Fig. 6: Validation of hrp2/3 deletion detection using the NOMADS16 panel.

a Diagram showing the location of the hrp2, hrp2 upstream and hrp2 downstream amplicons in the NOMADS16 panel, within a 50 kbp window of chromosome 8. The chromosome is represented by a dark grey horizontal line, on which thicker segments demarcate genes (labelled above) and their exons. The genomic extent of documented hrp2 deletions is displayed above the chromosome for lab strains Dd2 and HB3, and for a selection of three field strains^12,67. Amplicon positions are shown below in orange. b Same as in (a) but for hrp3 upstream, hrp3 and hrp3 downstream amplicons, shown in purple. Note Dd2 does not have a deletion within this windnow. c Heatmap displaying the normalised abundance of NOMADS16 panel amplicons (rows) across 48 mock samples (columns). The P. f. strain used in the mock sample (3D7, blue; Dd2, green; HB3, red; P. f. -negative, grey) and its parasitemia is indicated above the heatmap. The bottom six rows of the heatmap show amplicons designed for detection of hrp2 and hrp3 deletions. d Scatterplot showing the relationship between amplicon abundance (y-axis, in number of reads) and parasitemia (x-axis) for the hrp2 amplicon across all 48 mock samples. As in (c) the colour of points indicates the P. f. strain used in the mock sample. e Same as (d) but for the hrp3 amplicon. f Heatmap displaying the probability of deletion for each of the six amplicons designed to support hrp2/3 deletion detection (rows) across the 48 mock samples (columns) indicated in (c). Probabilities were calculated using a statistical model (Methods) that leverages all sixteen amplicons in NOMADS16 and estimates barcode misclassification/contamination rates from P. f. -negative samples. The expected deletions are detected with a very high degree of certainty (black squares). Uncertainty about P. f. -negative samples (deletion probability between 0.2 and 0.8) is expected as they have very few reads.