Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum

Scientific Reports
Lucky Ronald RuntuweneYutaka Suzuki

Abstract

Here, we report the application of a portable sequencer, MinION, for genotyping the malaria parasite Plasmodium falciparum. In the present study, an amplicon mixture of nine representative genes causing resistance to anti-malaria drugs is diagnosed. First, we developed the procedure for four laboratory strains (3D7, Dd2, 7G8, and K1), and then applied the developed procedure to ten clinical samples. We sequenced and re-sequenced the samples using the obsolete flow cell R7.3 and the most recent flow cell R9.4. Although the average base-call accuracy of the MinION sequencer was 74.3%, performing >50 reads at a given position improves the accuracy of the SNP call, yielding a precision and recall rate of 0.92 and 0.8, respectively, with flow cell R7.3. These numbers increased significantly with flow cell R9.4, in which the precision and recall are 1 and 0.97, respectively. Based on the SNP information, the drug resistance status in ten clinical samples was inferred. We also analyzed K13 gene mutations from 54 additional clinical samples as a proof of concept. We found that a novel amino-acid changing variation is dominant in this area. In addition, we performed a small population-based analysis using 3 and 5 cases (K13) and 10 and ...Continue Reading

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Citations

Sep 21, 2018·PloS One·Christian NsanzabanaIveth J Gonzalez
Jan 29, 2019·GigaScience·Victoria ShabardinaWojciech Makałowski
Nov 2, 2018·Journal of Clinical Microbiology·Michelle SuTimothy D Read
Sep 3, 2019·Journal of Cellular and Molecular Medicine·Xiaoling YuJun Lin
Dec 11, 2019·Tropical Medicine and Infectious Disease·Christian Nsanzabana
Oct 5, 2019·Journal of Human Genetics·Arthur Elia MonganLucky Ronald Runtuwene
May 1, 2019·Development, Growth & Differentiation·Nobuaki Kono, Kazuharu Arakawa
Dec 21, 2019·International Journal for Parasitology·Larissa CalarcoJohn Ellis
Aug 2, 2021·International Journal for Parasitology. Drugs and Drug Resistance·Yaye Die NdiayeSarah K Volkman
Aug 28, 2021·Nanomaterials·Xiaoqing ZengDeqiang Wang
Sep 4, 2021·Journal of Parasitic Diseases : Official Organ of the Indian Society for Parasitology·Laxman Kumar MurmuTapan Kumar Barik
Dec 16, 2021·PloS One·Harrison J LambElizabeth M Ross

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Datasets Mentioned

BETA
DRA005565

Methods Mentioned

BETA
genotyping
PCR
Illumina sequencing
Illumina sequencings
Metrichor Sequencing

Software Mentioned

LAST
Albacore
Poretools
BWA
BWA MEM
Metrichor
Nanopolish
MinION
MEM
ONT

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