Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Muzamil Mahdi Abdel Hamid; Mohamed Hassan Abdelraheem; Desmond Omane Acheampong; Ambroise Ahouidi; Mozam Ali; Jacob Almagro-Garcia; Alfred Amambua-Ngwa; Chanaki Amaratunga; Lucas Amenga-Etego; Ben Andagalu; Tim Anderson; Voahangy Andrianaranjaka; Ifeyinwa Aniebo; Enoch Aninagyei; Felix Ansah; Patrick O. Ansah; Tobias Apinjoh; Paulo Arnaldo; Elizabeth Ashley; Sarah Auburn; Gordon A. Awandare; Hampate Ba; Vito Baraka; Alyssa Barry; Philip Bejon; Gwladys I. Bertin; Maciej F. Boni; Steffen Borrmann; Teun Bousema; Marielle Bouyou-Akotet; Oralee Branch; Peter C. Bull; Huch Cheah; Keobouphaphone Chindavongsa; Thanat Chookajorn; Kesinee Chotivanich; Antoine Claessens; David J. Conway; Vladimir Corredor; Erin Courtier; Alister Craig; Umberto D'Alessandro; Souleymane Dama; Nicholas Day; Brigitte Denis; Mehul Dhorda; Mahamadou Diakite; Abdoulaye Djimde; Christiane Dolecek; Arjen Dondorp; Seydou Doumbia; Chris Drakeley; Eleanor Drury; Patrick Duffy; Diego F. Echeverry; Thomas G. Egwang; Sonia Maria Mauricio Enosse; Berhanu Erko; Rick M. Fairhurst; Abdul Faiz; Caterina A. Fanello; Mark Fleharty; Matthew Forbes; Mark Fukuda; Dionicia Gamboa; Anita Ghansah; Lemu Golassa; Sonia Goncalves; G. L.Abby Harrison; Sara Anne Healy; Jason A. Hendry; Anastasia Hernandez-Koutoucheva; Tran Tinh Hien; Catherine A. Hill; Francis Hombhanje; Amanda Hott; Ye Htut; Mazza Hussein; Mallika Imwong; Deus Ishengoma; Scott A. Jackson; Chris G. Jacob; Julia Jeans; Kimberly J. Johnson; Claire Kamaliddin; Edwin Kamau; Jon Keatley; Theerarat Kochakarn; Drissa S. Konate; Abibatou Konaté; Aminatou Kone; Dominic P. Kwiatkowski; Myat P. Kyaw; Dennis Kyle; Mara Lawniczak; Samuel K. Lee; Martha Lemnge; Pharath Lim; Chanthap Lon; Kovana M. Loua; Celine I. Mandara; Jutta Marfurt; Kevin Marsh; Richard James Maude; Mayfong Mayxay; Oumou Maïga-Ascofaré; Olivo Miotto; Toshihiro Mita; Victor Mobegi; Abdelrahim Osman Mohamed; Olugbenga A. Mokuolu; Jaqui Montgomery; Collins Misita Morang’a; Ivo Mueller; Kathryn Murie; Paul N. Newton; Thang Ngo Duc; Thuy Nhien Nguyen; Thuy Nhien Nguyen; Tuyen Nguyen Thi Kim; Hong Nguyen Van; Harald Noedl; Francois Nosten; Rintis Noviyanti; Vincent Ntui Njock Ntui; Alexis Nzila; Lynette Isabella Ochola-Oyier; Harold Ocholla; Abraham Oduro; Irene Omedo; Marie A. Onyamboko; Jean Bosco Ouedraogo; Kolapo Oyebola; Wellington Aghoghovwia Oyibo; Richard Pearson; Norbert Peshu; Aung P. Phyo; Christopher V. Plowe; Ric N. Price; Sasithon Pukrittayakamee; Huynh Hong Quang; Milijaona Randrianarivelojosia; Julian C. Rayner; Pascal Ringwald; Anna Rosanas-Urgell; Eduard Rovira-Vallbona; Valentin Ruano-Rubio; Lastenia Ruiz; David Saunders; Alex Shayo; Peter Siba; Victoria J. Simpson; Mahamadou S. Sissoko; Christen Smith; Xin Zhuan Su; Colin Sutherland; Shannon Takala-Harrison; Arthur Talman; Livingstone Tavul; Ngo Viet Thanh; Vandana Thathy; Aung Myint Thu; Mahamoudou Toure; Antoinette Tshefu; Federica Verra; Joseph Vinetz; Thomas E. Wellems; Jason Wendler; Nicholas J. White; Georgia Whitton; William Yavo; Rob W. van der Pluijm

doi:10.12688/wellcomeopenres.18681.1

Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Ben Andagalu, Tim Anderson, Voahangy Andrianaranjaka, Ifeyinwa Aniebo, Enoch Aninagyei, Felix Ansah, Patrick O. Ansah, Tobias Apinjoh, Paulo Arnaldo, Elizabeth Ashley, Sarah AuburnGordon A. Awandare, Hampate Ba, Vito Baraka, Alyssa Barry, Philip Bejon, Gwladys I. Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Marielle Bouyou-Akotet, Oralee Branch, Peter C. Bull, Huch Cheah, Keobouphaphone Chindavongsa, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David J. Conway, Vladimir Corredor, Erin Courtier, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas Day, Brigitte Denis, Mehul Dhorda, Mahamadou Diakite, Abdoulaye Djimde, Christiane Dolecek, Arjen Dondorp, Seydou Doumbia, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Sonia Maria Mauricio Enosse, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, Mark Fleharty, Matthew Forbes, Mark Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, G. L.Abby Harrison, Sara Anne Healy, Jason A. Hendry, Anastasia Hernandez-Koutoucheva, Tran Tinh Hien, Catherine A. Hill, Francis Hombhanje, Amanda Hott, Ye Htut, Mazza Hussein, Mallika Imwong, Deus Ishengoma, Scott A. Jackson, Chris G. Jacob, Julia Jeans, Kimberly J. Johnson, Claire Kamaliddin, Edwin Kamau, Jon Keatley, Theerarat Kochakarn, Drissa S. Konate, Abibatou Konaté, Aminatou Kone, Dominic P. Kwiatkowski, Myat P. Kyaw, Dennis Kyle, Mara Lawniczak, Samuel K. Lee, Martha Lemnge, Pharath Lim, Chanthap Lon, Kovana M. Loua, Celine I. Mandara, Jutta Marfurt, Kevin Marsh, Richard James Maude, Mayfong Mayxay, Oumou Maïga-Ascofaré, Olivo Miotto, Toshihiro Mita, Victor Mobegi, Abdelrahim Osman Mohamed, Olugbenga A. Mokuolu, Jaqui Montgomery, Collins Misita Morang’a, Ivo Mueller, Kathryn Murie, Paul N. Newton, Thang Ngo Duc, Thuy Nhien Nguyen, Thuy Nhien Nguyen, Tuyen Nguyen Thi Kim, Hong Nguyen Van, Harald Noedl, Francois Nosten, Rintis Noviyanti, Vincent Ntui Njock Ntui, Alexis Nzila, Lynette Isabella Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A. Onyamboko, Jean Bosco Ouedraogo, Kolapo Oyebola, Wellington Aghoghovwia Oyibo, Richard Pearson, Norbert Peshu, Aung P. Phyo, Christopher V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Huynh Hong Quang, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Anna Rosanas-Urgell, Eduard Rovira-Vallbona, Valentin Ruano-Rubio, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Mahamadou S. Sissoko, Christen Smith, Xin Zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Arthur Talman, Livingstone Tavul, Ngo Viet Thanh, Vandana Thathy, Aung Myint Thu, Mahamoudou Toure, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E. Wellems, Jason Wendler, Nicholas J. White, Georgia Whitton, William Yavo, Rob W. van der Pluijm

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Abstract

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Original language	English
Article number	22
Journal	Wellcome Open Research
Volume	8
DOIs	https://doi.org/10.12688/wellcomeopenres.18681.1
Publication status	Published - 2023

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10.12688/wellcomeopenres.18681.1

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Abdel Hamid, M. M., Abdelraheem, M. H., Acheampong, D. O., Ahouidi, A., Ali, M., Almagro-Garcia, J., Amambua-Ngwa, A., Amaratunga, C., Amenga-Etego, L., Andagalu, B., Anderson, T., Andrianaranjaka, V., Aniebo, I., Aninagyei, E., Ansah, F., Ansah, P. O., Apinjoh, T., Arnaldo, P., Ashley, E., ... van der Pluijm, R. W. (2023). Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Research, 8, [22]. https://doi.org/10.12688/wellcomeopenres.18681.1

@article{be4640d861f447cc9def9bf8d8ed6c84,

title = "Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples",

abstract = "We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.",

keywords = "data resource, genomic epidemiology, genomics, malaria, plasmodium falciparum",

author = "{Abdel Hamid}, {Muzamil Mahdi} and Abdelraheem, {Mohamed Hassan} and Acheampong, {Desmond Omane} and Ambroise Ahouidi and Mozam Ali and Jacob Almagro-Garcia and Alfred Amambua-Ngwa and Chanaki Amaratunga and Lucas Amenga-Etego and Ben Andagalu and Tim Anderson and Voahangy Andrianaranjaka and Ifeyinwa Aniebo and Enoch Aninagyei and Felix Ansah and Ansah, {Patrick O.} and Tobias Apinjoh and Paulo Arnaldo and Elizabeth Ashley and Sarah Auburn and Awandare, {Gordon A.} and Hampate Ba and Vito Baraka and Alyssa Barry and Philip Bejon and Bertin, {Gwladys I.} and Boni, {Maciej F.} and Steffen Borrmann and Teun Bousema and Marielle Bouyou-Akotet and Oralee Branch and Bull, {Peter C.} and Huch Cheah and Keobouphaphone Chindavongsa and Thanat Chookajorn and Kesinee Chotivanich and Antoine Claessens and Conway, {David J.} and Vladimir Corredor and Erin Courtier and Alister Craig and Umberto D'Alessandro and Souleymane Dama and Nicholas Day and Brigitte Denis and Mehul Dhorda and Mahamadou Diakite and Abdoulaye Djimde and Christiane Dolecek and Arjen Dondorp and Seydou Doumbia and Chris Drakeley and Eleanor Drury and Patrick Duffy and Echeverry, {Diego F.} and Egwang, {Thomas G.} and Enosse, {Sonia Maria Mauricio} and Berhanu Erko and Fairhurst, {Rick M.} and Abdul Faiz and Fanello, {Caterina A.} and Mark Fleharty and Matthew Forbes and Mark Fukuda and Dionicia Gamboa and Anita Ghansah and Lemu Golassa and Sonia Goncalves and Harrison, {G. L.Abby} and Healy, {Sara Anne} and Hendry, {Jason A.} and Anastasia Hernandez-Koutoucheva and Hien, {Tran Tinh} and Hill, {Catherine A.} and Francis Hombhanje and Amanda Hott and Ye Htut and Mazza Hussein and Mallika Imwong and Deus Ishengoma and Jackson, {Scott A.} and Jacob, {Chris G.} and Julia Jeans and Johnson, {Kimberly J.} and Claire Kamaliddin and Edwin Kamau and Jon Keatley and Theerarat Kochakarn and Konate, {Drissa S.} and Abibatou Konat{\'e} and Aminatou Kone and Kwiatkowski, {Dominic P.} and Kyaw, {Myat P.} and Dennis Kyle and Mara Lawniczak and Lee, {Samuel K.} and Martha Lemnge and Pharath Lim and Chanthap Lon and Loua, {Kovana M.} and Mandara, {Celine I.} and Jutta Marfurt and Kevin Marsh and Maude, {Richard James} and Mayfong Mayxay and Oumou Ma{\"i}ga-Ascofar{\'e} and Olivo Miotto and Toshihiro Mita and Victor Mobegi and Mohamed, {Abdelrahim Osman} and Mokuolu, {Olugbenga A.} and Jaqui Montgomery and Morang{\textquoteright}a, {Collins Misita} and Ivo Mueller and Kathryn Murie and Newton, {Paul N.} and {Ngo Duc}, Thang and Nguyen, {Thuy Nhien} and Nguyen, {Thuy Nhien} and {Nguyen Thi Kim}, Tuyen and {Nguyen Van}, Hong and Harald Noedl and Francois Nosten and Rintis Noviyanti and Ntui, {Vincent Ntui Njock} and Alexis Nzila and Ochola-Oyier, {Lynette Isabella} and Harold Ocholla and Abraham Oduro and Irene Omedo and Onyamboko, {Marie A.} and Ouedraogo, {Jean Bosco} and Kolapo Oyebola and Oyibo, {Wellington Aghoghovwia} and Richard Pearson and Norbert Peshu and Phyo, {Aung P.} and Plowe, {Christopher V.} and Price, {Ric N.} and Sasithon Pukrittayakamee and Quang, {Huynh Hong} and Milijaona Randrianarivelojosia and Rayner, {Julian C.} and Pascal Ringwald and Anna Rosanas-Urgell and Eduard Rovira-Vallbona and Valentin Ruano-Rubio and Lastenia Ruiz and David Saunders and Alex Shayo and Peter Siba and Simpson, {Victoria J.} and Sissoko, {Mahamadou S.} and Christen Smith and Su, {Xin Zhuan} and Colin Sutherland and Shannon Takala-Harrison and Arthur Talman and Livingstone Tavul and Thanh, {Ngo Viet} and Vandana Thathy and Thu, {Aung Myint} and Mahamoudou Toure and Antoinette Tshefu and Federica Verra and Joseph Vinetz and Wellems, {Thomas E.} and Jason Wendler and White, {Nicholas J.} and Georgia Whitton and William Yavo and {van der Pluijm}, {Rob W.}",

note = "Funding Information: This study was conducted by MalariaGEN, and was made possible by clinical parasite samples contributed by partner studies, whose investigators are represented in the author list and in the associated data release ( https://www.malariagen.net/resource/34 ). This research was supported in part by the Intramural Research Programme of the NIH, NIAID. In addition, the authors would like to thank the following individuals who contributed to partner studies, making this study possible: Dr Eugene Laman for work in sample collection in the Republic of Guinea; Dr Abderahmane Tandia and Dr Yacine Deh and Dr Samuel Assefa for work in sample collection in Mauritania; Dr Ibrahim Sanogo, Dr Sekou F. Traore and Dr Merepen dite Agnes Guindo for work in sample collection in Mali; Dr James Abugri and Dr Nicholas Amoako for work coordinating sample collection in Ghana. Genome sequencing was undertaken by the Wellcome Sanger Institute and we thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contribution. The views expressed here are solely those of the authors and do not reflect the views, policies or positions of the U.S. Government or Department of Defense. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. The investigators have adhered to the policies for protection of human subjects as prescribed in AR 70–25. PR is a staff member of the World Health Organization. PR alone is responsible for the views expressed in this publication and they do not necessarily represent the decisions, policy or views of the World Health Organization. Publisher Copyright: Copyright: {\textcopyright} 2023 MalariaGEN et al.",

year = "2023",

doi = "10.12688/wellcomeopenres.18681.1",

language = "English",

volume = "8",

journal = "Wellcome Open Research",

issn = "2398-502X",

publisher = "F1000 Research Ltd.",

}

Abdel Hamid, MM, Abdelraheem, MH, Acheampong, DO, Ahouidi, A, Ali, M, Almagro-Garcia, J, Amambua-Ngwa, A, Amaratunga, C, Amenga-Etego, L, Andagalu, B, Anderson, T, Andrianaranjaka, V, Aniebo, I, Aninagyei, E, Ansah, F, Ansah, PO, Apinjoh, T, Arnaldo, P, Ashley, E, Auburn, S, Awandare, GA, Ba, H, Baraka, V, Barry, A, Bejon, P, Bertin, GI, Boni, MF, Borrmann, S, Bousema, T, Bouyou-Akotet, M, Branch, O, Bull, PC, Cheah, H, Chindavongsa, K, Chookajorn, T, Chotivanich, K, Claessens, A, Conway, DJ, Corredor, V, Courtier, E, Craig, A, D'Alessandro, U, Dama, S, Day, N, Denis, B, Dhorda, M, Diakite, M, Djimde, A, Dolecek, C, Dondorp, A, Doumbia, S, Drakeley, C, Drury, E, Duffy, P, Echeverry, DF, Egwang, TG, Enosse, SMM, Erko, B, Fairhurst, RM, Faiz, A, Fanello, CA, Fleharty, M, Forbes, M, Fukuda, M, Gamboa, D, Ghansah, A, Golassa, L, Goncalves, S, Harrison, GLA, Healy, SA, Hendry, JA, Hernandez-Koutoucheva, A, Hien, TT, Hill, CA, Hombhanje, F, Hott, A, Htut, Y, Hussein, M, Imwong, M, Ishengoma, D, Jackson, SA, Jacob, CG, Jeans, J, Johnson, KJ, Kamaliddin, C, Kamau, E, Keatley, J, Kochakarn, T, Konate, DS, Konaté, A, Kone, A, Kwiatkowski, DP, Kyaw, MP, Kyle, D, Lawniczak, M, Lee, SK, Lemnge, M, Lim, P, Lon, C, Loua, KM, Mandara, CI, Marfurt, J, Marsh, K, Maude, RJ, Mayxay, M, Maïga-Ascofaré, O, Miotto, O, Mita, T, Mobegi, V, Mohamed, AO, Mokuolu, OA, Montgomery, J, Morang’a, CM, Mueller, I, Murie, K, Newton, PN, Ngo Duc, T, Nguyen, TN, Nguyen, TN, Nguyen Thi Kim, T, Nguyen Van, H, Noedl, H, Nosten, F, Noviyanti, R, Ntui, VNN, Nzila, A, Ochola-Oyier, LI, Ocholla, H, Oduro, A, Omedo, I, Onyamboko, MA, Ouedraogo, JB, Oyebola, K, Oyibo, WA, Pearson, R, Peshu, N, Phyo, AP, Plowe, CV, Price, RN, Pukrittayakamee, S, Quang, HH, Randrianarivelojosia, M, Rayner, JC, Ringwald, P, Rosanas-Urgell, A, Rovira-Vallbona, E, Ruano-Rubio, V, Ruiz, L, Saunders, D, Shayo, A, Siba, P, Simpson, VJ, Sissoko, MS, Smith, C, Su, XZ, Sutherland, C, Takala-Harrison, S, Talman, A, Tavul, L, Thanh, NV, Thathy, V, Thu, AM, Toure, M, Tshefu, A, Verra, F, Vinetz, J, Wellems, TE, Wendler, J, White, NJ, Whitton, G, Yavo, W & van der Pluijm, RW 2023, 'Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples', Wellcome Open Research, vol. 8, 22. https://doi.org/10.12688/wellcomeopenres.18681.1

TY - JOUR

T1 - Pf7

T2 - An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

AU - Abdel Hamid, Muzamil Mahdi

AU - Abdelraheem, Mohamed Hassan

AU - Acheampong, Desmond Omane

AU - Ahouidi, Ambroise

AU - Ali, Mozam

AU - Almagro-Garcia, Jacob

AU - Amambua-Ngwa, Alfred

AU - Amaratunga, Chanaki

AU - Amenga-Etego, Lucas

AU - Andagalu, Ben

AU - Anderson, Tim

AU - Andrianaranjaka, Voahangy

AU - Aniebo, Ifeyinwa

AU - Aninagyei, Enoch

AU - Ansah, Felix

AU - Ansah, Patrick O.

AU - Apinjoh, Tobias

AU - Arnaldo, Paulo

AU - Ashley, Elizabeth

AU - Auburn, Sarah

AU - Awandare, Gordon A.

AU - Ba, Hampate

AU - Baraka, Vito

AU - Barry, Alyssa

AU - Bejon, Philip

AU - Bertin, Gwladys I.

AU - Boni, Maciej F.

AU - Borrmann, Steffen

AU - Bousema, Teun

AU - Bouyou-Akotet, Marielle

AU - Branch, Oralee

AU - Bull, Peter C.

AU - Cheah, Huch

AU - Chindavongsa, Keobouphaphone

AU - Chookajorn, Thanat

AU - Chotivanich, Kesinee

AU - Claessens, Antoine

AU - Conway, David J.

AU - Corredor, Vladimir

AU - Courtier, Erin

AU - Craig, Alister

AU - D'Alessandro, Umberto

AU - Dama, Souleymane

AU - Day, Nicholas

AU - Denis, Brigitte

AU - Dhorda, Mehul

AU - Diakite, Mahamadou

AU - Djimde, Abdoulaye

AU - Dolecek, Christiane

AU - Dondorp, Arjen

AU - Doumbia, Seydou

AU - Drakeley, Chris

AU - Drury, Eleanor

AU - Duffy, Patrick

AU - Echeverry, Diego F.

AU - Egwang, Thomas G.

AU - Enosse, Sonia Maria Mauricio

AU - Erko, Berhanu

AU - Fairhurst, Rick M.

AU - Faiz, Abdul

AU - Fanello, Caterina A.

AU - Fleharty, Mark

AU - Forbes, Matthew

AU - Fukuda, Mark

AU - Gamboa, Dionicia

AU - Ghansah, Anita

AU - Golassa, Lemu

AU - Goncalves, Sonia

AU - Harrison, G. L.Abby

AU - Healy, Sara Anne

AU - Hendry, Jason A.

AU - Hernandez-Koutoucheva, Anastasia

AU - Hien, Tran Tinh

AU - Hill, Catherine A.

AU - Hombhanje, Francis

AU - Hott, Amanda

AU - Htut, Ye

AU - Hussein, Mazza

AU - Imwong, Mallika

AU - Ishengoma, Deus

AU - Jackson, Scott A.

AU - Jacob, Chris G.

AU - Jeans, Julia

AU - Johnson, Kimberly J.

AU - Kamaliddin, Claire

AU - Kamau, Edwin

AU - Keatley, Jon

AU - Kochakarn, Theerarat

AU - Konate, Drissa S.

AU - Konaté, Abibatou

AU - Kone, Aminatou

AU - Kwiatkowski, Dominic P.

AU - Kyaw, Myat P.

AU - Kyle, Dennis

AU - Lawniczak, Mara

AU - Lee, Samuel K.

AU - Lemnge, Martha

AU - Lim, Pharath

AU - Lon, Chanthap

AU - Loua, Kovana M.

AU - Mandara, Celine I.

AU - Marfurt, Jutta

AU - Marsh, Kevin

AU - Maude, Richard James

AU - Mayxay, Mayfong

AU - Maïga-Ascofaré, Oumou

AU - Miotto, Olivo

AU - Mita, Toshihiro

AU - Mobegi, Victor

AU - Mohamed, Abdelrahim Osman

AU - Mokuolu, Olugbenga A.

AU - Montgomery, Jaqui

AU - Morang’a, Collins Misita

AU - Mueller, Ivo

AU - Murie, Kathryn

AU - Newton, Paul N.

AU - Ngo Duc, Thang

AU - Nguyen, Thuy Nhien

AU - Nguyen Thi Kim, Tuyen

AU - Nguyen Van, Hong

AU - Noedl, Harald

AU - Nosten, Francois

AU - Noviyanti, Rintis

AU - Ntui, Vincent Ntui Njock

AU - Nzila, Alexis

AU - Ochola-Oyier, Lynette Isabella

AU - Ocholla, Harold

AU - Oduro, Abraham

AU - Omedo, Irene

AU - Onyamboko, Marie A.

AU - Ouedraogo, Jean Bosco

AU - Oyebola, Kolapo

AU - Oyibo, Wellington Aghoghovwia

AU - Pearson, Richard

AU - Peshu, Norbert

AU - Phyo, Aung P.

AU - Plowe, Christopher V.

AU - Price, Ric N.

AU - Pukrittayakamee, Sasithon

AU - Quang, Huynh Hong

AU - Randrianarivelojosia, Milijaona

AU - Rayner, Julian C.

AU - Ringwald, Pascal

AU - Rosanas-Urgell, Anna

AU - Rovira-Vallbona, Eduard

AU - Ruano-Rubio, Valentin

AU - Ruiz, Lastenia

AU - Saunders, David

AU - Shayo, Alex

AU - Siba, Peter

AU - Simpson, Victoria J.

AU - Sissoko, Mahamadou S.

AU - Smith, Christen

AU - Su, Xin Zhuan

AU - Sutherland, Colin

AU - Takala-Harrison, Shannon

AU - Talman, Arthur

AU - Tavul, Livingstone

AU - Thanh, Ngo Viet

AU - Thathy, Vandana

AU - Thu, Aung Myint

AU - Toure, Mahamoudou

AU - Tshefu, Antoinette

AU - Verra, Federica

AU - Vinetz, Joseph

AU - Wellems, Thomas E.

AU - Wendler, Jason

AU - White, Nicholas J.

AU - Whitton, Georgia

AU - Yavo, William

AU - van der Pluijm, Rob W.

N1 - Funding Information: This study was conducted by MalariaGEN, and was made possible by clinical parasite samples contributed by partner studies, whose investigators are represented in the author list and in the associated data release ( https://www.malariagen.net/resource/34 ). This research was supported in part by the Intramural Research Programme of the NIH, NIAID. In addition, the authors would like to thank the following individuals who contributed to partner studies, making this study possible: Dr Eugene Laman for work in sample collection in the Republic of Guinea; Dr Abderahmane Tandia and Dr Yacine Deh and Dr Samuel Assefa for work in sample collection in Mauritania; Dr Ibrahim Sanogo, Dr Sekou F. Traore and Dr Merepen dite Agnes Guindo for work in sample collection in Mali; Dr James Abugri and Dr Nicholas Amoako for work coordinating sample collection in Ghana. Genome sequencing was undertaken by the Wellcome Sanger Institute and we thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contribution. The views expressed here are solely those of the authors and do not reflect the views, policies or positions of the U.S. Government or Department of Defense. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. The investigators have adhered to the policies for protection of human subjects as prescribed in AR 70–25. PR is a staff member of the World Health Organization. PR alone is responsible for the views expressed in this publication and they do not necessarily represent the decisions, policy or views of the World Health Organization. Publisher Copyright: Copyright: © 2023 MalariaGEN et al.

PY - 2023

Y1 - 2023

N2 - We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

AB - We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

KW - data resource

KW - genomic epidemiology

KW - genomics

KW - malaria

KW - plasmodium falciparum

UR - http://www.scopus.com/inward/record.url?scp=85150355807&partnerID=8YFLogxK

U2 - 10.12688/wellcomeopenres.18681.1

DO - 10.12688/wellcomeopenres.18681.1

M3 - Article

AN - SCOPUS:85150355807

SN - 2398-502X

VL - 8

JO - Wellcome Open Research

JF - Wellcome Open Research

M1 - 22

ER -

Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

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