RT Journal Article SR Electronic T1 Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples JF bioRxiv FD Cold Spring Harbor Laboratory SP 835389 DO 10.1101/835389 A1 Noam B. Teyssier A1 Anna Chen A1 Elias M Duarte A1 Rene Sit A1 Bryan Greenhouse A1 Sofonias K. Tessema YR 2019 UL http://biorxiv.org/content/early/2019/11/08/835389.abstract AB Background Whole-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.Results At 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.Conclusions Overall, 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.