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Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six\n            <jats:named-content content-type=\"genus-species\">Plasmodium falciparum<\/jats:named-content>\n            genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse\n            <jats:named-content content-type=\"genus-species\">P. falciparum<\/jats:named-content>\n            reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.\n          <\/jats:p>","DOI":"10.1128\/jcm.00235-16","type":"journal-article","created":{"date-parts":[[2016,3,24]],"date-time":"2016-03-24T04:26:28Z","timestamp":1458793588000},"page":"1500-1511","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":53,"title":["A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India"],"prefix":"10.1128","volume":"54","author":[{"given":"Pavitra N.","family":"Rao","sequence":"first","affiliation":[{"name":"Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swapna","family":"Uplekar","sequence":"additional","affiliation":[{"name":"Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sriti","family":"Kayal","sequence":"additional","affiliation":[{"name":"National Institute of Technology, Raurkela, Odisha, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prashant K.","family":"Mallick","sequence":"additional","affiliation":[{"name":"National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nabamita","family":"Bandyopadhyay","sequence":"additional","affiliation":[{"name":"National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonal","family":"Kale","sequence":"additional","affiliation":[{"name":"National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Om P.","family":"Singh","sequence":"additional","affiliation":[{"name":"National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akshaya","family":"Mohanty","sequence":"additional","affiliation":[{"name":"Institute of Life Sciences, Bhubaneswar, Odisha, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjib","family":"Mohanty","sequence":"additional","affiliation":[{"name":"Ispat General Hospital, Raurkela, Odisha, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel C.","family":"Wassmer","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Division of Parasitology, New York University School of Medicine, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane M.","family":"Carlton","sequence":"additional","affiliation":[{"name":"Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","unstructured":"WHO\/UNICEF. 2015. 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