Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study

• DOI: 10.1101/2021.09.15.21263521
• Publication Date: 2021-09-22T19:35:19Z
• Authors: Emily LaVerriere; Philipp Schwabl; Manuela Carrasquilla; Aimee R. Taylor; Zachary M. Johnson; Meg Shieh; Ruchit Panchal; Timothy J. Straub; Rebecca Kuzma; Sean Watson; Caroline O. Buckee; Carolina M. Andrade; Silvia Portugal; Peter D. Crompton; Boubacar Traore; Julian C. Rayner; Vladimir Corredor; Kashana James; Horace Cox; Angela M. Early; Bronwyn L. MacInnis; Daniel E. Neafsey
• Keywords: Amplicon

Abstract Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, shows strong potential genomic epidemiology infectious disease. AmpSeq data microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, determining the effectiveness therapeutics. We describe design comparative evaluation two new assays Plasmodium falciparum malaria parasites: a four-locus panel (‘4CAST’) composed highly diverse antigens, 129-locus (‘AMPLseq’) markers, loci relatedness, locus to detect vivax co-infections. explore performance each various public health use cases with silico simulations as well empirical experiments. find that smaller 4CAST performs reliably across wide range parasitemia levels without DNA pre-amplification, could be informative evaluating number distinct parasite strains within samples (complexity infection), recrudescent infections therapeutic efficacy studies. The AMPLseq similarly existing panels comparable size relatedness measurement, despite differences approach used designing panel. Finally, we R package (paneljudge) facilitates estimation, provide general guidance on implementation