Quantitative analysis of DNA levels in maternal plasma in normal and Down syndrome pregnancies

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.

Cell-free fetal nucleic acids as prenatal biomarkers

INTRODUCTION

Cell-free fetal nucleic acids in maternal plasma or serum have become important tools in the pursuance of new methods for non-invasive prenatal diagnosis, such as the determination of fetal blood groups and fetal gender. During these pioneering explorations, elevations in the concentration of these new-found biological analytes were noted in several pregnancy-related disorders, including preterm labor, pre-eclampsia and malimplantation. As these elevations appeared to occur before onset of clinical symptoms, it was proposed that such analyses might assist in screening for at-risk pregnancies. A major problem with these early studies is that they relied on the quantitation of Y-chromosome-specific gene sequences, and as such could be applied only in those cases where the fetus was male. Recent developments that might permit gender-independent analysis include epigenetic markers, as well as the analysis of cell-free placentally derived mRNA species.

AREAS COVERED

This article focuses specifically on prognostic markers, which enable at-risk pregnancies to be identified, allowing the modification of pregnancy management and in turn improvement of pregnancy outcome. The authors also provide their opinion on the progress and future challenges that lie ahead.

EXPERT OPINION

Accurate quantification of fetal nucleic acids and the specificity of these elevations for particular disorders remain controversial issues. Regarding the multifactorial etiology of some pregnancy disorders, the use of fetal nucleic acids as prenatal markers is restricted to well-defined high-risk groups.

Prenatal sonographic features of fetuses in trisomy 13 pregnancies. IV

Prenatal ultrasound is a powerful tool to detect structural abnormalities associated with the fetuses in trisomy 13 pregnancies. This article provides a comprehensive review of the prenatal sonographic markers of trisomy 13 in the first trimester, including fetal nuchal translucency thickness, fetal heart rate, fetal nasal bone, fetal tricuspid regurgitation, ductus venous flow, fetal crown-rump length, fetal trunk and head volume, fetal frontomaxillary facial angle, gestational sac volume and umbilical cord diameter, along with biochemical markers such as maternal serum free beta-human chorionic gonadotropin, maternal serum pregnancy-associated plasma protein-A, maternal serum placental growth factor, and the fetal and total cell-free DNA concentration in the maternal circulation.

Persistence of male hematopoietic CD34+ cells in the circulation of women does not affect prenatal diagnostic techniques

OBJECTIVE

We aimed to verify whether fetal microchimerism, because of persisting fetal hematopoietic CD34(+) cells from previous pregnancies, could interfere with the development of genetic tests based on using these cells, isolated from maternal blood for the diagnosis of fetal aneuploidies.

STUDY DESIGN

CD34(+) cells, isolated from blood of parous women with at least 1 son and nulliparous women, were analyzed by using qualitative polymerase chain reaction (PCR), quantitative PCR, and fluorescence in situ hybridization (FISH) to establish whether these molecular techniques are concurrently capable of detecting circulating male DNA.

RESULTS

By qualitative PCR, male DNA was found both in parous and nulliparous women, whereas by quantitative PCR and FISH analyses, no male DNA or male nuclei were revealed except in 1 cultured CD34(+) sample from a nulliparous woman.

CONCLUSION

Fetal hematopoietic CD34(+) cells can be used in the noninvasive prenatal testing of fetal aneuploidies because the presence of fetal microchimerism does not affect fetal diagnosis in current pregnancies.

Prenatal diagnosis: update on invasive versus noninvasive fetal diagnostic testing from maternal blood

The modern obstetrics care includes noninvasive prenatal diagnosis testing such as first trimester screening performed between 11 and 14 weeks' gestation and second trimester screening performed between 15 and 20 weeks. In these screening tests, biochemical markers are measured in the maternal blood with or without ultrasound for fetal nuchal translucency with reported accuracy of up to 90%. Invasive procedures, including amniocentesis or chorionic villi sampling, are used to achieve over 99% accuracy. During these procedures direct fetal material is examined and, therefore, these tests are highly accurate with the caveat of a small risk for pregnancy loss. Much research now focuses on other noninvasive highly accurate and risk-free tests that will identify fetal material in the maternal blood. Fetal cells and fetal DNA/RNA provide fetal information but are hard to find in an overwhelming background of maternal cells and in the absence of specific fetal cell markers. The most experience has been accumulated with fetal rhesus and fetal sex determination from maternal blood, with an accuracy of up to 100% by using gene sequences that are absent from maternal blood. Although not clinically applicable yet, fetal cells, fetal DNA/RNA and fetal proteomics in combination with cutting edge technology are described to prenatally diagnose aneuploidies and single-gene disorders.

Non-invasive fetal sex determination: impact on clinical practice

Prenatal fetal sex determination is undertaken in women at high risk of serious genetic disorders affecting a specific sex. Traditionally, this is undertaken by invasive testing, usually chorionic villus sampling, which carries a risk of miscarriage of around 1%. The identification of cell-free fetal DNA in the maternal circulation has allowed the development of 'non-invasive prenatal diagnostic tests', which permit fetal sex determination without risk to the pregnancy.

Circulating nucleic acids in plasma/serum

Since the discovery of circulating nucleic acids in plasma in 1948, many diagnostic applications have emerged. For example, diagnostic and prognostic potentials of circulating tumour-derived DNA have been demonstrated for many types of cancer. The parallel development of fetal-derived DNA detection in maternal plasma has opened up the possibility of non-invasive prenatal diagnosis and monitoring of many pregnancy-associated disorders. In this regard, non-invasive fetal rhesus blood group genotyping has already been translated to clinical practice. Other applications of circulating DNA in traumatology and transplant monitoring have also been reported. The more recent discoveries of circulating tumour-derived RNA and fetal-derived RNA have proven to be equally important as their DNA counterparts. Successful prenatal diagnosis of Down's syndrome by fetal RNA analysis has recently been reported. However, the definite origin and release mechanisms of circulating nucleic acids have remained incompletely understood, with cell death being suggested to be associated with such nucleic acid release. Pre-analytical standardisation will become increasingly relevant when comparing data from different laboratories. In conclusion, studies of circulating nucleic acids have promised exciting developments in molecular diagnostics in the years to come.

Elevated levels of total (maternal and fetal) β-globin DNA in maternal blood from first trimester pregnancies with trisomy 21

BACKGROUND

Elevated levels of circulating fetal DNA have been observed in maternal plasma when a trisomy 21 fetus is confirmed. However, these studies have been limited to pregnancies carrying a male fetus. We sought to quantify total (fetal and maternal) DNA from dried blood spots (DBS) for use as an additional factor in multi-parameter prenatal screening for aneuploidy.

METHODS

Maternal DBS were obtained from the NICHD-sponsored multi-center cohort (BUN) study. Seventeen confirmed trisomy 21 (mean gestational age 12.23 +/- 0.77 weeks) cases were each matched by gestational age to euploid controls (n = 30). DNA was extracted and quantitative PCR was performed to measure four non-chromosome 21 loci, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (12p13), beta-globin (11p15.5), beta-actin (7p15-12) and p53 (17p13.1).

RESULTS

Beta-globin DNA levels were significantly elevated (P = 0.003) in 13 of 17 trisomy 21 cases (4.08 +/- 1.78 Geq/ml x 10(5)) compared with matched controls (2.35 +/- 1.84 Geq/ml x 10(5)). Following conversion of beta-globin concentrations into multiples of the median (MoM), MoM for trisomy 21 cases was 2.8 compared with 1.0 in euploid cases. No significant differences in levels of circulating GAPDH, beta-actin and p53 sequences were detected.

CONCLUSIONS

This work demonstrates differential levels of circulating beta-globin DNA in maternal blood of euploid and trisomy 21 cases. Sequence-specific quantification could provide an additional measure to improve non-invasive methods of prenatal screening to detect trisomy 21 using dried blood. Beta-globin in particular is an attractive biomarker that could contribute to enhance multiple serum parameter testing in the first trimester.

Reduction in diagnostic and therapeutic interventions by non-invasive determination of fetal sex in early pregnancy

OBJECTIVE

This study reviews our clinical experience of non-invasive techniques for early sex determination. It assesses the effectiveness of these techniques at reducing invasive prenatal testing for X-linked genetic disease or for ambiguous development of the external genitalia.

METHODS

A prospective cohort study of 30 pregnancies was referred to a tertiary unit for prenatal diagnosis. Fetal gender was determined using two non-invasive techniques: analysis of free fetal DNA (ffDNA) in maternal plasma and ultrasound visualisation. The results were compared to fetal gender determined by invasive testing or at birth.

RESULTS

Fetal gender was accurately determined by analysis of ffDNA at a mean of 10 + 1 (7 + 6 to 14 + 1) weeks' gestation in all cases. Ultrasound assessment was accurate in 20 of the 23 cases where this was attempted at 12 + 0 (10 + 4 to 14 + 1) weeks' gestation, but could not be determined in the remaining 3 cases. Thirteen of 28 (46%) women chose not to have invasive testing on the basis of these findings.

CONCLUSIONS

Both the techniques appear to offer an accurate means of assessing fetal gender, giving parents the option of avoiding invasive testing in the 50% of cases where the fetus would not be affected. The molecular technique is performed at an earlier gestation, but female fetal status is predicted by a negative test result. Ultrasound cannot be applied until 11 weeks' gestation but diagnostic signs are sought in both sexes. Combining these approaches offers a highly sensitive method of non-invasive determination of gender in high-risk pregnancies. Health professionals, clinical geneticists and genetics associates, in particular, who refer women at high risk should be aware of these non-invasive options for prenatal sex determination.

Free fetal DNA in maternal circulation: a potential prognostic marker for chromosomal abnormalities?

OBJECTIVES

Previous studies on the association of fetal cell-free (cf)DNA levels in maternal circulation have produced conflicting results but the sample sizes were small and based on archived material. We aimed to quantify the levels of fetal and total cfDNA on prospectively collected samples, to understand their correlation with other variables and to clarify their diagnostic value.

METHODS

DNA from pre-CVS maternal plasma was extracted from 264 controls, 72 trisomy 21, 24 trisomy 18, 12 trisomy 13, 16 Turner's syndrome and 8 triploidy first-trimester pregnancies and quantified using real-time PCR. beta-globin was used to determine total cfDNA levels and DYS14 and SRY assays to determine fetal cfDNA levels.

RESULTS

Fetal cfDNA levels (DYS14) showed correlation with crown rump length (CRL) (p = 0.004), BMI (p = 0.01) and storage time (p = 0.007) while there was an inverse correlation of total cfDNA levels with nuchal translucency (NT) (p = 0.001). No significant difference was observed between the levels of fetal cfDNA in controls and aneuploidy cases.

CONCLUSION

Quantification of fetal and total cfDNA in maternal circulation showed inverse correlation between NT and total cfDNA levels. Our results also suggest that fetal cfDNA is not an ideal prognostic marker for chromosomal abnormalities in first-trimester pregnancies.

Non-invasive fetal sex determination using real-time PCR

OBJECTIVE

The aim of this study was to evaluate the specificity and sensitivity of the real-time quantitative PCR method for fetal gender determination in early pregnancy.

METHODS

Blood samples were collected from 46 pregnant women prior to amniocentesis. DNA was extracted from maternal plasma using a QIAmp DNA Blood Mini Kit. DNA samples were subjected to real-time quantitative PCR amplification of SRY (as a fetus-specific marker) and beta-globin (as a marker for total plasma DNA) genes.

RESULTS

The beta-globin gene sequence was detected in all samples. The SRY gene was detected in 25 of 28 plasma samples from women with male fetuses and in none of the 18 samples from women with female fetuses (sensitivity 89.2% and specificity 100%). The fetal gender was correctly determined in 43 (93.5%) of 46 maternal plasma samples. The concentration of the beta-globin gene ranged from 161 to 25,568 genome-equivalents (GE)/mL (median 1051.1), while the concentration of the SRY gene ranged from 5 to 166 GE/mL (median 27.4). The percentage of free fetal DNA ranged from 0.1% to 46.1% (median 2.0%).

CONCLUSION

Amplification of fetal DNA from maternal plasma by real-time quantitative PCR is a promising method for fetal sex determination in early pregnancy. However, further studies are necessary before this procedure can be included into a clinical routine.

Non-invasive diagnosis of fetal sex; utilisation of free fetal DNA in maternal plasma and ultrasound

Non-invasive prenatal diagnosis is now a clinical reality, using both early ultrasound and molecular DNA methods. Technical advances in the sensitivity of the polymerase chain reaction (PCR), coupled with the finding that significant levels of fetal DNA (ffDNA) are found in maternal plasma and serum, has enabled the ready detection of paternally inherited genes or polymorphisms. Routine maternal plasma-based genotyping is now available for the determination of fetal sex and RHD blood group status (Van der Schoot et al., 2003). This review touches briefly on the ultrasound diagnoses and then focuses on the application of free ffDNA for fetal sex determination, indicating the Y-chromosome targets exploited in this strategy and the merits of their utilisation.

Cell-free fetal DNA in maternal blood: kinetics, source and structure

The kinetics and structure of cell-free fetal DNA in maternal plasma is currently under investigation. Plasma fetal DNA seems quite stable albeit cleared rapidly following birth, suggesting continuous fetal DNA release into the maternal circulation during pregnancy. However, to understand better the kinetics of circulating DNA, studies to determine the biological (structural) form in which fetal and maternal DNA exist and the mechanisms underlying variation in plasma are warranted to ensure quantitative diagnostic reliability. It is likely that circulating fetal DNA is released from fetal and/or placental cells undergoing apoptosis. Thus, the majority of fetal DNA is proposed to circulate in membrane-bound vesicles (apoptotic bodies). This review summarizes the latest reports in this field.

Increased total cell-free DNA in the serum of pregnant women carrying a fetus affected by trisomy 21

OBJECTIVE

Analysis of the levels of cell-free fetal and total DNA in serum of women carrying a male fetus affected by trisomy 21, and comparison of these levels with those in women carrying a normal male fetus.

METHODS

DNA was extracted from archived second-trimester maternal serum samples collected as part of a prenatal screening program. A total of 10 cases with trisomy 21 male fetuses were compared with 10 controls (male fetuses) with samples matched for duration of storage and gestational age. Real-time quantitative PCR of the SRY and albumin genes was used to quantify fetal and total DNA respectively.

RESULTS

The median fetal DNA level in the group of 10 pregnancies with trisomy 21 was 31.98 cell-equivalents per mL compared to 34.06 in the control group. The difference was not significant. The median total DNA level in women with a trisomy 21 fetus was significantly higher (P = 0.029) than that in controls (36 152.6 vs 5832.81 cell-equivalents per mL).

CONCLUSIONS

Although we could not confirm previous studies of an increased amount of fetal DNA in pregnancies affected by trisomy 21, we did find increased levels of total DNA. The possible reasons for these observations are discussed with respect to previous findings. Larger studies are needed to elucidate the true value, if any, of measurement of fetal and total DNA in maternal serum in the context of prenatal screening for chromosomal abnormalities.