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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
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Journal Article
High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
2017
Overview
Genetic polymorphisms in
P. falciparum
can be used to indicate the parasite’s susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in
pfcrt
,
pfmdr1
,
pfdhfr
,
pfdhps
, as well as the entire length of
pfK13
, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8–100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in
pfK13
are absent from the studied area of Guinea-Bissau, while the
pfmdr1
86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 45/77
/ 631/337
/ Antimalarials - pharmacology
/ Antimalarials - therapeutic use
/ High-Throughput Nucleotide Sequencing
/ Humanities and Social Sciences
/ Humans
/ Malaria
/ Malaria, Falciparum - drug therapy
/ Malaria, Falciparum - epidemiology
/ Malaria, Falciparum - parasitology
/ Mutation
/ Plasmodium falciparum - drug effects
/ Plasmodium falciparum - genetics
/ Polymorphism, Single Nucleotide
/ Protozoan Proteins - genetics
/ Science
/ Single-nucleotide polymorphism
