Size Distributions of Maternal and Fetal DNA in Maternal Plasma

Abstract

Background:The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive prenatal diagnosis. Despite the rapid expansion in clinical applications, the molecular characteristics of plasma DNA in pregnant women remain unclear. Methods: We investigated the size distribution of plasma DNA in 34 nonpregnant women and 31 pregnant women, using a panel of quantitative PCR assays with different amplicon sizes targeting the leptin gene. We also determined the size distribution of fetal DNA in maternal plasma by targeting the SRY gene. Results: The median percentages of plasma DNA with size >201 bp were 57% and 14% for pregnant and nonpregnant women, respectively (P <0.001, MannWhitney test). The median percentages of fetal-derived DNA with sizes >193 bp and >313 bp were 20% and 0%, respectively, in maternal plasma. Conclusion: Plasma DNA molecules are mainly short DNA fragments. The DNA fragments in the plasma of pregnant women are significantly longer than those in the plasma of nonpregnant women, and the maternalderived DNA molecules are longer than the fetal-derived ones.

Next generation sequencing of SNPs for non-invasive prenatal diagnosis: challenges and feasibility as illustrated by an application to β-thalassaemia

“…This depends on the position of the SNP on the amplicon in terms on where the fetal fragment is cut, as well as on the size of the fetal fragment. Fetal-derived DNA molecules are o300 bp 7 showing a prominence at 143 bp. 25 The amplicon sizes of our fragments were between 170 bp and 268 bp and therefore, fragments longer than 146 bp, in combination with the position of the SNP on the amplicon, are expected to result in the amplification of only a fraction of the fetal molecules present in the maternal plasma resulting in falsenegative results.…”

“…Theoretically, a non-present fetal allele gives a calculated fetal fraction of 0, whereas the fetal fraction DNA in the maternal circulation can be as low as 3% with an average of 10%. 6,7 We used a cutoff of 2.5%, which is somewhat below the minimum value. We consider the fetal allele detected if f is larger than 2.5% for at least two out of three replicates.…”

“…[4][5][6] However, this poses a technical challenge as fetal DNA represents a minor population in maternal plasma, exacerbated by the fragmentation of fetal DNA. 7,8 As the advent of next generation sequencing (NGS), a lot of effort has been concentrated on exploiting this technology for the measurement of aneuploidies in maternal plasma. [9][10][11][12][13][14] Using this technology, non-invasive prenatal diagnostic (NIPD) for trisomy 21, 18 and 13 has recently reached the clinical setting by analysing the relative amount of chromosomes in circulating cell-free DNA from maternal plasma.…”

Cell‐free fetal DNA in celomic fluid

“…However, it is very unlikely that fetal cfDNA from the early amniotic fluid could reach the maternal circulation because exchange at the level of the yolk sac is mainly unidirectional towards the fetus and the amniotic membrane is practically impermeable to large molecules 8 . Given that the estimated size of fetal cfDNA in maternal circulation is 100-300 base pairs 9 , which is equivalent to about 30-90 kDa, and the transfer through the amniotic membrane is negligible for molecules of similar size (e.g. human albumin), it appears that the source of cfDNA in the amniotic fluid is the fetus and the source in the maternal serum is the placenta.…”

Sonographic findings of uterine sacculation during pregnancy

“…However, it is very unlikely that fetal cfDNA from the early amniotic fluid could reach the maternal circulation because exchange at the level of the yolk sac is mainly unidirectional towards the fetus and the amniotic membrane is practically impermeable to large molecules 8 . Given that the estimated size of fetal cfDNA in maternal circulation is 100-300 base pairs 9 , which is equivalent to about 30-90 kDa, and the transfer through the amniotic membrane is negligible for molecules of similar size (e.g. human albumin), it appears that the source of cfDNA in the amniotic fluid is the fetus and the source in the maternal serum is the placenta.…”