Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections
- Author(s)
- Lerch, A; Koepfli, C; Hofmann, NE; Messerli, C; Wilcox, S; Kattenberg, JH; Betuela, I; O'Connor, L; Mueller, I; Felger, I;
- Details
- Publication Year 2017,Volume 18,Issue #1,Page 864
- Journal Title
- BMC Genomics
- Publication Type
- Journal Article
- Abstract
- Background: Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis protocols are needed for genotyping in epidemiological studies and drug efficacy trials of P. falciparum. Methods: Targeted sequencing of molecular marker csp and novel marker cpmp was conducted in duplicate on mixtures of parasite culture strains and 37 field samples. A protocol allowing to multiplex up to 384 samples in a single sequencing run was applied. Software "HaplotypR" was developed for data analysis. Results: Cpmp was highly diverse (He = 0.96) in contrast to csp (He = 0.57). Minority clones were robustly detected if their frequency was >1%. False haplotype calls owing to sequencing errors were observed below that threshold. Conclusions: To reliably detect haplotypes at very low frequencies, experiments are best performed in duplicate and should aim for coverage of >10'000 reads/amplicon. When compared to length polymorphic marker msp2, highly multiplexed amplicon sequencing displayed greater sensitivity in detecting minority clones. © 2017 The Author(s).
- Publisher
- BioMed Central
- Research Division(s)
- Systems Biology And Personalised Medicine; Population Health And Immunity
- Publisher's Version
- https://doi.org/10.1186/s12864-017-4260-y
- Open Access at Publisher's Site
https://doi.org/10.1186/s12864-017-4260-y- Terms of Use/Rights Notice
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Creation Date: 2017-11-29 08:58:13
Last Modified: 2017-11-30 08:34:44