Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance

Table 2 DNA recovery rate of different DNA isolation methods and dilutions quantified by ddPCR targeting the tRNA gene

DNA isolation method	Sample input	DNA recovery rate in % by ddPCR (± SD)
DNA isolation method	Sample input	10,000 p/µL	1000 p/µL	100 p/µL	10p/µL
NucleoMag Blood 200 μL Kit
	50 μL whole blood	98.3% (± 11.9)	94.7% (± 6.3)	97.2% (± 13.3)	88.3% (± 14.4)
	50 μL DBS	8.2% (± 1.5)	11.1% (± 1.3)	20.8% (± 7.5)	18.8% (± 11.0)
	50 μL DBS (short lysis)	3.6% (± 0.4)	6.9% (± 3.0)	9.2% (± 4.9)	6.0% (± 4.6)
	5 × 3 mm punches DBS	1.1% (± 0.5)	2.2% (± 0.3)	1.8% (± 0.3)	3.0% (± 1.7)
QIAamp DNA Blood Mini Kit
	50 μL whole blood	25.4% (± 8.0)	33.2% (± 11.0)	31.7% (± 5.3)	16.8% (± 8.5)
	50 μL DBS	2.4% (± 0.5)	2.6% (± 0.2)	2.5% (± 0.5)	2.3% (± 2.0)
	5 × 3 mm punches DBS	2.4% (± 0.5)	2.0% (± 0.4)	3.2% (± 0.1)	3.5% (± 3.4)
Tween-Chelex
	50 μL DBS	15.6% (± 2.8)	17.7% (± 4.0)	17.5% (± 2.0)	21.7% (± 7.2)
	5 × 3 mm punches DBS	9.3% (± 2.2)	9.7% (± 1.8)	8.7% (± 1.0)	8.9% (± 4.1)

Recovery is calculated as DNA copies per µL extracted DNA compared to parasites per µL blood in the initial sample. Elution volume for all extractions except Tween-Chelex was 50 µL. Thus, for 5 × 3 mm punches, DNA was diluted 3.33-fold compared to the initial sample. For Tween-Chelex extractions, the elution volume was 250 µL for 50 µL DBS, and 70 µL for 5 × 3 mm punches. DNA was thus diluted ~ fivefold. As data in the table is given as genomes per µL, the total recovery (i.e., total genomes in eluate) is fivefold higher

ISSN: 1475-2875