High-Resolution Profiling of Fetal DNA Clearance from Maternal Plasma by Massively Parallel Sequencing

Abstract

BACKGROUND:With the advent of massively parallel sequencing (MPS), DNA analysis can now be performed in a genomewide manner. Recent studies have demonstrated the high precision of MPS for quantifying fetal DNA in maternal plasma. In addition, paired-end sequencing can be used to determine the size of each sequenced DNA fragment. We applied MPS in a highresolution investigation of the clearance profile of circulating fetal DNA.

Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA

“…These data provide genome-level evidence that the placenta is the predominant source of fetal-derived DNA molecules in maternal plasma and represent a major step forward, compared with previous evidence based on selected loci (31 ). The reversal of the methylation profile in the postdelivery maternal plasma sample to become more similar to that of the maternal blood cells suggests that the fetal DNA molecules were removed from the maternal circulation (34 ). Calculation of the fetal DNA concentrations based on SNP markers of the fetus indeed showed that the concentration changed from 33.9% before delivery to just 4.5% in the postdelivery sample.…”

Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation‐negative early‐onset and high‐risk breast cancer patients

“…Although we cannot exclude BC dormancy or early‐stage second tumors, circulating tumor cells in these patients occur at very low concentrations of one tumor cell in the background of millions of blood cells and have an average half‐life of only 1–3 h after separation 40, 41. Similarly, cell‐free circulating DNA has a half‐life of approximately 14 h and is rapidly cleared from blood, if not replenished from apoptotic/necrotic cells every few hours 42. Moreover, the vast majority of cell‐free DNA fragments are between 180 and 200 bp,43, 44 and cannot be amplified by our DBS assays, which targets regions between 379 and 597 bp in length.…”

Potentials, challenges and limitations of a molecular characterization of circulating tumor DNA for the management of cancer patients

“…In general, the release of ctDNA is thought to be a fluctuating, stochastic process rather than a continuous process. Due to the fact that cfDNA is cleared rapidly from the maternal plasma after delivery [34,35], most data on stability and half-life of cfDNA come from fetal DNA studies. Recent data from Dennis Lo's group suggests an initial rapid phase, with a mean half-life of 1 h and a subsequent slow phase, with a mean half-life of 13 h [35].…”

“…Due to the fact that cfDNA is cleared rapidly from the maternal plasma after delivery [34,35], most data on stability and half-life of cfDNA come from fetal DNA studies. Recent data from Dennis Lo's group suggests an initial rapid phase, with a mean half-life of 1 h and a subsequent slow phase, with a mean half-life of 13 h [35]. These data were confirmed in healthy subjects performing extensive exercise [36].…”

“…Two studies from Lo's group and Snyder and colleagues, respectively, contributed immensely to the present knowledge of cfDNA origin. In pregnant women, for example, it was shown that the placenta is the origin of fetal cfDNA (cffDNA) detectable in the maternal circulation whereas cffDNA ranged from 12.1 to 41.0% of overall cfDNA [35]. Moreover, these studies showed that cfDNA circulating in the blood of transplant recipients originated from the donor genome suggesting that cfDNA can be used to detect an organ-specific signature.…”