{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T20:14:20Z","timestamp":1791490460587,"version":"4.3.4"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,25]],"date-time":"2020-08-25T00:00:00Z","timestamp":1598313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1132226"],"award-info":[{"award-number":["OPP1132226"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["098051"],"award-info":[{"award-number":["098051"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["090770"],"award-info":[{"award-number":["090770"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity\u2005=\u20050.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites\/\u00b5L). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiaa527","type":"journal-article","created":{"date-parts":[[2020,8,24]],"date-time":"2020-08-24T07:07:43Z","timestamp":1598252863000},"page":"1227-1237","source":"Crossref","is-referenced-by-count":73,"title":["Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the\n                    <i>Plasmodium falciparum<\/i>\n                    Heterozygome"],"prefix":"10.1093","volume":"225","author":[{"given":"Sofonias K","family":"Tessema","sequence":"first","affiliation":[{"name":"EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9639-2894","authenticated-orcid":false,"given":"Nicholas J","family":"Hathaway","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noam B","family":"Teyssier","sequence":"additional","affiliation":[{"name":"EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, 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M","family":"Duarte","sequence":"additional","affiliation":[{"name":"EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilson","family":"Simone","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a, Manhi\u00e7a, Mozambique"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Colborn","sequence":"additional","affiliation":[{"name":"Clinton Health Access Initiative, Maputo, Mozambique"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Saute","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a, Manhi\u00e7a, 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