Magnus ManskeOlivo MiottoSusana CampinoSarah AuburnJacob Almagro-GarciaGareth MaslenJack O'BrienAbdoulaye DjimdeOgobara DoumboIssaka ZongoJean Bosco OuedraogoPascal MichonIvo MuellerPeter SibaAlexis NzilaSteffen BorrmannSteven M. KiaraKevin MarshHongying JiangXin Zhuan SuChanaki AmaratungaRick FairhurstDuong SocheatFrancois NostenMallika ImwongNicholas J. WhiteMandy SandersElisa AnastasiDan AlcockEleanor DrurySamuel OyolaMichael A. QuailDaniel J. TurnerValentin Ruano-RubioDushyanth JyothiLucas Amenga-EtegoChristina HubbartAnna JeffreysKate RowlandsColin SutherlandCally RoperValentina ManganoDavid ModianoJohn C. TanMichael T. FerdigAlfred Amambua-NgwaDavid J. ConwayShannon Takala-HarrisonChristopher V. PloweJulian C. RaynerKirk A. RockettTaane G. ClarkChris I. NewboldMatthew BerrimanBronwyn MacInnisDominic P. KwiatkowskiWellcome Trust Sanger InstituteUniversity of OxfordMahidol UniversityMenzies School of Health ResearchWellcome Trust Centre for Human GeneticsUniversity of Bamako Faculty of Medicine, Pharmacy and Odonto-StomatologyInstitut de Recherche en Sciences de la SantéPapua New Guinea Institute of Medical ResearchWellcome Trust Research Laboratories NairobiNational Institute of Allergy and Infectious DiseasesCambodia National Malaria CentreShoklo Malaria Research UnitNavrongo Health CentreLondon School of Hygiene & Tropical MedicineUniversita degli Studi di Roma La SapienzaUniversity of Notre DameMedical Research Council Laboratories GambiaUniversity of Maryland, BaltimoreWeatherall Institute of Molecular Medicine2018-06-112018-06-112012-07-19Nature. Vol.487, No.7407 (2012), 375-37914764687002808362-s2.0-84863982076https://repository.li.mahidol.ac.th/handle/20.500.14594/15243Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P.falciparum genome. © 2012 Macmillan Publishers Limited. All rights reserved.Mahidol UniversityMultidisciplinaryArticleSCOPUS10.1038/nature11174