Noninvasive prenatal diagnosis of fetal Rhesus D: ready for Prime(r) Time

Sensitivity of fetal RHD screening for safe guidance of targeted anti-D immunoglobulin prophylaxis: prospective cohort study of a nationwide programme in the Netherlands

OBJECTIVE

 To determine the accuracy of non-invasive fetal testing for the RHD gene in week 27 of pregnancy as part of an antenatal screening programme to restrict anti-D immunoglobulin use to women carrying a child positive for RHD DESIGN:  Prospectively monitoring of fetal RHD testing accuracy compared with serological cord blood typing on introduction of the test. Fetal RHD testing was performed with a duplex real time quantitative polymerase chain reaction, with cell-free fetal DNA isolated from 1 mL of maternal plasma The study period was between 4 July 2011 and 7 October 2012. The proportion of women participating in screening was determined.

SETTING

 Nationwide screening programme, the Netherlands. Tests are performed in a centralised setting.

PARTICIPANTS

 25 789 RhD negative pregnant women.

MAIN OUTCOME MEASURES

 Sensitivity, specificity, false negative rate, and false positive rate of fetal RHD testing compared with serological cord blood typing; proportion of technical failures; and compliance to the screening programme.

RESULTS

 A fetal RHD test result and serological cord blood result were available for 25 789 pregnancies. Sensitivity for detection of fetal RHD was 99.94% (95% confidence interval 99.89% to 99.97%) and specificity was 97.74% (97.43% to 98.02%). Nine false negative results for fetal RHD testing were registered (0.03%, 95% confidence interval 0.01% to 0.06%). In two cases these were due to technical failures. False positive fetal RHD testing results were registered for 225 samples (0.87%, 0.76% to 0.99%). Weak RhD expression was shown in 22 of these cases, justifying anti-D immunoglobulin use. The negative and positive predictive values were 99.91% (95% confidence interval 99.82% to 99.95%) and 98.60% (98.40% to 98.77%), respectively. More than 98% of the women participated in the screening programme.

CONCLUSIONS

 Fetal RHD testing in week 27 of pregnancy as part of a national antenatal screening programme is highly reliable and can be used to target both antenatal and postnatal anti-D immunoglobulin use.

Recent advances in prenatal genetic screening and testing

The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.

Maternal mosaicism of sex chromosome causes discordant sex chromosomal aneuploidies associated with noninvasive prenatal testing

OBJECTIVE

To investigate the clinical efficiency of noninvasive prenatal test (NIPT) identifying fetal chromosomal aneuploidies.

MATERIALS AND METHODS

In the present study, 917 women with high-risk pregnancies were invited to participate in an NIPT trial based on an Illumina HiSeq massively parallel sequencing platform. Abnormal cases in NIPT were validated by karyotyping and fluorescence in situ hybridization (FISH) analysis. All of the participants' infants were examined clinically and followed up for at least 6 months.

RESULTS

A total of 35 (3.82%) high-risk pregnancies were detected with abnormal results in NIPT, which included 25 cases (2.73%) of trisomy 21 (Tri21), four cases (0.44%) of trisomy 18 (Tri18), four cases (0.44%) of Turner syndrome (45, X), one cases (0.11%) of Klinefelter's syndrome (47, XXY), and one cases (0.11%) with lower X chromosome concentration. Further validation indicated that one case of Tri18 and the case with lower X chromosome concentration were false positive results (0.22%) in NIPT. Furthermore, it was found that the false positive case with lower X chromosome concentration in NIPT was caused by maternal sex chromosomal mosaicism (45, X and 46, XX).

CONCLUSION

Our findings indicated that maternal mosaicism of sex chromosome could cause discordant sex chromosomal aneuploidies associated with NIPT. We highly recommended that maternal karyotype should be confirmed for the cases with abnormal results in NIPT.

Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex

BACKGROUND

There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT).

METHODS

We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing.

RESULTS

Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%–100%) cases of trisomy 21, 16/16 (95% CI, 79.4%–100%) cases of trisomy 18, 5/5 (95% CI, 47.8%–100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%–100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%–100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction.

CONCLUSIONS

The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.

Epsilon globin gene expression in developing human fetal tissues

OBJECTIVE

The discovery of free fetal DNA in plasma of pregnant women has opened a new avenue for non-invasive prenatal diagnosis. We hypothesized that epsilon (ɛ)-globin gene expression could serve as a positive control for the presence of fetal nucleic acid.

STUDY DESIGN

We measured ɛ-globin mRNA in human fetal tissues and compared concentrations with that measured in adult non-pregnant and pregnant samples. Total RNA was isolated from fetal marrow, liver, blood, and placenta (10-24 weeks gestation), from adult peripheral blood mononuclear cells, and from maternal plasma. RNA was reverse transcribed and quantitative polymerase chain reaction performed for ɛ-globin expression.

RESULTS

ɛ-globin gene expression was detected in all fetal samples, was detected in plasma of pregnant women, but was negligible in non-pregnant samples. Relative ɛ-globin gene expression was significantly greater in fetal blood compared to fetal liver, and was minimally expressed in placenta. ɛ-globin gene expression decreased at the highest gestational ages in fetal blood, while expression was greatest at 15-19 weeks in fetal marrow.

CONCLUSION

Fetal ɛ-globin gene expression is significantly greater than adult expression and is increased in maternal plasma compared to non-pregnant samples. ɛ-globin gene expression might serve as a positive control when determining the presence of fetal nucleic acid in total nucleic acid isolated from maternal plasma.

Correlation between the Amount of Anti-D Antibodies and IgG Subclasses with Severity of Haemolytic Disease of Foetus and Newborn

AIM

The aim of this study was to investigate the influence of subclasses to IgG anti-D on the intensity of hemolytic disease of fetus and newborn (HDFN) at 45 fetuses/newborns with symptoms of mild and severe HDFN in Republic of Macedonia.

MATERIAL AND METHODS

In retrospective and prospective studies, in a period of 10 years, from 2004 to 2014, there have been immunohemathology tests performed on 22 009 samples on serums of pregnant women.

RESULTS

At 37.78% of the total number of tested patients, IgG1 and IgG3 was the reason for severe HDFN. At 17.77% of the total number of tested patients, which had only IgG1detected, was the reason for serious intensity of HDFN. The correlation of the titer to anti-D antibodies in the mother's serum and the intensity of HDFN were researched in 48 newborns. The titers between 1:8 and 1:32 resulted in 3 cases of HDFN with symptoms of severe disease and in 4 cases there were no signs of HDFN. At 12 women that had a titre between 1:32 and 1:512, five of the newborns developed severe HDFN, and seven had symptoms of mild and weak intensity form. In 3 cases the titer was higher than 512, and out of them one newborn had weak symptoms of HDFN, one developed severe HDFN and one ended with foetal death. Only in one case the titer reached a value higher than 1000, and it ended with a fetal death.

CONCLUSIONS

The titers of the pregnant women serum those are lower than 32 and those higher than 1000 can well predict HDFN. The titers of anti-D antibodies between 64 and 512 have no exact predictive value. IgG1 and IgG3 subclasses of anti-D have no predictive value by themselves, and cannot foresee the outcome of HDFN. The research study results suggest that IgG1 and IgG3 should be included in a multi - parameter protocol for evaluation of the HDFN intensity. They can give a real assessment of the expected HDFN intensity in combination with the titer hight and the significance of the antibodies.

Non-Invasive Prenatal RHD Genotyping Using Cell-Free Fetal DNA from Maternal Plasma: An Italian Experience

BACKGROUND

This study assessed the diagnostic accuracy of a non-invasive approach to fetal RHD genotyping using cell-free fetal DNA in maternal plasma and a combination of methodological strategies.

METHODS

Real-time PCR (qPCR) was performed on 216 RhD-negative women between weeks 10+0 and 14+6 of gestation (1st qPCR). qPCR was repeated (2nd qPCR) to increase the amount of each sample for analysis, on 95 plasma aliquots that were available from first trimester blood collection (group 1) and on 13 samples that were collected between weeks 18+0 and 25+6 of gestation (group 2). qPCR was specific for exons 5 and 7 of the RHD gene (RHD5 and RHD7). The results were interpreted according to the number of positive replicates of both exons.

RESULTS

1st qPCR: diagnostic accuracy was of 93.3%. Diagnostic accuracy increased from 90.5% (1st qPCR) to 93.7% (2nd qPCR) in group 1 and from 84.6% (1st qPCR) to 92.3% (2nd qPCR) in group 2. These increments were not statistically significant.

CONCLUSION

Our approach to RHD genotyping in early pregnancy yielded high diagnostic accuracy. Increasing the amount of DNA analyzed in each sample did not improve significantly the diagnostic accuracy of the test.

Non-invasive prenatal testing: ethics and policy considerations

New technologies analyzing fetal DNA in maternal blood have led to the wide commercial availability of non-invasive prenatal testing (NIPT). We present here for clinicians the ethical and policy issues related to an emerging practice option. Although NIPT presents opportunities for pregnant women, particularly women who are at increased risk of having a baby with an abnormality or who are otherwise likely to access invasive prenatal testing, NIPT brings significant ethics and policy challenges. The ethical issues include multiple aspects of informed decision-making, such as access to counselling about the possible results of the test in advance of making a decision about participation in NIPT. Policy considerations include issues related to offering and promoting a privately available medical strategy in publicly funded institutions. Ethics and policy considerations merge in NIPT with regard to sex selection and support for persons living with disabilities.

Noninvasive prenatal screening for fetal trisomies 21, 18, 13 and the common sex chromosome aneuploidies from maternal blood using massively parallel genomic sequencing of DNA

OBJECTIVE

The objective of this study was to validate the clinical performance of massively parallel genomic sequencing of cell-free deoxyribonucleic acid contained in specimens from pregnant women at high risk for fetal aneuploidy to test fetuses for trisomies 21, 18, and 13; fetal sex; and the common sex chromosome aneuploidies (45, X; 47, XXX; 47, XXY; 47, XYY).

STUDY DESIGN

This was a prospective multicenter observational study of pregnant women at high risk for fetal aneuploidy who had made the decision to pursue invasive testing for prenatal diagnosis. Massively parallel single-read multiplexed sequencing of cell-free deoxyribonucleic acid was performed in maternal blood for aneuploidy detection. Data analysis was completed using sequence reads unique to the chromosomes of interest.

RESULTS

A total of 3430 patients were analyzed for demographic characteristics and medical history. There were 137 fetuses with trisomy 21, 39 with trisomy 18, and 16 with trisomy 13 for a prevalence rate of the common autosomal trisomies of 5.8%. There were no false-negative results for trisomy 21, 3 for trisomy 18, and 2 for trisomy 13; all 3 false-positive results were for trisomy 21. The positive predictive values for trisomies 18 and 13 were 100% and 97.9% for trisomy 21. A total of 8.6% of the pregnancies were 21 weeks or beyond; there were no aneuploid fetuses in this group. All 15 of the common sex chromosome aneuploidies in this population were identified, although there were 11 false-positive results for 45,X. Taken together, the positive predictive value for the sex chromosome aneuploidies was 48.4% and the negative predictive value was 100%.

CONCLUSION

Our prospective study demonstrates that noninvasive prenatal analysis of cell-free deoxyribonucleic acid from maternal plasma is an accurate advanced screening test with extremely high sensitivity and specificity for trisomy 21 (>99%) but with less sensitivity for trisomies 18 and 13. Despite high sensitivity, there was modest positive predictive value for the small number of common sex chromosome aneuploidies because of their very low prevalence rate.

Noninvasive prenatal screening by next-generation sequencing

Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.

Non-Invasive Screening Tools for Down's Syndrome: A Review

Down's syndrome (DS) is the most common genetic cause of developmental delay with an incidence of 1 in 800 live births, and is the predominant reason why women choose to undergo invasive prenatal diagnosis. However, as invasive tests are associated with around a 1% risk of miscarriage new non-invasive tests have been long sought after. Recently, the most promising approach for non-invasive prenatal diagnosis (NIPD) has been provided by the introduction of next generation sequencing (NGS) technologies. The clinical application of NIPD for DS detection is not yet applicable, as large scale validation studies in low-risk pregnancies need to be completed. Currently, prenatal screening is still the first line test for the detection of fetal aneuploidy. Screening cannot diagnose DS, but developing a more advanced screening program can help to improve detection rates, and therefore reduce the number of women offered invasive tests. This article describes how the prenatal screening program has developed since the introduction of maternal age as the original "screening" test, and subsequently discusses recent advances in detecting new screening markers with reference to both proteomic and bioinformatic techniques.

Prenatal screening methods for aneuploidies

Aneuploidies are a major cause of perinatal morbidity and mortality. Therefore, it is the most common indication for invasive prenatal diagnosis. Initially, screening for aneuploidies started with maternal age risk estimation. Later on, serum testing for biochemical markers and ultrasound markers were added. Women detected to be at high-risk for aneuploidies were offered invasive testing. New research is now focusing on non-invasive prenatal testing using cell-free fetal DNA in maternal circulation. The advantage of this technique is the ability to reduce the risk of miscarriage associated with invasive diagnostic procedures. However, this new technique has its own set of technical limitations and ethical issues at present and careful consideration is required before broad implementation.

Circulating cell-free fetal DNA for the detection of RHD status and sex using reflex fetal identifiers

OBJECTIVE

To determine the sensitivity and specificity of circulating cell-free fetal DNA in determining the fetal RHD status and fetal sex.

METHODS

Maternal blood was collected in each trimester of pregnancy from RhD negative nonalloimmunized women. Whole blood was centrifuged, separated into plasma and buffy coat, and frozen at -80°C. DNA analysis was conducted via allele-specific primer extensions for exons 4, 5, and 7 of the RHD gene and for a 37-base pair insertion in exon 4 (RHD pseudogene; psi) three Y-chromosome sequences (SRY, DBY, and TTY2), and an extraction control (TGIFL-like X/Y). RhD serotyping on cord blood and gender assessment of the newborns were entered into a Web-based database.

RESULTS

One hundred twenty women were enrolled. The median gestational age at the first venipuncture was 12.4 (range: 10.6-13.9) weeks with 120 samples drawn; 118 samples were drawn at 17.6 (16-20.9) weeks; and 113 samples at 28.7 (27.9-33.9) weeks. Overall accuracy for RHD was 99.1%, 99.1%, and 98.1% for each trimester and was 99.1%, 99.1%, and 100% for fetal sex determination.

CONCLUSIONS

Fetal RHD genotyping and sex can be very accurately determined in all three trimesters using circulating cell-free fetal DNA in the maternal circulation.

MeDIP real-time qPCR of maternal peripheral blood reliably identifies trisomy 21

OBJECTIVE

To reevaluate the efficiency of the 12 differentially methylated regions (DMRs) used in the methylated DNA immunoprecipitation (MeDIP) real-time quantitative polymerase chain reaction (real-time qPCR) based approach, develop an improved version of the diagnostic formula and perform a larger validation study.

METHODS

Twelve selected DMRs were checked for copy number variants in the Database of Genomic Variants. The DMRs located within copy number variants were excluded from the analysis. One hundred and seventy-five maternal peripheral blood samples were used to reconstruct and evaluate the new diagnostic formula and for a larger-scale blinded validation study using MeDIP real-time qPCR.

RESULTS

Seven DMRs entered the final model of the prediction equation and a larger blinded validation study demonstrated 100% sensitivity and 99.2% specificity. No significant evidence for association was observed between cell free fetal DNA concentration and D value.

CONCLUSION

The MeDIP real-time qPCR method for noninvasive prenatal diagnosis of trisomy 21 was confirmed and revalidated in 175 samples with satisfactory results demonstrating that it is accurate and reproducible. We are currently working towards simplification of the method to make it more robust and therefore easily, accurately, and rapidly reproduced and adopted by other laboratories. Nevertheless, larger scale validation studies are necessary before the MeDIP real-time qPCR-based method could be applied in clinical practice.

From prenatal genomic diagnosis to fetal personalized medicine: progress and challenges

Thus far, the focus of personalized medicine has been the prevention and treatment of conditions that affect adults. Although advances in genetic technology have been applied more frequently to prenatal diagnosis than to fetal treatment, genetic and genomic information is beginning to influence pregnancy management. Recent developments in sequencing the fetal genome combined with progress in understanding fetal physiology using gene expression arrays indicate that we could have the technical capabilities to apply an individualized medicine approach to the fetus. Here I review recent advances in prenatal genetic diagnostics, the challenges associated with these new technologies and how the information derived from them can be used to advance fetal care. Historically, the goal of prenatal diagnosis has been to provide an informed choice to prospective parents. We are now at a point where that goal can and should be expanded to incorporate genetic, genomic and transcriptomic data to develop new approaches to fetal treatment.

Non-invasive prenatal diagnosis of aneuploidies: new technologies and clinical applications

Non-invasive prenatal diagnosis (NIPD) has substantial medical importance as it targets the development of safer and more effective methods to avoid the risk of fetal loss associated with currently used invasive methods. Several approaches have been demonstrated as being proof-of concept for NIPD of chromosomal aneuploidies. These approaches include cell-based and cell-free detection methods, involving the investigation of fetal cells in the maternal circulation, formaldehyde treatment of maternal plasma, DNA methylation studies using sodium bisulfite or restriction enzymes, protein-based studies, identification of fetal-specific mRNAs and digital polymerase chain reaction (PCR) approaches, and recently next-generation sequencing and methylated DNA immunoprecipitation real-time quantitative PCR-based approaches. Although all these NIPD methods have both advantages and limitations, some are moving closer to clinical implementation. Biotechnology companies dedicated to the development of NIPD tests such as the sequencing- or methylation-based approaches are finalizing large clinical trials. It is expected that these new technologies will facilitate safer, more sensitive and accurate prenatal diagnostic tests in the near future. In this review, we highlight the most recent advances in methods for NIPD of aneuploidies, and we discuss their future implications in clinical practice.

Tracking fetal development through molecular analysis of maternal biofluids

Current monitoring of fetal development includes fetal ultrasonography, chorionic villus sampling or amniocentesis for chromosome analysis, and maternal serum biochemical screening for analytes associated with aneuploidy and open neural tube defects. Over the last 15 years, significant advances in noninvasive prenatal diagnosis (NIPD) via cell-free fetal (cff) nucleic acids in maternal plasma have resulted in the ability to determine fetal sex, RhD genotype, and aneuploidy. Cff nucleic acids in the maternal circulation originate primarily from the placenta. This contrasts with cff nucleic acids in amniotic fluid, which derive from the fetus, and are present in significantly higher concentrations than in maternal blood. The fetal origin of cff nucleic acids in the amniotic fluid permits the acquisition of real-time information about fetal development and gene expression. This review seeks to provide a comprehensive summary of the molecular analysis of cff nucleic acids in maternal biofluids to elucidate mechanisms of fetal development, physiology, and pathology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.

Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21

The trials performed worldwide toward noninvasive prenatal diagnosis (NIPD) of Down's syndrome (or trisomy 21) have shown the commercial and medical potential of NIPD compared to the currently used invasive prenatal diagnostic procedures. Extensive investigation of methylation differences between the mother and the fetus has led to the identification of differentially methylated regions (DMRs). In this study, we present a strategy using the methylated DNA immunoprecipitation (MeDiP) methodology in combination with real-time quantitative PCR (qPCR) to achieve fetal chromosome dosage assessment, which can be performed noninvasively through the analysis of fetal-specific DMRs. We achieved noninvasive prenatal detection of trisomy 21 by determining the methylation ratio of normal and trisomy 21 cases for each tested fetal-specific DMR present in maternal peripheral blood, followed by further statistical analysis. The application of this fetal-specific methylation ratio approach provided correct diagnosis of 14 trisomy 21 and 26 normal cases.

Multiplexed analysis of circulating cell-free fetal nucleic acids for noninvasive prenatal diagnostic RHD testing

OBJECTIVE

The objective of the study was the evaluation of a novel multiplex assay to detect fetal Rh blood group D-antigen gene (RHD) loci in maternal plasma from RhD-negative, pregnant women.

STUDY DESIGN

An RHD genotyping assay was designed to detect exons 4, 5, 7, and 10 and RHDΨ (pseudogene) of the RHD gene along with a Y chromosome-specific assay and a generic polymerase chain reaction amplification control. Plasma samples from 150 RhD-negative pregnant women were assayed for fetal RHD genotype using the MassARRAY system.

RESULTS

The fetal RHD status of 148 of 150 samples (98.7%) was correctly classified; 86 (57.3%) and 62 (41.3%) were positive and negative, respectively.

CONCLUSION

This study demonstrates that noninvasive prenatal diagnostics with a single-reaction multiplexed assay is a viable path toward routine characterization of fetal RHD genotypes using circulating cell-free fetal DNA in maternal plasma on the MassARRAY system and is perhaps preferable to serologic testing as currently used clinically.

Molecular genetics and clinical applications for RH

Rhesus is the clinically most important protein-based blood group system. It represents the largest number of antigens and the most complex genetics of the 30 known blood group systems. The RHD and RHCE genes are strongly homologous. Some genetic complexity is explained by their close chromosomal proximity and unusual orientation, with their tail ends facing each other. The antigens are expressed by the RhD and the RhCE proteins. Rhesus exemplifies the correlation of genotype and phenotype, facilitating the understanding of general genetic mechanisms. For clinical purposes, genetic diagnostics of Rhesus antigens will improve the cost-effective development of transfusion medicine.

Insights into fetal and neonatal development through analysis of cell-free RNA in body fluids

The use of cell-free nucleic acids in the circulation of pregnant women for noninvasive prenatal diagnosis is arguably one of the hottest current topics in prenatal medicine. Between 1997 and the present era this field has gone from basic research to clinical application for diagnosis of fetal gender and Rhesus D status. Over the next few years it is likely that noninvasive prenatal diagnosis for Down syndrome will also be possible. Here we summarize current and future clinical applications of analyzing cell-free fetal DNA and RNA in both maternal and neonatal body fluids, including maternal plasma, serum, whole blood, amniotic fluid, and neonatal saliva. We describe methods to evaluate normal and abnormal fetal and neonatal development using gene expression microarrays. We also discuss the ways in which differentially-regulated gene lists can advance knowledge of both fetal and neonatal biology, as well as suggest novel possibilities for fetal and neonatal treatment.

MALDI-TOF mass array analysis of RASSF1A and SERPINB5 methylation patterns in human placenta and plasma

Differences in DNA methylation patterns between placenta and blood cells of pregnant women have been suggested as potential biomarkers for noninvasive prenatal diagnostic strategies, including for common obstetrical complications, such as preeclampsia. New findings in epigenetic origins of fetal or placental disorders may improve our ability for optimal management of these conditions. Using a novel high-throughput mass spectrometry on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass array, we compared the quantitative methylation changes of RASSF1 and SERPINB5 (also known as MASPIN) genes in placenta and plasma samples. We analyzed the methylation status of a total of 3569 CpG dinucleotides on these two genes in 83 different samples: 50 plasma samples (20 from pregnant women and 30 from nonpregnant women) and 33 placenta tissue samples (25 from normal pregnancies and eight from preeclamptic pregnancies). The aim of this study was to assess the utility of epigenetic changes as biomarkers for noninvasive prenatal diagnostic procedures. Using a two-way hierarchical cluster analysis, significantly different methylation levels of the RASSF1 gene were found between placenta (normal and preeclamptic) and plasma samples of pregnant women. Although the SERPINB5 gene was hypomethylated in placenta DNA more than in plasma DNA, it did not demonstrate significant differences between studied groups. The MALDI-TOF mass spectrometry analysis of placenta and plasma DNA methylation patterns may serve as a tool for the study of gender-independent biomarkers in noninvasive prenatal diagnosis.

Sharpening the Tools: A summary of a National Institutes of Health workshop on new technologies for detection of fetal cells in maternal blood for early prenatal diagnosis

In 2003 the National Institute of Child Health and Human Development (NICHD) sponsored a workshop entitled "Sharpening the Tools", which was designed to explore the then current state of prenatal diagnosis and screening using fetal cells in maternal blood. The goals of the workshop were to: review the then current state of the field and assess present capabilities, identify future research needs and challenges in this area, identify promising new and innovative approaches for future exploration, and provide a written summary of the conference for public distribution. The workshop featured brief presentations by experts from a wide range of scientific fields and by innovative bioengineering and technology leaders from academic centers and private industry. The workshop was divided into presentations on target cells, target approaches for separation, genetic and protein analysis, and "out of the box" (bioengineering) approaches. The passage of time since the workshop has allowed an objective assessment of where the research has progressed. A 2006 update on the field is included at the end of the summary.

Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies

The use of epigenetic differences between maternal whole blood and fetal (placental) DNA is one of the main areas of interest for the development of noninvasive prenatal diagnosis of aneuploidies. However, the lack of detailed chromosome-wide identification of differentially methylated sites has limited the application of this approach. In this study, we describe an analysis of chromosome-wide methylation status using methylation DNA immunoprecipitation coupled with high-resolution tiling oligonucleotide array analysis specific for chromosomes 21, 18, 13, X, and Y using female whole blood and placental DNA. We identified more than 2000 regions of differential methylation between female whole blood and placental DNA on each of the chromosomes tested. A subset of the differentially methylated regions identified was validated by real-time quantitative polymerase chain reaction. Additionally, correlation of these regions with CpG islands, genes, and promoter regions was investigated. Between 56 to 83% of the regions were located within nongenic regions whereas only 1 to 11% of the regions overlapped with CpG islands; of these, up to 65% were found in promoter regions. In summary, we identified a large number of previously unreported fetal epigenetic molecular markers that have the potential to be developed into targets for noninvasive prenatal diagnosis of trisomy 21 and other common aneuploidies. In addition, we demonstrated the effectiveness of the methylation DNA immunoprecipitation approach in the enrichment of hypermethylated fetal DNA.

Isolation of serum nucleic acids for fetal DNA analysis: comparison of manual and automated extraction methods

OBJECTIVES

To investigate the performance of an automated system for the extraction of cell-free DNA of maternal and fetal origin from stored serum samples for subsequent quantitative real-time polymerase chain reaction (PCR) analysis.

METHODS

Thirty-two maternal blood samples between the early second trimester and term were obtained. Cell-free DNA was extracted from replicate stored sera using a column-based manual isolation procedure and with an automated system, the MagNA Pure LC Instrument. Real-time quantitative PCR for the ubiquitous glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and male-specific DYS14 loci was performed.

RESULTS

The extraction yields for both total and fetal DNA and the quality of the purified nucleic acids were similar for the automated system or the manual procedure. However, the number of false-negative results in samples collected early in pregnancy was reduced with the automated extraction. Furthermore, the extraction rate by the automated system was highly reproducible over time.

CONCLUSIONS

We validated the use of an automated extraction system for the isolation of fetal DNA from stored serum. This procedure might be exploited in the future for high-throughput non-invasive fetal gene analysis of archived serum samples.

Non-invasive fetal RHD genotyping tests: a systematic review of the quality of reporting of diagnostic accuracy in published studies

Articles reporting the diagnostic accuracy of non-invasive prenatal diagnostic (NIPD) tests for RHD genotyping using fetal material extracted from maternal blood have been published steadily for over a decade. Health care providers in Europe have started to use this technology for management of the small number of sensitised pregnancies (ca. 220-600 per annum in the Netherlands, Germany, France and the UK). Scientists and clinicians are also advocating widespread implementation for the far larger number of non-sensitised RhD-negative pregnancies (ca. 34,000-125,000 per annum in the same countries). Large-scale, prospective trials are only now underway. Estimates of the technical performance of these tests are currently based on results from small-scale studies, together with formal meta-analysis. The issue of early assessment of test performance is one faced by many new genetic tests. As part of a wider study we have investigated the quality of reporting of diagnostic accuracy in publications and produced guidelines for future studies. A systematic search of the literature identified 27 papers which met predefined inclusion criteria. All 27 papers were, first, assessed against an international quality (STARD) checklist for reporting of diagnostic accuracy and, second, against our own in-house NIPD proforma to assess the implications of the quality of reporting specifically for the RhD NIPD test. Authors were found to generally present an optimistic view of NIPD, bearing in mind weaknesses identified in reporting and conduct of their studies and the analysis of results, as evidenced by the low STARD scores. The NIPD proforma identified that specific biases were potentially introduced through selective population sampling and/or failure to report the make-up of the population tested, omission of inconclusive results, inconsistencies in the handling of repeat results on a sample, and lack of adequate controls. These factors would inevitably affect the validity of diagnostic accuracy as reported in individual publications, as well as any subsequent meta-analyses. Together, published reports to date may provide a biased picture of the actual potential of NIPD testing for fetal RHD genotyping. Generalisation of the available evidence on diagnostic accuracy, especially to large-scale implementation of NIPD testing of non-sensitised women, will also require that decision makers consider further aspects such as test reliability and cost of routine testing in clinical practice. It is recommended that all studies of diagnostic accuracy of NIPD tests adhere to the STARD quality checklist in order to improve reporting, thereby, minimising bias and increasing the comparability of studies. Researchers should also consider specific shortcomings for NIPD and avoid selective participant sampling; report population characteristics; report handling of replicate sampling as well as their failure rates; and include controls for genotypes tested in the study. Furthermore, meta-analyses should consider the quality, as well as the sample size, of NIPD studies in their analysis. Larger trials, required to produce results that are valid and meaningful for clinical practice, must also adhere to these reporting standards.

Large-scale blood group genotyping: clinical implications

The molecular background of blood group antigen expression of the major clinically significant blood group antigens has been largely accomplished. Despite this large body of work, blood group phenotype prediction by genotyping has a marginal supporting role in the routine blood bank. It has however had a major impact in the prenatal determination of fetal blood group status in the management of haemolytic disease of the fetus and newborn. In the past few years several high throughput systems have been in development that have the potential capacity to perform genotyping on a mass scale. Such systems have been designed for use on donor- and patient-derived DNA and provide much more comprehensive information regarding an individuals blood group than is possible by using serological methods alone. DNA-based typing methodology is easier to standardize than serology and has the potential to replace it as a front line diagnostic in blood banks. This review overviews the current situation in this area and attempts to predict how blood group genotyping will evolve in the future.

High throughput non-invasive determination of foetal Rhesus D status using automated extraction of cell-free foetal DNA in maternal plasma and mass spectrometry

PURPOSE

To examine the potential high throughput capability and efficiency of an automated DNA extraction system in combination with mass spectrometry for the non-invasive determination of the foetal Rhesus D status.

METHODS

A total of 178 maternal plasma samples from RHD-negative pregnant women were examined, from which DNA was extracted using the automated Roche MagNA Pure system. Presence of the foetal RHD gene was detected by PCR for RHD exon 7 and subsequent analysis using the Sequenom MassArray mass spectrometric system.

RESULTS

We determined that as little as 15 pg of RHD-positive genomic DNA could be detected in a background of 585 pg of RHD-negative genomic DNA. The analysis of the clinical samples yielded a sensitivity and specificity of 96.1 and 96.1%, respectively.

CONCLUSION

Our study indicated that automated DNA extraction in combination with mass spectrometry permits the determination of foetal Rhesus D genotype with an accuracy comparable to the current approaches using real-time PCR.

The changing face of haemolytic disease of the newborn

The diagnosis, acute management and follow-up of neonates with haemolytic disease of the newborn (HDN) still represents a significant area of activity for maternity/neonatal services. ABO incompatability is now the single largest cause of HDN in the western world. However, with increasing knowledge at the molecular level, and closer liaison between neonatal paediatricians and haematologists, the diagnosis of non-immune causes of HDN is increasing. As these conditions have an inherited basis and therefore have implications for other family members (or future children), it remains a high priority for all neonatal paediatricians to achieve an accurate diagnosis in all cases of HDN. As the efficacy of phototherapy increases the role of exchange transfusion in acute management is rapidly decreasing. This makes gauging the appropriate time to intervene with exchange transfusion a difficult clinical decision, and guidelines appropriate to the spectrum of contemporary disease are required. In the future intravenous immunoglobulin and/or intramuscular metalloporphyrins may further reduce the need for exchange transfusion and continue to change the spectrum of HDN faced by neonatal paediatricians.

Recent progress in non-invasive prenatal diagnosis

Although the first finding that fetal cells can enter the maternal circulation was made more than a century ago, it is still unclear if this finding will be translated into a clinically useful diagnostic tool in the foreseeable future. However, significant progress has been made via the analysis of cell-free fetal DNA in maternal plasma/serum and clinical services are now already being offered for the determination of fetal rhesus D status and sex. Currently, however, this technology is really only suited for the analysis of fetal genetic loci completely absent from the maternal genome. The detection of more subtle fetal genetic traits, such as point mutations involved in Mendelian disorders (thalassaemia, cystic fibrosis), is considerably more complex. Preliminary reports indicate that the detection of fetal aneuploidies might be possible using epigenetically modified genes, e.g. maspin on chromosome 18. Additionally, an exiting recent development is that it might be feasible to detect Down syndrome via the quantitative assessment of placentally derived cell-free mRNA of chromosome-21-specific genes such as PLAC4.

Non-invasive prenatal diagnosis and determination of fetal Rh status

RhD blood group incompatibility between a pregnant woman and her fetus can result in maternal alloimmunization and consequent haemolytic disease of the newborn (HDN) in subsequent pregnancies. The D-negative blood group is found in 15% of whites, 3-5% of black Africans, and is rare in Asians. Recent technological advances in non-invasive prenatal determination of the fetal RHD status using cell-free fetal DNA (cffDNA) have opened new avenues for the management of D-negative pregnant women. In this review applications for the high risk women, as well as potential for routine screening will be discussed. The use of non-invasive prenatal diagnosis and the management of other blood incompatibilities will also be discussed.

Routine fetal RHD genotyping with maternal plasma: a four-year experience in Belgium

BACKGROUND

The objective was to evaluate the diagnostic value of RHD fetal genotyping from the plasma of D- mothers as soon as 10 weeks' gestation in a routine clinical practice in Belgium.

STUDY DESIGN AND METHODS

A prospective study was conducted between November 2002 and December 2006. DNA extraction was performed in an automated closed tube system. Fetal RHD/SRY genotypes were detected in the plasma of 563 pregnant mothers by real-time polymerase chain reaction (PCR) targeting multiple exons 4, 5, and 10 of the RHD gene and targeting an SRY gene sequence. These were compared to the D phenotypes determined in the 581 babies they delivered.

RESULTS

By combining amplification of three exons, the concordance rate of fetal RHD genotypes in maternal plasma and newborn D phenotypes at delivery was 100 percent (99.8% including one unusual false-positive). The presence of nonfunctional RHD genes and the absence of a universal fetal marker, irrespective of fetal sex, did not influence the accuracy of fetal RhD status prediction. The RHD genotyping from 18 twin pregnancies was also assessed. Five weak D women were excluded from the RHD fetal genotyping prediction. Three discrepant results (0.5%) between predicted fetal genotype and cord blood phenotype were not confirmed by the baby phenotypes from venipuncture blood.

CONCLUSION

Prenatal prediction of fetal RHD by targeting multiple exons from the maternal plasma with real-time PCR is highly sensitive and accurate. Over 4 years, this experience has highly modified our management of D- pregnant women.

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.

Blood product replacement in the perinatal period

OBJECTIVE

In this article, we will describe some of the special compatibility testing procedures and blood component preparation and modification techniques used in intrauterine and neonatal transfusion medicine. We also will review the transfusion therapy used in hemolytic disease of the fetus and newborn (HDFN) and fetal and neonatal alloimmune thrombocytopenia (FNAIT).

FINDING

Transfusion therapy in the fetus and neonate requires blood typing and compatibility testing techniques not routinely used for adults. These include: cord blood testing, special attention to the volume and speed of infusion, cytomegalovirus risk reduction, and routine irradiation of cellular blood components. The treatment of HDFN and FNAIT involves phenotyping and/or genotyping of fetal and paternal red blood cells and platelets. In FNAIT, platelet products are chosen based on the absence of platelet-specific antigens.

CONCLUSION

Fetal and neonatal transfusion medicine require special attention to the unique anatomic and physiologic features of early human development.

Haemolytic disease of the newborn

The changing management of haemolytic disease of the newborn is reviewed