Fetal DNA in maternal serum: does it persist after pregnancy?

Cell-free fetal DNA coming in all sizes and shapes

Cell‐free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non‐invasively from maternal blood. Through the years, evidence has accumulated to show that cell‐free fetal DNA molecules are derived from placental tissues, are mainly of short DNA fragments and have rapid post‐delivery clearance profiles. But questions regarding how they come to being short molecules from placental cells and in which physical forms do they exist remained largely unanswered until recently. We now know that the distributions of ending sites of cell‐free DNA molecules are non‐random across the genome and bear correlations with the chromatin structures of cells from which they have originated. Such an insight offers ways to deduce the tissue‐of‐origin of these molecules. Besides, the physical nature and sequence characteristics of the ends of each cell‐free DNA molecule provide tell‐tale signs of how the DNA fragmentation processes are orchestrated by nuclease enzymes. These realizations offered opportunities to develop methods for enriching cell‐free fetal DNA to facilitate non‐invasive prenatal diagnostics. Here we aimed to collate what is known about the biological and physical characteristics of cell‐free fetal DNA into one article and explain the implications of these observations.

What’s already known about this topic?

Cell‐free fetal DNA originates from placental tissues and circulates in maternal plasma as a minor population in the form of short fragments which disappears from maternal circulation rapidly after delivery.

What does this study add?

Cell‐free DNA studies at the per molecule per nucleotide level documented the detailed genomic distributions, fragment end characteristics and physical forms of cell‐free DNA unveiling the fine feature differences between maternal and fetal DNA as well as their intricate relationships with the chromatin structure of the cells‐of‐origin. These studies have substantially bridged the knowledge gaps in the biology of cell‐free fetal DNA and may provide insights on how to enhance prenatal tests based on their analyses.

Optimization of diagnostic strategy for non-invasive cell-free foetal RHD determination from maternal plasma

BACKGROUND AND OBJECTIVES

The aim of the study was to optimize routine non-invasive prenatal detection of fetal RHD gene from plasma of RhD-negative pregnant women (the median of gestational age was 25 weeks, range 10-38) to detect RhD materno-fetal incompatibility and to avoid the redundant immunoprophylaxis.

MATERIALS AND METHODS

Initially only one exon of RHD gene (exon 10) was investigated in 281 plasma samples (144 verified after delivery), in the second phase three RHD exons (5, 7, 10) were analyzed in 246 samples of plasma and maternal genomic DNA (204 verified) by real-time PCR method. Detection of Y-chromosomal sequence DYS-14 and five X-chromosomal insertion/deletion polymorphisms was used to confirm the fetal cfDNA detectability in plasma. Specific polymorphisms in RHD gene were detected by sequence-specific primer PCR in nine samples.

RESULTS

When only the RHD exon 10 was tested, 2·8% of verified samples were false positive and 3·5% false negative. With three RHD exons (5, 7, 10) and maternal genomic DNA testing, only one case was false negative (0·5%). Nine samples were inconclusive due to RHD-positive results in maternal genomic DNA. These samples were analyzed for specific mutations in RHD gene. Combination of both methods for fetal cfDNA verification succeeded in 75% of tested group.

CONCLUSION

Implementation of analysis of three RHD exons and maternal genomic DNA to routine practice lowers dramatically the ratio of false positive and negative results. This method enables more accurate determination of fetal RHD status with the reduction of unnecessary medical care and RhD immunoprophylaxis.

High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing

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 high-resolution investigation of the clearance profile of circulating fetal DNA.

METHODS

Using paired-end MPS, we analyzed serial samples of maternal plasma collected from 13 women after cesarean delivery. We also studied the transrenal excretion of circulating fetal DNA in 3 of these individuals by analyzing serial urine samples collected after delivery.

RESULTS

The clearance of circulating fetal DNA occurred in 2 phases, with different kinetics. The initial rapid phase had a mean half-life of approximately 1 h, whereas the subsequent slow phase had a mean half-life of approximately 13 h. The final disappearance of circulating fetal DNA occurred at about 1 to 2 days postpartum. Although transrenal excretion was involved in the clearance of circulating fetal DNA, it was not the major route. Furthermore, we observed significant changes in the size profiles of circulating maternal DNA after delivery, but we did not observe such changes in circulating fetal DNA.

CONCLUSIONS

MPS of maternal plasma and urinary DNA permits high-resolution study of the clearance profile of circulating fetal DNA.

Non-invasive prenatal diagnostic test accuracy for fetal sex using cell-free DNA a review and meta-analysis

Background

Cell-free fetal DNA (cffDNA) can be detected in maternal blood during pregnancy, opening the possibility of early non-invasive prenatal diagnosis for a variety of genetic conditions. Since 1997, many studies have examined the accuracy of prenatal fetal sex determination using cffDNA, particularly for pregnancies at risk of an X-linked condition. Here we report a review and meta-analysis of the published literature to evaluate the use of cffDNA for prenatal determination (diagnosis) of fetal sex. We applied a sensitive search of multiple bibliographic databases including PubMed (MEDLINE), EMBASE, the Cochrane library and Web of Science.

Results

Ninety studies, incorporating 9,965 pregnancies and 10,587 fetal sex results met our inclusion criteria. Overall mean sensitivity was 96.6% (95% credible interval 95.2% to 97.7%) and mean specificity was 98.9% (95% CI = 98.1% to 99.4%). These results vary very little with trimester or week of testing, indicating that the performance of the test is reliably high.

Conclusions

Based on this review and meta-analysis we conclude that fetal sex can be determined with a high level of accuracy by analyzing cffDNA. Using cffDNA in prenatal diagnosis to replace or complement existing invasive methods can remove or reduce the risk of miscarriage. Future work should concentrate on the economic and ethical considerations of implementing an early non-invasive test for fetal sex.

Genomic analysis of fetal nucleic acids in maternal blood

The 15 years since the discovery of fetal DNA in maternal plasma have witnessed remarkable developments in noninvasive prenatal diagnosis. An understanding of biological parameters governing this phenomenon, such as the concentration and molecular size of circulating fetal DNA, has guided its diagnostic applications. Early efforts focused on the detection of paternally inherited sequences, which were absent in the maternal genome, in maternal plasma. Recent developments in precise measurement technologies such as digital polymerase chain reaction (PCR) have allowed the detection of minute allelic imbalances in plasma and have catalyzed analysis of single-gene disorders such as the hemoglobinopathies and hemophilia. The advent of massively parallel sequencing has enabled the robust detection of fetal trisomies in maternal plasma. Recent proof-of-concept studies have detected a chromosomal translocation and a microdeletion and have deduced a genome-wide genetic map of a fetus from maternal plasma. Understanding the ethical, legal, and social aspects in light of such rapid developments is thus a priority for future research.

Clinical application of fetal sex determination using cell-free fetal DNA in pregnant carriers of X-linked genetic disorders

As the first step in prenatal diagnosis of X-linked genetic disorders, chorionic villus sampling (CVS) for fetal sex determination is generally performed at 11-13 weeks of gestation. However, as the procedure-related miscarriage rate of CVS is 0.5-1.0%, non-invasive methods such as PCR of cell-free fetal DNA (cff-DNA) in maternal plasma are preferable. Here, we determined fetal sex at 9-12 weeks of gestation using PCR of cff-DNA in three pregnant carriers of Duchenne muscular dystrophy. The fetal sex was accurately determined in all three cases, as confirmed by ultrasound and amniocentesis at 16 weeks (for the two female fetuses) and CVS at 12 weeks (for the one male fetus). This procedure could avoid unnecessary CVS in female fetuses.

Effect of labor on postpartum clearance of cell-free fetal DNA from the maternal circulation

OBJECTIVE

The aim of this study was to compare the effect of mode of delivery on the postpartum clearance of cell-free fetal (cff) DNA.

METHODS

Women who gave birth to a single-term male infant by any mode of delivery had blood collected on three occasions: within 3 h of birth, on day 1-2 postpartum and at 2 weeks postpartum. The SRY sequence was used as a marker of cff DNA, and was detected using conventional PCR.

RESULTS

Eighty-seven women were included in the study. There were 28 women in the elective caesarean section group and 59 in the labor group. Cell-free fetal DNA was detected in 38/87 (44%) of women within 3 h of birth. There was a significant difference between the group that labored and the group that did not (54 vs 21%, p = 0.003). Twelve percent of women who labored had persistent cff DNA on day 1-2 postpartum, compared with none of the women who delivered without labor. No woman had DNA that persisted up to 2 weeks postpartum.

CONCLUSION

The presence of labor increases the rate of detectable DNA in women within 3 h of birth and on day 1-2 postpartum. Postpartum clearance was completed by 2 weeks in all women tested regardless of mode of delivery.

Noninvasive prenatal diagnosis of aneuploidy using cell-free nucleic acids in maternal blood: promises and unanswered questions

The discovery of cell-free fetal (cff) DNA and RNA in the maternal circulation has driven developments in noninvasive prenatal diagnosis (NIPD) for the past decade. Detection of paternally derived alleles in cff DNA is becoming well established. Now much interest is focussing on NIPD of fetal chromosomal abnormalities, such as trisomy 21, which is a considerable challenge because this demands accurate quantitative measurements of the amounts of specific cff DNA or cff RNA sequences in maternal blood samples. Emerging strategies for distinguishing and quantifying the fetal nucleic acids in the maternal circulation promise continued development of the field, and pose a number of unanswered questions.

Placenta Accreta: A Review of Current Advances in Prenatal Diagnosis

Placenta accreta is a life-threatening obstetrical condition requiring a multidisciplinary approach. Despite identified obstetrical risk factors, the diagnosis is often made at the time of delivery. Recent advances in biology could allow a prenatal screening of placenta accreta with the identification of biological markers in maternal blood including cell-free fetal DNA, placental mRNA, and DNA microarray. These promising technologies can detect the presence of anomalies and should play a future role in developing a better understanding of placental invasion. Ultrasound imaging is popular due to its low cost and accessibility and widely used for the screening of placenta location and potential abnormal development. This exam is associated with high sensitivity and specificity for diagnosis of placenta accreta when specific defined criteria are used for the diagnosis. A placental MRI provides a morphological description, as well as recently demonstrated topographical information that optimizes diagnosis and surgical management. The screening of placenta accreta should be improved with the use of a combination of these diagnostic techniques and benefit high-risk populations with a reduction in morbidity.

Polymerase-chain-reaction-based detection of fetal rhesus D and Y-chromosome-specific DNA in the whole blood of pregnant women during different trimesters of pregnancy

OBJECTIVE

The aim of this study was to determine whether or not a noninvasive procedure utilizing maternal peripheral blood as the source of DNA and polymerase chain reaction (PCR) could be used to detect fetal rhesus D (RhD) status as well as fetal gender during different gestational stages of pregnancy.

MATERIALS AND METHODS

Maternal blood samples were obtained from 54 RhD-negative pregnant women during the first trimester (6-13 weeks, n = 14), second trimester (14-26 weeks, n = 26) and third trimester (27-40 weeks, n = 14). Genomic DNA was extracted from the whole blood and analyzed by seminested and nested PCR for detection of DNA sequences corresponding to RhD (n = 54) and Y chromosome (n = 48) using RhD and Y-chromosome-specific oligonucleotide primers, respectively. The seminested/nested PCR results were compared with the RhD status and gender of the babies after delivery.

RESULTS

The sensitivity and specificity of seminested PCR for detection of fetal RhD positivity in whole blood of pregnant women were 81 and 100%, respectively, while the sensitivity and specificity of nested PCR for detection of male fetuses, using Y-chromosome-specific DNA as a marker, were 96 and 91%, respectively. There were no significant differences in the PCR results with samples obtained from women at different gestational stages of pregnancy.

CONCLUSION

Seminested and nested PCRs for detection of fetal RhD and gender status, respectively, by using the blood of pregnant women during different gestational stages of pregnancy, are reliable noninvasive procedures with high sensitivity and specificity.

Use of maternal plasma for non-invasive prenatal diagnosis of fetal ABO genotypes

BACKGROUND

Measurement of free fetal DNA in maternal plasma opened a door for non-invasive prenatal diagnosis. Prenatal diagnosis of fetal ABO genotypes can provide a basis for the prevention and therapy of maternal-fetal incompatibility. We identified fetal ABO genotypes using fetal DNA in plasma from pregnant women with blood group O. The aim of the study was to investigate the accuracy and feasibility of this method.

METHODS

A total of 105 blood group O women in middle or late pregnancy were enrolled. Fetal DNA in maternal plasma and genomic DNA in umbilical vein blood from newborns were extracted using a QIAamp DNA Blood Kit. DNA was amplified to identify ABO genotypes by PCR with sequence-specific primers (PCR-SSP). The genotype results were evaluated using serologic tests for ABO phenotyping.

RESULTS

Using DNA from umbilical vein blood, ABO genotypes of 105 newborns were successfully identified by PCR-SSP. Using fetal DNA from maternal plasma, 88.6% (93/105) fetal ABO genotypes was correct; 12 false results were from 66 pregnant women with fetuses of type non-O. The accuracy in middle pregnancy was lower than that in late pregnancy, although the difference was not significant (0.05<p<0.10).

CONCLUSIONS

It is feasible to use measurement of fetal DNA in plasma from pregnant women with blood group O for prenatal diagnosis of fetal ABO genotypes. The method is useful for the diagnosis and therapy of ABO maternal-fetal incompatibility and hemolytic disease of the newborn.

Prenatal diagnosis using cell-free nucleic acids in maternal body fluids: A decade of progress

The ability to detect cell-free fetal nucleic acids in pregnant women has greatly evolved over the past decade. Dozens of papers have explored the biology, kinetics, and clinical significance of both cell-free fetal DNA and mRNA in the maternal circulation. As a result, our overall understanding of fetal nucleic acid trafficking has expanded. To date, two applications, gender determination and fetal RhD status, have translated into clinical medicine. However, with advanced molecular techniques such as mass spectrometry, real-time quantitative polymerase chain reaction, and gene expression arrays, the ease with which fetal genes can be detected within the mother has greatly improved. Newly identified placental and fetal mRNA transcripts as well as an epigenetically modified placental DNA marker, maspin, have universal applicability. Global expression analyses of fetal mRNA in both amniotic fluid and blood provide new insights into fetal development and pathology. Prenatal diagnosis is poised to evolve from detection of aneuploidy to detection of deviation from normal development, which should provide novel opportunities for fetal treatment.

Evaluation of prenatal RHD typing strategies on cell-free fetal DNA from maternal plasma

BACKGROUND

The discovery of cell-free fetal DNA in maternal plasma led to the development of assays to predict the fetal D status with RHD-specific sequences. Few assays are designed in such a way that the fetus can be typed in RHDpsi mothers and that RHDpsi fetuses are correctly typed. Owing to the limited knowledge about the mechanism responsible for the presence of fetal DNA in maternal plasma, precautions in developing prenatal genotyping strategies must be made.

STUDY DESIGN AND METHODS

Real-time quantitative (RQ)-polymerase chain reaction (PCR) assays were developed for prenatal diagnostic use with cell-free fetal DNA from maternal plasma. An RQ-PCR assay on RHD exon 5 (amplicon 361 bp), negative on RHDpsi, was developed with genomic DNA and evaluated with cell-free fetal DNA. A previously published RHD exon 5 RQ-PCR (amplicon 82 bp) was duplexed with an in-house developed RHD exon 7 RQ-PCR and evaluated with cell-free fetal DNA from pregnant D-RHDpsi+ women.

RESULTS

The RHD exon 5 361 bp assay showed on cell-free plasma DNA from D- women carrying a D+ fetus, low amplification levels, resulting in high Ct values and false-negative results. Owing to fragmentation of cell-free plasma DNA, too few DNA stretches of sufficient length (> 360 bp) are present. The RHD exon 5 82 bp and exon 7 RQ-PCR duplex was evaluated with RHDpsi+ cell-free plasma DNA and showed complete specificity and maximal sensitivity.

CONCLUSION

Assays designed for prenatal genotyping should be developed and evaluated on cell-free plasma DNA. Prenatal RHD typing is accurate with the RHD exon 5 82 bp and exon 7 duplex strategy.

Identification of fetal gender in maternal blood is a helpful tool in the prenatal diagnosis of haemophilia

Fetal DNA identification in maternal circulation has provided a new approach for non-invasive prenatal diagnosis. However, fetal DNA can persist in maternal blood long after the delivery, severely hampering this possibility. We addressed the issue of fetal DNA persistence in maternal blood. Thus, we investigated cell-free fetal DNA as a reliable approach in prenatal diagnosis of haemophilia. Forty non-pregnant women, who had had at least a male fetus, 29 control pregnant women, and 14 pregnant women, carriers of hemophilia A or B. The assessment of Y-chromosomal sequences was performed by analysing SRY and amelogenin genes using PCR-based techniques. A protocol consisting of double centrifugation at full speed followed by plasma filtration hampered the detection of Y chromosome-specific sequence in non-pregnant women. In 29 control pregnant women, blinded determination of fetal sex confirmed the specificity and sensitivity of the method applied. In 14 pregnant carriers of hemophilia, the investigation revealed a male fetus in nine pregnancies. Excluding the three cases in which a spontaneous miscarriage occurred, the sensitivity and specificity of fetal sex prediction by SRY and amelogenin gene analyses were both 100% as compared with the invasive approach and the fetal sex outcome at birth (six males and five females). Because of its high accuracy in prediction, fetal gender determination with cell-free fetal DNA in maternal plasma may be a useful tool in prenatal diagnosis of haemophilia allowing for the avoidance of invasive procedures for female fetuses.

Fetal blood group genotyping from DNA from maternal plasma: an important advance in the management and prevention of haemolytic disease of the fetus and newborn

The cloning of blood group genes and subsequent identification of the molecular bases of blood group polymorphisms has made it possible to predict blood group phenotypes from DNA with a reasonable degree of accuracy. The major application of this technology, which has now become the standard of care, is the determination of a fetal RHD genotype in women with anti-D, to assess whether the fetus is at risk of haemolytic disease of the fetus and newborn (HDFN). Initially, the procurement of fetal DNA required the invasive procedures of amniocentesis or chorionic villus sampling. Since the discovery of fetal DNA in maternal plasma in 1997, the technology of detecting an RHD gene in this very small quantity of fetal DNA has developed rapidly, so that non-invasive fetal D typing can now be provided as a diagnostic service for D-negative pregnant women with anti-D. Within a few years, it is probable that fetuses of all D-negative pregnant women will be tested for RHD, to establish whether the mother requires antenatal anti-D immunoglobulin prophylaxis.

Circulating Fetal DNA: Its Origin and Diagnostic Potential—A Review

OBJECTIVE

In contrast to the traditional teaching that the placenta forms an impermeable barrier, multiple studies show that both intact fetal cells and cell-free nucleic acids circulate freely in maternal blood. Complications of pregnancy, such as pre-eclampsia, or fetal cytogenetic abnormalities, such as trisomy 21, increase transfusion of both intact fetal cells and cell-free fetal nucleic acids into the maternal circulation. The objective of our research is to show that abnormal feto-maternal trafficking of nucleic acids is associated with fetal and placental pathology, and that these observations may lead to novel non-invasive diagnostic and screening tests.

METHODS

Real-time quantitative PCR amplification of DYS1 is used to measure the levels of male fetal DNA in case-control sets of serum or plasma taken from pregnant women. In our laboratory, we use DYS1, a Y-chromosome specific gene, as a uniquely fetal DNA marker for the development of gestation-specific normal values and theoretical models.

RESULTS

Women carrying fetuses with trisomies 21 or 13 (but not 18) have increased levels of fetal DNA in their fresh or archived serum and/or plasma samples. Women destined to develop pre-eclampsia have a characteristic bi-phasic elevation of cell-free fetal DNA that precedes clinical symptoms. Data obtained from a variety of clinical scenarios suggest that the placenta is the predominant source of the circulating fetal nucleic acids, although apoptotic haematopoietic cells may contribute to the pool as well.

CONCLUSIONS

Fetal cell-free DNA is elevated in a number of conditions associated with placental pathology. Widespread clinical implementation of fetal DNA as a screening tool awaits discovery of a reliable gender-independent marker, which may be DNA polymorphisms, epigenetic markers, or mRNA. Fetal cell-free nucleic acids have potential for non-invasive monitoring of placental pathology.

Earliest gestational age for fetal sexing in cell-free maternal plasma

OBJECTIVES

To evaluate at what gestational age fetal DNA can reliably be detected at the earliest in maternal plasma.

METHODS

We performed consecutive blood sampling in the first trimester of pregnancy in 17 women who were pregnant after in vitro fertilization (IVF) or intrauterine insemination (IUI). DNA was isolated and the Y-chromosome specific SRY was amplified by real-time polymerase chain reaction (PCR). We likewise studied 31 women prior to invasive prenatal diagnosis procedures for test validation purposes. All test results were compared to cytogenetic sex or sex at birth.

RESULTS

The earliest SRY detection was at a gestational age of 5 weeks and 2 days. In none of 4 pregnancies ending in a miscarriage was SRY detected. We detected SRY in maternal plasma in 1 of 2 patients (50%) carrying a male fetus at a gestational age of 5 weeks, in 4 of 5 (80%) at a gestational age of 7 weeks, in 4 of 4 (100%) at a gestational age of 9 weeks. In all 7 women pregnant with a male fetus, the correct fetal sex was detected by 10 weeks. In none of the 6 patients who delivered a girl was SRY detected. In the validation group, SRY was detected in 13 of the 13 male, and none of the 18 female fetuses.

CONCLUSIONS

We conclude that real-time PCR of the SRY gene promises to be a reliable technique for early fetal sexing in maternal plasma.