{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T16:02:37Z","timestamp":1791648157771,"version":"4.3.4"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T00:00:00Z","timestamp":1614297600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T00:00:00Z","timestamp":1614297600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill & 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"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Malar J"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. The effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification were evaluated on the quality and fidelity of WGS data recovered from DBS.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Low parasite density mock DBS samples were created, extracted either with Tween-Chelex or QIAamp, treated with or without McrBC, and amplified with one of three different amplification techniques (two sWGA primer sets and one rWGA). Extraction conditions were evaluated on performance of sequencing depth, percentiles of coverage, and expected SNP concordance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>At 100 parasites\/\u03bcL, Chelex-Tween-McrBC samples had higher coverage (5\u00a0\u00d7 depth\u2009=\u200993% genome) than QIAamp extracted samples (5\u00a0\u00d7 depth\u2009=\u200976% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12936-021-03630-4","type":"journal-article","created":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T08:03:39Z","timestamp":1614326619000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":63,"title":["Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4001-6296","authenticated-orcid":false,"given":"Noam B.","family":"Teyssier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elias M.","family":"Duarte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rene","family":"Sit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Greenhouse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofonias K.","family":"Tessema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,2,26]]},"reference":[{"key":"3630_CR1","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.ajic.2016.05.015","volume":"45","author":"P Tang","year":"2017","unstructured":"Tang P, Croxen MA, Hasan MR, Hsiao WWL, Hoang LM. Infection control in the new age of genomic epidemiology. Am J Infect Control. 2017;45:170\u20139.","journal-title":"Am J Infect Control"},{"key":"3630_CR2","doi-asserted-by":"publisher","first-page":"e22213","DOI":"10.1371\/journal.pone.0022213","volume":"6","author":"S Auburn","year":"2011","unstructured":"Auburn S, Campino S, Clark TG, Djimde AA, Zongo I, Pinches R, et al. An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLoS ONE. 2011;6:e22213.","journal-title":"PLoS ONE"},{"key":"3630_CR3","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1475-2875-11-41","volume":"11","author":"M Venkatesan","year":"2012","unstructured":"Venkatesan M, Amaratunga C, Campino S, Auburn S, Koch O, Lim P, et al. Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples. Malar J. 2012;11:41.","journal-title":"Malar J"},{"key":"3630_CR4","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1645\/GE-1706.1","volume":"95","author":"Y Wang","year":"2009","unstructured":"Wang Y, Nair S, Nosten F, Anderson TJC. Multiple displacement amplification for malaria parasite DNA. J Parasitol. 2009;95:253\u20135.","journal-title":"J Parasitol"},{"key":"3630_CR5","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1093\/dnares\/dsu028","volume":"21","author":"SO Oyola","year":"2014","unstructured":"Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, et al. Optimized whole-genome amplification strategy for extremely AT-biased template. DNA Res. 2014;21:661\u201371.","journal-title":"DNA Res"},{"key":"3630_CR6","doi-asserted-by":"publisher","first-page":"R73","DOI":"10.1186\/gb-2011-12-8-r73","volume":"12","author":"A Melnikov","year":"2011","unstructured":"Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, et al. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 2011;12:R73.","journal-title":"Genome Biol"},{"issue":"10","key":"3630_CR7","first-page":"2174","volume":"5","author":"M Smith","year":"2012","unstructured":"Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, et al. An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS. Open Genomics J. 2012;5(10):2174.","journal-title":"Open Genomics J"},{"key":"3630_CR8","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1186\/1471-2164-13-262","volume":"13","author":"AT Bright","year":"2012","unstructured":"Bright AT, Tewhey R, Abeles S, Chuquiyauri R, Llanos-Cuentas A, Ferreira MU, et al. Whole genome sequencing analysis of Plasmodium vivax using whole genome capture. BMC Genomics. 2012;13:262.","journal-title":"BMC Genomics"},{"key":"3630_CR9","doi-asserted-by":"publisher","first-page":"R1220","DOI":"10.1016\/j.cub.2016.10.016","volume":"26","author":"S Marciniak","year":"2016","unstructured":"Marciniak S, Prowse TL, Herring DA, Klunk J, Kuch M, Duggan AT, et al. Plasmodium falciparum malaria in 1st-2nd century CE southern Italy. Curr Biol. 2016;26:R1220\u20132.","journal-title":"Curr Biol"},{"key":"3630_CR10","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1128\/JCM.02507-12","volume":"51","author":"SO Oyola","year":"2013","unstructured":"Oyola SO, Gu Y, Manske M, Otto TD, O\u2019Brien J, Alcock D, et al. Efficient depletion of host DNA contamination in malaria clinical sequencing. J Clin Microbiol. 2013;51:745\u201351.","journal-title":"J Clin Microbiol"},{"key":"3630_CR11","doi-asserted-by":"publisher","first-page":"e02257","DOI":"10.1128\/mBio.02257-16","volume":"8","author":"AN Cowell","year":"2017","unstructured":"Cowell AN, Loy DE, Sundararaman SA, Valdivia H, Fisch K, Lescano AG, et al. Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium vivax from unprocessed clinical samples. MBio. 2017;8:e02257-e2316.","journal-title":"MBio"},{"key":"3630_CR12","doi-asserted-by":"publisher","first-page":"11078","DOI":"10.1038\/ncomms11078","volume":"7","author":"SA Sundararaman","year":"2016","unstructured":"Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, et al. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Commun. 2016;7:11078.","journal-title":"Nat Commun"},{"key":"3630_CR13","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1186\/s12936-016-1641-7","volume":"15","author":"SO Oyola","year":"2016","unstructured":"Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, et al. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malar J. 2016;15:597.","journal-title":"Malar J"},{"key":"3630_CR14","doi-asserted-by":"publisher","first-page":"9873","DOI":"10.1038\/s41598-019-46398-z","volume":"9","author":"ED Benavente","year":"2019","unstructured":"Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, et al. Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations. Sci Rep. 2019;9:9873.","journal-title":"Sci Rep"},{"key":"3630_CR15","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s12936-018-2232-6","volume":"17","author":"S Nag","year":"2018","unstructured":"Nag S, Kofoed P-E, Ursing J, Lemvigh CK, Alles\u00f8e RL, Rodrigues A, et al. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots. Malar J. 2018;17:91.","journal-title":"Malar J"},{"key":"3630_CR16","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1093\/infdis\/jiw304","volume":"214","author":"AM Guggisberg","year":"2016","unstructured":"Guggisberg AM, Sundararaman SA, Lanaspa M, Moraleda C, Gonz\u00e1lez R, Mayor A, et al. Whole-genome sequencing to evaluate the resistance landscape following antimalarial treatment failure with fosmidomycin-clindamycin. J Infect Dis. 2016;214:1085\u201391.","journal-title":"J Infect Dis"},{"key":"3630_CR17","doi-asserted-by":"publisher","first-page":"565","DOI":"10.4269\/ajtmh.1995.52.565","volume":"52","author":"CV Plowe","year":"1995","unstructured":"Plowe CV, Djimde A, Bouare M, Doumbo O, Wellems TE. Pyrimethamine and proguanil resistance-conferring mutations in Plasmodium falciparum dihydrofolate reductase: polymerase chain reaction methods for surveillance in Africa. Am J Trop Med Hyg. 1995;52:565\u20138.","journal-title":"Am J Trop Med Hyg"},{"key":"3630_CR18","doi-asserted-by":"publisher","first-page":"e1001788","DOI":"10.1371\/journal.pmed.1001788","volume":"12","author":"N Hofmann","year":"2015","unstructured":"Hofmann N, Mwingira F, Shekalaghe S, Robinson LJ, Mueller I, Felger I. Ultra-sensitive detection of Plasmodium falciparum by amplification of multi-copy subtelomeric targets. PLoS Med. 2015;12:e1001788.","journal-title":"PLoS Med"},{"key":"3630_CR19","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303 3997 [Internet]. 2013; Available from: http:\/\/arxiv.org\/abs\/1303.3997"},{"key":"3630_CR20","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics"},{"key":"3630_CR21","doi-asserted-by":"crossref","unstructured":"Auwera GAV der, Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, et al. From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1\u201333.","DOI":"10.1002\/0471250953.bi1110s43"},{"key":"3630_CR22","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1006\/jmbi.1999.2894","volume":"290","author":"D Panne","year":"1999","unstructured":"Panne D, Raleigh EA, Bickle TA. The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis. J Mol Biol. 1999;290:49\u201360.","journal-title":"J Mol Biol"},{"key":"3630_CR23","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1186\/s12936-020-03195-8","volume":"19","author":"Z Shah","year":"2020","unstructured":"Shah Z, Adams M, Moser KA, Shrestha B, Stucke EM, Laufer MK, et al. Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples. Malar J. 2020;19:135.","journal-title":"Malar J"}],"container-title":["Malaria Journal"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12936-021-03630-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12936-021-03630-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12936-021-03630-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T08:11:26Z","timestamp":1614327086000},"score":1,"resource":{"primary":{"URL":"https:\/\/malariajournal.biomedcentral.com\/articles\/10.1186\/s12936-021-03630-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,26]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["3630"],"URL":"https:\/\/doi.org\/10.1186\/s12936-021-03630-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-69257\/v1","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-69257\/v3","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-69257\/v2","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-69257\/v4","asserted-by":"object"},{"id-type":"doi","id":"10.1101\/835389","asserted-by":"object"}]},"ISSN":["1475-2875"],"issn-type":[{"value":"1475-2875","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,26]]},"assertion":[{"value":"30 August 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 February 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 February 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"116"}}