hmmIBD: software to infer pairwise identity by descent between haploid genotypes.
Stephen F. Schaffner,Stephen F. Schaffner,Aimee R. Taylor,Aimee R. Taylor,Wesley P. Wong,Dyann F. Wirth,Dyann F. Wirth,Daniel E. Neafsey,Daniel E. Neafsey +8 more
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TLDR
Fast and accurate software for detecting IBD in malaria parasite genetic data sampled from one or two populations is presented and will likely be a useful feature for malaria elimination efforts, since it could facilitate identification of imported malaria cases.Abstract:
A number of recent malaria studies have used identity by descent (IBD) to study epidemiological processes relevant to malaria control. In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available. The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations. Code for all tests is freely available. The utility of hmmIBD for detecting IBD across populations was demonstrated using Plasmodium falciparum data from Cambodia and Ghana. Alongside an existing method, hmmIBD was highly accurate, sensitive and specific. It is fast, requiring only 70 s on average to analyse 50 whole genome sequences on a laptop computer, and scales linearly in the number of pairwise comparisons. Treatment of different populations under hmmIBD improves detection of IBD across populations. Fast and accurate software for detecting IBD in malaria parasite genetic data sampled from one or two populations is presented. The latter will likely be a useful feature for malaria elimination efforts, since it could facilitate identification of imported malaria cases. Software is robust to possible misspecification of the genotyping error and the recombination rate. However, exclusion of data in regions whose rates vary greatly from their genome-wide average is recommended.read more
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An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN,Ambroise D. Ahouidi,Mozam Ali,Jacob Almagro-Garcia,Jacob Almagro-Garcia,Alfred Amambua-Ngwa,Alfred Amambua-Ngwa,Chanaki Amaratunga,Roberto Amato,Roberto Amato,Lucas Amenga-Etego,Ben Andagalu,Tim J. Anderson,Voahangy Andrianaranjaka,Tobias O. Apinjoh,Cristina V. Ariani,Elizabeth A. Ashley,Sarah Auburn,Gordon A. Awandare,Hampate Ba,Vito Baraka,Vito Baraka,Alyssa E. Barry,Alyssa E. Barry,Alyssa E. Barry,Philip Bejon,Gwladys I. Bertin,Maciej F. Boni,Steffen Borrmann,Teun Bousema,Teun Bousema,OraLee H. Branch,Peter C. Bull,Peter C. Bull,George B.J. Busby,Thanat Chookajorn,Kesinee Chotivanich,Antoine Claessens,Antoine Claessens,David J. Conway,Alister Craig,Alister Craig,Umberto D'Alessandro,Souleymane Dama,Nicholas P. J. Day,Brigitte Denis,Mahamadou Diakite,Abdoulaye Djimde,Christiane Dolecek,Arjen M. Dondorp,Chris Drakeley,Eleanor Drury,Patrick E. Duffy,Diego F. Echeverry,Thomas G. Egwang,Berhanu Erko,Rick M. Fairhurst,Abdul Faiz,Caterina A. Fanello,Mark M. Fukuda,Dionicia Gamboa,Anita Ghansah,Lemu Golassa,Sónia Gonçalves,William L Hamilton,William L Hamilton,G. L. Abby Harrison,Lee Hart,Christa Henrichs,Tran Tinh Hien,Catherine A. Hill,Abraham Hodgson,Christina Hubbart,Mallika Imwong,Deus S. Ishengoma,Scott A. Jackson,Christopher G Jacob,Ben Jeffery,Anna E. Jeffreys,Kimberly J. Johnson,Dushyanth Jyothi,Claire Kamaliddin,Edwin Kamau,Mihir Kekre,Krzysztof Kluczynski,Theerarat Kochakarn,Theerarat Kochakarn,Abibatou Konaté,Dominic P. Kwiatkowski,Dominic P. Kwiatkowski,Myat Phone Kyaw,Pharath Lim,Chanthap Lon,Kovana M. Loua,Oumou Maïga-Ascofaré,Oumou Maïga-Ascofaré,Cinzia Malangone,Magnus Manske,Jutta Marfurt,Kevin Marsh,Kevin Marsh,Mayfong Mayxay,Mayfong Mayxay,Alistair Miles,Alistair Miles,Olivo Miotto,Olivo Miotto,Olivo Miotto,Victor A. Mobegi,Olugbenga A. Mokuolu,Jacqui Montgomery,Ivo Mueller,Paul N. Newton,Thuy Nguyen,Thuy-Nhien Nguyen,Harald Noedl,François Nosten,Rintis Noviyanti,Alexis Nzila,Lynette Isabella Ochola-Oyier,Harold Ocholla,Harold Ocholla,Abraham Oduro,Irene Omedo,Marie A. Onyamboko,Jean-Bosco Ouédraogo,Kolapo Oyebola,Kolapo Oyebola,Richard D. Pearson,Richard D. Pearson,Norbert Peshu,Aung Pyae Phyo,Christopher V. Plowe,Ric N. Price,Ric N. Price,Sasithon Pukrittayakamee,Milijaona Randrianarivelojosia,Julian C. Rayner,Pascal Ringwald,Kirk A. Rockett,Kirk A. Rockett,Katherine Rowlands,Lastenia Ruiz,David L. Saunders,Alex Shayo,Peter Siba,Victoria Simpson,Jim Stalker,Xin-zhuan Su,Colin J. Sutherland,Shannon Takala-Harrison,Livingstone Tavul,Vandana Thathy,Vandana Thathy,Antoinette Tshefu,Federica Verra,Joseph M. Vinetz,Joseph M. Vinetz,Thomas E. Wellems,Jason P. Wendler,Nicholas J. White,Ian J. Wright,William Yavo,Htut Ye +163 more
TL;DR: A new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries aims to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
Journal ArticleDOI
Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea.
Olivo Miotto,Makoto Sekihara,Shin-Ichiro Tachibana,Masato Yamauchi,Richard D. Pearson,Richard D. Pearson,Roberto Amato,Sónia Gonçalves,Somya Mehra,Rintis Noviyanti,Jutta Marfurt,Sarah Auburn,Sarah Auburn,Sarah Auburn,Ric N. Price,Ric N. Price,Ric N. Price,Ivo Mueller,Mie Ikeda,Toshiyuki Mori,Makoto Hirai,Livingstone Tavul,Manuel W Hetzel,Manuel W Hetzel,Moses Laman,Alyssa E. Barry,Pascal Ringwald,Jun Ohashi,Francis Hombhanje,Dominic P. Kwiatkowski,Dominic P. Kwiatkowski,Toshihiro Mita +31 more
TL;DR: It is suggested that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity.
Journal ArticleDOI
Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance.
Luana Mathieu,Luana Mathieu,Horace Cox,Angela M. Early,Angela M. Early,Sachel Mok,Yassamine Lazrek,Jeanne-Celeste Paquet,Maria-Paz Ade,Naomi W. Lucchi,Quacy Grant,Venkatachalam Udhayakumar,Jean S F Alexandre,Magalie Demar,Pascal Ringwald,Daniel E. Neafsey,Daniel E. Neafsey,David A. Fidock,Lise Musset +18 more
TL;DR: It is reported that mutant pfk13 has emerged independently in Guyana, with genome analysis indicating an evolutionary origin distinct from Southeast Asia, and these data place local malaria control efforts at risk in the Guiana Shield.
Journal ArticleDOI
Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.
Aimee R. Taylor,Aimee R. Taylor,Stephen F. Schaffner,Gustavo C. Cerqueira,Standwell Nkhoma,Tim J. Anderson,Kanlaya Sriprawat,Aung Pyae Phyo,François Nosten,François Nosten,Daniel E. Neafsey,Daniel E. Neafsey,Caroline O. Buckee +12 more
TL;DR: In this article, the authors use data collected from four clinics with a catchment area spanning approximately 120 km of the Thai-Myanmar border to compare the ability of divergence (FST) and relatedness based on identity by descent (IBD) to resolve spatial connectivity between malaria parasites collected from proximal clinics.
Journal ArticleDOI
Plasmepsin II–III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum
Selina Bopp,Pamela Magistrado,Wesley P. Wong,Stephen F. Schaffner,Stephen F. Schaffner,Angana Mukherjee,Pharath Lim,Mehul Dhorda,Chanaki Amaratunga,Charles J. Woodrow,Elizabeth A. Ashley,Nicholas J. White,Nicholas J. White,Arjen M. Dondorp,Arjen M. Dondorp,Rick M. Fairhurst,Frédéric Ariey,Didier Menard,Dyann F. Wirth,Dyann F. Wirth,Sarah K. Volkman,Sarah K. Volkman,Sarah K. Volkman +22 more
TL;DR: A bimodal dose−response curve of Cambodian isolates exposed to PPQ is found, with the area under the curve correlating with in vitro PPQ resistance, and the importance of Plasmepsin II–III copy number to PPZ resistance is shown.
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