An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
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 previou...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal article |
| Language: | English |
| Published: |
F1000Research
2022
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| _version_ | 1797107417626968064 |
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| author | Adam, I Alam, MS Alemu, S Amaratunga, C Amato, R Andrianaranjaka, V Anstey, N Aseffa, A Ashley, E Assefa, A Auburn, S Barber, B Barry, A Batista Pereira, D Cao, J Chau, NH Chotivanich, K Chu, C Dondorp, A Drury, E Echeverry, D Erko, B Espino, F Fairhurst, R Faiz, A Fernanda Villegas, M Gao, Q Golassa, L Goncalves, S Grigg, M Hamedi, Y Hien, TT Htut, Y Johnson, K Karunaweera, N Khan, W Krudsood, S Kwiatkowski, D Lacerda, M Ley, B Lim, P Liu, Y Llanos-Cuentas, A Lon, C Lopera-Mesa, T Marfurt, J Michon, P Miotto, O Mohammed, R Nosten, F Price, R |
| author2 | MalariaGEN |
| author_facet | MalariaGEN Adam, I Alam, MS Alemu, S Amaratunga, C Amato, R Andrianaranjaka, V Anstey, N Aseffa, A Ashley, E Assefa, A Auburn, S Barber, B Barry, A Batista Pereira, D Cao, J Chau, NH Chotivanich, K Chu, C Dondorp, A Drury, E Echeverry, D Erko, B Espino, F Fairhurst, R Faiz, A Fernanda Villegas, M Gao, Q Golassa, L Goncalves, S Grigg, M Hamedi, Y Hien, TT Htut, Y Johnson, K Karunaweera, N Khan, W Krudsood, S Kwiatkowski, D Lacerda, M Ley, B Lim, P Liu, Y Llanos-Cuentas, A Lon, C Lopera-Mesa, T Marfurt, J Michon, P Miotto, O Mohammed, R Nosten, F Price, R |
| author_sort | Adam, I |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T07:14:17Z |
| format | Journal article |
| id | oxford-uuid:bc33c3a2-8b88-4be7-8b5b-d14c0d98982e |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:14:17Z |
| publishDate | 2022 |
| publisher | F1000Research |
| record_format | dspace |
| spelling | oxford-uuid:bc33c3a2-8b88-4be7-8b5b-d14c0d98982e2022-07-25T16:16:20ZAn open dataset of Plasmodium vivax genome variation in 1,895 worldwide samplesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:bc33c3a2-8b88-4be7-8b5b-d14c0d98982eEnglishSymplectic ElementsF1000Research2022Adam, IAlam, MSAlemu, SAmaratunga, CAmato, RAndrianaranjaka, VAnstey, NAseffa, AAshley, EAssefa, AAuburn, SBarber, BBarry, ABatista Pereira, DCao, JChau, NHChotivanich, KChu, CDondorp, ADrury, EEcheverry, DErko, BEspino, FFairhurst, RFaiz, AFernanda Villegas, MGao, QGolassa, LGoncalves, SGrigg, MHamedi, YHien, TTHtut, YJohnson, KKarunaweera, NKhan, WKrudsood, SKwiatkowski, DLacerda, MLey, BLim, PLiu, YLlanos-Cuentas, ALon, CLopera-Mesa, TMarfurt, JMichon, PMiotto, OMohammed, RNosten, FPrice, RMalariaGENThis 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. |
| spellingShingle | Adam, I Alam, MS Alemu, S Amaratunga, C Amato, R Andrianaranjaka, V Anstey, N Aseffa, A Ashley, E Assefa, A Auburn, S Barber, B Barry, A Batista Pereira, D Cao, J Chau, NH Chotivanich, K Chu, C Dondorp, A Drury, E Echeverry, D Erko, B Espino, F Fairhurst, R Faiz, A Fernanda Villegas, M Gao, Q Golassa, L Goncalves, S Grigg, M Hamedi, Y Hien, TT Htut, Y Johnson, K Karunaweera, N Khan, W Krudsood, S Kwiatkowski, D Lacerda, M Ley, B Lim, P Liu, Y Llanos-Cuentas, A Lon, C Lopera-Mesa, T Marfurt, J Michon, P Miotto, O Mohammed, R Nosten, F Price, R An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title_full | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title_fullStr | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title_full_unstemmed | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title_short | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples |
| title_sort | open dataset of plasmodium vivax genome variation in 1 895 worldwide samples |
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