MalDeepSeq panel: A targeted ultra-deep sequencing approach to trace drug resistance markers in Plasmodium falciparum.
JSON
Salazar YEAR, Rezende AM, Puça MCSB, Lagström S, Fletcher D, Muwanguzi-Karugaba J, Sutherland CJ, Beshir KB, Mascarenhas MEP, Louzada J, Oliveira-Ferreira J, Djimde A, Lopes D, de Sousa TN, Gil JP
Cell Reports Methods - (-) 101509 [2026-06-25; online 2026-06-25]
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.
NGI Stockholm (Genomics Production) [Service]
National Genomics Infrastructure [Service]
PubMed 42349411
DOI 10.1016/j.crmeth.2026.101509
Crossref 10.1016/j.crmeth.2026.101509
pii: S2667-2375(26)00210-9