Fig. 1
MAD4HatTer is a multi-purpose malaria amplicon sequencing panel. A. Primer pools to amplify targets in 5 categories are grouped into two modules (Diversity and Resistance). R1 refers to two primer pools: R1.1, the original pool, and R1.2, a reduced version of primer pool R1.1 designed to increase sensitivity. The recommended configuration to maximize information retrieval and sensitivity for low parasitemia samples are two mPCR reactions, one with D1 and R1.2 primers, and one with R2 primers (solid lines). Supplementary Tables 1–5 contain complete details on primer pools and targets. B. Chromosomal locations of all targets in the P. falciparum genome (not including non-falciparum targets). Note that the Diagnostic Resistance category includes targets in and around hrp2 and hrp3 as well as targets in chromosome 11 that are often duplicated when hrp3 is deleted44 and length controls in other chromosomes. C. Simplified workflow for library preparation and sequencing, highlighting the need for two multiplexed PCR reactions when using primer pools R1 and R2 which are incompatible due to tiling over some genes of interest. A more detailed scheme can be found in Supplementary Figure 1, and a full protocol, including didactic materials, can be found online78.
