Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study.
Authors
Taylor, Aimee R
Johnson, Zachary M
Straub, Timothy J
Kuzma, Rebecca
Watson, Sean
Buckee, Caroline O
Andrade, Carolina M
Portugal, Silvia
Crompton, Peter D
Traore, Boubacar
Rayner, Julian C
Corredor, Vladimir
James, Kashana
Cox, Horace
Early, Angela M
MacInnis, Bronwyn L
Neafsey, Daniel E
Publication Date
2022-08Journal Title
Mol Ecol Resour
ISSN
1755-098X
Publisher
Wiley
Language
en
Type
Article
This Version
AO
VoR
Metadata
Show full item recordCitation
LaVerriere, E., Schwabl, P., Carrasquilla, M., Taylor, A. R., Johnson, Z. M., Shieh, M., Panchal, R., et al. (2022). Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study.. Mol Ecol Resour https://doi.org/10.1111/1755-0998.13622
Description
Funder: British Council; Id: http://dx.doi.org/10.13039/501100000308
Funder: Broad Institute; Id: http://dx.doi.org/10.13039/100013114
Funder: National Institute of Allergy and Infectious Diseases; Id: http://dx.doi.org/10.13039/100000060
Funder: Bill and Melinda Gates Foundation; Id: http://dx.doi.org/10.13039/100000865
Funder: Division of Intramural Research, National Institute of Allergy and Infectious Diseases; Id: http://dx.doi.org/10.13039/100006492
Abstract
Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for the genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, such as by measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ("4CAST") composed of highly diverse antigens, and a 129-locus panel ("AMPLseq") composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitaemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for the genomic epidemiology of infectious disease.
Keywords
RESOURCE ARTICLE, RESOURCE ARTICLES, amplicon sequencing, epidemiology, genome, genotyping, malaria, relatedness
Sponsorship
National Institutes of Health (R01AI141544)
Identifiers
men13622
External DOI: https://doi.org/10.1111/1755-0998.13622
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336823
Rights
Licence:
http://creativecommons.org/licenses/by/4.0/
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