Wellcome open research · 2022

An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples.

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MalariaGEN, Adam Ishag, Alam Mohammad Shafiul, Alemu Sisay, Amaratunga Chanaki, Amato Roberto, Andrianaranjaka Voahangy, Anstey Nicholas M, Aseffa Abraham, Ashley Elizabeth, Assefa Ashenafi, Auburn Sarah, Barber Bridget E, Barry Alyssa, Batista Pereira Dhelio, Cao Jun, Chau Nguyen Hoang, Chotivanich Kesinee, Chu Cindy, Dondorp Arjen M, Drury Eleanor, Echeverry Diego F, Erko Berhanu, Espino Fe, Fairhurst Rick, Faiz Abdul, Fernanda Villegas María, Gao Qi, Golassa Lemu, Goncalves Sonia, Grigg Matthew J, Hamedi Yaghoob, Hien Tran Tinh, Htut Ye, Johnson Kimberly J, Karunaweera Nadira, Khan Wasif, Krudsood Srivicha, Kwiatkowski Dominic P, Lacerda Marcus, Ley Benedikt, Lim Pharath, Liu Yaobao, Llanos-Cuentas Alejandro, Lon Chanthap, Lopera-Mesa Tatiana, Marfurt Jutta, Michon Pascal, Miotto Olivo, Mohammed Rezika, Mueller Ivo, Namaik-Larp Chayadol, Newton Paul N, Nguyen Thuy-Nhien, Nosten Francois, Noviyanti Rintis, Pava Zuleima, Pearson Richard D, Petros Beyene, Phyo Aung P, Price Ric N, Pukrittayakamee Sasithon, Rahim Awab Ghulam, Randrianarivelojosia Milijaona, Rayner Julian C, Rumaseb Angela, Siegel Sasha V, Simpson Victoria J, Thriemer Kamala, Tobon-Castano Alberto, Trimarsanto Hidayat, Urbano Ferreira Marcelo, Vélez Ivan D, Wangchuk Sonam, Wellems Thomas E, White Nicholas J, William Timothy, Yasnot Maria F, Yilma Daniel

Аннотация

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax 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 dhfr, dhps and mdr1 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 P. vivax and to accelerate genomic surveillance for malaria control and elimination.

An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples.

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