2016
A Worldwide Map of Plasmodium falciparum K13-Propeller Polymorphisms
Ménard D, Khim N, Beghain J, Adegnika A, Shafiul-Alam M, Amodu O, Rahim-Awab G, Barnadas C, Berry A, Boum Y, Bustos M, Cao J, Chen J, Collet L, Cui L, Thakur G, Dieye A, Djallé D, Dorkenoo M, Eboumbou-Moukoko C, Espino F, Fandeur T, Ferreira-da-Cruz M, Fola A, Fuehrer H, Hassan A, Herrera S, Hongvanthong B, Houzé S, Ibrahim M, Jahirul-Karim M, Jiang L, Kano S, Ali-Khan W, Khanthavong M, Kremsner P, Lacerda M, Leang R, Leelawong M, Li M, Lin K, Mazarati J, Ménard S, Morlais I, Muhindo-Mavoko H, Musset L, Na-Bangchang K, Nambozi M, Niaré K, Noedl H, Ouédraogo J, Pillai D, Pradines B, Quang-Phuc B, Ramharter M, Randrianarivelojosia M, Sattabongkot J, Sheikh-Omar A, Silué K, Sirima S, Sutherland C, Syafruddin D, Tahar R, Tang L, Touré O, Tshibangu-wa-Tshibangu P, Vigan-Womas I, Warsame M, Wini L, Zakeri S, Kim S, Eam R, Berne L, Khean C, Chy S, Ken M, Loch K, Canier L, Duru V, Legrand E, Barale J, Stokes B, Straimer J, Witkowski B, Fidock D, Rogier C, Ringwald P, Ariey F, Mercereau-Puijalon O. A Worldwide Map of Plasmodium falciparum K13-Propeller Polymorphisms. New England Journal Of Medicine 2016, 374: 2453-2464. PMID: 27332904, PMCID: PMC4955562, DOI: 10.1056/nejmoa1513137.Peer-Reviewed Original ResearchConceptsK13 mutationsRing-stage survival assayK13-propeller polymorphismsPlasmodium falciparum resistanceA578S mutationParasite clearanceRare nonsynonymous mutationsFalciparum resistanceAntimalarial resistanceArtemisinin resistanceNationwide surveillanceGlobal burdenSentinel sitesGeographic disparitiesSurvival assaysP. falciparum genesMalariaPropeller domainMajor determinantArtemisininMutationsNonsynonymous mutationsSuch resistancePolymorphismPatients
2012
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
Preston M, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo J, Nosten F, Anderson T, Clark T. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics 2012, 28: 2983-2985. PMID: 22976080, PMCID: PMC3496337, DOI: 10.1093/bioinformatics/bts557.Peer-Reviewed Original ResearchConceptsNext-generation sequencing dataUser-defined groupsGenomic regionsVariant call format filesSingle nucleotide polymorphismsDrug resistance genesSequence dataSequencing dataStructural variantsImportant antigenicSequence file formatsInformative markersPlasmodium falciparumDifferent continentsFile formatFormat fileUser manualReal timeAnalysis toolsGenesVariantsDeletionPolymorphismVarBFalciparumCharacterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data
Auburn S, Campino S, Miotto O, Djimde A, Zongo I, Manske M, Maslen G, Mangano V, Alcock D, MacInnis B, Rockett K, Clark T, Doumbo O, Ouédraogo J, Kwiatkowski D. Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data. PLOS ONE 2012, 7: e32891. PMID: 22393456, PMCID: PMC3290604, DOI: 10.1371/journal.pone.0032891.Peer-Reviewed Original ResearchConceptsHost diversityIllumina GA platformMultiplicity of infectionGenome-wide datasetsPopulation-level diversitySingle-molecule sequencing technologiesNext-generation sequence dataPlasmodium falciparum diversityMsp-1 locusGenetic divergenceSequence dataSequencing technologiesNumber of clonesLevel diversityNovel insightsDiversityP. falciparum fieldLociMSP-1PCRRelative proportionsNew statistical approachSNPsClonesReduced sensitivity
2011
An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing
Auburn S, Campino S, Clark T, Djimde A, Zongo I, Pinches R, Manske M, Mangano V, Alcock D, Anastasi E, Maslen G, MacInnis B, Rockett K, Modiano D, Newbold C, Doumbo O, Ouédraogo J, Kwiatkowski D. An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing. PLOS ONE 2011, 6: e22213. PMID: 21789235, PMCID: PMC3138765, DOI: 10.1371/journal.pone.0022213.Peer-Reviewed Original Research