An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved]
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...
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| Format: | Article |
| Language: | English |
| Published: |
Wellcome
2022-04-01
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| Series: | Wellcome Open Research |
| Subjects: | |
| Online Access: | https://wellcomeopenresearch.org/articles/7-136/v1 |
| _version_ | 1818504024788303872 |
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| author | Sonia Goncalves Lemu Golassa Wasif Khan Sisay Alemu Mohammad Shafiul Alam Pharath Lim Elizabeth Ashley Nicholas M Anstey Bridget E Barber Jutta Marfurt Ashenafi Assefa Dhelio Batista Pereira Alyssa Barry Nguyen Hoang Chau Jun Cao Fe Espino Cindy Chu Ivo Mueller María Fernanda Villegas Rick Fairhurst Thuy-Nhien Nguyen Yaghoob Hamedi Matthew J Grigg Rintis Noviyanti Ye Htut Tran Tinh Hien Nadira Karunaweera Kimberly J Johnson Dominic P Kwiatkowski Srivicha Krudsood Francois Nosten Benedikt Ley Marcus Lacerda Alejandro Llanos-Cuentas Yaobao Liu Tatiana Lopera-Mesa Milijaona Randrianarivelojosia Chanthap Lon Sasithon Pukrittayakamee Rezika Mohammed Pascal Michon Paul N Newton Chayadol Namaik-larp Richard D Pearson Julian C Rayner Zuleima Pava Aung P Phyo Beyene Petros Awab Ghulam Rahim Ric N Price Sasha V Siegel Angela Rumaseb Kamala Thriemer Victoria J Simpson Marcelo Urbano Ferreira Alberto Tobon-Castano Sonam Wangchuk Ivan D Vélez Nicholas J White Thomas E Wellems Maria F Yasnot Arjen M. Dondorp Timothy William Daniel Yilma Sarah Auburn Hidayat Trimarsanto Abraham Aseffa Qi Gao Roberto Amato Voahangy Andrianaranjaka Ishag Adam Kesinee Chotivanich Olivo Miotto Chanaki Amaratunga Eleanor Drury Diego F. Echeverry Berhanu Erko Abdul Faiz |
| author_facet | Sonia Goncalves Lemu Golassa Wasif Khan Sisay Alemu Mohammad Shafiul Alam Pharath Lim Elizabeth Ashley Nicholas M Anstey Bridget E Barber Jutta Marfurt Ashenafi Assefa Dhelio Batista Pereira Alyssa Barry Nguyen Hoang Chau Jun Cao Fe Espino Cindy Chu Ivo Mueller María Fernanda Villegas Rick Fairhurst Thuy-Nhien Nguyen Yaghoob Hamedi Matthew J Grigg Rintis Noviyanti Ye Htut Tran Tinh Hien Nadira Karunaweera Kimberly J Johnson Dominic P Kwiatkowski Srivicha Krudsood Francois Nosten Benedikt Ley Marcus Lacerda Alejandro Llanos-Cuentas Yaobao Liu Tatiana Lopera-Mesa Milijaona Randrianarivelojosia Chanthap Lon Sasithon Pukrittayakamee Rezika Mohammed Pascal Michon Paul N Newton Chayadol Namaik-larp Richard D Pearson Julian C Rayner Zuleima Pava Aung P Phyo Beyene Petros Awab Ghulam Rahim Ric N Price Sasha V Siegel Angela Rumaseb Kamala Thriemer Victoria J Simpson Marcelo Urbano Ferreira Alberto Tobon-Castano Sonam Wangchuk Ivan D Vélez Nicholas J White Thomas E Wellems Maria F Yasnot Arjen M. Dondorp Timothy William Daniel Yilma Sarah Auburn Hidayat Trimarsanto Abraham Aseffa Qi Gao Roberto Amato Voahangy Andrianaranjaka Ishag Adam Kesinee Chotivanich Olivo Miotto Chanaki Amaratunga Eleanor Drury Diego F. Echeverry Berhanu Erko Abdul Faiz |
| author_sort | Sonia Goncalves |
| collection | DOAJ |
| 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 | 2024-12-10T21:31:35Z |
| format | Article |
| id | doaj.art-af8eb4064e9d44ab99a763d933cf62d1 |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-12-10T21:31:35Z |
| publishDate | 2022-04-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-af8eb4064e9d44ab99a763d933cf62d12022-12-22T01:32:47ZengWellcomeWellcome Open Research2398-502X2022-04-01719696An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved]Sonia Goncalves0Lemu Golassa1https://orcid.org/0000-0002-1216-8711Wasif Khan2Sisay Alemu3Mohammad Shafiul Alam4https://orcid.org/0000-0001-8330-5499Pharath Lim5Elizabeth Ashley6https://orcid.org/0000-0002-7620-4822Nicholas M Anstey7Bridget E Barber8https://orcid.org/0000-0003-1066-7960Jutta Marfurt9Ashenafi Assefa10Dhelio Batista Pereira11https://orcid.org/0000-0002-7761-5498Alyssa Barry12Nguyen Hoang Chau13Jun Cao14Fe Espino15https://orcid.org/0000-0003-1690-1711Cindy Chu16https://orcid.org/0000-0001-9465-8214Ivo Mueller17María Fernanda Villegas18Rick Fairhurst19Thuy-Nhien Nguyen20https://orcid.org/0000-0002-4101-5706Yaghoob Hamedi21Matthew J Grigg22Rintis Noviyanti23Ye Htut24Tran Tinh Hien25Nadira Karunaweera26https://orcid.org/0000-0003-3985-1817Kimberly J Johnson27Dominic P Kwiatkowski28https://orcid.org/0000-0002-5023-0176Srivicha Krudsood29Francois Nosten30https://orcid.org/0000-0002-7951-0745Benedikt Ley31https://orcid.org/0000-0002-5734-0845Marcus Lacerda32Alejandro Llanos-Cuentas33Yaobao Liu34Tatiana Lopera-Mesa35Milijaona Randrianarivelojosia36Chanthap Lon37Sasithon Pukrittayakamee38Rezika Mohammed39Pascal Michon40Paul N Newton41Chayadol Namaik-larp42Richard D Pearson43https://orcid.org/0000-0002-7386-3566Julian C Rayner44https://orcid.org/0000-0002-9835-1014Zuleima Pava45Aung P Phyo46https://orcid.org/0000-0002-0383-9624Beyene Petros47Awab Ghulam Rahim48Ric N Price49https://orcid.org/0000-0003-2000-2874Sasha V Siegel50Angela Rumaseb51Kamala Thriemer52Victoria J Simpson53Marcelo Urbano Ferreira54https://orcid.org/0000-0002-5293-9090Alberto Tobon-Castano55Sonam Wangchuk56Ivan D Vélez57Nicholas J White58Thomas E Wellems59https://orcid.org/0000-0003-3899-8454Maria F Yasnot60https://orcid.org/0000-0001-8081-4212Arjen M. Dondorp61https://orcid.org/0000-0001-5190-2395Timothy William62Daniel Yilma63https://orcid.org/0000-0001-6058-2696Sarah Auburn64Hidayat Trimarsanto65Abraham Aseffa66Qi Gao67Roberto Amato68Voahangy Andrianaranjaka69Ishag Adam70Kesinee Chotivanich71Olivo Miotto72https://orcid.org/0000-0001-8060-6771Chanaki Amaratunga73Eleanor Drury74Diego F. Echeverry75https://orcid.org/0000-0003-0301-4478Berhanu Erko76Abdul Faiz77https://orcid.org/0000-0002-3460-7535Wellcome Sanger Institute, Hinxton, UKAklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, EthiopiaInfectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, BangladeshArmauer Hansen Research Unit (AHRI), Addis Ababa, EthiopiaInfectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, BangladeshNational Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USALao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic RepublicGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaMenzies School of Health Research, Darwin, AustraliaGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaEthiopian Public Health Institute, Addis Ababa, EthiopiaCentro de Pesquisa em Medicina Tropical de Rondônia, Porto Velho, BrazilWalter and Eliza Hall Institute, Parkville, AustraliaOxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, VietnamNational Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, ChinaResearch Institute for Tropical Medicine, Department of Health, Manila, PhilippinesShoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, ThailandWalter and Eliza Hall Institute, Parkville, AustraliaCentro de Investigaciones Clinicas, Cali, ColombiaNational Institutes of Health (NIH), Bethesda, USACentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UKInfectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, IranGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaEijkman Institute for Molecular Biology, Jakarta, IndonesiaDepartment of Medical Research, Yangon, MyanmarOxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, VietnamUniversity of Colombo, Colombo, Sri LankaWellcome Sanger Institute, Hinxton, UKWellcome Sanger Institute, Hinxton, UKMahidol University, Bangkok, ThailandCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UKGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaInstituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, BrazilCayetano Heredia University, Lima, PeruNational Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, ChinaUniversidad de Antioquia, Medellin, ColombiaInstitut Pasteur de Madagascar, Antananarivo, MadagascarNational Institute of Allergy and Infectious Diseases, Phnom Penh, CambodiaMahidol University, Bangkok, ThailandDepartment of Internal Medicine, University of Gondar, Gondar, EthiopiaNational University of Vanuatu, Port-Vila, VanuatuLao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic RepublicUmphang Hospital, Tak, ThailandWellcome Sanger Institute, Hinxton, UKCambridge Institute for Medical Research, University of Cambridge, Cambridge, UKCentro Internacionale de Entrenamiento e Investigaciones Medicas, Cali, ColombiaMahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, ThailandAddis Ababa University, Addis Ababa, EthiopiaNangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, AfghanistanGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaWellcome Sanger Institute, Hinxton, UKGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaWellcome Sanger Institute, Hinxton, UKUniversidade de São Paulo, São Paulo, BrazilUniversidad de Antioquia, Medellin, ColombiaRoyal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, BhutanUniversity of Antioquia, Medellin, ColombiaCentre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UKNational Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USAGrupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, ColombiaMahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, ThailandClinical Research Centre, Queen Elizabeth Hospital, Sabah, MalaysiaJimma University, Jimma, EthiopiaGlobal and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, AustraliaEijkman Institute for Molecular Biology, Jakarta, IndonesiaArmauer Hansen Research Unit (AHRI), Addis Ababa, EthiopiaNational Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, ChinaWellcome Sanger Institute, Hinxton, UKUniversité d'Antananarivo, Antananarivo, MadagascarFaculty of Medicine, University of Khartoum, Khartoum, SudanMahidol University, Bangkok, ThailandWellcome Sanger Institute, Hinxton, UKNational Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USAWellcome Sanger Institute, Hinxton, UKDepartamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, ColombiaAklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, EthiopiaDev Care Foundation, Dhaka, BangladeshThis 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.https://wellcomeopenresearch.org/articles/7-136/v1malaria plasmodium vivax genomics data resource genomic epidemiologyeng |
| spellingShingle | Sonia Goncalves Lemu Golassa Wasif Khan Sisay Alemu Mohammad Shafiul Alam Pharath Lim Elizabeth Ashley Nicholas M Anstey Bridget E Barber Jutta Marfurt Ashenafi Assefa Dhelio Batista Pereira Alyssa Barry Nguyen Hoang Chau Jun Cao Fe Espino Cindy Chu Ivo Mueller María Fernanda Villegas Rick Fairhurst Thuy-Nhien Nguyen Yaghoob Hamedi Matthew J Grigg Rintis Noviyanti Ye Htut Tran Tinh Hien Nadira Karunaweera Kimberly J Johnson Dominic P Kwiatkowski Srivicha Krudsood Francois Nosten Benedikt Ley Marcus Lacerda Alejandro Llanos-Cuentas Yaobao Liu Tatiana Lopera-Mesa Milijaona Randrianarivelojosia Chanthap Lon Sasithon Pukrittayakamee Rezika Mohammed Pascal Michon Paul N Newton Chayadol Namaik-larp Richard D Pearson Julian C Rayner Zuleima Pava Aung P Phyo Beyene Petros Awab Ghulam Rahim Ric N Price Sasha V Siegel Angela Rumaseb Kamala Thriemer Victoria J Simpson Marcelo Urbano Ferreira Alberto Tobon-Castano Sonam Wangchuk Ivan D Vélez Nicholas J White Thomas E Wellems Maria F Yasnot Arjen M. Dondorp Timothy William Daniel Yilma Sarah Auburn Hidayat Trimarsanto Abraham Aseffa Qi Gao Roberto Amato Voahangy Andrianaranjaka Ishag Adam Kesinee Chotivanich Olivo Miotto Chanaki Amaratunga Eleanor Drury Diego F. Echeverry Berhanu Erko Abdul Faiz An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] Wellcome Open Research malaria plasmodium vivax genomics data resource genomic epidemiology eng |
| title | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] |
| title_full | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] |
| title_fullStr | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] |
| title_full_unstemmed | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] |
| title_short | An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved] |
| title_sort | open dataset of plasmodium vivax genome variation in 1 895 worldwide samples version 1 peer review 2 approved |
| topic | malaria plasmodium vivax genomics data resource genomic epidemiology eng |
| url | https://wellcomeopenresearch.org/articles/7-136/v1 |
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