Highly multiplex molecular inversion probe panel in Plasmodium falciparum targeting common SNPs approximates whole genome sequencing assessments for selection and relatedness

IntroductionThe use of next-generation sequencing technologies (NGS) to study parasite populations and their response and evolution to interventions is important to support malaria control and elimination efforts. While whole genome sequencing (WGS) is optimal in terms of assessing the entire genome, it is costly for numerous samples. Targeted approaches selectively enriching for sequence of interest are more affordable but sometimes lack adequate information content for key analyses. MethodsWe have developed a highly-multiplexed molecular inversion probe (MIP) panel (IBC2FULL) targeting single nucleotide polymorphisms (SNPs) with [≥] 5% minor allele frequency (MAF) in sub-Saharan African regions from publicly available Plasmodium falciparum WGS. We optimized the panel alone and in combination with antimalarial drug resistance MIPs in laboratory P. falciparum strains at different parasitemias, and validated it by sequencing field isolates from Democratic Republic of Congo, Ethiopia, Ghana, Mali, Rwanda, Tanzania and Uganda and evaluating population structure, identity-by-descent (IBD), signals of selection, and complexity of infection (COI) ResultsThe new panel IBC2FULL consisted of 2,128 MIP microhaplotypes (containing 4,264 common SNPs) spaced by 5.1 - 18.4 kb across the entire genome. While these microhaplotypes were developed based on variation from sub-Saharan African WGS, 59.3% (2,529) of SNPs were also common in South-East Asia. The MIPs were balanced to produce more uniform and higher depth coverage at low parasitemia (100 parasites/L) along with MIPs targeting antimalarial drug resistance genes. Comparing targeted regions extracted from public WGS, IBC2FULL provided higher resolution of local population structure in sub-Saharan Africa than current PCR-based targeted sequencing panels. Sequencing field samples, IBC2FULL approximated WGS measures of relatedness, population structure, and COI. Interestingly, genome-wide analysis of extended haplotype homozygosity detected the same major peaks of selection as WGS. We also chose a subset of 305 high performing probes to create a core panel (IBC2CORE) that produced high-quality data for basic population genomic analysis and accurate estimation of COI. DiscussionIBC2FULL and IBC2CORE provide an improved platform for malaria genomic epidemiology and biology that can approximate WGS for many applications and is deployable for malaria molecular surveillance in resource-limited settings.