Improving Fetal Fraction of Noninvasive Prenatal Screening Samples Collected in EDTA-Gel Tubes Using Gel Size Selection A Head-To-Head Comparison of Methods

The aim of this study was to compare the use of EDTA-gel blood collection tubes with and without size selection to cell-stabilizing collection tubes for remote blood sampling for noninvasive prenatal screening (NIPS). Sixty-one pregnant women at 10 to 14 weeks' gestation undergoing NIPS were recruited. Participants were phlebotomized with Streck and EDTA-gel tubes. EDTA-gel tubes were centrifuged before shipping. Libraries prepared from cell-free DNA (cfDNA) extracted from both types of tubes were sequenced on Illumina NextSeq 500, and fetal fraction was estimated using SeqFF. EDTA-gel tube libraries were size selected on agarose gel to eliminate cfDNA fragments > 160 bp and resequenced. The main outcome measure was fetal fraction expressed as percentage of total cfDNA sequenced, calculated from sequence read counts (SeqFF). Streck tube samples showed an average 1% higher fetal fraction than centrifuged EDTA-gel tubes without size selection. This difference increased with temperature. When EDTA-gel samples' libraries were size selected, the mean fetal fraction increased from 7% to 13%, with no sample having fetal fraction < 4%. Using EDTA-gel tubes reduces NIPS sampling cost and tube processing time in the laboratory. Also, using EDTA-gel tubes does not lead to cfDNA degradation. Size selection increases fetal fraction, reduces the number of test failures, increases NIPS clinical performance, and may be helpful in situations asking for a higher fetal fraction, such as twin pregnancies or screening for sub-chromosomal imbalances.