Fetal genome profiling at 5 weeks of gestation after noninvasive isolation of trophoblast cells from the endocervical canal

A novel aptamer-based probe for the identification and enrichment of trophoblast cells

Trophoblast cells, which are shed into the maternal reproductive tract, are emerging as a valuable source for prenatal diagnostic cells. However, the current enrichment efficiency of these cells is inadequate for clinical purposes. The reliance on antibody-based cell recognition methods has been a significant barrier to developing more effective enrichment techniques. In our research, we employed systematic evolution of ligands by exponential enrichment (SELEX) technology to identify three aptamers that can specifically bind to the HLA-G protein, a unique marker on the surface of trophoblast cells. Through a process of meticulous truncation and optimization, we successfully developed the highly effective nucleic acid aptamer H4-2. Utilizing H4-2, we engineered a novel circulating microfluidic system that achieves an impressive 65 % enrichment efficiency for trophoblast cells. This advancement holds substantial promise for enhancing prenatal diagnostic methods that rely on intact foetal cells.

Limitations of Semi-Automated Immunomagnetic Separation of HLA-G-Positive Trophoblasts from Papanicolaou Smears for Prenatal Genetic Diagnostics

Background: In prenatal genetic diagnostics, the detection of single-gene defects relies on chorionic villus sampling (CVS) and amniocentesis, which carry a miscarriage risk of 0.2-0.3%. To mitigate this risk, fetal trophoblasts have been isolated from a Papanicolaou smear using Trophoblast Retrieval and Isolation from the Cervix (TRIC). However, this method is labor-intensive and has been shown to be challenging to implement in clinical practice. Here, we describe our experiences in using semi-automated immunomagnetic cell sorting for isolating trophoblasts from clinically obtained Papanicolaou smears during ongoing pregnancies. Methods: Using HLA-G-positive Jeg-3 and HLA-G-negative HeLa cell lines in 10%, 1%, and 0.1% dilutions, we tested and optimized the isolation of HLA-G-positive cells using FACS and semi-automated immunomagnetic cell sorting. We used the latter technique for isolation of HLA-G-positive cells from Papanicolaou smears collected from 26 pregnant women, gestational age between 6 and 20 weeks, who underwent CVS. Results: In four independent dilution series, the mean percentages of Jeg-3 cells went from 7.1% to 53.5%, 0.9% to 32.6%, and 0.4% to 2.6% (7.5, 36, and 6.5-fold enrichment, respectively) using immunomagnetic cell sorting. After sorting of the Papanicolaou smears, HLA-G-positive cells were moderately increased in the positive (14.61 vs. 11.63%) and decreased in the negative fraction (7.87 vs. 11.63%) compared to baseline pre-sorting. However, we could not identify fetal cells using XY-chromosomal FISH in a male sample. Conclusions: Our study supports previous findings that careful sampling of fetal cells from Papanicolaou smears in a clinical context poses significant challenges to cell retrieval.

Non-Invasive Prenatal Diagnosis of Chromosomal and Monogenic Disease by a Novel Bioinspired Micro-Nanochip for Isolating Fetal Nucleated Red Blood Cells

Purpose

Fetal nucleated red blood cells (fNRBCs) in the peripheral blood of pregnant women contain comprehensive fetal genetic information, making them an ideal target for non-invasive prenatal diagnosis (NIPD). However, challenges in identifying, enriching, and detecting fNRBCs limit their diagnostic potential.

Methods

To overcome these obstacles, we developed a novel biomimetic chip, replicating the micro-nano structure of red rose petals on polydimethylsiloxane (PDMS). The surface was modified with gelatin nanoparticles (GNPs) and affinity antibodies to enhance cell adhesion and facilitate specific cell identification. We subsequently investigated the chip's characteristics, along with its in vitro capture and release system, and conducted further experiments using peripheral blood samples from pregnant women.

Results

In the cell line capture and release assay, the chip achieved a cell capture efficiency of 90.4%. Following metalloproteinase-9 (MMP-9) enzymatic degradation, the release efficiency was 84.08%, with cell viability at 85.97%. Notably, fNRBCs can be captured from the peripheral blood of pregnant women as early as 7 weeks of gestation. We used these fNRBCs to diagnose a case of single-gene disease and instances of chromosomal aneuploidies, yielding results consistent with those obtained from amniotic fluid punctures.

Conclusion

This novel chip not only enables efficient enrichment of fNRBCs for NIPD but also extends the diagnostic window for genetic and developmental disorders to as early as 7 weeks of gestation, potentially allowing for earlier interventions. By improving the accuracy and reliability of NIPD, this technology could reduce reliance on invasive diagnostic techniques, offering a new pathway for diagnosing fetal genetic conditions in clinical practice.

Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities

Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.

A Novel Paradigm for Non-Invasive Prenatal Genetic Screening: Trophoblast Retrieval and Isolation from the Cervix (TRIC)

As the prevalence of pregnancies with advanced maternal age increases, the risk of fetal chromosomal abnormalities is on the rise. Therefore, prenatal genetic screening and diagnosis have become essential elements in contemporary obstetrical care. Trophoblast retrieval and isolation from the cervix (TRIC) is a non-invasive procedure that can be utilized for prenatal genetic diagnosis. The method involves the isolation of fetal cells (extravillous trophoblasts) by transcervical sampling; along with its non-invasiveness, TRIC exhibits many other advantages such as its usefulness in early pregnancy at 5 weeks of gestation, and no interference by various fetal and maternal factors. Moreover, the trophoblast yields from TRIC can provide valuable information about obstetrical complications related to abnormal placentation even before clinical symptoms arise. The standardization of this clinical tool is still under investigation, and the upcoming advancements in TRIC are expected to meet the increasing need for a safe and accurate option for prenatal diagnosis.

Genetics in prenatal diagnosis

The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.

Tricky TRIC: A replication study using trophoblast retrieval and isolation from the cervix to study genetic birth defects

OBJECTIVE

Noninvasive Prenatal Diagnosis has recently been introduced for a limited number of monogenetic disorders. However, the majority of DNA diagnostics still require fetal material obtained using an invasive test. Recently, a novel technique, TRIC (Trophoblast Retrieval and Isolation from the Cervix), has been described, which collects fetal trophoblast cells by endocervical sampling. Since this technique has not been successfully replicated by other groups, we aimed to achieve this in the current study.

METHOD

Pregnant women referred for transvaginal chorionic villous sampling (CVS) were asked for an endocervical sample prior to CVS. The TRIC samples were processed to isolate trophoblast DNA. TRIC DNA was used in ForenSeq to determine the amount of maternal DNA contamination, and for Sanger sequencing in case of a monogenic disorder.

RESULTS

23%-44% of samples had a sufficiently high fetal DNA fraction to allow genetic testing, as calculated by Sanger sequencing and ForenSeq, respectively.

CONCLUSION

We have been able to successfully replicate the TRIC protocol, although with a much lower success rate as described by the original study performing TRIC. As we obtained the samples in the actual clinical setting envisioned, the method in its current setup is not advisable for use in prenatal diagnostics.

Whole-Chromosome Karyotyping of Fetal Nucleated Red Blood Cells Using the Ion Proton Sequencing Platform

The current gold standard for the definitive diagnosis of fetal aneuploidy uses either chorionic villus sampling (CVS) or amniocentesis, both of which are which are invasive procedures carrying a procedure-related risk of miscarriage of up to 0.1-0.2%. Non-invasive prenatal diagnosis using fetal nucleated red blood cells (FNRBCs) isolated from maternal peripheral venous blood would remove this risk of miscarriage since these cells can be isolated from the mother's blood. We aimed to detect whole-chromosome aneuploidies from single nucleated fetal red blood cells using whole-genome amplification followed by massively parallel sequencing performed on a semiconductor sequencing platform. Twenty-six single cells were picked from the placental villi of twelve patients thought to have a normal fetal genotype and who were undergoing elective first-trimester surgical termination of pregnancy. Following karyotyping, it was subsequently found that two of these cases were also abnormal (one trisomy 15 and one mosaic genotype). One single cell from chorionic villus samples for two patients carrying a fetus with trisomy 21 and two single cells from women carrying fetuses with T18 were also picked. Pooled libraries were sequenced on the Ion Proton and data were analysed using Ion Reporter software. We correctly classified fetal genotype in all 24 normal cells, as well as the 2 T21 cells, the 2 T18 cells, and the two T15 cells. The two cells picked from the fetus with a mosaic result by CVS were classified as unaffected, suggesting that this was a case of confined placental mosaicism. Fetal sex was correctly assigned in all cases. We demonstrated that semiconductor sequencing using commercially available software for data analysis can be achieved for the non-invasive prenatal diagnosis of whole-chromosome aneuploidy with 100% accuracy.

Rarity of fetal cells in exocervical samples for noninvasive prenatal diagnosis

OBJECTIVES

The possibility to isolate fetal cells from pregnant women cervical samples has been discussed for five decades but is not currently applied in clinical practice. This study aimed at offering prenatal genetic diagnosis from fetal cells obtained through noninvasive exocervical sampling and immuno-sorted based on expression of HLA-G.

METHODS

We first developed and validated robust protocols for cell detection and isolation on control cell lines expressing (JEG-3) or not (JAR) the HLA-G antigen, a specific marker for extravillous trophoblasts. We then applied these protocols to noninvasive exocervical samples collected from pregnant women between 6 and 14 weeks of gestational age. Sampling was performed through insertion and rotation of a brush at the ectocervix close to the external os of the endocervical canal. Finally, we attempted to detect and quantify trophoblasts in exocervical samples from pregnant women by ddPCR targeting the male SRY locus.

RESULTS

For immunohistochemistry, a strong specific signal for HLA-G was observed in the positive control cell line and for rare cells in exocervical samples, but only in non-fixative conditions. HLA-G positive cells diluted in HLA-G negative cells were isolated by flow cytometry or magnetic cell sorting. However, no HLA-G positive cells could be recovered from exocervical samples. SRY gene was detected by ddPCR in exocervical samples from male (50%) but also female (27%) pregnancies.

CONCLUSIONS

Our data suggest that trophoblasts are too rarely and inconstantly present in noninvasive exocervical samples to be reliably retrieved by standard immunoisolation techniques and therefore cannot replace the current practice for prenatal screening and diagnosis.

Specific innate immune cells uptake fetal antigen and display homeostatic phenotypes in the maternal circulation

Pregnancy represents a period when the mother undergoes significant immunological changes to promote tolerance of the fetal semi-allograft. Such tolerance results from the exposure of the maternal immune system to fetal antigens (Ags), a process that has been widely investigated at the maternal-fetal interface and in the adjacent draining lymph nodes. However, the peripheral mechanisms of maternal-fetal crosstalk are poorly understood. Herein, we hypothesized that specific innate immune cells interact with fetal Ags in the maternal circulation. To test this hypothesis, a mouse model was utilized in which transgenic male mice expressing the chicken ovalbumin (OVA) Ag under the beta-actin promoter were allogeneically mated with wild-type females to allow for tracking of the fetal Ag. Fetal Ag-carrying Ly6G+ and F4/80+ cells were identified in the maternal circulation, where they were more abundant in the second half of pregnancy. Such innate immune cells displayed unique phenotypes: while Ly6G+ cells expressed high levels of MHC-II and CD80 together with low levels of pro-inflammatory cytokines, F4/80+ cells up-regulated the expression of CD86 as well as the anti-inflammatory cytokines IL-10 and TGF-β. In vitro studies using allogeneic GFP+ placental particles revealed that maternal peripheral Ly6G+ and F4/80+ cells phagocytose fetal Ags in mid and late murine pregnancy. Importantly, cytotrophoblast-derived particles were also engulfed in vitro by CD15+ and CD14+ cells from women in the second and third trimester, providing translational evidence that this process also occurs in humans. Collectively, this study demonstrates novel interactions between specific maternal circulating innate immune cells and fetal Ags, thereby shedding light on the systemic mechanisms of maternal-fetal crosstalk.

Research Progress in Isolation and Enrichment of Fetal Cells from Maternal Blood

Prenatal diagnosis is an important means of early diagnosis of genetic diseases, which can effectively reduce the risk of birth defects. Free fetal cells, as a carrier of intact fetal genetic material, provide hope for the development of high-sensitivity and high-accuracy prenatal diagnosis technology. However, the number of fetal cells is small and it is difficult to apply clinically. In recent years, noninvasive prenatal diagnosis (NIPD) technology for fetal genetic material in maternal peripheral blood has developed rapidly, which makes it possible to diagnose genetic diseases by fetal cells in maternal peripheral blood. This article reviewed the current status of fetal cell separation and enrichment technology and its application in noninvasive prenatal diagnosis technology.

Overview and recent developments in cell-based noninvasive prenatal testing

Investigators have long been interested in the natural phenomenon of fetal and placental cell trafficking into the maternal circulation. The scarcity of these circulating cells makes their detection and isolation technically challenging. However, as a DNA source of fetal origin not mixed with maternal DNA, they have the potential of considerable benefit over circulating cell-free DNA-based noninvasive prenatal genetic testing (NIPT). Endocervical trophoblasts, which are less rare but more challenging to recover are also being investigated as an approach for cell-based NIPT. We review published studies from around the world describing both forms of cell-based NIPT and highlight the different approaches' advantages and drawbacks. We also offer guidance for developing a sound cell-based NIPT protocol.

Enrichment of Placental Trophoblast Cells from Clinical Cervical Samples Using Differences in Surface Adhesion on an Inclined Plane

Placental trophoblast cells present in cervical samples have great potential towards non-invasive prenatal testing. However, cervical samples are highly heterogeneous, largely comprised of maternal cervical cells with only a small quantity of trophoblast cells. In order to use these rare cells for diagnostic applications, there is a need to enrich and isolate them from the heterogeneous maternal sample. Our goal was to investigate the use of gravitational flow on an inclined surface and optimize parameters including angle of incline, surface material, incubation time on the surface, solution volume, and device channel width in order to identify a design allowing label-free enrichment of trophoblast cells. In this work we detail the development of a new method and device for controlling cell adhesion to a surface vs. rolling into a collection area. The enrichment device design was developed for ease of use by non-specialized personal and on a slide surface for the ability to be directly integrated onto an automatic cell picker instrument, which can be used for downstream single cell isolation. JEG-3 trophoblast cells were used with clinical cervical samples to present the effect of the different optimization parameters on enrichment. We further provide an assessment of the impact shear stress and thickness of the liquid layer has on cell enrichment. We found that this method provides a maximum JEG-3 enrichment using polystyrene surfaces at a 50° incline with a 5 min incubation period prior to inclined flow. This resulted in a 396 ± 52% increase in purity of the trophoblast cells from the clinical cervical samples as confirmed using human leukocyte antigen G (HLA-G) antibody staining with fluorescence imaging to identify JEG-3 cells. Ultimately, this method is inexpensive, quick, and has the potential for direct integration into fetal cell isolation platforms.

Isolation of mesenchymal stem cells from Pap smear samples

Objective

Exploiting their ability to differentiate into mesenchymal lineages like cartilage, bone, fat, and muscle, and to elicit paracrine effects, mesenchymal stem cells (MSCs) are widely used in clinical settings to treat tissue injuries and autoimmune disorders. One of accessible sources of MSC is the samples used for Papanicolaou (Pap) test, which is a cervical screening method for detecting potentially pre-cancerous and cancerous alterations in the cervical cells and to diagnose genetic abnormalities in fetuses. This study aimed to identify and isolate the stem cells from Pap smear samples collected from pregnant women, and to trace the origin of these cells to maternal or fetal tissue, and characterize their stem cell properties.

Methods

To investigate the possibility and efficiency of establishing MSC lines from the Pap smear samples, we were able to establish 6 cell lines from Pap smear samples from 60 pregnant women at different stages of gestation.

Results

The 3 cell lines randomly selected among the 6 established in this study, displayed high proliferation rates, several characteristics of MSCs, and the capacity to differentiate into adipocytes, osteocytes, and chondrocytes. Our study identified that the stem cell lines obtainable from Pap smear sampling were uterine cervical stromal cells (UCSCs) and had 10% efficiency of establishment.

Conclusion

Despite their low efficiency of establishment, human UCSCs from Pap smear samples can become a simple, safe, low-cost, and donor-specific source of MSCs for stem cell therapy and regenerative medicine.

Optimization Protocol of Fixation Method for Trophoblast Retrieval from the Cervix (TRIC): A Preliminary Study

Extravillous trophoblast cells (EVTs) secreted by the uterine cavity may help overcome limitations associated with prenatal testing currently in use. EVTs are isolated using a routine safe liquid-based Pap test (called ThinPrep); however, the ThinPrep solution contains alcohol that hinders the isolation of intact EVTs. We compared the trophoblastic cell isolation efficiency of two different methods of fixation: Thinprep (pre-fixation method) and formalin (post-fixation method). We analyzed EVTs from 20 pregnant women (5-20 weeks of gestation) who underwent invasive prenatal testing. The percentages of placental β-human chorionic gonadotropin (β-hCG)-expressing cells were calculated. The presence of XY chromosomes were used to confirm pure trophoblast cells by fluorescence in situ hybridization. The β-hCG-positive cells obtained from pre- and post-fixation were 66.4 ± 13.3% and 83.2 ± 8.1% (p = 0.003), respectively, and fluorescence-positive cells were 11.1 ± 2.1% and 23.8 ± 4.8%, respectively (p = 0.001). Post-fixation was found to be more efficient in isolating non-trophoblast cells than pre-fixation. For the successful clinical application of trophoblast retrieval and isolation from the cervix in prenatal genetic testing, each step should be optimized for consistent and reliable results.

Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases

Noninvasive prenatal detection of monogenic diseases based on cell-free DNA is hampered by challenges in obtaining a sufficient fraction and adequate quality of fetal DNA. Analyzing rare trophoblastic cells from Papanicolaou smears carrying the entire fetal genome provides an alternative method for noninvasive detection of monogenic diseases. However, intracellular labeling for identification of target cells can affect the quality of DNA in varying degrees. Here, a new approach is developed for nondestructive identification of rare fetal cells from abundant maternal cells based on endoplasmic reticulum staining and linear discriminant analysis (ER-LDA). Compared with traditional methods, ER-LDA has little effect on cell quality, allowing trophoblastic cells to be analyzed on the single-cell level. Using ER-LDA, high-purity of trophoblastic cells can be identified and isolated at single cell resolution from 60 pregnancies between 4 and 38 weeks of gestation. Pathogenic variants, including -SEA/ deletion mutation and point mutations, in 11 fetuses at risk for α- or β-thalassemia can be accurately detected by this test. The detection platform can also be extended to analyze the mutational profiles of other monogenic diseases. This simple, low-cost, and noninvasive test can provide valuable fetal cells for fetal genotyping and holds promise for prenatal detection of monogenic diseases.

Status of medical genomics and genetics education in maternal-fetal medicine: survey of program directors and clinical fellows in the USA

Objective: The study aimed to assess the current state of medical genetics and genomics (MGG) education amongst maternal-fetal medicine (MFM) program directors (PDs) and clinical fellows.Methods: An online questionnaire was generated and distributed to all current program directors and fellows in ACGME-accredited MFM fellowships across the USA in 2018.Results: A total of 13 program directors and 54 MFM fellows responded to our survey. Of the respondents, 73% of the MFM fellows mentioned having dedicated structured MGG rotations as part of their training. Only 12% of fellows reported a high level of satisfaction with their programs' structured MGG rotations and almost 40% reported dissatisfaction, compared to 56% of PDs who reported very high satisfaction. Furthermore, 84% of PDs reported high levels of satisfaction with MGG didactics currently in place compared to only 24% of fellows sharing the same opinion. When compared to PDs, fellows reported a significantly lower satisfaction score toward their MGG rotations (p < .05) and didactic sessions (p < .05). More than 62% of PDs were satisfied with the number of MGG-faculty in their division compared to 80% of fellows who thought more faculty is needed. Thirty-eight percent of PDs quoted curricular overload and lack of time as the most important obstacles to MGG education, compared to 43% of fellows citing a limited number of genetics services providers as the most important obstacles to their MGG education.Conclusion: MFM fellows and PDs differ in their satisfaction with the current state of MGG didactics and rotations in their programs, the number of MGG faculty in their divisions, and the perceived obstacles to MGG education . Our study illustrates the need for MGG curriculum development in MFM fellowships as this subspecialty relies heavily on the use of genetics and genomics services.

Nanostructured Substrates for Detection and Characterization of Circulating Rare Cells: From Materials Research to Clinical Applications

Circulating rare cells in the blood are of great significance for both materials research and clinical applications. For example, circulating tumor cells (CTCs) have been demonstrated as useful biomarkers for "liquid biopsy" of the tumor. Circulating fetal nucleated cells (CFNCs) have shown potential in noninvasive prenatal diagnostics. However, it is technically challenging to detect and isolate circulating rare cells due to their extremely low abundance compared to hematologic cells. Nanostructured substrates offer a unique solution to address these challenges by providing local topographic interactions to strengthen cell adhesion and large surface areas for grafting capture agents, resulting in improved cell capture efficiency, purity, sensitivity, and reproducibility. In addition, rare-cell retrieval strategies, including stimulus-responsiveness and additive reagent-triggered release on different nanostructured substrates, allow for on-demand retrieval of the captured CTCs/CFNCs with high cell viability and molecular integrity. Several nanostructured substrate-enabled CTC/CFNC assays are observed maturing from enumeration and subclassification to molecular analyses. These can one day become powerful tools in disease diagnosis, prognostic prediction, and dynamic monitoring of therapeutic response-paving the way for personalized medical care.

Considerations for whole exome sequencing unique to prenatal care

Whole exome sequencing (WES) is increasingly being used in the prenatal setting. The emerging data support the clinical utility of prenatal WES based on its diagnostic yield, which can be as high as 80% for certain ultrasound findings. However, detailed practice and laboratory guidelines, addressing the indications for prenatal WES and the surrounding technical, interpretation, ethical, and counseling issues, are still lacking. Herein, we review the literature and summarize the most recent findings and applications of prenatal WES. This review offers specialists and clinical genetic laboratorians a body of evidence and expert opinions that can serve as a resource to assist in their practice. Finally, we highlight the emerging technologies that promise a future of prenatal WES without the risks associated with invasive testing.

Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?

Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of NGS-based genetic testing in the context of rare disease diagnosis. We highlight the role of artificial intelligence (AI) in enhancing understanding and prioritization of variance in the clinical setting and propose deep learning frameworks for further investigation.

Noninvasive prenatal testing: from aneuploidy to single genes

Noninvasive prenatal testing has undergone rapid advances in the last few years. Although researchers have long known about circulating pregnancy-based cell-free fragments of DNA in maternal plasma, it was the introduction of massively parallel sequencing that allowed noninvasive prenatal testing to become a widely used clinical test. This review will begin with an in-depth analysis of the use of noninvasive prenatal testing for aneuploidy, including common causes for inaccurate and/or discordant results. It will also review the ongoing expansion of noninvasive prenatal testing to include copy number variants and select single-gene disorders. Finally, integrated throughout the review is a comparison of noninvasive prenatal testing to more traditional screening methods along with some medical and ethical implications of the widespread use of this new technology.

A Rapid Method for Label-Free Enrichment of Rare Trophoblast Cells from Cervical Samples

Extravillous trophoblasts (EVTs) have the potential to provide the entire fetal genome for prenatal testing. Previous studies have demonstrated the presence of EVTs in the cervical canal and the ability to retrieve a small quantity of these cells by cervical sampling. However, these small quantities of trophoblasts are far outnumbered by the population of cervical cells in the sample, making isolation of the trophoblasts challenging. We have developed a method to enrich trophoblast cells from a cervical sample using differential settling of the cells in polystyrene wells. We tested the addition of small quantities of JEG-3 trophoblast cell line cells into clinical samples from standard Pap tests taken at 5 to 20 weeks of gestation to determine the optimal work flow. We observed that a 4 min incubation in the capture wells led to a maximum in JEG-3 cell settling on the surface (71 ± 10% of the initial amount added) with the removal of 91 ± 3% of the cervical cell population, leading to a 700% enrichment in JEG-3 cells. We hypothesized that settling of mucus in the cervical sample affects the separation. Finally, we performed a proof-of-concept study using our work flow and CyteFinder cell picking to verify enrichment and pick individual JEG-3 and trophoblast cells free of cervical cells. Ultimately, this work provides a rapid, facile, and cost-effective method for enriching native trophoblasts from cervical samples for use in subsequent non-invasive prenatal testing using methods including single cell picking.

The national blueprint for pregnancy/birth longitudinal cohorts to study factor VIII immunogenicity: NHLBI State of the Science (SOS) Workshop on factor VIII inhibitors

INTRODUCTION

Patients with haemophilia can develop inhibitors to exogenous coagulation factors. Some patients are tolerant to factor, while those who develop inhibitors do so early in life. Genetics and environmental factors are known to contribute to inhibitor risk. However, it is not yet possible to predict inhibitor formation or treatment responsiveness in individuals. We hypothesize that factors in the antenatal/neonatal period inform inhibitor risk development.

AIM

To consider the design of longitudinal studies beginning in the antenatal/neonatal period and the use of new technologies to better understand haemophilia inhibitors.

METHODS

A working group was formed for the NHLBI State of the Science Workshop: Factor VIII Inhibitors: Generating a National Blueprint for Future Research to solicit input from the US haemophilia community and international collaborators to consider design of pregnancy/birth longitudinal cohorts that leverage -omics, existing phenotypic data, and in silico modelling to study inhibitors.

RESULTS

An antenatal/neonatal longitudinal cohort should begin with enrolment of pregnant genetic carriers of haemophilia and span the at-risk period for inhibitor development in the child. Data and samples from the mother, placenta, neonate and young child can be obtained that are amenable to existing assays, genomics and other -omics studies. Data can inform in silico prediction and mathematical models.

CONCLUSION

A longitudinal study beginning before birth offers the unique opportunity to study factors that influence inhibitor development prior to exposure. Advances in -omics and computational biology can study complex phenotypes in this rare disease. This study could be accomplished through interdisciplinary efforts and patient community engagement.

Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing

Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.

Endocervical trophoblast for interrogating the fetal genome and assessing pregnancy health at five weeks

Prenatal testing for fetal genetic traits and risk of obstetrical complications is essential for maternal-fetal healthcare. The migration of extravillous trophoblast (EVT) cells from the placenta into the reproductive tract and accumulation in the cervix offers an exciting avenue for prenatal testing and monitoring placental function. These cells are obtained with a cervical cytobrush, a routine relatively safe clinical procedure during pregnancy, according to published studies and our own observations. Trophoblast retrieval and isolation from the cervix (TRIC) obtains hundreds of fetal cells with >90% purity as early as five weeks of gestation. TRIC can provide DNA for fetal genotyping by targeted next-generation sequencing with single-nucleotide resolution. Previously, we found that known protein biomarkers are dysregulated in EVT cells obtained by TRIC in the first trimester from women who miscarry or later develop intrauterine growth restriction or preeclampsia. We have now optimized methods to stabilize RNA during TRIC for subsequent isolation and analysis of trophoblast gene expression. Here, we report transcriptomics analysis demonstrating that the expression profile of TRIC-isolated trophoblast cells was distinct from that of maternal cervical cells and included genes associated with the EVT phenotype and invasion. Because EVT cells are responsible for remodeling the maternal arteries and their failure is associated with pregnancy disorders, their molecular profiles could reflect maternal risk, as well as mechanisms underlying these disorders. The use of TRIC to analyze EVT genomes, transcriptomes and proteomes during ongoing pregnancies could provide new tools for anticipating and managing both fetal genetic and maternal obstetric disorders.

Noninvasive Prenatal Diagnostics: Recent Developments Using Circulating Fetal Nucleated Cells

PURPOSE OF REVIEW

The purpose of this review is to highlight recent research advances in noninvasive prenatal diagnostic methods.

RECENT FINDINGS

Recent studies developing noninvasive prenatal diagnostic (NIPD) methods have been focused on either fetal nucleated red blood cells (fNRBCs) or circulating trophoblasts (cTBs). Enriched cTBs were successfully utilized for whole genome profiling and short tandem repeat (STR) identification to confirm feto-maternal relationship. However, further analysis of isolated fNRBCs remains confined to examining fetal cytogenetics.

SUMMARY

Invasive prenatal diagnostic procedures, amniocentesis and chorionic villus sampling, are the gold standard for the diagnosis of fetal chromosomal abnormalities and genetic disorders. Meanwhile, noninvasive techniques of analyzing circulating cell-free fetal DNA (cffDNA) have been limited to screening tools and are highly fragmented and confounded by maternal DNA. By detecting circulating fetal nucleated cells (CFNCs) we are able to noninvasively confirm fetal chromosomal abnormalities, truly realizing the concept of "noninvasive prenatal diagnostics". The primary technical challenge is the enrichment of the low abundance of CFNCs in maternal peripheral blood. For any cell-based NIPD method, both fetal whole genome profiling and confirmation of the feto-parental relationship are essential. This has been successfully performed using enriched and isolated cTBs, making cTB a better candidate for NIPD. cTB enumeration also correlates with abnormal fetal or placental development. On the other hand, downstream analysis of fNRBCs remains limited to examining fetal sex and aneuploidies. Furthermore, trophoblast-based NIPD via an endocervical sample is also promising because of reduced dilution from hematologic cells.

A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing

New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from maternal blood, CFCs have a strong potential to bridge the gap between the diagnostic sensitivity of invasive procedures and the desirable noninvasive nature of cell-free fetal DNA (cffDNA). Considering the rapid advances in both rare cell isolation and low-input DNA analysis, we argue here that CFC-based noninvasive prenatal testing is poised to be implemented clinically in the near future.

Bi-stream CNN Down Syndrome screening model based on genotyping array

BACKGROUND

Human Down syndrome (DS) is usually caused by genomic micro-duplications and dosage imbalances of human chromosome 21. It is associated with many genomic and phenotype abnormalities. Even though human DS occurs about 1 per 1,000 births worldwide, which is a very high rate, researchers haven't found any effective method to cure DS. Currently, the most efficient ways of human DS prevention are screening and early detection.

METHODS

In this study, we used deep learning techniques and analyzed a set of Illumina genotyping array data. We built a bi-stream convolutional neural networks model to screen/predict the occurrence of DS. Firstly, we built image input data by converting the intensities of each SNP site into chromosome SNP maps. Next, we proposed a bi-stream convolutional neural network (CNN) architecture with nine layers and two branch models. We further merged two CNN branch models into one model in the fourth convolutional layer, and output the prediction in the last layer.

RESULTS

Our bi-stream CNN model achieved 99.3% average accuracies, and very low false-positive and false-negative rates, which was necessary for further applications in disease prediction and medical practice. We further visualized the feature maps and learned filters from intermediate convolutional layers, which showed the genomic patterns and correlated SNPs variations in human DS genomes. We also compared our methods with other CNN and traditional machine learning models. We further analyzed and discussed the characteristics and strengths of our bi-stream CNN model.

CONCLUSIONS

Our bi-stream model used two branch CNN models to learn the local genome features and regional patterns among adjacent genes and SNP sites from two chromosomes simultaneously. It achieved the best performance in all evaluating metrics when compared with two single-stream CNN models and three traditional machine-learning algorithms. The visualized feature maps also provided opportunities to study the genomic markers and pathway components associated with Human DS, which provided insights for gene therapy and genomic medicine developments.

Thalassemia in the laboratory: pearls, pitfalls, and promises

Thalassemia is one of the most common hereditary disorders of the developing world, and it is associated with severe anemia and transfusion dependence. The global health burden of thalassemia has increased as a result of human mobility and migration in recent years. Depending on inherited mutations, thalassemia patients exhibit distorted hemoglobin (Hb) patterns and deviated red cell indices, both of which can be used to support identification by diagnostic tools. Diagnostic approaches vary depending on the target population and the aim of the testing. Current methods, which are based on Hb patterns, are used for first-line screening, whereas molecular testing is needed for conformation of the results and for prenatal and preimplantation genetic diagnosis. In the present paper, we review the diagnostic parameters, pitfalls, interfering factors, and methods; currently available best-practice guidelines; quality assurance and standardization of the procedures; and promising laboratory technologies for the future of thalassemia diagnosis.

Trophoblast retrieval and isolation from the cervix: origins of cervical trophoblasts and their potential value for risk assessment of ongoing pregnancies

BACKGROUND

Early during human development, the trophoblast lineage differentiates to commence placentation. Where the placenta contacts the uterine decidua, extravillous trophoblast (EVT) cells differentiate and invade maternal tissues. EVT cells, identified by expression of HLA-G, invade into uterine blood vessels (endovascular EVT), as well as glands (endoglandular EVT), and open such luminal structures towards the intervillous space of the placenta. Endoglandular invasion diverts the contents of uterine glands to the intervillous space, while glands near the margin of the placenta that also contain endoglandular EVT cells open into the reproductive tract. Cells of the trophoblast lineage have thus been recovered from the uterine cavity and endocervical canal. An emerging non-invasive technology [trophoblast retrieval and isolation from the cervix (TRIC)] isolates and examines EVT cells residing in the cervix to explore their origin, biology and relationship to pregnancy and fetal status.

OBJECTIVE AND RATIONALE

This review explores the origins and possible uses of trophoblast cells obtained during ongoing pregnancies (weeks 5-20) by TRIC. We hypothesize that endoglandular EVT cells at the margins of the expanding placenta enter the uterine cavity and are carried together with uterine secretion products to the cervix where they can be retrieved from a Papanicolaou (Pap) smear. The advantages of TRIC for investigation of human placentation and prenatal testing will be considered. Evidence from the literature, and from archived in utero placental histological sections, is presented to support these hypotheses.

SEARCH METHODS

We used 52 out of 80 publications that appeared between 1966 and 2017 and were found by searching the PubMed and Google Scholar databases. The studies described trophoblast invasion of uterine vessels and glands, as well as trophoblast cells residing in the reproductive tract. This was supplemented with literature on human placental health and disease.

OUTCOMES

The literature describes a variety of invasive routes taken by EVT cells at the fetal-maternal interface that could displace them into the reproductive tract. Since the 1970s, investigators have attempted to recover trophoblast cells from the uterus or cervix for prenatal diagnostics. Trophoblast cells from Pap smears obtained at 5-20 weeks of gestation have been purified (>95% β-hCG positive) by immunomagnetic isolation with nanoparticles linked to anti-HLA-G (TRIC). The isolated cells contain the fetal genome, and have an EVT-like expression profile. Similar EVT-like cells appear in the lumen of uterine glands and can be observed entering the uterine cavity along the margins of the placenta, suggesting that they are the primary source of cervical trophoblast cells. Cells isolated by TRIC can be used to accurately genotype the embryo/fetus by targeted next-generation sequencing. Biomarker protein expression quantified in cervical trophoblast cells after TRIC correlates with subsequent pregnancy loss, pre-eclampsia and fetal growth restriction. A key remaining question is the degree to which EVT cells in the cervix might differ from those in the basal plate and placental bed.

WIDER IMPLICATIONS

TRIC could one day provide a method of risk assessment for maternal and fetal disease, and reveal molecular pathways disrupted during the first trimester in EVT cells associated with placental maldevelopment. As perinatal interventions emerge for pregnancy disorders and inherited congenital disorders, TRIC could provide a key diagnostic tool for personalized precision medicine in obstetrics.

Noninvasive prenatal diagnosis for single gene disorders

PURPOSE OF REVIEW

Noninvasive prenatal diagnosis for single gene disorders is coming to fruition in its clinical utility. The presence of cell-free DNA in maternal plasma has been recognized for many years, and a number of applications have developed from this. Noninvasive prenatal diagnosis for single gene disorders has lagged behind due to complexities of technology development, lack of investment and the need for validation samples for rare disorders.

RECENT FINDINGS

Publications are emerging demonstrating a variety of technical approaches and feasibility of clinical application. Techniques for analysis of cell-free DNA including digital PCR, next-generation sequencing and relative haplotype dosage have been used most often for assay development. Analysis of circulating fetal cells in the maternal blood is still being investigated as a viable alternative and more recently transcervical trophoblast cells. Studies exploring ethical and social issues are generally positive but raise concerns around the routinization of prenatal testing.

SUMMARY

Further work is necessary to make testing available to all patients with a pregnancy at risk of a single gene disorder, and it remains to be seen if the development of more powerful technologies such as isolation and analysis of single cells will shift the emphasis of noninvasive prenatal diagnosis. As testing becomes possible for a wider range of conditions, more ethical questions will become relevant.

Quo vadis, trophoblast? Exploring the new ways of an old cell lineage

Trophoblast cells are the first embryonic lineage to differentiate during human development, and are needed to sustain fetal life through their role in constructing a placenta. As the fetus grows, the trophoblast rapidly expands and further differentiates to produce an extravillous subtype that invades the maternal tissues. Some of the extravillous trophoblast cells find their way into the reproductive tract, and can be safely captured by noninvasive collection from the endocervical canal, similarly to a Pap smear. We are developing a new technology for investigating trophoblast cells residing in the cervix to better understand their development, and to glean information from them about pregnancy status. Trophoblast retrieval and isolation from the cervix (TRIC) efficiently isolates hundreds of trophoblast cells without limitations due to early gestational age, maternal obesity, or uteroplacental insufficiency disorders. Cells that appear to be extravillous trophoblast, based on their molecular phenotype, can be purified from Pap smears obtained between 5 and 20 weeks of gestation, using magnetic nanoparticles coupled to an antibody recognizing HLA-G that they specifically produce. Information about fetal genotype and adverse pregnancy outcomes has been obtained using TRIC, and could one day provide assessment of maternal and fetal risk of disease. As perinatal interventions for placental disorders and inherited congenital disorders emerge, TRIC could provide a key diagnostic tool for personalize precision pregnancy management.

Imprinted NanoVelcro Microchips for Isolation and Characterization of Circulating Fetal Trophoblasts: Toward Noninvasive Prenatal Diagnostics

Circulating fetal nucleated cells (CFNCs) in maternal blood offer an ideal source of fetal genomic DNA for noninvasive prenatal diagnostics (NIPD). We developed a class of nanoVelcro microchips to effectively enrich a subcategory of CFNCs, i.e., circulating trophoblasts (cTBs) from maternal blood, which can then be isolated with single-cell resolution by a laser capture microdissection (LCM) technique for downstream genetic testing. We first established a nanoimprinting fabrication process to prepare the LCM-compatible nanoVelcro substrates. Using an optimized cTB-capture condition and an immunocytochemistry protocol, we were able to identify and isolate single cTBs (Hoechst+/CK7+/HLA-G+/CD45-, 20 μm > sizes > 12 μm) on the imprinted nanoVelcro microchips. Three cTBs were polled to ensure reproducible whole genome amplification on the cTB-derived DNA, paving the way for cTB-based array comparative genomic hybridization (aCGH) and short tandem repeats analysis. Using maternal blood samples collected from expectant mothers carrying a single fetus, the cTB-derived aCGH data were able to detect fetal genders and chromosomal aberrations, which had been confirmed by standard clinical practice. Our results support the use of nanoVelcro microchips for cTB-based noninvasive prenatal genetic testing, which holds potential for further development toward future NIPD solution.

Expanding Use of cfDNA Screening in Pregnancy: Current and Emerging Ethical, Legal, and Social Issues

Purpose of Review

In 2011, screening platforms became available in the US that detect and analyze fragments of cell-free placental DNA (cfDNA) in maternal blood serum. Marketed as noninvasive prenatal tests (NIPT), cfDNA screening is more accurate than previously available serum screening tests for certain aneuploidies. The combination of a noninvasive procedure, high specificity and sensitivity, and lower false positive rates for some aneuploidies (most notably Down's syndrome) has led to broad clinician and patient adoption. New ethical, legal, and social issues arise from the increased use and expanded implementation of cfDNA in pregnancy.

Recent Findings

Recently, several professional associations have amended their guidelines on cfDNA, removing language recommending its use in only "high-risk" pregnancies in favor of making cfDNA screening an available option for women with "low-risk" pregnancies as well. At the same time, commercial cfDNA screening laboratories continue to expand the range of available test panels. As a result, the future of prenatal screening will likely include a broader range of genetic tests in a wider range of patients.

Summary

This article addresses the ethical, legal, and social issues related to the shift in guidance and expanded use of cfDNA in pregnant women, including concerns regarding routinized testing, an unmet and increasing demand for genetic counseling services, social and economic disparities in access, impact on groups living with disabling conditions, and provider liability.