{"entity": "publication", "iuid": "cd185537d6c1427a862c3a4040bcd21c", "timestamp": "2026-07-17T09:59:02.707Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd185537d6c1427a862c3a4040bcd21c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd185537d6c1427a862c3a4040bcd21c"}}, "title": "MalDeepSeq panel: A targeted ultra-deep sequencing approach to trace drug resistance markers in Plasmodium falciparum.", "authors": [{"family": "Salazar", "given": "Yanka E A R", "initials": "YEAR"}, {"family": "Rezende", "given": "Antonio M", "initials": "AM"}, {"family": "Pu\u00e7a", "given": "Maria C S B", "initials": "MCSB"}, {"family": "Lagstr\u00f6m", "given": "Sonja", "initials": "S"}, {"family": "Fletcher", "given": "Danielle", "initials": "D"}, {"family": "Muwanguzi-Karugaba", "given": "Julian", "initials": "J"}, {"family": "Sutherland", "given": "Colin J", "initials": "CJ"}, {"family": "Beshir", "given": "Khalid B", "initials": "KB"}, {"family": "Mascarenhas", "given": "Maria E P", "initials": "MEP"}, {"family": "Louzada", "given": "Jaime", "initials": "J"}, {"family": "Oliveira-Ferreira", "given": "Joseli", "initials": "J"}, {"family": "Djimde", "given": "Abdoulaye", "initials": "A"}, {"family": "Lopes", "given": "Dinora", "initials": "D"}, {"family": "de Sousa", "given": "Tais N", "initials": "TN"}, {"family": "Gil", "given": "Jos\u00e9 P", "initials": "JP"}], "type": "journal article", "published": "2026-06-25", "journal": {"title": "Cell Reports Methods", "issn": "2667-2375", "pages": "101509", "issn-l": null}, "abstract": "The emergence of drug-resistant Plasmodium falciparum highlights the need for tools to detect minor parasite subpopulations before resistant lineages expand. We developed and validated a targeted ultra-deep sequencing framework for the full-length sequences of 48 antimalarial resistance genes. Performance was evaluated using 3D7:Dd2 mock mixtures and clinical samples after selective whole-genome amplification. The panel achieved high depth and breadth, including for dried blood spot samples. Using Dd2-fixed markers, Mutect2 and HaplotypeCaller reproduced expected variant-allele frequencies, with Mutect2 exhibiting lower global bias and error. A conservative truth set derived from Dd2-pure controls yielded perfect recall and no false-positives in 3D7 controls, with high recovery of true Dd2 variants in mock mixtures for both callers. In clinical samples, the panel captured within-host diversity and minority resistance alleles. Overall, these results demonstrate that targeted deep sequencing offers a cost-efficient, high-resolution approach for routine molecular surveillance of emerging drug resistance.", "doi": "10.1016/j.crmeth.2026.101509", "pmid": "42349411", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S2667-2375(26)00210-9"}], "notes": [], "created": "2026-07-14T18:12:00.160Z", "modified": "2026-07-14T18:12:00.163Z"}