Assessment of Nanopore adaptive sampling for Plasmodium whole-genome sequencing. Plasmodium adaptive sampling

The predominance of human DNA in a malaria patient blood sample requires time-consuming lab procedures to filter out human DNA or enrich Plasmodium DNA. Here, we investigated the potential of adaptive sampling to enrich for Plasmodium DNA while sequencing unenriched patient blood samples on a minION device. For our initial tests (Biosample: SAMEA112148332), we compared adaptive sampling to regular sequencing on a dilution series of human DNA (Promega G304A) mixed with Plasmodium falciparum 3D7 DNA. This produced a series of nine samples, labeled barcode 01 through barcode 09, with Plasmodium DNA concentrations ranging from 0% to 100%, in the following increments: 0, 0.1, 0.5, 1, 5, 10, 50, 90, and 100%. For each sample, the accession numbers for reads of Plasmodium falciparum and Promega G304A are sequentially organized, corresponding to both regular and adaptive sequencing methods. For instance, for the initial sample, the accession number ERR10502669 is assigned to the adaptive mode reads of Plasmodium falciparum, ERR10502670 to Promega G304A in adaptive mode, ERR10502671 to Plasmodium falciparum in regular mode, and ERR10502672 to Promega G304A in regular mode. This numeric sequence is consistently applied across the dataset. Further analysis was conducted on three patient samples using the minION's adaptive sampling capability. One patient sample underwent comparative analysis with both adaptive sampling and conventional sequencing post-selective whole-genome amplification (sWGA). We evaluated the quality of the sequencing data for its relevance in clinical settings. The sequences aligned with the Plasmodium falciparum reference genome have been deposited with the following sample accessions: ERS14258238, ERS14258239, and ERR12164889 for adaptive sampling; and an additional accession ERR12164890 for the sWGA-enhanced regular sequencing method.