2021
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley E, Auburn S, Awandare G, Ba H, Baraka V, Barry A, Bejon P, Bertin G, Boni M, Borrmann S, Bousema T, Branch O, Bull P, Busby G, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp A, Drakeley C, Drury E, Duffy P, Echeverry D, Egwang T, Erko B, Fairhurst R, Faiz A, Fanello C, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton W, Harrison G, Hart L, Henrichs C, Hien T, Hill C, Hodgson A, Hubbart C, Imwong M, Ishengoma D, Jackson S, Jacob C, Jeffery B, Jeffreys A, Johnson K, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski D, Kyaw M, Lim P, Lon C, Loua K, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu O, Montgomery J, Mueller I, Newton P, Nguyen T, Nguyen T, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier L, Ocholla H, Oduro A, Omedo I, Onyamboko M, Ouedraogo J, Oyebola K, Pearson R, Peshu N, Phyo A, Plowe C, Price R, Pukrittayakamee S, Randrianarivelojosia M, Rayner J, Ringwald P, Rockett K, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson V, Stalker J, Su X, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems T, Wendler J, White N, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research 2021, 6: 42. DOI: 10.12688/wellcomeopenres.16168.1.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsStrong geographic differentiationGenome variation dataHigh-quality genotypesGeographic differentiationGenome variationGenetic evidenceShort indelsEvolutionary processesStructural variantsMosquito stagesNumber variantsData-sharing networksNucleotide polymorphismsVariation dataWorldwide sampleAnalysis pipelineGenomic epidemiologyMarker of resistanceDrug resistanceSurveillance toolkitIndelsGenesLociVariants
2016
Artesunate-Amodiaquine and Artemether-Lumefantrine Therapies and Selection of Pfcrt and Pfmdr1 Alleles in Nanoro, Burkina Faso
Sondo P, Derra K, Nakanabo S, Tarnagda Z, Kazienga A, Zampa O, Valéa I, Sorgho H, Owusu-Dabo E, Ouédraogo J, Guiguemdé T, Tinto H. Artesunate-Amodiaquine and Artemether-Lumefantrine Therapies and Selection of Pfcrt and Pfmdr1 Alleles in Nanoro, Burkina Faso. PLOS ONE 2016, 11: e0151565. PMID: 27031231, PMCID: PMC4816516, DOI: 10.1371/journal.pone.0151565.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAllelesAmodiaquineAntimalarialsArtemether, Lumefantrine Drug CombinationArtemisininsBurkina FasoChildDrug CombinationsEthanolaminesFemaleFluorenesGene FrequencyGenotypeHost-Parasite InteractionsHumansMalaria, FalciparumMaleMembrane Transport ProteinsMiddle AgedMultidrug Resistance-Associated ProteinsMultivariate AnalysisParasitemiaPlasmodium falciparumPolymorphism, Single NucleotideProtozoan ProteinsTreatment OutcomeConceptsPfmdr1 allelesTreatment failureArtemether-lumefantrine therapyPfcrt K76TSingle nucleotide polymorphismsRestriction fragment length polymorphism methodFragment length polymorphism methodPotential beneficial effectsLength polymorphism methodArtesunate-AmodiaquineRecurrent parasitaemiaTreatment regimenACT resistanceCombination therapyK76TPfmdr1 geneClinical trialsTreatment outcomesMultivariate analysisDay 0PfcrtMalaria controlBlood spotsBeneficial effectsPolymorphism method
2015
Dynamic of plasmodium falciparum chloroquine resistance transporter gene Pfcrt K76T mutation five years after withdrawal of chloroquine in Burkina Faso
Sondo P, Derra K, Tarnagda Z, Nakanabo S, Zampa O, Kazienga A, Valea I, Sorgho H, Ouedraogo J, Guiguemde T, Tinto H. Dynamic of plasmodium falciparum chloroquine resistance transporter gene Pfcrt K76T mutation five years after withdrawal of chloroquine in Burkina Faso. Pan African Medical Journal 2015, 21: 101. PMID: 26516402, PMCID: PMC4606025, DOI: 10.11604/pamj.2015.21.101.6437.Peer-Reviewed Original Research
2014
A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
Preston M, Campino S, Assefa S, Echeverry D, Ocholla H, Amambua-Ngwa A, Stewart L, Conway D, Borrmann S, Michon P, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Pain A, Bousema T, Drakeley C, Fairhurst R, Sutherland C, Roper C, Clark T. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature Communications 2014, 5: 4052. PMID: 24923250, PMCID: PMC4082634, DOI: 10.1038/ncomms5052.Peer-Reviewed Original ResearchConceptsMajor public health problemValuable public health toolSingle nucleotide polymorphismsPublic health problemDrug-resistant parasitesPublic health toolPlasmodium falciparum strainsGlobal eradication campaignHealth problemsFalciparum strainsCase managementHealth toolsPlasmodium falciparumParasite migrationElimination areaEradication campaignApicoplast genomeParasitesPolymorphismInfectionMalariaInternational air travelFalciparumSelection of Drug Resistance-Mediating Plasmodium falciparum Genetic Polymorphisms by Seasonal Malaria Chemoprevention in Burkina Faso
Somé A, Zongo I, Compaoré Y, Sakandé S, Nosten F, Ouédraogo J, Rosenthal P. Selection of Drug Resistance-Mediating Plasmodium falciparum Genetic Polymorphisms by Seasonal Malaria Chemoprevention in Burkina Faso. Antimicrobial Agents And Chemotherapy 2014, 58: 3660-3665. PMID: 24733476, PMCID: PMC4068591, DOI: 10.1128/aac.02406-14.Peer-Reviewed Original ResearchConceptsSeasonal malaria chemopreventionAQ/SPMalaria chemopreventionSingle nucleotide polymorphismsP. falciparum crtPfcrt 76TResistance-mediating polymorphismsMalaria control measuresPCR-positive samplesMonthly DPPfdhfr 108NPfdhfr 51IPfmdr1 86YSulfadoxine-pyrimethamineTreatment armsDevelopment of resistanceTransmission seasonControl groupP. falciparumSNP prevalenceGenetic polymorphismsRegular useAntifolate antimalarialsMonthsBurkina Faso
2013
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
Preston M, Assefa S, Ocholla H, Sutherland C, Borrmann S, Nzila A, Michon P, Hien T, Bousema T, Drakeley C, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Fairhurst R, Conway D, Roper C, Clark T. PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation. The Journal Of Infectious Diseases 2013, 209: 1808-1815. PMID: 24338354, PMCID: PMC4017360, DOI: 10.1093/infdis/jit812.Peer-Reviewed Original ResearchConceptsGenomic variationSingle nucleotide polymorphismsHigh-quality single nucleotide polymorphismsHigh-throughput sequencingInter-population differencesGenetic barcodesPlasmodium biologyGenetic variabilityGenomic dataInformative variantsDrug resistanceParasite populationsDifferential phenotypesLaboratory strainsMalaria parasitesNovel mutationsGlobal public health challengeNew insightsPf isolatesMalaria-endemic regionsPublic health challengePlasmodium falciparum speciesMedicine applicationsWeb-based resourcesClinical studies
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 toolsGenesVariantsDeletionPolymorphismVarBFalciparum