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

Communicable Diseases Genomics Humans Malaria Malaria, Vivax / epidemiology Plasmodium falciparum / genetics Plasmodium vivax / genetics
amplicon sequencing epidemiology genome genotyping malaria relatedness

Journal

Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604

Informations de publication

Date de publication:
Aug 2022
Historique:
revised: 05 03 2022
received: 15 09 2021
accepted: 05 04 2022
pubmed: 20 4 2022
medline: 7 7 2022
entrez: 19 4 2022
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1111/1755-0998.13622 PMID: 35437908 PMC: PMC9288814
pubmed: 35437908
doi: 10.1111/1755-0998.13622
pmc: PMC9288814
mid: NIHMS1819057
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

2285-2303

Subventions

Organisme : NIH HHS
ID : R01AI141544
Pays : United States
Organisme : Broad Institute
Organisme : National Institute of Allergy and Infectious Diseases
Organisme : British Council
Organisme : NIAID NIH HHS
ID : R01 AI141544
Pays : United States
Organisme : Division of Intramural Research, National Institute of Allergy and Infectious Diseases
Organisme : Bill and Melinda Gates Foundation
Organisme : NIAID NIH HHS
ID : U19 AI110818
Pays : United States

Informations de copyright

© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

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Auteurs

Emily LaVerriere (E)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
ORCID: 0000-0002-4750-4199

Philipp Schwabl (P)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
ORCID: 0000-0002-1244-945X

Manuela Carrasquilla (M)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Max Planck Institute for Infection Biology, Berlin, Germany.
ORCID: 0000-0002-7953-4376

Aimee R Taylor (AR)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

Zachary M Johnson (ZM)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Meg Shieh (M)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
ORCID: 0000-0002-0483-5000

Ruchit Panchal (R)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
ORCID: 0000-0002-4664-4501

Timothy J Straub (TJ)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Rebecca Kuzma (R)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Sean Watson (S)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

Caroline O Buckee (CO)

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

Carolina M Andrade (CM)

Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.

Silvia Portugal (S)

Max Planck Institute for Infection Biology, Berlin, Germany.
Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.

Peter D Crompton (PD)

Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA.

Boubacar Traore (B)

Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali.

Julian C Rayner (JC)

Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

Vladimir Corredor (V)

Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia.

Kashana James (K)

Guyana National Malaria Control Program, Ministry of Health, Georgetown, Guyana.

Horace Cox (H)

Guyana Vector Control Services, Ministry of Health, Georgetown, Guyana.

Angela M Early (AM)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Bronwyn L MacInnis (BL)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Daniel E Neafsey (DE)

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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Classifications MeSH

questionsmedicales.fr › États, signes et symptômes pathologiques › Processus pathologiques › Caractéristiques de la maladie › Maladies transmissibles › Design and implementation of multiplexed...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Design and implementation of multiplexed...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Design and implementation of multiplexed...
questionsmedicales.fr › Infection › Maladies vectorielles › Paludisme › Design and implementation of multiplexed...
questionsmedicales.fr › Infection › Maladies vectorielles › Paludisme › Paludisme à Plasmodium vivax › Design and implementation of multiplexed...
questionsmedicales.fr › Eucaryotes › Alveolata › Apicomplexa › Haemosporida › Plasmodium › Plasmodium falciparum › Design and implementation of multiplexed...
questionsmedicales.fr › Eucaryotes › Alveolata › Apicomplexa › Haemosporida › Plasmodium › Plasmodium vivax › Design and implementation of multiplexed...