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

From: 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

Marker ID Chromosome Recipient Donor Control gDNA MagNAPure IDEAL LabTurbo24 AB Chemagic 360
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
  1. Quality warning: * (yellow): coverage: 1000–10,000 X, ** (red): coverage < 1000 X
  2. NC not calculated, DL detection limit