Qualitative and quantitative comparison of cell-free DNA and cell-free fetal DNA isolation by four (semi-)automated extraction methods: impact in two clinical applications: chimerism quantification and noninvasive prenatal diagnosis

Table 3 Chimerism results of the different isolation methods using NGS and ddPCR techniques

Marker ID	Chromosome	Recipient	Donor	Control gDNA		MagNAPure		IDEAL		LabTurbo24 AB		Chemagic 360
Marker ID	Chromosome	Recipient	Donor	100%	15%	10%	1%	10%	1%	10%	1%	10%	1%
NGS chimerism
1	1	+/−	−/−	100	14.7	16.2**	0.1*	0**	0*	21.8*	4.6	10.6**	5.7*
3	1	+/−	+/+	100	12.8*	3.6**	0*	0**	8.8*	12.7*	2.6	0**	3.3**
8	6	+/−	−/−	100*	18.8*	13.9*	0	0**	2.3*	16.2*	4.9*	12.8**	4*
9	7	+/−	+/+	100*	30.2*	35.8**	0*	0**	2.9*	12.3*	1.9	0**	0.7**
11	8	−/−	+/+	99.1*	18.8*	19.4*	0*	0**	1.5*	10.4*	2.3	5.7**	1.2*
12	9	+/+	−/−	98.1	16.5*	10.6**	0*	0**	3.9*	12.7*	1.2	15**	2.4*
22	20	−/−	+/+	98.9	17.1	7.1**	0**	100**	2.6**	24*	1.8	0**	1.4**
23	22	+/−	+/+	100*	16*	14.8*	0	0**	0*	17.5*	2.8*	8.1**	1*
Average (%)				99.5	18.1	15.2	0	12.5	2.7	16	2.7	6.5	2.4
SD				0.7	5.3	9.8	0	35.4	2.8	4.9	1.3	6.1	1.8
ddPCR chimerism
Total droplets				22,512	21,496	22,286	22,685	21,481	21,253	16,812	18,665	19,207	19,115
RPP30 positive droplets				13,184	11,256	94	84	40	29	124	128	55	40
Y-marker positive droplets				7121	914	0	0	0	0	4	1	0	0
% chimerism (Y-marker heterozygous × 2)				108%	16%	NC	NC	NC	NC	6%	< DL NC	NC	NC

Quality warning: * (yellow): coverage: 1000–10,000 X, ** (red): coverage < 1000 X
NC not calculated, DL detection limit

ISSN: 1479-5876