Performance of noninvasive prenatal screening for fetal sex chromosome aneuploidies in a cohort of 116,862 pregnancies

BACKGROUND

Noninvasive prenatal screening (NIPS) has shown good performance in screening common aneuploidies. However, its performance in detecting fetal sex chromosome aneuploidies (SCAs) needs to be evaluated in a large cohort.

RESEARCH DESIGN AND METHODS

In this retrospective observation, a total of 116,862 women underwent NIPS based on DNA nanoball sequencing from 2015 to 2022. SCAs were diagnosed based on karyotyping or chromosomal microarray analysis (CMA). Among them, 2,084 singleton pregnancies received karyotyping and/or CMA. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NIPS for fetal SCAs were evaluated.

RESULTS

The sensitivity was 97.7% (95%CI, 87.7-99.9), 87.3% (95% CI, 76.5-94.4), 96.1% (95%CI, 86.5-99.5), and 95.7% (95% CI, 78.1-99.9), the PPV was 25.8% (95%CI, 19.2-33.2), 80.9% (95%CI, 69.5-89.4), 79.0% (95%CI, 66.8-88.3), and 53.7% (95%CI, 37.4-69.3) for 45,X, 47,XXY, 47,XXX, and 47,XYY, respectively. The specificity was 94.1% (95%CI, 93.0-95.1) for 45,X, and more than 99.0% for sex chromosome trisomy (SCT). The NPV was over 99.0% for all.

CONCLUSIONS

NIPS screening for fetal SCAs has high sensitivity, specificity and NPV. The PPV of SCAs was moderate, but that of 45,X was lower than that of SCTs. Invasive prenatal diagnosis should be recommended for high-risk patients.

Electrochemical impedance biosensor based on Y chromosome-specific sequences for fetal sex determination

A new electrochemical biosensor based on the sequence of chromosome Y (SRY) has been introduced to determine the gender of the fetus. At first, the DNA probe was designed based on the SRY gene sequence on chromosome Y. Then, a suitable functional group was added to the DNA probe, and it has been immobilized on the surface of the electrode modified with a nanocomposite containing Cu(OH)2 @N-C n-boxes. This substrate causes more DNA probes to connect to the electrode surface by increasing the effective surface area. The presence of the SRY sequence in the DNA sample extracted from blood was detected by the electrochemical signal of the bio-sensor. After optimizing the parameters, the fabricated genosensor showed linear responses in the two concentration ranges containing 0.5 fM to 50 pM and 50 pM to 500 nM. The limit of detection (LOD) for the proposed method was 0.16 fM. The proposed genosensor has been successfully used to determine the gender of the fetus using cell-free fetal DNA (cffDNA) in the blood plasma of several pregnant mothers. This method has advantages such as being simple, portable, accurate, and non-invasive for early determination of the gender of the fetus and early diagnosis of X-linked genetic disorders.

[Towards a generalization of non-invasive prenatal diagnosis of single-gene disorders? Assesment and outlook]

OBJECTIVES

The screening of fetal aneuploidies and non-invasive prenatal diagnosis of monogenic diseases (NIPD-MD) both rely on the study of free fetal DNA in maternal circulation, but their respective rise was unequal. Development of NIPD-MD has taken longer as it represents a less attractive commercial dynamic for industry, but also because it usually involves the development of tailored tests specific to each pathogenic variant.

METHODS

We have carried out a review of the literature on the various indications and technologies involved in the use of NIPD-MM. We present its current implementation and its development in France.

RESULTS

To date, NIPD-MD has been routinely offered in France for several years by the laboratories of the French NIPD-MD network but remains mostly limited to the exclusion of paternal or de novo variants, the exclusion DPNI-MD. Indeed, it is still difficult to study the transmission of maternal variants from circulating free DNA analysis, due to its biological complexity: coexistence and predominance of similar DNA sequences of maternal origin. Different strategies, either direct or indirect, are being evaluated to establish fetal status regardless of the parental origin of the disease or its transmission mode. The emergence of commercial screening solutions for monogenic diseases complements the arsenal of prenatal exploration tools for these diseases.

CONCLUSION

The multitude of existing technologies and protocols may complicate the information provided during antenatal consultations, but mastery of know-how and knowledge of ethical issues of NIPD-MD will ensure optimal service and better management of pregnancies at risk of transmitting monogenic disease.

Association between the first and second trimester cell free DNA fetal fraction and spontaneous preterm birth

OBJECTIVE

To evaluate whether the fetal fraction of cell-free DNA at the first and second trimesters is associated with spontaneous preterm birth.

METHODS

This was a retrospective cohort study with singleton pregnancies who underwent noninvasive prenatal testing. According to pregnancy outcome, eligible patients were divided into a delivery group ≥37 weeks of pregnancy (term group) and <37 weeks of pregnancy (spontaneous preterm group). Stepwise linear regression was used to identify maternal characteristics associated with the fetal fraction of cell-free DNA. Logistic regression analysis was performed to evaluate the association between the fetal fraction of cell-free DNA and spontaneous preterm birth, adjusted for confounding factors.

RESULTS

14,020 cases were included in the study, 13292 cases (94.81%) in the term group and 728 cases (5.19%) in the spontaneous preterm group. The cell-free fraction of fetal DNA was inversely correlated with maternal age and body mass index. Positively correlated with gestational age, fertility, and assisted reproductive technology. After adjusting for the covariates, logistic regression analysis revealed no statistically significant association between the fetal fraction of cell-free DNA and spontaneous preterm birth.

CONCLUSION

In our original study, we found no association between the fetal fraction on NIPT and subsequent spontaneous preterm birth.

Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility

Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.

Noninvasive Prenatal Diagnosis of Beta-Thalassemia Disease by Using Digital PCR Analysis of Cell-Free Fetal DNA in Maternal Plasma

INTRODUCTION

Prenatal diagnosis of thalassemia disease was usually based on invasive technique. Noninvasive diagnosis using cell-free fetal DNA (cff-DNA) was described with various laboratory techniques. The aim of this study was to identify the performance of dPCR for analyzing cff-DNA in maternal plasma to diagnose fetal beta-thalassemia diseases.

METHODS

Thirty-five couples at risk of fetal beta-thalassemia disease caused by four common mutations of HBB were enrolled at 12-18 weeks. The dPCR assay was designed to detect and quantify paternally inherited beta-thalassemia allele (PIB) and maternally inherited beta-thalassemia allele (MIB) from cff-DNA in maternal plasma.

RESULTS

Of 29 couples with different paternal/maternal mutations, all cases who inherited paternal mutation had detectable PIB-M. The MIB-mutant/wild-type (MIB-M/MIB-N) ratio in the mothers whose fetuses did not inherit maternal mutation was 0.87 ± 0.07 which was significantly lower than that of the mothers whose fetuses inherited maternal mutation, 1.01 ± 0.05. The sensitivity and specificity of MIB-M/MIB-N ratio >0.95 in predicting fetus inheriting maternal mutation were 100 and 92.3%, respectively. In four couples with same paternal/maternal mutation, IB-M/IB-N ratio of >0.95 correctly predicted the presence of an inheritance of at least one beta-thalassemia allele. In two couples with paternal Hb E/beta-thalassemia, the presence of PIB-M and the MIB-M/MIB-N ratio of >0.95 correctly predicted the presence of paternal/maternal mutations, respectively.

CONCLUSIONS

The method of analyzing cff-DNA in maternal plasma by dPCR is efficient for prenatal diagnosis of beta-thalassemia.

Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders

Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.

Extracellular DNA levels and cytokine profiles in preterm birth: a cohort study

PURPOSE

The content of eight different cytokines, cell-free DNA (cfDNA) and cell-free fetal DNA (cffDNA) in women's plasma during preterm birth (PB) was studied. The purpose of this study was to identify the relationships between the investigated factors and determine their prognostic significance.

METHODS

Venous blood samples were collected from 45 women with PB and 35 women with full-term labor at 22-31 and 32-36 weeks of gestation, as well as from 17 women during labor at 39-40 weeks of gestation. The concentration of IL-2, IL-4, IL-6, IL-8, IL-10, GM-CSF, IFN-γ and TNF-α cytokines in peripheral blood plasma was measured by multiplex method. The level of cfDNA and cffDNA was evaluated using PCR analysis.

RESULTS

It was found that, the level of IL-6, IL-8 and cfDNA in the blood was significantly increased in women with PB at 22-31 weeks of gestation (p = 0.044, p = 0.001, p < 0.001) and 32-36 weeks of gestation (p = 0.025, p = 0.001, p = 0.002) compared to women with physiological pregnancy at the same terms. The level of cffDNA (p = 0.014) was significantly increased in women with PB at 32-36 weeks of gestation. The IL-8 content had a significant correlation with the cfDNA level in women with PB at all stages of labor and with the cffDNA level in the group who gave birth at 32-36 weeks of gestation. There was no correlation between IL-8, cfDNA and cffDNA, but there was consistency with other cytokines at all studied terms and during delivery in the term-delivery group.

CONCLUSION

The results of the study suggest that cfDNA is a potential marker of PB and show that the aberrant relationship between cfDNA and IL-8 may be important in the genesis of PB.

Amniotic fluid stem cells and the cell source repertoire for non-invasive prenatal testing

Cell-free fetal DNA (cffDNA)-based non-invasive prenatal testing (NIPT) is considered to be a very promising screening tool for pregnant women with an increased risk of fetal aneuploidy. Already millions of women worldwide underwent NIPT. However, due to the observed false-positive and false-negative results, this screening approach does not fulfil the criteria of a diagnostic test. Accordingly, positive results still require risk-carrying invasive prenatal testing, such as amniocentesis or chorionic villus sampling (CVS), for confirmation. Such hurdles need to be overcome before NIPT could become a diagnostic approach widely used in the general population. Here we discuss new evidence that besides the placenta amniotic fluid stem cells (AFSCs) could also represent an origin of cffDNA in the mother’s blood. A comprehensive picture of the involved cell source repertoire could pave the way to more reliable interpretations of NIPT results and ameliorate counselling of advice-seeking patients.

Fetomaternal microchimerism and genetic diagnosis: On the origins of fetal cells and cell-free fetal DNA in the pregnant woman

During pregnancy several types of fetal cells and fetal stem cells, including pregnancy-associated progenitor cells (PAPCs), traffic into the maternal circulation. Whereas they also migrate to various maternal organs and adopt the phenotype of the target tissues to contribute to regenerative processes, fetal cells also play a role in the pathogenesis of maternal diseases. In addition, cell-free fetal DNA (cffDNA) is detectable in the plasma of pregnant women. Together they constitute the well-known phenomenon of fetomaternal microchimerism, which inspired the concept of non-invasive prenatal testing (NIPT) using maternal blood. An in-depth knowledge concerning the origins of these fetal cells and cffDNA allows a more comprehensive understanding of the biological relevance of fetomaternal microchimerism and has implications for the ongoing expansion of resultant clinical applications.

Contingent prenatal screening for frequent aneuploidies with cell-free fetal DNA analysis

OBJECTIVE

To analyze the results of contingent screening for common aneuploidies at our center from June 2017 to June 2019.

MATERIALS AND METHODS

Traditional screening tests were performed using a combination of biochemical markers and ultrasound measurements in the first and second trimesters to assess the risk of trisomies 21 (T21), 18 (T18) and 13 (T13). Cell-free DNA (cf-DNA) testing was offered (Harmony test) to pregnant women at high risk (>1/280 for T21 and > 1/150 for T13 and T18) and a normal early morphology scan. In positive cases, prenatal sampling was strongly recommended to confirm the results by gold standard methods (QF-PCR and karyotyping). Newborns' phenotypes were corroborated after birth in all cases.

RESULTS

In this prospective study, 8153 pregnant women were enrolled, resulting in 390 at high risk according to traditional screening tests. cfDNA testing was offered to 383 women. Traditional screening tests showed a false negative rate of 9.68% for T21. Traditional test sensitivity for T21 was 90.3%, for a false positive rate of 4.17% and a positive predictive value of 7.6%. The positive and negative predictive value for cfDNA testing was 100%. The approach used avoided invasive procedures in 91.3% of women at high risk. The prevalence of chromosomal abnormalities in the population analyzed was 1 in 164, and 1 in 210 for T21.

CONCLUSIONS

Our results show that offering cf-DNA testing to women at high risk in traditional tests (including those with risks >1 in 50) significantly reduces false positives and, therefore, the number of invasive tests. Extending the use of cf-DNA testing to intermediate risk categories may be cost effective.

Label-free E-DNA biosensor based on PANi-RGO-G*NPs for detection of cell-free fetal DNA in maternal blood and fetal gender determination in early pregnancy

In this study, a DYS14 aptamer/polyaniline-reduced graphene oxide-gold nanoparticles/gold (Apt/PANi-RGO-G*NPs/Au) electrode was fabricated to detect the Y-chromosome DYS14 DNA sequence in cffDNA in the blood plasma of pregnant women and used on real and laboratory samples with high success rate. The electrochemical properties of the prepared E-DNA biosensor were characterized by CV, SWV, XRD, and EIS. The E-DNA biosensor morphological characteristics were investigated by TEM, SEM, and EDX. Phosphorothioate was used to link the aptamer to PANi-RGO-G*NPs modified gold electrode. This is due to control of the adsorption polarity and increase adsorption stability. Under optimized conditions, the linear range of the analytical technique with respect to the logarithm of the target sequence concentration was 1.0 × 10^-16-1.0 × 10^-8 M, the detection limit was 4.26 × 10^-17 M, and the limit of quantitation was 1.422 × 10^-16 M. The E-DNA biosensor displayed high selectivity and sensitivity, high efficiency, and acceptable repeatability. For fetal sex detection, 12 pregnant women from the 5th to the 15th week of gestation participated in the study. Results indicated the fabricated Apt/PANi-RGO-G*NPs/Au E-DNA biosensor to be appropriate for fetal sex determination in pregnant women between the 7th and 9th week of gestation. Notably, this method can be used as a model for the study of pathogens like bacteria and viruses.

Noninvasive prenatal screening for fetal sex chromosome aneuploidies

INTRODUCTION

Sex chromosome aneuploidies (SCAs) are among the most common chromosome abnormalities observed in humans. Manifestations include low fertility, infertility, delayed language development, and dysfunction in motor development. Noninvasive prenatal screening (NIPS) based on cell-free fetal DNA from the peripheral blood of pregnant women is increasingly used for the screening of fetal chromosome abnormalities, including screening for fetal gender and fetal sex chromosome aneuploidy. A systematic review of the literature about NIPS for SCAs is needed.

AREAS COVERED

This review evaluated a vast array of published studies focusing on the clinical significance, detection methods, performance of NIPS for SCAs, and the management of positive SCA results following screening with the aim of facilitating a comprehensive and systematic understanding of NIPS for SCAs.

EXPERT COMMENTARY

Looking forward, NIPS is expected to become the primary screening test for common aneuploidies as well as other chromosome abnormalities, including some micro-deletions and micro-duplications, with the potential to transition from a screening test to a prenatal diagnosis method. Ultimately, the goal is to provide a safe and accurate method for increasing early diagnosis to improve long-term outcomes for the SCA patients and families by well- informed health care providers.

The Setup and Application of Reference Material in Sequencing-Based Noninvasive Prenatal Testing

INTRODUCTION

The sequencing-based noninvasive prenatal testing (NIPT) has been successfully integrated into clinical practice and facilitated the early detection of fetal chromosomal anomalies. However, a comprehensive reference material to evaluate and quality control NIPT services from different NIPT providers remains unavailable.

METHODS

In this study, we established a set of NIPT reference material consisting of 192 simulated samples. Most of the potential factors influencing the accuracy of NIPT, such as fetal fraction, mosaicism, and interfering substances, were included in the reference material. We compared the performance of chromosomal abnormalities detection on 3 widely used sequencers (NextSeq 500, BGISEQ-500, and Ion Proton) based on the reference material.

RESULTS

All 3 sequencers provided highly accurate and reliable results to samples with ≥3.5% fetal fractions and high percentage of mosaicism.

CONCLUSIONS

The established reference material can serve as a universal standard quality control for the current and new-coming NIPT providers based on various sequencers.

A fetal reduction from twin to singleton based on sonography and cell-free fetal DNA testing: A sequential approach to old pitfalls

OBJECTIVE

We examined the potential value of combining ultrasound and non-invasive prenatal screening (NIPS) of maternal blood to screen for major aneuploidies as an early approach before selective fetal reduction from twin pregnancy to singleton.

STUDY DESIGN

The sample was composed of pregnant women with di-chorionic di-amniotic twins who chose to undergo fetal reduction to singleton at 12-24 weeks of gestation. These women were asked to provide a blood sample for cell-free fetal DNA (cffDNA) testing prior to fetal reduction.

RESULTS

A total of 24 pregnant women with a twin pregnancy prior to fetal reduction to singleton were enrolled. There were 8 cases with structural anomalies (33.3%) in one twin that dictated fetal reduction. The proportion of patients who underwent selective fetal reduction for fetal abnormalities was larger than in several other studies. The NIPS identified 1 case of Trisomy 13 (4.2%). The other 15 cases (62.5%) had no structural or chromosomal anomalies. The decision to undergo elective reduction of twin pregnancy to singleton was made for social reasons or upon the parents' request. Given the 33% of structural anomalies in the cohort, a cost analysis indicated that this procedure was 6.6-fold less expensive (vs. 4.6-fold with 4% structural anomalies in other publications) than conducting invasive procedures for the entire cohort.

CONCLUSION

The findings suggest that an early anatomical scan and cffDNA can increase the overall safety margin and reduce interventional procedures before elective reduction of twin pregnancy to singleton. However, a larger cohort is needed to confirm these results.

Prenatal RHD genotyping in Croatia: preliminary results

OBJECTIVES

Croatian Institute of Transfusion Medicine (CITM) implemented non-invasive fetal RHD genotyping as a request for targeted antenatal anti-D prophylaxis. The diagnostic performance of in-house RT-PCR method for fetal RHD genotyping and preliminary results are analyzed.

MATERIALS AND METHODS

Evaluation included results of RHD genotyping for 205 RhD negative pregnant women, 12-36th week of gestation, whose samples were received in period between 2015 and 2020. QIAsymphony SP DSP Virus Midi Kit was used for cffDNA extraction on QIAsymphony SP platform (Qiagen, Germany). Fragments of RHD exons 7 and 10 and later exon 5 were RT-PCR amplified. As internal controls, amplification of SRY gene or RASSF1A fragment and β-actin genes digested with BsTUI were used.

RESULTS

We identified 70.72% (145/205) positive and 28.78% (59/205) negative fetal RHD genotypes. We had one inconclusive result (0.50%) due to the interference of maternal DNA with variant genotype RHD*09.02.00/01/*01N.01. When compared to newborns RhD phenotypes, no false negative and three false positive results (3/199, 1.50%) were observed. The test yielded 100% sensitivity and 95.08% specificity, while diagnostic accuracy was 98.48%. We were able to determine one case of fetal variant genotype RHD*04.04/*01N.01 inherited from the father. The negative and positive predictive test values were 100% and 97.86%, respectively.

CONCLUSION

Automated cffDNA extraction and RT-PCR amplification of fetal RHD exons 5,7,10 and fragments of SRY, RASSF1A genes represents highly reliable system for determining fetal RHD status which enables targeted antenatal anti-D prophylaxis. To obtain high specificity of cffDNA extraction, strict and thoroughly cleaning procedures are required.

Noninvasive Fetal Sex Determination by Real-Time PCR and TaqMan Probes

Background

Noninvasive fetal sex determination by analyzing Y chromosome-specific sequences is very useful in the management of cases related to sex-linked genetic diseases. The aim of this study was to establish a non-invasive fetal sex determination test using Real-Time PCR and specific probes.

Methods

The study was a prospective observational cohort study conducted from August 2018 to September 2019. Venous blood samples were collected from 25 Iranian pregnant women at weeks 7 to 25 of gestation. Cell-free DNA (cfDNA) was isolated from the plasma of samples and fetal sex was determined by SRY gene analysis using the Real-Time PCR technique. In the absence of SRY detection, the presence of fetal DNA was investigated using cfDNA treated with BstUI enzyme and PCR for the epigenetic marker RASSF1A.

Results

Of the total samples analyzed, 48% were male and 52% female. The RASSF1A assay performed on SRY negative cases also confirmed the presence of cell-free fetal DNA. Genotype results were in full agreement with neonate gender, and the accuracy of noninvasive fetal sex determination was 100%.

Conclusion

Fetal sex determination using the strategy applied in this study is noninvasive and highly accurate and can be exploited in the management of sex-linked genetic diseases.

Non-invasive prenatal testing for management of haemolytic disease of the fetus and newborn induced by maternal alloimmunisation

Anti-D immunoglobulin prophylaxis reduces the risk of RhD negative women becoming alloimmunised to the RhD antigen and is a major preventative strategy in reducing the burden of haemolytic disease of the fetus and newborn (HDFN). HDFN also arises from other maternal red cell antibodies, with the most clinically significant, after anti-D, being anti-K, anti-c and anti-E. Among the 39 human blood group systems advanced genomic technologies are still revealing novel or rare antigens involved in maternal alloimmunisation. Where clinically significant maternal antibodies are detected in pregnancy, non-invasive prenatal testing (NIPT) of cell-free fetal DNA provides a safe way to assess the fetal blood group antigen status. This provides information as to the risk for HDFN and thus guides management strategies. In many countries, NIPT fetal RHD genotyping as a diagnostic test using real-time PCR has already been integrated into routine clinical care for the management of women with allo-anti-D to assess the risk for HDFN. In addition, screening programs have been established to provide antenatal assessment of the fetal RHD genotype in non-alloimmunised RhD negative pregnant women to target anti-D prophylaxis to those predicted to be carrying an RhD positive baby. Both diagnostic and screening assays exhibit high accuracy (over 99 %). NIPT fetal genotyping for atypical (other than RhD) blood group antigens presents more challenges as most arise from a single nucleotide variant. Recent studies show potential for genomic and digital technologies to provide a personalised medicine approach with NIPT to assess fetal blood group status for women with other (non-D) red cell antibodies to manage the risk for HDFN.

Evaluation of beta-thalassemia in the fetus through cffDNA with multiple polymorphisms as a haplotype in the beta-globin gene

OBJECTIVE

Invasive biopsy during the pregnancy is associated with an abortion risk of approximately 1% for the fetus. Free fetal DNA in maternal plasma is an excellent source of genetic material for prenatal molecular diagnoses. This study was conducted to investigate beta-thalassemia mutation in the fetus through maternal blood with multiple polymorphisms as haplotypes in the beta-globin gene.

METHODS

In this study, a total of 33 beta-thalassemia carrier (minor) couples were genotyped by ARMS-PCR for IVSII-IG>A mutation. During pregnancy, 10mL of blood was collected from pregnant women, and DNA was extracted by the magnetic bead-based extraction, and fetal DNA was enriched with AMPure XP kit. Five polymorphisms in 4 haplotype groups were evaluated by the Sanger Sequencing method. Finally, results were compared with those of the invasion method.

RESULTS

Participants in study were 33 couples, mean age of the men was 26±5 years, and mean age of women was 23±4 years, and mean MCV, MCH, HbA2 blood parameters were 62.4±5.3, 19.6±3.1, 4.2±2.1 respectively. A total of 33 fetuses were genotyped for IVSII-IG>A mutation. Nine fetuses were affected, 10 fetuses were normal and 14 fetuses were carrier of beta-thalassemia. Sensitivity and specificity of Sanger Sequencing were equal to 88.8% and 91.6% respectively. Positive and negative predictive values were obtained as 80% and 95.6%, respectively.

CONCLUSION

Mutational status of the fetus can be assessed by determining inheritance of paternally-derived alleles based on detection of haplotype-associated SNP in maternal plasma. Magnetic-based DNA extraction and fetal DNA enrichment are very simple and easy to perform and have satisfactory accuracy.

Non-invasive prenatal diagnosis and screening for monogenic disorders

Cell-free fetal DNA (cffDNA) can be detected in the maternal circulation from 4 weeks gestation, and is present with cell-free maternal DNA at a level of between 5 % and 20 %. Cell-free DNA (cfDNA) can be extracted from a maternal blood sample and, although it is not possible to separate the fetal from the maternal cfDNA, it has enabled non-invasive prenatal diagnosis (NIPD) without the associated miscarriage risk that accompanies invasive testing. NIPD for monogenic diseases was first reported in 2000 and since then there have been many proof of principle studies showing how analysis of cfDNA can provide a definitive diagnosis early in pregnancy for a wide range of single gene diseases. Testing for a number of these diseases has been available in the UK National Health Service (NHS) since 2012. This review highlights the main techniques that are being used for NIPD and discusses the technical limitations of the methods, as well as the advances that are being made to overcome some of the issues. NIPD is technologically challenging for a number of reasons. Firstly, because it requires the detection of low level fetal variants in a high maternal background. For de novo and paternally-inherited variants this has been achieved through the use of techniques such as next-generation sequencing (NGS) and digital PCR to detect variants in the cffDNA that are not present in the maternal cfDNA. However, for maternally-inherited variants this is much more challenging and relies on dosage-based techniques to detect small differences in the levels of mutant and wild-type alleles. Alongside the technical advances that are making NIPD more widely available in both the public healthcare and commercial settings, it is crucial that we continue to monitor the social and ethical impact to ensure that patients are being offered safe and accurate testing.

Inflammation-mediated generation and inflammatory potential of human placental cell-free fetal DNA

Introduction

Circulating DNA can be pro-inflammatory when detected by leukocytes via toll-like receptor 9 (TLR9). Cell-free fetal DNA (cff-DNA) of placental origin, circulates in pregnancy, and increased concentrations are seen in conditions associated with placental and maternal inflammation such as pre-eclampsia. However, whether cff-DNA is directly pro-inflammatory in pregnant women and what regulates cff-DNA levels in pregnancy are unknown.

Methods

Using a human term placental explant model, we examined whether induction of placental inflammation can promote cff-DNA release, and the capacity of this cff-DNA to stimulate peripheral blood mononuclear cells (PBMCs) from pregnant women.

Results

We demonstrate lipopolysaccharide (LPS)-mediated inflammation in placental explants and induced apoptosis after 24 h. However, this did not increase levels of cff-DNA generation compared to controls. Furthermore, the methylation status of the cff-DNA, was not altered by LPS-induced inflammation. Cff-DNA did not elicit production of inflammatory cytokines from PBMCs, in contrast to exposure to LPS or the TLR9 agonist CpG-ODN. Finally, we demonstrate that cff-DNA acquired directly from pregnant women did not differ in methylation status from placental extracted DNA, or from placental explant generated cell-free DNA, and that, unlike Escherichia coli DNA, this cff-DNA has a low level of unmethylated CpG sequences.

Discussion

Our data suggest that placental inflammation does not increase release of cff-DNA and that placental cff-DNA is not pro-inflammatory to circulating PBMCs. It thus seems unlikely that high levels of cff-DNA are either a direct consequence or cause of inflammation observed in obstetric complications.

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Cell-free fetal DNA was generated using a human placental explant model.

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Lipopolysaccharide causes inflammation and cell death in placental explants.

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Inflammation does not increase cell-free fetal DNA release from placental explants.

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Generated DNA does not elicit inflammation from blood cells from pregnant women.

Recent advances in non-invasive fetal HPA-1a typing

Non-invasive fetal HPA-1a typing is a valuable tool to identify the pregnancies at risk of fetal and neonatal alloimmune thrombocytopenia (FNAIT). At present, prenatal determination of the fetus HPA-1a type is performed for diagnostic purposes in pregnancies of HPA-1 alloimmunized women with history of a previous fetus or child with FNAIT. Different approaches have been used to determine the fetal HPA-1a genotype from cell-free fetal DNA (cffDNA) in the mother's plasma, mainly based on real-time PCR. Due to the single nucleotide polymorphism (SNP) between the HPA-1a and HPA-1b allelic sequences, a robust and accurate detection of the fetal genotype is challenging, and the sensitivity of most assays is still limited early in pregnancy. Nowadays, the availability of technologies such as next generation sequencing (NGS) or digital PCR offers unprecedented possibilities of analyzing cell-free DNA (cfDNA)-amplified sequences with very high coverage and high sensitivity. In addition, other interesting approaches using variant sequence enrichment strategies have been recently described. In particular, coamplification at lower denaturation temperature PCR (COLD-PCR) offers a simple and sensitive strategy for noninvasive fetal HPA-1 typing. These novel approaches are explained in more detail in this review. Despite no population-based FNAIT screening programs have so far been implemented, the perspectives in terms of treatment and prevention are changing and less costly high-throughput maternal HPA-1a typing methods have been developed. Altogether, this may lead to the implementation of fetal HPA-1a typing with a broader scope in the future, playing a critical role within FNAIT screening programs.

Psychological and social consequences of non-invasive prenatal testing (NIPT): a scoping review

Background

Genomics-based noninvasive prenatal tests (NIPT) allow screening for chromosomal anomalies such as Down syndrome (trisomy 21). The technique uses cell-free fetal DNA (cffDNA) that circulates in the maternal blood and is detectable from 5 weeks of gestation onwards. Parents who choose to undergo this relatively new test (introduced in 2011) might be aware of its positive features (i.e. clinical safety and ease of use); however, they might be less aware of the required decisions and accompanying internal conflicts following a potential positive test result. To show the evidence on psychological and social consequences of the use of NIPT, we conducted a scoping review.

Methods

We systematically searched four electronic databases (MEDLINE (Ovid), Cochrane Library (Wiley), CINAHL (EBSCO) and PsychINFO (EBSCO)) for studies that investigated the psychological or social consequences of the use of NIPT by pregnant women or expecting parents. The search was limited to studies published between 2011 and August 8, 2018. We identified 2488 studies and, after removal of duplicates, screened 2007 titles and abstracts, and then assessed 99 articles in full text (both screenings were done independently in duplicate). We included 7 studies in our analysis.

Results

Five studies assessed anxiety, psychological distress and/or decisional regret among women with validated psychological tests like the Spielberger State Trait-Anxiety Inventory (STAI), the Pregnancy-Related Anxiety Questionnaire-Revised (PRAQ-R), the Kessler Psychological Distress Scale (K6) or the Decisional Regret Scale (DRS). Two studies assessed women’s experiences with and feelings after NIPT in interviews or focus groups. The included studies were heterogeneous in location, study setting, inclusion criteria, outcome assessment, and other characteristics.

Conclusions

Only few studies on psychological consequences of NIPT have been identified. The studies assessed only short-term psychological consequences of NIPT at baseline and/or after receiving the results or after giving birth. Studies show that short term anxiety decreased when women received negative NIPT results and that decisional regret was generally low. We could not identify studies on long term consequences of NIPT, as well as studies on women’s partners’ short and long term outcomes, nor on social consequences of NIPT.

Cell-Free Fetal DNA in the Early and Late First Trimester

OBJECTIVE

The aim of this work was to investigate the association between maternal and fetal characteristics and the fetal fraction at 8-14 weeks' gestation, with emphasis on the change in the fetal fraction upon repeat sampling.

METHOD

One sample for cell-free DNA (cfDNA) testing was collected at the same time as the biochemical markers for combined first trimester screening (visit 1) and another at the nuchal translucency scan (visit 2). Chromosome-selective cfDNA analysis was performed on frozen plasma.

RESULTS

Overall, 321 women were included at visit 1, and 307 had a repeat blood sampling. A fetal fraction was obtained in 532 samples (238 samples with repeat fetal fraction). The fetal fraction decreased with maternal BMI (p < 0.001), was lower in Asian women (p = 0.03), and increased with β-hCG levels (p < 0.001) and gestational age (p = 0.04). Before 10 weeks' gestation, the fetal fraction was lower (p = 0.02), as was the probability of a sufficient fetal fraction (p = 0.03) after adjustment for maternal BMI. Asian women had a higher increase in fetal fraction upon repeat sampling (p < 0.001).

CONCLUSION

Before 10 weeks' gestation, the fetal fraction is significantly lower but seems to increase more rapidly compared to later gestations. Presently, combined first trimester screening with cfDNA testing should not include samples before 10 weeks' gestation.

Evaluation of droplet digital PCR for non-invasive prenatal diagnosis of phenylketonuria

This study was carried out to establish a non-invasive prenatal diagnosis method for phenylketonuria (PKU) based on droplet digital PCR (ddPCR) and to evaluate its accuracy by comparison with conventional invasive diagnostic methods. A total of 24 PKU pedigrees that required prenatal diagnosis were studied, in which the genetic mutations in the probands and parents were unambiguous. Prenatal diagnosis of sibling fetuses was performed using traditional invasive prenatal diagnostic methods as a standard. At the same time, cell-free DNA (cfDNA) was extracted from maternal plasma and the fetal genes contained within were typed and quantified using ddPCR method. Invasive prenatal diagnosis determined that 3 of the 24 fetuses were affected, 8 of them were normal, and 13 were heterozygous carriers of pathogenic mutations. Successful non-invasive prenatal diagnosis analysis of PAH gene mutations was performed for 8 of the families using ddPCR method. Non-invasive prenatal diagnosis results were consistent with the results of the invasive prenatal diagnoses and no false positive or false negative results were found. In conclusion, this study is the first to establish non-invasive prenatal diagnosis of PKU based on ddPCR. The method showed high sensitivity and specificity from cfDNA, indicating that ddPCR is a reliable non-invasive prenatal diagnosis tool for PKU diagnosis. Graphical abstract.

Successful early fetal sex determination using cell-free fetal DNA isolated from maternal capillary blood: A pilot study

OBJECTIVES

The discovery of cell-free fetal DNA (cffDNA) fragments in maternal plasma made it possible to determine fetal sex at early stages of pregnancy without carrying a risk miscarriage, which is especially important for the management of X-linked genetic abnormalities. The vast majority of studies used cffDNA extracted from maternal venous blood, excluding the possibility of capillary sampling for those who cannot tolerate venipuncture. This study evaluates the possibility of fetal sex determination using cffDNA isolated from capillary blood of women with early gestational pregnancies.

STUDY DESIGN

Samples were obtained from 24 pregnant women from the Ukrainian population, whose gestational age varied between 5th to 10th weeks. Sex determination was performed using real-time quantitative PCR of SRY male-specific markers. Results were compared to the known fetal sex (detected by next-generation sequencing during the preimplantation genetic testing procedure) to calculate the test accuracy.

RESULTS

Results demonstrated 85.71-100% sensitivity and 100% specificity of the test. Cohen's Kappa coefficient of agreement in sex determination test varied from 0.8 to 1.0 (P < 0.00001).

CONCLUSION

This test, which is the first known so far detailed report of successful early fetal sex determination using cffDNA isolated from maternal capillary blood, is a reliable alternative to traditional venipuncture.

Cell-Free DNA: Applications in Different Diseases

Since its discovery in human blood plasma about 70 years ago, circulating cell-free DNA (cfDNA) has become an attractive subject of research as noninvasive disease biomarker. The interest in clinical applications has gained an exponential increase, making it a popular and potential target in a wide range of research areas.cfDNA can be found in different body fluids, both in healthy and not healthy subjects. The recent and rapid development of new molecular techniques is promoting the study and the identification of cfDNA, holding the key to minimally invasive diagnostics, improving disease monitoring, clinical decision, and patients' outcome.cfDNA has already given a huge impact on prenatal medicine, and it could become, in the next future, the standard of care also in other fields, from oncology to transplant medicine and cardiovascular diseases.

Screening of fetal chromosomal aneuploidy diseases using noninvasive prenatal testing in twin pregnancies

OBJECTIVES

This study was aimed to report the clinical characteristics of fetal chromosomal aneuploidy diseases using noninvasive prenatal testing (NIPT) in twin pregnancies and analyze the results in terms of chorionicity, conception, and fetal fraction.

METHODS

A total of 1160 women with twin pregnancies were recruited from 1 October 2015, to 1 August 2017. Next-generation sequencing technology was used to detect fetal aneuploidies, such as trisomy 21, trisomy 18, trisomy 13 and trisomy X.

RESULTS

Aneuploidy was detected using NIPT in 26 fetuses, among which 18 fetal aneuploidies occurred in only one fetus of the twins. The rate of aneuploidy was 1.3% for dichorionic diamniotic twins and 0.5% for monochorionic diamniotic twins, respectively. The rate of aneuploidy was 1.2% for spontaneous pregnancy group and 1.1% for assisted reproductive technologies group.

CONCLUSION

In this study, detection of trisomy 21, trisomy 18, trisomy 13, and X abnormality in twin pregnancies was confirmed to be accurate. The aneuploidies mostly occurred in only one fetus of the twins, and trisomy 21 was the most common type. The prenatal diagnostic standard for NIPT in singleton pregnancies could perform well in twin pregnancies, which means NIPT can be popularized as routine prenatal screening in twin pregnancies.

Noninvasive Antenatal Screening for Fetal RHD in RhD Negative Women to Guide Targeted Anti-D Prophylaxis

RhD negative pregnant women who carry an RhD positive fetus are at risk of immunization against the D antigen, which may result in hemolytic disease of the fetus and the newborn. Predicting the fetal RhD status by noninvasive antenatal screening for the fetal RhD gene (RHD) can guide targeted use of antenatal anti-D prophylaxis.Cell-free fetal DNA is extracted from maternal plasma from RhD negative pregnant women at a gestational age of 25 weeks. A real-time PCR-based detection of two RHD exons enables reliable prediction of the fetal RhD status to determine the administration of antenatal prophylaxis, as well as postnatal prophylaxis.

Effect of cell-free fetal DNA on spontaneous preterm labor

Inflammatory phenomenon, including cell-free fetal DNA (cffDNA), is one of the various causes of preterm delivery. Always, there is a trend in the prediction and prevention of preterm labor. Herein, the aim of this study is to assess the value of cffDNA levels in serum of pregnant women for prediction of spontaneous preterm labor. A case–control study with nonrandomized convenience sampling was conducted. One hundred women qualifying for the study were enrolled. The participants were divided into two groups of healthy nulliparous pregnant women (n = 50) and nulliparous pregnant women experiencing preterm labor (n = 50). Then, venous blood was sampled from each participant and its plasma was separated and analyzed. The mean age of women in the experimental group was 22.90 years with the standard deviation of 4.04, while in the control group these two values were 23.78 and 4.37, respectively. In the experimental group, 29 patients (58%), and in the control group, 27 patients (54%) had cffDNA. The mean of the counted DNA in the experimental group was 2080/03 with the standard deviation of 909/792 while the same values for the control group were 1183/26 and 620/720, in the same order. The statistical analysis revealed that this difference was meaningful at P = 0.001. Furthermore, in the experimental group, cffDNA increased with increase in the age and the difference was meaningful. Finally, increasing pregnancy age in the experimental group led to an increase in the number of cffDNA (P = 0.001). The results of this study indicated that the cumulative frequency of preterm labor for women with positive cffDNA was significantly higher. High levels of cells' DNA in the serum of pregnant mothers increase the risk of spontaneous preterm labor. These observations may have implications for preterm labor.

Direct comparison of QIAamp DSP Virus Kit and QIAamp Circulating Nucleic Acid Kit regarding cell-free fetal DNA isolation from maternal peripheral blood

BACKGROUND

Blood of pregnant women contains cell-free fetal DNA (cffDNA), which is widely used in non-invasive prenatal diagnosis. The modern laboratory equipment market provides huge variety of commercial kits for isolation of circulating nucleic acids, but unfortunately none of them are standardized for isolation of cffDNA, which is a crucial step for success of subsequent analysis.

AIM

To compare DSPVK and CNAK in terms of cffDNA, cell-free total DNA (cftDNA) yield and resulting cffDNA fraction, as well as to try to explain the possible difference between the efficacy of these kits.

METHODS

Peripheral blood samples were collected from 18 healthy pregnant women (6^th-14th week of pregnancy) and from 12 healthy unpregnant subjects. cftDNA was isolated using QIAamp Circulating Nucleic Acid Kit (CNAK) (Qiagen, Germany) and QIAamp DSP Virus Kit (DSPVK) (Qiagen, Germany) from 1 ml of plasma of each sample. Methylation-sensitive restriction was carried out to isolate cffDNA. Yield of cffDNA and cftDNA was quantified using digital PCR. To explain the difference in resulting efficacy of these two kits PCR inhibitors analysis was performed, as well as the optimal plasma input for DSPVK was investigated.

RESULTS

Yield of cffDNA using CNAK was statistically significantly higher than using DSPVK (167.62 (125.34-192.47) vs 52.88 (35.48-125.42) GEq/mL, p < 0.001). The same applies to cftDNA yield, CNAK appears to be statistically significantly superior to DSPVK (743.42 (455.02-898.33) vs 371.07 (294.37-509.89) GEq/mL, p < 0.001). cffDNA fraction using CNAK was also higher than using DSVPK (24.75 (14.5-31.53) vs 14.20 (6.88-25.83) %, p = 0.586), although the difference was not statistically significant due to inconsistency of DSPVK results from sample to sample. PCR inhibitors analysis uncovered increased amount of PCR inhibitors in CNAK cftDNA solution, compared to DSPVK (p = 0.002). Usage of 0.5 mL of plasma for cftDNA extraction with DSPVK over 1 mL demonstrates almost 1.8 times higher cftDNA output (p = 0.028), which suggests that this kit is not so viable for volumes of plasma larger than 0.5 mL.

CONCLUSIONS

We recommend CNAK over DSPVK for quantitative analysis of cffDNA. Nevertheless, DSPVK is definitely suitable for qualitative analysis as well as for research with limited budget, since it is almost 3 times cheaper than CNAK.

Effective Fetal Epigenetic Biomarkers for Noninvasive Fetal Trisomy 21 Detections

INTRODUCTION

Recently, we identified three novel fetal-specific epigenetic DNA regions (FSERs) on chromosome 21 for detection of noninvasive fetal trisomy 21 (T21). In this study, the diagnostic accuracies of the three FSERs were assessed on a larger panel of the first-trimester pregnant women.

MATERIAL AND METHODS

This study was conducted with maternal plasma collected from 167 pregnant women carrying 155 chromosomally normal and 12 T21 fetuses (10-13 gestational weeks). Accuracies of FSERs for noninvasive prenatal test of fetal T21 were estimated by the area under the receiver operator characteristic curve (AUC).

RESULTS

The levels of all FSERs increased in pregnant women with T21 fetuses when compared with controls (p < 0.001 for all). The levels of the three FSERs did not differ according to maternal age, body mass index, and fetal sex at maternal blood sampling (p > 0.05 for all). In noninvasive fetal T21 detection, the AUC of FSER1, FSER2, and FSER3 were 0.859 (95% CI: 0.746-0.972), 0.919 (95% CI: 0.856-0.982), and 0.868 (95% CI: 0.746-0.990), respectively.

DISCUSSION

The findings of this study suggest that all FSERs may be useful for noninvasive fetal T21 detection, regardless of maternal age, body mass index, and fetal sex.

A Broad Test Based on Fluorescent-Multiplex PCR for Noninvasive Prenatal Diagnosis of Cystic Fibrosis

BACKGROUND

Analysis of cell-free fetal DNA in maternal plasma is very promising for early diagnosis of monogenic diseases. However, it has been limited by the need to set up patient- or disease-specific custom-made approaches. Here we propose a universal test based on fluorescent multiplex PCR and size fragment analysis for an indirect diagnosis of cystic fibrosis (CF).

METHODS

The test, based on haplotyping, includes nine intra- and extragenic short tandem repeats of the CFTR locus, the coamplification of p.Phe508del (the most frequent mutation in CF patients worldwide), and a specific SRY sequence. The assay is able to determine the inherited paternal allele.

RESULTS

Our simple approach was successfully applied to 30 couples and provided clear results from the maternal plasma. The mean rate of informative markers was sufficient to propose it for use in indirect diagnosis.

CONCLUSIONS

This noninvasive prenatal diagnosis test, focused on indirect diagnosis of CF, offers many advantages over current methods: it is simple, rapid, and cost-effective. It allows for the testing of a large number of couples with high risk of CF, whatever the familial mutation of the CFTR gene. It provides an alternative method to reduce the number of invasive tests.

Genetic Counselors' Perspectives About Cell-Free DNA: Experiences, Challenges, and Expectations for Obstetricians

The expansion of cell-free fetal DNA (cfDNA) screening for a larger and diverse set of genetic variants, in addition for use among the low-risk obstetric population, presents important clinical challenges for all healthcare providers involved in the delivery of prenatal care. It is unclear how to leverage the different members of the healthcare team to respond to these challenges. We conducted interviews with 25 prenatal genetic counselors to understand their experience with the continued expansion of cfDNA screening. Participants supported the use of cfDNA screening for the common autosomal aneuploidies, but noted some reservations for its use to identify fetal sex and microdeletions. Participants reported several barriers to ensuring that patients have the information and support to make informed decisions about using cfDNA to screen for these different conditions. This was seen as a dual-sided problem, and necessitated additional education interventions that addressed patients seeking cfDNA screening, and obstetricians who introduce the concepts of genetic risk and cfDNA to patients. In addition, participants noted that they have a professional responsibility to educate obstetricians about cfDNA so they can be prepared to be gatekeepers of counseling and education about this screening option for use among the general obstetric population.

Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies

Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.

Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing

Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.

The biological basis and prevention of preterm birth

The time of birth is a critical determinant of perinatal and long-term outcomes. Preterm birth is still the first cause of infant mortality and morbidity; unfortunately, rates of preterm birth remain high in both high- and low-resource countries, ranging from 5% to 18%. Preterm parturition is a syndrome, which can be induced by various factors such as infection, cervical pathology, uterine overdistension, progesterone deficiency, vascular alterations (utero-placental ischemia, decidual hemorrhage), maternal and fetal stress, allograft reaction, allergic phenomena, and probably other several unknown factors. These various etiologies can lead to the pathological activation of a common pathway of decidua/fetal membranes, which causes uterine contractility, cervical ripening, and rupture of membranes. Moreover, the mechanisms responsible for these processes have been identified, which involve receptors, chemokines, and inflammatory cytokines. It is very important to understand the cellular and biochemical pathways responsible for preterm labor to identify, treat, and prevent negative outcome in a timely manner. Clinicians and researchers play a key role in improving biochemical knowledge on preterm delivery, identifying risk factors, and shaping interventions that can address this complex syndrome.

Evaluation of extraction methods for methylated cell-free fetal DNA from maternal plasma

PURPOSE

Recently, fetal placenta-specific epigenetic regions (FSERs) have been identified for quantification of cell-free fetal DNA (cff-DNA) for non-invasive prenatal testing (NIPT). The aim of this study was to evaluate the efficiencies of a column-based kit and magnetic bead-based kit for quantification of methylated FSERs from maternal plasma.

METHODS

Maternal plasma was extracted from normal pregnant women within the gestational age of 10~13 weeks (n = 24). Total cell-free DNA (cf-DNA) was extracted using a column-based kit and magnetic bead-based kit from the plasma of the same pregnant woman, respectively. Methylated FSERs were enriched from the extracted total cf-DNA using a methyl-CpG-binding domain-based protein method. The four FSERs were simultaneously quantified by multiplex real-time polymerase chain reaction.

RESULTS

Methylated FSERs were detected in all samples extracted from both kits. However, the amplification of FSERs showed significant differences in the extraction efficiency of methylated FSERs between the two extraction methods. The Ct values of methylated FSERs extracted using the column-based kit were significantly lower than those obtained using the magnetic bead-based kit (P < 0.001 for all FSERs). The quantity of methylated FSERs was significantly higher for extracted DNA using the column-based kit than that extracted using the magnetic bead-based kit (P < 0.001 for all FSERs). Time and cost for the process of extraction were similar for the column kit and magnetic bead-based kit.

CONCLUSIONS

Our findings demonstrate that the column-based kit was more effective than the magnetic bead-based kit for isolation of methylated FSERs from maternal plasma as assessed by FSER detection.

The Use of Ultrasound as a Potential Adjunct to Cell-Free Fetal DNA Screening for Aneuploidy at Weill Cornell Medical College, New York, USA

Objective  To evaluate the utility of ultrasound in identifying fetuses with uncommon chromosomal abnormalities that would be considered not detectable by cell-free fetal deoxyribonucleic acid (cfDNA). Study Design  We performed a retrospective study of fetuses with chromosomal abnormalities that would be undetectable by cfDNA, who underwent an 11- to 14-week ultrasound from 2006 to 2016. Results  There were 43 pregnancies included. First-trimester ultrasound revealed a fetal abnormality in 19 (44.2%) cases, of which 13 (30.2%) had a thickened nuchal translucency. There were an additional four fetuses with second-trimester sonographic abnormalities. Overall, 23 (53.5%) fetuses were found to have a major anomaly diagnosed by ultrasound. The rate of first-trimester sonographic abnormalities varied widely based on category of chromosomal abnormalities with high rates seen with triploidy (87.5%) and autosomal trisomy (80%) and lower rates seen with structurally abnormal chromosomes (33.3%), trisomy mosaicism (27.3%), other forms of mosaicism (11.1%), and deletions or duplications (25.0%), p  < 0.001. Conclusion  The majority of fetuses with uncommon chromosomal abnormalities in our cohort had major sonographic anomalies. The use of first-trimester ultrasound with nuchal translucency measurement may offer utility in identifying fetuses with risk of aneuploidy that would not be detectable with cfDNA.

Obstetric professionals' perceptions of non-invasive prenatal testing for Down syndrome: clinical usefulness compared with existing tests and ethical implications

BACKGROUND

While non-invasive prenatal testing (NIPT) for fetal aneuploidy is commercially available in many countries, little is known about how obstetric professionals in non-Western populations perceive the clinical usefulness of NIPT in comparison with existing first-trimester combined screening (FTS) for Down syndrome (DS) or invasive prenatal diagnosis (IPD), or perceptions of their ethical concerns arising from the use of NIPT.

METHODS

A cross-sectional survey among 327 obstetric professionals (237 midwives, 90 obstetricians) in Hong Kong.

RESULTS

Compared to FTS, NIPT was believed to: provide more psychological benefits and enable earlier consideration of termination of pregnancy. Compared to IPD, NIPT was believed to: provide less psychological stress for high-risk women and more psychological assurance for low-risk women, and offer an advantage to detect chromosomal abnormalities earlier. Significant differences in perceived clinical usefulness were found by profession and healthcare sector: (1) obstetricians reported more certain views towards the usefulness of NIPT than midwives and (2) professionals in the public sector perceived less usefulness of NIPT than the private sector. Beliefs about earlier detection of DS using NIPT were associated with ethical concerns about increasing abortion. Participants believing that NIPT provided psychological assurance among low-risk women were less likely to be concerned about ethical issues relating to informed decision-making and pre-test consultation for NIPT.

CONCLUSIONS

Our findings suggest the need for political debate initially on how to ensure pregnant women accessing public services are informed about commercially available more advanced technology, but also on the potential implementation of NIPT within public services to improve access and equity to DS screening services.

Cell-free fetal DNA testing in prenatal diagnosis: Recommendations of the Polish Gynecological Society and the Polish Human Genetics Society

This paper contains a joint position of the Polish Gynecological Society and Polish Human Genetics Society on the cell-free fetal DNA testing in prenatal diagnosis. We present situations where the cell-free fetal DNA testing should be applied and cases in which performing of the test is not useful. We indicate what diagnostic steps should be performed before the test and how the test results should be interpreted and followed.

Pre-eclampsia: Molecular events to biomarkers

Pre-eclampsia is a hypertensive disorder in pregnancy, which accounts for 10-15% of the maternal and perinatal mortality worldwide. Abnormal placental development and tissue hypoxia are its main etiologic factors. The present diagnostic methods of blood pressure monitoring and renal function evaluation are insufficient in the early detection of pre-eclampsia. Since molecular events portent well ahead of the disease onset, biomarker research for the early diagnosis of pre-eclampsia has recently generated ambitious clinical targets. However, no clinically validated biomarker has so far been reported for the prediction of pre-eclampsia. Therefore, this review takes stock of the current understanding of pre-eclampsia from a molecular biology perspective and critically evaluates the following diagnostic potentials claimed for the biomarkers: placental proteins, angiogenic markers, and cell-free fetal DNA (cffDNA) in maternal circulation. Though the emerging evidences in favor of the fetal-specific epigenetic marker, hypermethylated RASSF1A of cffDNA, are highlighted, it pitches for a broader strategy of 'combination biomarker approach' for the reliable forecasting and triaging of pre-eclampsia.

Analysis of first-trimester combined test results in preparation for a cell-free fetal DNA era

OBJECTIVE

To survey experience with the first-trimester combined test (FCT) for trisomy 21 (T21) in different risk score groups to determine the most useful clinical application of cell-free fetal DNA (cffDNA) screening.

METHODS

In a retrospective study, the records of FCT results obtained at a center in Turkey between January 2009 and January 2014 were reviewed. The FCT results and rates of uptake of invasive diagnostic testing were compared among different risk score groups.

RESULTS

FCT results were available for 4804 pregnancies; 276 (5.7%) had IDT results. Ten (72.7%) of 11 cases of T21 had a risk score of 1:300 or more. The IDT uptake rates were 54.5%, 51.9%, and 47.4% at risk scores of 1:100 or more, 1:200 or more, and 1:300 or more, respectively. In the group at intermediate risk (1:1001-1:3000), no pregnancy had an FCT result of both low pregnancy-associated plasma protein A and high free β-human chorionic gonadotropin, but 30 (3.9%) of 766 pregnancies had both advanced maternal age and high β-human chorionic gonadotropin.

CONCLUSION

cffDNA screening should be used to optimize IDT uptake in pregnancies with a risk score of 1:101-1:1000. The selective power of the FCT diminishes beyond the 1:1001 score and cffDNA screening cannot yet be recommended routinely.

Screening and Testing in Multiples

The choice of screening or invasive procedure in twin pregnancies is a personal choice of whether the patient wishes to take a small risk of having a baby with a serious disorder versus a small risk of having a complication because she wishes to avoid that. How to interpret such risks has profound effects on the perceived value of techniques, either leading to a decision to screening or going directly to chorionic villus sampling. There are profound issues surrounding the data and the interpretation of the data. No single short review can exhaustively examine all of the issues.

Prevalence of RhD status and clinical application of non-invasive prenatal determination of fetal RHD in maternal plasma: a 5 year experience in Cyprus

BACKGROUND

After the discovery that cell-free fetal DNA (cffDNA) is circulating in the maternal plasma of pregnant women, non-invasive prenatal diagnosis for fetal RhD in maternal plasma in RhD negative women at risk for haemolytic disease of the newborn (HDN) was clinically established and used by many laboratories. The objectives of this study are: (a) to assess the feasibility and report our experiences of the routine implementation of fetal RHD genotyping by analysis of cffDNA extracted from maternal plasma of RhD negative women at risk of HDN, and (b) to estimate the RhD phenotype frequencies, the RHD genotype frequencies and the RhD zygosity in the Cypriot population.

METHODS

cffDNA was extracted from maternal plasma of 73 RhD negative pregnant women. Real-Time Multiplex-PCR was used to amplify regions of RHD gene in exons 4, 5 and 10. RhD phenotypes were determined on 445 random samples using conventional agglutination slide test.

RESULTS

The fetus was predicted to be positive in 53 cases and negative in 18 cases. Two of cases were identified as D-variants, weak D type-1 and 11. The frequency of RhD negative homozygosity in the Cypriot population was estimated to be 7.2%, while the frequencies of RHD hemizygosity and RhD positive homozygosity was calculated to be 39.2 and 53.6%, respectively.

CONCLUSION

Fetal RHD genotyping can be accurately determined using cffDNA from maternal plasma. The implementation of the test has eliminated all use of unnecessary anti-D and reduced the total use of anti-D by 25.3% while achieving appropriate management of the RhD negative pregnancies.

Cell-free DNA: Comparison of Technologies

Cell-free fetal DNA screening for Down syndrome has gained rapid acceptance over the past few years with increasing market penetration. Three main laboratory methodologies are currently used: a massive parallel shotgun sequencing (MPSS), a targeted massive parallel sequencing (t-MPS) and a single nucleotide polymorphism (SNP) based approach. Although each of these technologies has its own advantages and disadvantages, the performance of all was shown to be comparable and superior to that of traditional first-trimester screening for the detection of trisomy 21 in a routine prenatal population. Differences in performance were predominantly shown for chromosomal anomalies other than trisomy 21. Understanding the limitations and benefits of each technology is essential for proper counseling to patients. These technologies, as well as few investigational technologies described in this review, carry a great potential beyond screening for the common aneuploidies.

The effect of chorionic villus sampling on the fraction of cell-free fetal DNA in maternal plasma

OBJECTIVE

This study aims to assess whether the fraction of cell-free fetal DNA (cffDNA) is different at 24 h or 7 days after chorionic villus sampling (CVS), compared to subjects that do not undergo CVS.

METHODS

Pregnant women undergoing CVS for genetic testing and matched subjects undergoing first trimester combined screening alone were enrolled between 11(0/7) and 13(6/7) weeks gestation. The fractions of cffDNA were compared before the procedure, 24 h after and 7 days after between CVS patients and ultrasound-only patients.

RESULTS

Forty-five women underwent CVS and 45 had ultrasound alone. The women undergoing CVS were, on average, older (36.8 years versus 28.5 years, p=0.001) and had a higher baseline fraction of cffDNA than women in the comparison group (11.4% versus 9.8%, p=0.033). Both groups had a decrease in the mean fraction of cffDNA after 24 h. After 7 days, the trend of the mean fraction of cffDNA continued to decline in the CVS group but began to trend toward an increase in the ultrasound only group.

CONCLUSIONS

CVS does not significantly increase the fraction of cell free fetal (placental) DNA in the maternal plasma. A downward trend in cffDNA in maternal plasma is seen at 24 h and 7 days following CVS compared to baseline.

Evaluation of an Improved Non-invasive Fetal Sex Determination in Haemophilia A Patients

BACKGROUND

Haemophilia A (HA) is the most severe sex-linked bleeding disorder that is characterized with non-controlled and often threatening Haemorrhage. Routine fetal sex determination in early pregnancy with Haemophilia is based on invasive procedures that can be dangerous to the mother and fetus.

AIM

The goal of this study is to present an improved assay for the non-invasive fetal sex determination using a Real-Time duplex PCR on the free fetal DNA (ffDNA) obtained from the maternal serum of the HA carriers.

MATERIALS AND METHODS

Blood samples were eventually collected from 23 pregnant HA carriers between the 8(th) and 12(th) weeks of gestation, and after amplification by duplex-PCR of the single copy of Y chromosome-specific sequence (SRY), the product was then subjected to Real-Time PCR analysis.

RESULTS

Data were compared with the outcome of chorionic villus sampling (CVS) and indicated that the SRY sequence was detected in 6 of 6 serum samples from male pregnancies and that sequence was absent in 9 samples where the fetus was female. The remaining samples determined without having the CVS positive samples.

CONCLUSION

We tried to develop a Real-Time duplex PCR for accurate diagnosis of fetal gender early in the pregnancy of HA carriers. This study has brought up two remarkable points, the first is the method's improvement with high specificity in sex determination, especially in screening of prenatal sex-linked disorders in male gender and the second is that fresh serum samples would be a good source for this purpose, advocated by similar studies carried out in this regard.

EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples

OBJETIVES

The extracellular DNA occurring in plasma-EDTA and serum is a biomarker of growing interest, especially in prenatal diagnosis and oncology. The objectives of the present study were to compare the DNase activity in these specimens and to investigate its ex-vivo impact over the circulating cell-free DNA yield (ccfDNA), using the circulating cell-free fetal DNA (ccffDNA) as a tool.

DESIGN AND METHODS

EDTA-plasma and serum from women bearing male fetus were submitted to an endogenous DNase activity assay based on qPCR hydrolysis probe degradation, they were treated with DNAse I to investigate the action of an exogenous nuclease and also submitted to different temperature conditions to investigate the temperature-dependent degradation of the ccffDNA. In all instances, all male ccffDNA were quantified by qPCR targeting the Y chromosome-specific sequence DYS-14. Moreover, a serial dilution of EDTA was added to nonanticoagulated plasma and serum before the endogenous DNAse activity assay, to investigate the EDTA-mediated inhibition of the blood's DNase.

RESULTS

The endogenous nuclease activity was 14.9-fold higher in serum compared to EDTA-plasma. The DNAse I treatment did not alter the ccffDNA yields in EDTA-plasma, but completely degraded it in serum. The addition of increasing doses of EDTA to nonanticoagulated plasma and serum resulted in a stepwise inhibition of their nucleases activity. Finally, we observed a much more pronounced temperature-mediated decrease on the ccffDNA amount in serum compared to EDTA-plasma.

CONCLUSION

The exogenous and endogenous DNases are more active in serum, the anticoagulant EDTA indirectly inhibits blood DNases, and consequently ccfDNA is protected from the blood's DNase preanalytical impact in EDTA-plasma.