina A. Fanello, Philip Bejon, Julian C. Rayner, Lemu Golassa, Chris Drakeley, Nicholas P. J. Day, Thomas E. Wellems, Roberto Amato, Harald Noedl, Cristina V. Ariani, Alex Shayo, Arjen M. Dondorp, David L. Saunders, Rick M. Fairhurst, Catherine A. Hill, Christina Hubbart, Dominic P. Kwiatkowski, Olugbenga A. Mokuolu, Diego F. Echeverry, Alexis Nzila, Abdoulaye Djimde, Edwin Kamau, Chanaki Amaratunga, Myat Phone Kyaw, Chanthap Lon, Pharath Lim, Harold Ocholla, George B.J. Busby, Olivo Miotto, Kesinee Chotivanich, Christiane Dolecek, Ric N. Price, Kolapo Oyebola, Peter C. Bull, Dushyanth Jyothi, Brigitte Denis, Tobias O. Apinjoh, Lucas Amenga-Etego, Tim J. Anderson, Berhanu Erko, Mozam Ali, Claire Kamaliddin, Victor A. Mobegi, Hampate Ba, Christopher V. Plowe, Kimberly J. Johnson, Scott A. Jackson, Livingstone Tavul, Jacqui Montgomery, François Nosten, Thuy Nguyen, Abibatou Konaté, Mark M. Fukuda, Elizabeth A. Ashley, Dionicia Gamboa, William Yavo, G. L. Abby Harrison, Alfred Amambua-Ngwa, Mihir Kekre, Antoinette Tshefu, Tran Tinh Hien, Katherine Rowlands, Mahamadou Diakite, Ian J. Wright, Jason P. Wendler, Shannon Takala-Harrison, Htut Ye, Theerarat Kochakarn, Sónia Gonçalves, Vandana Thathy, Ben Jeffery, Kovana M. Loua, Ivo Mueller, Anna E. Jeffreys, Christa Henrichs, Teun Bousema, Antoine Claessens, Jean-Bosco Ouédraogo, Patrick E. Duffy, Voahangy Andrianaranjaka, Deus S. Ishengoma, Abraham Oduro, OraLee H. Branch, Abdul Faiz, Souleymane Dama, Federica Verra, Kirk A. Rockett, Gwladys I. Bertin, Oumou Maïga-Ascofaré, Milijaona Randrianarivelojosia, Irene Omedo, Norbert Peshu, LPHI - Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Intensive Care Medicine

Subjects
0301 basic medicine, Population genetics, Evolution, purl.org/pe-repo/ocde/ford#1.06.03 [https], 030231 tropical medicine, Plasmodium falciparum, Medicine (miscellaneous), Genomics, Single-nucleotide polymorphism, Drug resistance, Biology, General Biochemistry, Genetics and Molecular Biology, purl.org/pe-repo/ocde/ford#3.00.00 [https], 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genotype, parasitic diseases, medicine, qv_256, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Copy-number variation, Indel, Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Rapid diagnostic test failure, medicine.disease, biology.organism_classification, Genomic epidemiology, 3. Good health, wc_750, Malaria, Data resource, 030104 developmental biology, qx_510, qx_135, qu_470
Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Published
2021

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