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Get Free Access<ns3:p>This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of <ns3:italic>Plasmodium vivax</ns3:italic> collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the <ns3:italic>dhfr</ns3:italic>, <ns3:italic>dhps</ns3:italic> and <ns3:italic>mdr1</ns3:italic> loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of <ns3:italic>P. vivax</ns3:italic> and to accelerate genomic surveillance for malaria control and elimination.</ns3:p>
Ishag Adam, Mohammad Shafiul Alam, Sisay Getachew Alemu, Chanaki Amaratunga, Roberto Amato, Voahangy Andrianaranjaka, Nicholas M. Anstey, Abraham Aseffa, Elizabeth A. Ashley, Ashenafi Assefa, Sarah Auburn, Bridget E. Barber, Alyssa E. Barry, Dhélio B. Pereira, Jun Cao, Nguyen Hoang Chau, Kesinee Chotivanich, Cindy S. Chu, Arjen M. Dondorp, Eleanor Drury, Diego F. Echeverry, Berhanu Erko, Fe Esperanza Espino, Rick M. Fairhurst, Abdul Faiz, María Fernanda Villegas, Qi Gao, Lemu Golassa, Sónia Gonçalves, Matthew J. Grigg, Yaghoob Hamedi, Tran Tinh Hien, Ye Htut, Kimberly J. Johnson, Nadira D. Karunaweera, Wasif Ali Khan, Srivicha Krudsood, Dominic Kwiatkowski, Marcus Lacerda, Benedikt Ley, Pharath Lim, Yaobao Liu, Alejandro Llanos‐Cuentas, Chanthap Lon, Tatiana M. Lopera-Mesa, Jutta Marfurt, P Michon, Olivo Miotto, Rezika Mohammed, Ivo Müeller, Chayadol Namaik-larp, Paul N. Newton, Thuy-Nhien Nguyen, François Nosten, Rintis Noviyanti, Zuleima Pava, Richard D. Pearson, Beyene Petros, Aung Pyae Phyo, Ric N. Price, Sasithon Pukrittayakamee, Ghulam Rahim Awab, Milijaona Randrianarivelojosia, Julian C. Rayner, Angela Rumaseb, Sasha V. Siegel, Victoria J. Simpson, Kamala Thriemer, Alberto Tobón-Castaño, Hidayat Trimarsanto, Marcelo U. Ferreira, Iván Darío Vélez, Sonam Wangchuk, Thomas E. Wellems, Sir Nicholas White, Timothy William, María Fernanda Yasnot, Daniel Yilma (2022). An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples. Wellcome Open Research, 7, pp. 136-136, DOI: 10.12688/wellcomeopenres.17795.1.
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Type
Preprint
Year
2022
Authors
78
Datasets
0
Total Files
0
Language
English
Journal
Wellcome Open Research
DOI
10.12688/wellcomeopenres.17795.1
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