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Publication Metadata only Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum(2018-12-01) Lucky R. Runtuwene; Josef S.B. Tuda; Arthur E. Mongan; Wojciech Makalowski; Martin C. Frith; Mallika Imwong; Suttipat Srisutham; Lan Anh Nguyen Thi; Nghia Nguyen Tuan; Yuki Eshita; Ryuichiro Maeda; Junya Yamagishi; Yutaka Suzuki; Sam Ratulangi University; University of Tokyo; National Institute of Advanced Industrial Science and Technology; Hokkaido University; Mahidol University; Obihiro University of Agriculture and Veterinary Medicine; Westfälische Wilhelms-Universität Münster; National Institute of Hygiene and Epidemiology.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...© 2018 The Author(s). 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 antiPublication Metadata only Sequence variation does not confound the measurement of plasma PfHRP2 concentration in African children presenting with severe malaria(2012-08-20) Thiranut Ramutton; Ilse Ce Hendriksen; Juliet Mwanga-Amumpaire; George Mtove; Rasaq Olaosebikan; Antoinette K. Tshefu; Marie A. Onyamboko; Corine Karema; Kathryn Maitland; Ermelinda Gomes; Samwel Gesase; Hugh Reyburn; Kamolrat Silamut; Kesinee Chotivanich; Kamoltip Promnares; Caterina I. Fanello; Lorenz Von Seidlein; Nicholas Pj Day; Nicholas J. White; Arjen M. Dondorp; Mallika Imwong; Charles J. Woodrow; Mahidol University; University of Oxford; Mbarara University of Science and Technology; National Institute for Medical Research Tanga; Medical Research Council Laboratories Gambia; Kingasani Research Centre; Ministry of Health; Wellcome Trust Research Laboratories Nairobi; Hospital Central da Beira; London School of Hygiene & Tropical Medicine; Prince of Songkla University; Menzies School of Health Researchcountries contributing to the largest hospital-based severe malaria trial (AQUAMAT). The quantitative relationship between sequence polymorphism and PFHRP2 plasma concentration was examined in samples from selected sites in Mozambique and Tanzania. Results...: There was no evidence for deletion of either Pfhrp2 or Pfhrp3 in the 77 samples with lowest PFHRP2 plasma concentrations across the seven countries. Pfhrp2 sequence diversity was very high with no haplotypes shared among 66 samples sequenced. There was no correlationPublication Metadata only Genetic population of Plasmodium knowlesi during pre-malaria elimination in Thailand(2021-12-01) Rungniran Sugaram; Patcharida Boondej; Suttipat Srisutham; Chanon Kunasol; Watcharee Pagornrat; Usa Boonyuen; Arjen M. Dondorp; Aungkana Saejeng; Prayuth Sudathip; Mallika Imwong; Faculty of Tropical Medicine, Mahidol University; Chulalongkorn University; Thailand Ministry of Public Health; Nuffield Department of MedicineThailand, were observed and confirmed by nested PCR assay and DNA sequencing. To evaluate whether these pathogens were from different lineages, cluster analysis based on seven microsatellite genotyping markers and the merozoite surface protein 1 (pkmsp1...-resistance monitoring as part of routine case-based surveillance and responses, specimens were collected from malaria patients (n = 966) between 2018 and 2020. Thirty-one mono P. knowlesi infections (3.1%), most of which were from eastern and southernPublication Metadata only OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer(2019-04-01) Vivek Bhakta Mathema; Arjen M. Dondorp; Mallika Imwong; Churchill Hospital; Mahidol Universityand protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable... scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generatorPublication Open Access Sequence variation does not confound the measurement of plasma PfHRP2 concentration in African children presenting with severe malaria(2012-08-16) Thiranut Ramutton; Hendriksen, Ilse CE; Mwanga-Amumpaire, Juliet; Mtove, George; Olaosebikan, Rasaq; Tshefu, Antoinette K.; Onyamboko, Marie A.; Karema, Corine; Maitland, Kathryn; Gomes, Ermelinda; Gesase, Samwel; Reyburn, Hugh; Kamolrat Silamut; Kesinee Chotivanich; เกศินี โชติวานิช; Kamoltip Promnares; Fanello, Caterina I.; Seidlein, Lorenz von; Day, Nicholas P.J.; White, Nicholas J.; Dondorp, Arjen M.; Mallika Imwong; มัลลิกา อิ่มวงศ์; Woodrow, Charles J.; Woodrow, Charles J.; Mahidol University. Faculty of Tropical Medicine. Department of Clinical Tropical Medicine.; Mahidol University. Faculty of Tropical Medicine. Department of Molecular Tropical Medicine and Genetics.; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.countries contributing to the largest hospital-based severe malaria trial (AQUAMAT). The quantitative relationship between sequence polymorphism and PFHRP2 plasma concentration was examined in samples from selected sites in Mozambique and Tanzania.... RESULTS: There was no evidence for deletion of either Pfhrp2 or Pfhrp3 in the 77 samples with lowest PFHRP2 plasma concentrations across the seven countries. Pfhrp2 sequence diversity was very high with no haplotypes shared among 66 samples sequencedPublication Open Access Genetic marker suitable for identification and genotyping of Plasmodium ovale curtisi and Plasmodium ovale wallikeri.(2013-12) Naowarat Tanomsing; เนาวรัตน์ ถนอมสิงห์; Mallika Imwong; มัลลิกา อิ่มวงศ์; Sutherland, Colin J.; Dolecek,Christiane; Hien,Tran Tinh; Nosten, Francois; Day, Nicholas P. J.; White, Nicholas J.; Snounouh, Georges; Mallika Imwong; Mahidol University. Faculty of Tropical Medicine. Department of Molecular Tropical Medicine and Genetics.; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.; Mahidol University. Faculty of Tropical Medicine. Shoklo Malaria Research Unit.We present a seminested PCR method that specifically discriminates between Plasmodium ovale curtisi and P. ovale wallikeri with high sensitivity. The test is based on species-specific amplification of a size-polymorphic fragment... of the tryptophan-rich antigen gene, potra, which also permits discrimination of intraspecific sequence variants at this locus.Publication Open Access Practical PCR genotyping protocols for Plasmodium vivax using Pvcs and Pvmsp1.(2005-04-27) Mallika Imwong; มัลลิกา อิ่มวงศ์; Sasithon Pukrittayakamee; Grüner, Anne Charlotte; Rénia, Laurent; Letourneur, Frank; Sornchai Looareesuwan; ศรชัย หลูอารีย์สุวรรณ; White, Nicholas J.; Snounou, Georges; Mallika Imwong; Mahidol University. Faculty of Tropical Medicine. Department of Clinical Tropical Medicine.adverse events observed attributable to either combination. CONCLUSION: Overall, this study confirms that these two artemisinin-based combinations remain highly effective and result in equivalent therapeutic responses in the treatment of highly drugPublication Open Access FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.(2009-10-15) Steenkeste, Nicolas; Dillies, Marie-Agnès; Khim, Nimol; Sismeiro, Odile; Chy, Sophy; Lim, Pharath; Crameri, Andreas; Bouchier, Christiane; Mercereau-Puijalon, Odile; Beck, Hans-Peter; Mallika Imwong; มัลลิกา อิ่มวงศ์; Dondorp, Arjen M.; Socheat, Duong; Rogier, Christophe; Coppée, Jean- Yves; Ariey, Frédéric; Steenkeste, Nicolas; Mahidol University. Faculty of Tropical Medicineof FlexiChip were compared to ResMalChip microarray, using the same extension probes and with the same PCR products. In both cases, sequence results were used as gold standard to calculate sensitivity and specificity. FlexiChip results obtained with a set....021) and had a sensitivity of 95.88% and a specificity of 97.68% compared to the sequencing as the reference method. Moreover the method performed well compared to the results obtained in the reference laboratories, with 99.7% of identical results (kappaPublication Metadata only K13 mutations and pfmdr1 copy number variation in Plasmodium falciparum malaria in Myanmar(2016-02-24) Aye A. Win; Mallika Imwong; Myat P. Kyaw; Charles J. Woodrow; Kesinee Chotivanich; Borimas Hanboonkunupakarn; Sasithon Pukrittayakamee; Institute of Medicine (1); Mahidol University; Department of Medical Research (Lower Myanmar); Nuffield Department of Clinical Medicine© 2016 Win et al. Background: Artemisinin-based combination therapy has been first-line treatment for falciparum malaria in Myanmar since 2005. The wide extent of artemisinin resistance in the Greater Mekong sub-region and the presence of mefloquine... samples collected from patients with Plasmodium falciparum malarial infection in five malaria-endemic areas across Myanmar were analysed for kelch 13 sequence (k13) and pfmdr1 copy number variation. K13 mutations in the region corresponding to amino acidsPublication Metadata only Caractéristiques à l'échelle du génome des microsatellites de cinq espèces humaines de Plasmodium, spécialement Plasmodium malariae et P. ovale curtisi(2020-01-01) Vivek Bhakta Mathema; Supatchara Nakeesathit; Nicholas J. White; Arjen M. Dondorp; Mallika Imwong; Mahidol University; Nuffield Department of Clinical Medicine. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1-10 base pairs... microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18-29