Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples

Abstract

AbstractBackgroundWhole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. We evaluated the effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification on the quality and fidelity of WGS data recovered from DBS.ResultsAt 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5X depth = 93% genome) than QIAamp extracted samples (5X depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published.ConclusionsOverall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.