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Because trial participants usually harbour multi-clonal <jats:italic>P. falciparum<\/jats:italic> infections, deep amplicon sequencing (AmpSeq) was employed to improve sensitivity and reliability of minority clone detection. Paired samples from 32 drug trial participants were Illumina deep-sequenced for five molecular markers. Reads were analysed by custom-made software HaplotypR and trial outcomes compared to results from the previous standard genotyping method based on length-polymorphic markers. Diversity of AmpSeq markers in pre-treatment samples was comparable or higher than length-polymorphic markers. AmpSeq was highly reproducible with consistent quantification of co-infecting parasite clones within a host. Outcomes of the three best-performing markers, <jats:italic>cpmp, cpp<\/jats:italic> and <jats:italic>ama1-D3<\/jats:italic>, agreed in 26\/32 (81%) of patients. Discordance between the three markers performed per sample was much lower by AmpSeq (six patients) compared to length-polymorphic markers (eleven patients). Using AmpSeq for discrimination of recrudescence and new infection in antimalarial drug trials provides highly reproducible and robust characterization of clone dynamics during trial follow-up. AmpSeq overcomes limitations inherent to length-polymorphic markers. Regulatory clinical trials of antimalarial drugs will greatly benefit from this unbiased typing method.<\/jats:p>","DOI":"10.1038\/s41598-019-54203-0","type":"journal-article","created":{"date-parts":[[2019,11,28]],"date-time":"2019-11-28T11:03:21Z","timestamp":1574939001000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":68,"title":["Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs"],"prefix":"10.1038","volume":"9","author":[{"given":"Maria","family":"Gruenberg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3062-5901","authenticated-orcid":false,"given":"Anita","family":"Lerch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8326-4834","authenticated-orcid":false,"given":"Hans-Peter","family":"Beck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1255-2606","authenticated-orcid":false,"given":"Ingrid","family":"Felger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,11,28]]},"reference":[{"key":"54203_CR1","unstructured":"WHO. 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