Journal article

SNP barcodes provide higher resolution than microsatellite markers to measurePlasmodium vivaxpopulation genetics

Abebe A Fola, Eline Kattenberg, Zahra Razook, Dulcie Lautu-Gumal, Stuart Lee, Somya Mehra, Melanie Bahlo, James Kazura, Leanne J Robinson, Moses Laman, Ivo Mueller, Alyssa E Barry

MALARIA JOURNAL | BMC | Published : 2020

Abstract

BACKGROUND: Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS: Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were se..

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Grants

Awarded by National Health and Medical Research Council (NHMRC) of Australia


Awarded by NIH NIAID International Centers of Excellence in Malaria Research (ICEMR) Program for the South West Pacific


Awarded by NHMRC


Funding Acknowledgements

This study was made possible through a National Health and Medical Research Council (NHMRC) of Australia Project Grant Number GNT1027108. Funding for sample collection was provided by the NIH NIAID International Centers of Excellence in Malaria Research (ICEMR) Program for the South West Pacific U19 AI089686 and a Bill and Melinda Gates Foundation Grant (TransEpi Consortium). LJR, IM and MB are supported by NHMRC Research Fellowships (GNT1161627, GNT1155075, GNT1102971). The authors acknowledge the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support Scheme (IRIISS).