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

Precision medicine activities and opportunities for shaping maternal and neonatal health in Qatar

Precision Medicine (PM) is a transformative clinical medicine strategy that aims to revolutionize healthcare by leveraging biological information and biomarkers. In the context of maternal and neonatal health, PM enables personalized care from preconception through the postnatal period. Qatar has emerged as a key player in PM research, with dedicated programs driving advancements and translating cutting-edge research into clinical applications. This article delves into neonatal and maternal health in Qatar, emphasizing PM programs and initiatives that have been implemented. It also features noteworthy clinical cases that demonstrate the effectiveness of precision interventions. Furthermore, the article highlights the role of pharmacogenomics in addressing various maternal health conditions. The review further explores potential advancements in the application of PM in maternal and neonatal healthcare in Qatar.

Women's experiences with non-invasive prenatal testing in Switzerland: a qualitative analysis

BACKGROUND

Prenatal genetic testing, in particular non-invasive prenatal testing (NIPT), as well as screening for risks associated with pregnancy, and counseling, play pivotal roles in reproductive healthcare, offering valuable information about the health of the fetus to expectant parents. This study aims to delve into the perspectives and experiences of women considering genetic testing and screening during pregnancy, focusing on their decision-making processes and the implications for informed consent.

METHODS

A nationwide qualitative study was conducted in Switzerland, involving in-depth interviews with women who were 1 to 2 years post-partum, covered by basic compulsory Swiss insurance, including women with a migration background. Thematic analysis was employed to identify key themes and patterns in the data.

RESULTS

The findings underscore the significance of effective communication during prenatal counseling, suggesting that healthcare providers could not only convey technical information but also support women in their decision-making processes. Women need comprehensive information about genetic testing and its implications, as well as the reasons for screening during pregnancy, as there might be a need to bridge knowledge gaps and clarify misconceptions. Furthermore, the study highlights the multifaceted nature of decision-making, with women considering factors such as uncertainty, values, emotional responses, and societal support systems. The concept of acceptance emerged as a crucial theme, with some women expressing their readiness to love and accept their child, regardless of genetic anomalies or disabilities.

CONCLUSION

This study offers valuable insights into the perspectives and needs of women regarding prenatal genetic testing, screening, and counseling in Switzerland. It underscores the importance of enhancing the clinical interaction and informed consent process by providing comprehensive information, addressing misconceptions, and supporting women in decision-making about pregnancy management and the management of the child's health, following prenatal genetic testing, including NIPT. These findings can inform healthcare providers and policymakers in improving the quality of prenatal counseling, ensuring informed consent, and supporting women in making well-informed and meaningful decisions about genetic testing, and on the use of screening during pregnancy.

Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification

Complex diseases are caused by a combination of genetic, lifestyle, and environmental factors and comprise common noncommunicable diseases, including allergies, cardiovascular disease, and psychiatric and metabolic disorders. More than 25% of Europeans suffer from a complex disease, and together these diseases account for 70% of all deaths. The use of genomic, molecular, or imaging data to develop accurate diagnostic tools for treatment recommendations and preventive strategies, and for disease prognosis and prediction, is an important step toward precision medicine. However, for complex diseases, precision medicine is associated with several challenges. There is a significant heterogeneity between patients of a specific disease-both with regards to symptoms and underlying causal mechanisms-and the number of underlying genetic and nongenetic risk factors is often high. Here, we summarize precision medicine approaches for complex diseases and highlight the current breakthroughs as well as the challenges. We conclude that genomic-based precision medicine has been used mainly for patients with highly penetrant monogenic disease forms, such as cardiomyopathies. However, for most complex diseases-including psychiatric disorders and allergies-available polygenic risk scores are more probabilistic than deterministic and have not yet been validated for clinical utility. However, subclassifying patients of a specific disease into discrete homogenous subtypes based on molecular or phenotypic data is a promising strategy for improving diagnosis, prediction, treatment, prevention, and prognosis. The availability of high-throughput molecular technologies, together with large collections of health data and novel data-driven approaches, offers promise toward improved individual health through precision medicine.

Carbon-Based Flexible Devices for Comprehensive Health Monitoring

Traditional public health systems suffer from incomprehensive, delayed, and inefficient medical services. Convenient and comprehensive health monitoring has been highly sought after recently. Flexible and wearable devices are attracting wide attention due to their potential applications in wearable human health monitoring and care systems. Using carbon materials with overall superiorities can facilitate the development of wearable and flexible devices with various functions and excellent performance, which can comprehensively and real-time monitor human health status and prevent diseases. Herein, the latest advances in the rational design and controlled fabrication of carbon materials for applications in health-related flexible and wearable electronics are reviewed. The fabrication strategies, working mechanism, performance, and applications in health monitoring of carbon-based flexible devices, including electromechanical sensors, temperature/humidity sensors, chemical sensors, and flexible conductive wires/electrodes, are reviewed. Furthermore, integrating multiple carbon-based devices into multifunctional wearable systems is discussed. Finally, the existing challenges and future opportunities in this field are also proposed.

Airline Point-of-Care System on Seat Belt for Hybrid Physiological Signal Monitoring

With a focus on disease prevention and health promotion, a reactive and disease-centric healthcare system is revolutionized to a point-of-care model by the application of wearable devices. The convenience and low cost made it possible for long-term monitoring of health problems in long-distance traveling such as flights. While most of the existing health monitoring systems on aircrafts are limited for pilots, point-of-care systems provide choices for passengers to enjoy healthcare at the same level. Here in this paper, an airline point-of-care system containing hybrid electrocardiogram (ECG), breathing, and motion signals detection is proposed. At the same time, we propose the diagnosis of sleep apnea-hypopnea syndrome (SAHS) on flights as an application of this system to satisfy the inevitable demands for sleeping on long-haul flights. The hardware design includes ECG electrodes, flexible piezoelectric belts, and a control box, which enables the system to detect the original data of ECG, breathing, and motion signals. By processing these data with interval extraction-based feature selection method, the signals would be characterized and then provided for the long short-term memory recurrent neural network (LSTM-RNN) to classify the SAHS. Compared with other machine learning methods, our model shows high accuracy up to 84-85% with the lowest overfit problem, which proves its potential application in other related fields.

Ethical Aspects of Prenatal DNA Testing

Cell-free DNA (cfDNA) first-trimester screening for fetal aneuploidies, as a non-invasive, safe, and rather accurate method, has changed prenatal screening policies all over the world. Owing to aggressive marketing, cfDNA screening tests exhibit global popularity and a rapid spread in routine prenatal care. However, wide availability of the tests, together with observed difficulties in the test’s interpretation, bring to light several serious ethical concerns. To date it is vital to identify and address the most important ethical, legal, and social issues regarding prenatal screening tests. Furthermore, guidelines and restrictions in certain cfDNA screening advancements that may provide information regarding fetal genetic traits of unknown clinical significance, conditions with variable penetrance, or late-onset conditions, should be considered.

Same performance of exome sequencing before and after fetal autopsy for congenital abnormalities: toward a paradigm shift in prenatal diagnosis?

Prenatal exome sequencing could be complex because of limited phenotypical data compared to postnatal/portmortem phenotype in fetuses affected by multiple congenital abnormalities (MCA). Here, we investigated limits of prenatal phenotype for ES interpretation thanks to a blindly reanalysis of postmortem ES data using prenatal data only in fetuses affected by MCA and harboring a (likely)pathogenic variant or a variant of unknown significance (VUS). Prenatal ES identified all causative variant previously reported by postmortem ES (22/24 (92%) and 2/24 (8%) using solo-ES and trio-ES respectively). Prenatal ES identified 5 VUS (in four fetuses). Two of them have been previously reported by postmortem ES. Prenatal ES were negative for four fetuses for which a VUS were diagnosed after autopsy. Our study suggests that prenatal phenotype is not a limitation for implementing pES in the prenatal assessment of unsolved MCA to personalize fetal medicine and could influence indication of postmortem examination.

Electronic Textiles for Wearable Point-of-Care Systems

Traditional public health systems are suffering from limited, delayed, and inefficient medical services, especially when confronted with the pandemic and the aging population. Fusing traditional textiles with diagnostic, therapeutic, and protective medical devices can unlock electronic textiles (e-textiles) as point-of-care platform technologies on the human body, continuously monitoring vital signs and implementing round-the-clock treatment protocols in close proximity to the patient. This review comprehensively summarizes the research advances on e-textiles for wearable point-of-care systems. We start with a brief introduction to emphasize the significance of e-textiles in the current healthcare system. Then, we describe textile sensors for diagnosis, textile therapeutic devices for medical treatment, and textile protective devices for prevention, by highlighting their working mechanisms, representative materials, and clinical application scenarios. Afterward, we detail e-textiles' connection technologies as the gateway for real-time data transmission and processing in the context of 5G technologies and Internet of Things. Finally, we provide new insights into the remaining challenges and future directions in the field of e-textiles. Fueled by advances in chemistry and materials science, textile-based diagnostic devices, therapeutic devices, protective medical devices, and communication units are expected to interact synergistically to construct intelligent, wearable point-of-care textile platforms, ultimately illuminating the future of healthcare system in the Internet of Things era.

An ethical exploration of pregnancy related mHealth: does it deliver?

Many pregnant women use pregnancy related mHealth (PRmHealth) applications, encompassing a variety of pregnancy apps and wearables. These are mostly directed at supporting a healthier fetal development. In this article we argue that the increasing dominance of PRmHealth stands in want of empirical knowledge affirming its beneficence in terms of improved pregnancy outcomes. This is a crucial ethical issue, especially in the light of concerns about increasing pressures and growing responsibilities ascribed to pregnant women, which may, in turn, be reinforced by PRmHealth. A point can be made that it would be ethically askew if PRmHealth does not lead to improved pregnancy outcomes, while at the same time increasing maternal duties to closely monitor fetal development. We conclude that more research is needed to get a view on the benefits and burdens of PRmHealth in order to ethically assess whether the latter are proportionate to the former. If not, there is a case in saying that endorsement of PRmHealth is overdemanding.

Exosomes-a potential indicator and mediator of cleft lip and palate: a narrative review

Objective

This article summarizes the recent literature on noncoding ribonucleic acids (ncRNAs) in relation to cleft lip with or without palate and exosomes and their usage in craniofacial diseases.

Background

Cleft lip with or without cleft palate (CL/P) is a common congenital malformation with genetic and environmental risk factors that affects numerous children and families. Surgical procedures can correct deformations; however, residual sequelae remain after surgery. Studies exploring the pathogenesis of CL/P are crucial for its early diagnosis and treatment and can inform treatment strategy decisions, etiology searches, and treatment during pregnancy. Recently, research has shown that most disease-related genes are ncRNAs, which are important transcripts in the human transcriptome. ncRNAs include microRNAs, long noncoding RNAs, and circular RNAs. These ncRNAs play essential roles in various pathophysiological processes, including cell proliferation, migration, apoptosis, and epithelial-mesenchymal transition. Previous studies on protein-coding genes have identified a number of genes related to CL/P; however, the pathogenesis of CL/P has not yet been thoroughly explained. Exosomes are vehicles that transfer various bioactive molecules between cells and represent a new method of intercellular communication. Research has shown that exosomes are related to some craniofacial diseases.

Methods

We searched the PubMed database for recently published English-language articles using the following keywords: “cleft lip with or without palate,” “noncoding RNA,” “exosomes,” and “craniofacial diseases”. We then reviewed the retrieved articles.

Conclusions

As exosomes serve as cellular communicators and the palate consists of epithelial and mesenchymal cells, communication between the two cell types may affect its formation. Thus, exosomes could represent a new indicator and mediator of CL/P.

The fetus in the age of the genome

Due to a number of recent achievements, the field of prenatal medicine is now on the verge of a profound transformation into prenatal genomic medicine. This transformation is expected to not only substantially expand the spectrum of prenatal diagnostic and screening possibilities, but finally also to advance fetal care and the prenatal management of certain fetal diseases and malformations. It will come along with new and profound challenges for the normative framework and clinical care pathways in prenatal (and reproductive) medicine. To adequately address the potential ethically challenging aspects without discarding the obvious benefits, several agents are required to engage in different debates. The permissibility of the sequencing of the whole fetal exome or genome will have to be examined from a philosophical and legal point of view, in particular with regard to conflicts with potential rights of future children. A second requirement is a societal debate on the question of priority setting and justice in relation to prenatal genomic testing. Third, a professional-ethical debate and positioning on the goal of prenatal genomic testing and a consequential re-structuring of clinical care pathways seems to be important. In all these efforts, it might be helpful to envisage the unborn rather not as a fetus, not as a separate moral subject and a second "patient", but in its unique physical connection with the pregnant woman, and to accept the moral quandaries implicitly given in this situation.

Die Rechte zukünftiger Kinder im Kontext pränataler Diagnostik

Das Gendiagnostikgesetz (GenDG) verbietet seit 2010 die pränatale Diagnostik spätmanifestierender Erkrankungen (§ 15(2) GenDG). In seiner Begründung bezog sich der Gesetzgeber in Analogie zu internationalen Empfehlungen für den pädiatrischen Bereich vor allem auf das Recht des heranwachsenden Kindes bzw. des späteren Erwachsenen auf Nichtwissen. Mit diesem gesetzlichen Verbot hat Deutschland einen viel diskutierten Sonderweg in der Regulierung genetischer Pränataldiagnostik eingeschlagen. Seither jedoch hat sich nicht nur die Perspektive auf prädiktive Testungen im Kindesalter verändert. In zunehmendem Maße generieren auf das gesamte Genom abzielende Diagnostikangebote auch andere vorgeburtlich genetische Informationen, die – in ähnlicher Weise wie diejenigen zu spätmanifestierenden Erkrankungen eine potenzielle Gefahr für das Recht auf Nichtwissen der späteren Person darstellen. Es soll daher im Rahmen dieses Beitrages überprüft werden, inwiefern das deutsche Diagnostikverbot und dessen Bezug auf das Recht auf Nichtwissen des späteren Kindes eine tragfähige Basis zur Regulierung gendiagnostischer Untersuchungen in der Pränatalmedizin insgesamt darstellt bzw. zukünftig darstellen kann.

Untersucht wird der Argumentationsgang des Diagnostikverbotes im Hinblick auf spätmanifestierende Erkrankungen vor dem Hintergrund der Entwicklungen in der prädiktiven (genomischen) Diagnostik. Eine Analyse des normativen Begründungsrahmens zeigt, dass nach wie vor deutlicher Klärungsbedarf hinsichtlich der philosophisch-ethischen Fundierung wie auch hinsichtlich der Interpretation eines Rechts auf Nichtwissen eines (zukünftigen) Kindes im Kontext von genetischer Diagnostik besteht. Darüber hinaus müssen auch Interessen des (zukünftigen) Kindes an eventuell möglich werdender pränataler Behandlung oder Prävention von Erkrankungen in die Abwägung miteinbezogen werden.

Um zukünftigen Herausforderungen genomischer Pränataldiagnostik und -therapie begegnen zu können, müsste dringend geklärt werden, inwiefern Rechte zukünftiger Personen tatsächlich in der speziellen Situation der Schwangerschaft relevant sein können und mit welchen Pflichten diese für den Gesetzgeber, aber insbesondere auch für zukünftige Eltern und Ärzte einhergehen. Der Menschenrechtsdiskurs könnte hierfür eine tragfähige Basis und hilfreiche Strategien liefern.

Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model

Human fetuses with trisomy 21 (T21) have atypical brain development that is apparent sonographically in the second trimester. We hypothesize that by analyzing and integrating dysregulated gene expression and pathways common to humans with Down syndrome (DS) and mouse models we can discover novel targets for prenatal therapy. Here, we tested the safety and efficacy of apigenin, identified with this approach, in both human amniocytes from fetuses with T21 and in the Ts1Cje mouse model. In vitro, T21 cells cultured with apigenin had significantly reduced oxidative stress and improved antioxidant defense response. In vivo, apigenin treatment mixed with chow was administered prenatally to the dams and fed to the pups over their lifetimes. There was no significant increase in birth defects or pup deaths resulting from prenatal apigenin treatment. Apigenin significantly improved several developmental milestones and spatial olfactory memory in Ts1Cje neonates. In addition, we noted sex-specific effects on exploratory behavior and long-term hippocampal memory in adult mice, and males showed significantly more improvement than females. We demonstrated that the therapeutic effects of apigenin are pleiotropic, resulting in decreased oxidative stress, activation of pro-proliferative and pro-neurogenic genes (KI67, Nestin, Sox2, and PAX6), reduction of the pro-inflammatory cytokines INFG, IL1A, and IL12P70 through the inhibition of NFκB signaling, increase of the anti-inflammatory cytokines IL10 and IL12P40, and increased expression of the angiogenic and neurotrophic factors VEGFA and IL7. These studies provide proof of principle that apigenin has multiple therapeutic targets in preclinical models of DS.

Molecular Diagnostics and In Utero Therapeutics for Orofacial Clefts

Orofacial clefts and their management impose a substantial burden on patients, on their families, and on the health system. Under the current standard of care, affected patients are subjected to a lifelong journey of corrective surgeries and multidisciplinary management to replace bone and soft tissues, as well as restore esthetics and physiologic functions while restoring self-esteem and psychological health. Hence, a better understanding of the dynamic interplay of molecular signaling pathways at critical phases of palate development is necessary to pioneer novel prenatal interventions. Such pathways include transforming growth factor-β (Tgfβ), sonic hedgehog (Shh), wingless-integrated site (Wnt)/β-catenin, bone morphogenetic protein (Bmp), and fibroblast growth factor (Fgf) and its associated receptors, among others. Here, we summarize commonly used surgical methods used to correct cleft defects postnatally. We also review the advances made in prenatal diagnostics of clefts through imaging and genomics and the various in utero surgical corrections that have been attempted thus far. An overview of how key mediators of signaling that drive palatogenesis are emphasized in the context of the framework and rationale for the development and testing of therapeutics in animal model systems and in humans is provided. The pros and cons of in utero therapies that can potentially restore molecular homeostasis needed for the proper growth and fusion of palatal shelves are presented. The theme advanced throughout this review is the need to develop preclinical molecular therapies that could ultimately be translated into human trials that can correct orofacial clefts at earlier stages of development.

Update on molecular companion diagnostics - a future in personalized medicine beyond Sanger sequencing

INTRODUCTION

The merging of molecular diagnostics with personalized medicine has led to a surge in development of molecular-based companion diagnostics. Companion diagnostics, defined as 'a medical device, often an in vitro device, which provides information that is essential for the safe and effective use of a corresponding drug or biological product', are key to the appropriate utilization of several pharmacotherapies; primarily in the area of oncology.

AREAS COVERED

While most molecular companion diagnostics are targeted toward oncology, the potential to multiplex assays will contribute to an expansion in the applications of companion diagnostics for an increasing menu of disease states and conditions including areas such as infectious disease, cardiology, and hematology.

EXPERT OPINION

With this innovation comes the responsibility to ensure molecular companion diagnostic devices are robust and controlled against the detrimental effects of false positive/negative results. Additional important considerations, such as paired development with pharmaceutical companies and adherence to Food and Drug Administration and/or European Union guidelines, must be addressed. While the current number of companion diagnostics is relatively small, as molecular assays continue to be developed as companion diagnostics the world of personalized medicine will advance to meet the needs of an expanding portion of the patient population.

Down syndrome

Trisomy 21, the presence of a supernumerary chromosome 21, results in a collection of clinical features commonly known as Down syndrome (DS). DS is among the most genetically complex of the conditions that are compatible with human survival post-term, and the most frequent survivable autosomal aneuploidy. Mouse models of DS, involving trisomy of all or part of human chromosome 21 or orthologous mouse genomic regions, are providing valuable insights into the contribution of triplicated genes or groups of genes to the many clinical manifestations in DS. This endeavour is challenging, as there are >200 protein-coding genes on chromosome 21 and they can have direct and indirect effects on homeostasis in cells, tissues, organs and systems. Although this complexity poses formidable challenges to understanding the underlying molecular basis for each of the many clinical features of DS, it also provides opportunities for improving understanding of genetic mechanisms underlying the development and function of many cell types, tissues, organs and systems. Since the first description of trisomy 21, we have learned much about intellectual disability and genetic risk factors for congenital heart disease. The lower occurrence of solid tumours in individuals with DS supports the identification of chromosome 21 genes that protect against cancer when overexpressed. The universal occurrence of the histopathology of Alzheimer disease and the high prevalence of dementia in DS are providing insights into the pathology and treatment of Alzheimer disease. Clinical trials to ameliorate intellectual disability in DS signal a new era in which therapeutic interventions based on knowledge of the molecular pathophysiology of DS can now be explored; these efforts provide reasonable hope for the future.

Real-time particle-by-particle detection of erythrocyte-camouflaged microsensor with extended circulation time in the bloodstream

Personalized medicine offers great potential benefits for disease management but requires continuous monitoring of drugs and drug targets. For instance, the therapeutic window for lithium therapy of bipolar disorder is very narrow, and more frequent monitoring of sodium levels could avoid toxicity. In this work, we developed and validated a platform for long-term, continuous monitoring of systemic analyte concentrations in vivo. First, we developed sodium microsensors that circulate directly in the bloodstream. We used "red blood cell mimicry" to achieve long sensor circulation times of up to 2 wk, while being stable, reversible, and sensitive to sodium over physiologically relevant concentration ranges. Second, we developed an external optical reader to detect and quantify the fluorescence activity of the sensors directly in circulation without having to draw blood samples and correlate the measurement with a phantom calibration curve to measure in vivo sodium. The reader design is inherently scalable to larger limbs, species, and potentially even humans. In combination, this platform represents a paradigm for in vivo drug monitoring that we anticipate will have many applications in the future.

The brain-placental axis: Therapeutic and pharmacological relevancy to pregnancy

The placenta plays a critical role in mammalian reproduction. Although it is a transient organ, its function is indispensable to communication between the mother and fetus, and supply of nutrients and oxygen to the growing fetus. During pregnancy, the placenta is vulnerable to various intrinsic and extrinsic conditions which can result in increased risk of fetal neurodevelopmental disorders as well as fetal death. The placenta controls the neuroendocrine secretion in the brain as a means of adaptive processes to safeguard the fetus from adverse programs, to optimize fetal development and other physiological changes necessary for reproductive success. Although a wealth of information is available on neuroendocrine functions in pregnancy, they are largely limited to the regulation of hypothalamus-pituitary-adrenal/gonad (HPA/ HPG) axis, particularly the oxytocin and prolactin system. There is a major gap in knowledge on systems-level functional interaction between the brain and placenta. In this review, we aim to outline the current state of knowledge about the brain-placental axis with description of the functional interactions between the placenta and the maternal and fetal brain. While describing the brain-placental interactions, a special emphasis has been given on the therapeutics and pharmacology of the placental receptors to neuroligands expressed in the brain during gestation. As a key feature of this review, we outline the prospects of integrated pharmacogenomics, single-cell sequencing and organ-on-chip systems to foster priority areas in this field of research. Finally, we remark on the application of precision genomics approaches to study the brain-placental axis in order to accelerate personalized medicine and therapeutics to treat placental and fetal brain disorders.

Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis

BACKGROUND

Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution, and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications.

OBJECTIVES

The aim was to investigate the spectrum and characteristics of pathogenic copy number variants in prenatal genetic diagnosis and to provide recommendations for expanding the scope of noninvasive prenatal screening for microdeletions and microduplications.

STUDY DESIGN

This was a retrospective study of 1510 pregnant women who underwent invasive prenatal diagnostic testing by chromosomal microarray analysis. Prenatal samples were retrieved by amniocentesis or chorionic villus sampling and sent to our prenatal genetic diagnosis laboratory for chromosomal microarray analysis. The risk of carrying a fetus with pathogenic copy number variants is stratified by the patients' primary indication for invasive testing. We searched the literature for published prenatal chromosomal microarray data to generate a large cohort of 23,865 fetuses. The characteristics and spectrum of pathogenic copy number variants including the type of aberrations (gains or losses), genomic loci, sizes, and the mode of inheritance were studied.

RESULTS

Overall, 375 of 23,865 fetuses (1.6%) carried pathogenic copy number variants for any indication for invasive testing, and 44 of them (11.7%) involve 2 or more pathogenic copy number variants. A total of 428 pathogenic copy number variants were detected in these fetuses, of which 280 were deletions and 148 were duplications. Three hundred sixty (84.1%) were less than 5 Mb in size and 68 (15.9%) were between 5 and 10 Mb. The incidence of carrying a pathogenic copy number variant in the high-risk group is 1 in 36 and the low-risk group is 1 in 125. Parental inheritance study results were available for 311 pathogenic copy number variants, 71 (22.8%) were maternally inherited, 36 (11.6%) were paternally inherited, and 204 (65.6%) occurred de novo.

CONCLUSION

Collectively, pathogenic copy number variants are common in pregnancies. High-risk pregnancies should be offered invasive testing with chromosomal microarray analysis for the most comprehensive investigation. Detection limits on size, parental inheritance, and genomic distribution should be carefully considered before implementing copy number variant screening in expanded noninvasive prenatal screening.

Non-invasive Prenatal Testing Using Fetal DNA

Non-invasive prenatal diagnosis (NIPD) is based on fetal DNA analysis starting from a simple peripheral blood sample, thus avoiding risks associated with conventional invasive techniques. During pregnancy, the fetal DNA increases to approximately 3-13% of the total circulating free DNA in maternal plasma. The very low amount of circulating cell-free fetal DNA (ccffDNA) in maternal plasma is a crucial issue, and requires specific and optimized techniques for ccffDNA purification from maternal plasma. In addition, highly sensitive detection approaches are required. In recent years, advanced ccffDNA investigation approaches have allowed the application of non-invasive prenatal testing (NIPT) to determine fetal sex, fetal rhesus D (RhD) genotyping, aneuploidies, micro-deletions and the detection of paternally inherited monogenic disorders. Finally, complex and innovative technologies such as digital polymerase chain reaction (dPCR) and next-generation sequencing (NGS) (exhibiting higher sensitivity and/or the capability to read the entire fetal genome from maternal plasma DNA) are expected to allow the detection, in the near future, of maternally inherited mutations that cause genetic diseases. The aim of this review is to introduce the principal ccffDNA characteristics and their applications as the basis of current and novel NIPT.

OLIG2 Drives Abnormal Neurodevelopmental Phenotypes in Human iPSC-Based Organoid and Chimeric Mouse Models of Down Syndrome

Down syndrome (DS) is a common neurodevelopmental disorder, and cognitive defects in DS patients may arise from imbalances in excitatory and inhibitory neurotransmission. Understanding the mechanisms underlying such imbalances may provide opportunities for therapeutic intervention. Here, we show that human induced pluripotent stem cells (hiPSCs) derived from DS patients overproduce OLIG2⁺ ventral forebrain neural progenitors. As a result, DS hiPSC-derived cerebral organoids excessively produce specific subclasses of GABAergic interneurons and cause impaired recognition memory in neuronal chimeric mice. Increased OLIG2 expression in DS cells directly upregulates interneuron lineage-determining transcription factors. shRNA-mediated knockdown of OLIG2 largely reverses abnormal gene expression in early-stage DS neural progenitors, reduces interneuron production in DS organoids and chimeric mouse brains, and improves behavioral deficits in DS chimeric mice. Thus, altered OLIG2 expression may underlie neurodevelopmental abnormalities and cognitive defects in DS patients.

Circulating tumor DNA in advanced prostate cancer: transitioning from discovery to a clinically implemented test

The genomic landscape of metastatic castration-resistant prostate cancer (mCRPC) differs from that of the primary tumor and is dynamic during tumor progression. The real-time and repeated characterization of this process via conventional solid tumor biopsies is challenging. Alternatively, circulating cell-free DNA (cfDNA) containing circulating tumor DNA (ctDNA) can be obtained from patient plasma using minimally disruptive blood draws and is amenable to sequential analysis. ctDNA has high overlap with the genomic sequences of biopsies from metastases and has the advantage of being representative of multiple metastases. The availability of techniques with high sensitivity and specificity, such as next-generation sequencing (NGS) and digital PCR, has greatly contributed to the development of the cfDNA field and enabled the detection of genomic alterations at low ctDNA fractions. In mCRPC, a number of clinically relevant genomic alterations have been tracked in ctDNA, including androgen receptor (AR) aberrations, which have been shown to be associated with an adverse outcome to novel antiandrogen therapies, and alterations in homologous recombination repair (HRR) genes, which have been associated with a response to PARP inhibitors. Several clinical applications have been proposed for cfDNA analysis, including its use as a prognostic tool, as a predictive biomarker, to monitor tumor response and to identify novel mechanisms of resistance. To date, the cfDNA analysis has provided interesting results, but there is an urgent need for these findings to be confirmed in prospective clinical trials.

Film-Spotting chiral miniPEG-γPNA array for BRCA1 gene mutation detection

Peptide nucleic acids array technology is a method of greatly increasing the throughput of laboratory processes to efficiently perform large-scale genetic tests. Diethylene glycol-containing chiral γPNA (miniPEG-γPNA) is considered to be the best PNA derivative and one of the best candidates for gene detection, because it can hybridize DNA with greater affinity and sequence selectivity than DNA and ordinary aminoethylglycyl PNA (aegPNA). Herein, miniPEG-γPNA probes are synthesized by 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS) in a mild condition, and a new biochip fabrication method "Film-Spotting" is invented, by which γPNA arrays with regular pattern, uniform luminance, and very low fluorescence background are obtained easily and cheaply. The miniPEG-γPNA array can effectively distinguish the full matched and mismatched targets in SSarc buffer, serum and urine, and the detection limit of complementary DNA is less than 5.97 nM. A miniPEG-γPNA array for BRCA1 gene mutation (3099delT) detection is also fabricated with a very good detection performance. This work provides an effective avenue for the diagnosis of breast cancer biomarker and expands the application of miniPEG-γPNA in the field of biochip.

Dizygotic opposite-sex twins with surgically repaired concordant myelomeningocele conceived by in vitro fertilization using intracytoplasmic sperm injection: a case report and review of the literature

BACKGROUND

Myelomeningocele (MMC) is a common subtype of congenital neural tube defects (NTD). Although congenital malformations including NTD are more common in twins, concordance, especially in dizygotic twins, is extremely rare and is found mostly in same-sex twins. The role of genetic and environmental factors in the etiology of MMC is unclear.

CASE REPORT

Dizygotic twins of opposite sex were born at term to a 35-year-old woman conceived with in vitro fertilization (IVF) using intracytoplasmic sperm injection (ICSI). Prenatal ultrasonography (US) revealed concordant lumbosacral MMC at 18 weeks of gestation as well as ventriculomegaly and Arnold-Chiari malformation type II at 28 weeks. Both twins underwent surgical repair of the MMC within 48 h after birth and required a ventriculoperitoneal shunt in the second week of life.

DISCUSSION

The case presented raises questions concerning the etiology of MMC, since in twins, it is compelling to attribute the etiology to genetic factors. In the literature, 22 pairs of twins with concordant MMC have been reported, and of the 10 dizygotic twins described, four were of opposite sex. However, in monozygotic twins, most of the cases are non-concordant; therefore, the role of genetics remains unclear. In addition, environmental factors such as nutrition, metabolic folic acid deficiency, and assisted conception with IVF and ICSI might play a role as well.

CONCLUSION

The appearance of concordant MMC in opposite-sex dizygotic twins, conceived by IVF using ICSI, intrigues questions concerning the etiology of MMC. In such cases, genetic counseling and evaluation should be considered.

[France and Great-Britain at the age of genomic medicine: new ethical challenges in reproductive medicine]

The announcement of the French Plan 'France Médecine Génomique 2015' demonstrates the will of the public authorities to make genomic medicine one of the flagships of public health and scientific research. It is against this backdrop that France announced its cooperation with Great Britain, one of the global leaders in genomics. The cooperation at an international level requires a common normative framework that addresses the new ethical challenges presented by genomic medicine. In order for such a framework to be adapted to different national contexts, it is important to identify and analyse the emerging ethical questions in general as well as within their specific national contexts. This article discusses the international implications of genomic medicine, and more precisely, the rise of international competitiveness in France. In a next step, the article explores the ethical implications of genomic medicine by taking the prenatal context as a case study. Finally, the article reflects on the way national contexts impact on the emerging ethical questions in France, as compared to Great Britain.

Limits to the scope of non-invasive prenatal testing (NIPT): an analysis of the international ethical framework for prenatal screening and an interview study with Dutch professionals

Background

The introduction of non-invasive prenatal testing (NIPT) for foetal aneuploidies is currently changing the field of prenatal screening in many countries. As it is non-invasive, safe and accurate, this technique allows for a broad implementation of first-trimester prenatal screening, which raises ethical issues, related, for instance, to informed choice and adverse societal consequences. This article offers an account of a leading international ethical framework for prenatal screening, examines how this framework is used by professionals working in the field of NIPT, and presents ethical guidance for the expansion of the scope of prenatal screening in practice.

Methods

A comparative analysis of authoritative documents is combined with 15 semi-structured interviews with professionals in the field of prenatal screening in the Netherlands. Data were recorded, transcribed verbatim and analysed using thematic analysis.

Results

The current ethical framework consists of four pillars: the aim of screening, the proportionality of the test, justice, and societal aspects. Respondents recognised and supported this framework in practice, but expressed some concerns. Professionals felt that pregnant women do not always make informed choices, while this is seen as central to reproductive autonomy (the aim of screening), and that pre-test counselling practices stand in need of improvement. Respondents believed that the benefits of NIPT, and of an expansion of its scope, outweigh the harms (proportionality), which are thought to be acceptable. They felt that the out-of-pocket financial contribution currently required by pregnant women constitutes a barrier to access to NIPT, which disproportionally affects those of a lower socioeconomic status (justice). Finally, professionals recognised but did not share concerns about a rising pressure to test or discrimination of disabled persons (societal aspects).

Conclusions

Four types of limits to the scope of NIPT are proposed: NIPT should generate only test outcomes that are relevant to reproductive decision-making, informed choice should be (made) possible through adequate pre-test counselling, the rights of future children should be respected, and equal access should be guaranteed. Although the focus of the interview study is on the Dutch healthcare setting, insights and conclusions can be applied internationally and to other healthcare systems.

How should costs and cost-effectiveness be considered in prenatal genetic testing?

In January 2017, a group of experts in prenatal genetics attended a workshop at the Society of Maternal-Fetal Medicine meeting to review the evidence behind the costs and cost-effectiveness of prenatal genetic testing. Over the past decade, prenatal genetic testing options have dramatically expanded to include additional options with cell-free DNA (cfDNA) screening, as well as increased diagnostic abilities through chromosomal microarray analysis (CMA), gene panels, whole exome sequencing, and other tests. With these expanding technologies, it is important to consider the options available as well as the cost effectiveness of their use. Other important considerations are the effects of movements toward value-based health care; the role of professional societies, commercial laboratories, and insurers; disparities that exist in prenatal genetic testing; and outcomes for both patients and health care systems. Workshop participants identified key areas of research to advance our understanding of the costs and cost-effectiveness of prenatal genetic testing, which include (1) understanding the short- and long-term costs to patients and to health care systems with prenatal genetic tests; (2) elucidating the short- and long-term health outcomes for parents and children that are important to consider when comparing one testing strategy to another; (3) understanding the value underlying prenatal genetic testing to individuals and health care systems; and (4) identifying disparities in prenatal genetic testing, reasons for these disparities, and how to minimize them.

In Utero Administration of Drugs Targeting Microglia Improves the Neurodevelopmental Outcome Following Cytomegalovirus Infection of the Rat Fetal Brain

Congenital cytomegalovirus (CMV) infections represent one leading cause of neurodevelopmental disorders. Recently, we reported on a rat model of CMV infection of the developing brain in utero, characterized by early and prominent infection and alteration of microglia-the brain-resident mononuclear phagocytes. Besides their canonical function against pathogens, microglia are also pivotal to brain development. Here we show that CMV infection of the rat fetal brain recapitulated key postnatal phenotypes of human congenital CMV including increased mortality, sensorimotor impairment reminiscent of cerebral palsy, hearing defects, and epileptic seizures. The possible influence of early microglia alteration on those phenotypes was then questioned by pharmacological targeting of microglia during pregnancy. One single administration of clodronate liposomes in the embryonic brains at the time of CMV injection to deplete microglia, and maternal feeding with doxycyxline throughout pregnancy to modify microglia in the litters' brains, were both associated with dramatic improvements of survival, body weight gain, sensorimotor development and with decreased risk of epileptic seizures. Improvement of microglia activation status did not persist postnatally after doxycycline discontinuation; also, active brain infection remained unchanged by doxycycline. Altogether our data indicate that early microglia alteration, rather than brain CMV load per se, is instrumental in influencing survival and the neurological outcomes of CMV-infected rats, and suggest that microglia might participate in the neurological outcome of congenital CMV in humans. Furthermore this study represents a first proof-of-principle for the design of microglia-targeted preventive strategies in the context of congenital CMV infection of the brain.

A kinetically controlled, isothermal method for the detection of single nucleotide mismatches

We describe an isothermal, enzyme-free method to detect single nucleotide differences between oligonucleotides of close homology. The approach exploits kinetic differences in toe-hold-mediated, nucleic acid strand-displacement reactions to detect single nucleotide polymorphisms (SNPs) with essentially "digital" precision. The theoretical underpinning, experimental analyses, predictability, and accuracy of this new method are reported. We demonstrate detection of biologically relevant SNPs and single nucleotide differences in the let-7 family of microRNAs. The method is adaptable to microarray formats, as demonstrated with on-chip detection of SNP variants involved in susceptibility to the therapeutic agents abacavir, Herceptin, and simvastatin.

Key Ethical Issues in Prenatal Genetics: An Overview

The clinical integration of prenatal genetic technologies raises a series of important medical and ethical considerations for patients, families, health care providers, health care systems, and society. It is critical to recognize, understand, and address these issues in conjunction with the continued development of new prenatal genetic screens and tests. This article discusses some of the lead ethical issues as a starting point to further understanding their ramifications on patients, families, communities, and health care providers.

The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study

OBJECTIVE

Pregnancy is accompanied by dramatic physiological changes in maternal plasma proteins. Characterization of the maternal plasma proteome in normal pregnancy is an essential step for understanding changes to predict pregnancy outcome. The objective of this study was to describe maternal plasma proteins that change in abundance with advancing gestational age and determine biological processes that are perturbed in normal pregnancy.

STUDY DESIGN

A longitudinal study included 43 normal pregnancies that had a term delivery of an infant who was appropriate for gestational age without maternal or neonatal complications. For each pregnancy, 3 to 6 maternal plasma samples (median, 5) were profiled to measure the abundance of 1125 proteins using multiplex assays. Linear mixed-effects models with polynomial splines were used to model protein abundance as a function of gestational age, and the significance of the association was inferred via likelihood ratio tests. Proteins considered to be significantly changed were defined as having the following: (1) >1.5-fold change between 8 and 40 weeks of gestation; and (2) a false discovery rate-adjusted value of P < .1. Gene ontology enrichment analysis was used to identify biological processes overrepresented among the proteins that changed with advancing gestation.

RESULTS

The following results were found: (1) Ten percent (112 of 1125) of the profiled proteins changed in abundance as a function of gestational age; (2) of the 1125 proteins analyzed, glypican-3, sialic acid-binding immunoglobulin-type lectin-6, placental growth factor, C-C motif-28, carbonic anhydrase 6, prolactin, interleukin-1 receptor 4, dual-specificity mitogen-activated protein kinase 4, and pregnancy-associated plasma protein-A had more than a 5-fold change in abundance across gestation (these 9 proteins are known to be involved in a wide range of both physiological and pathological processes, such as growth regulation, embryogenesis, angiogenesis immunoregulation, inflammation etc); and (3) biological processes associated with protein changes in normal pregnancy included defense response, defense response to bacteria, proteolysis, and leukocyte migration (false discovery rate, 10%).

CONCLUSION

The plasma proteome of normal pregnancy demonstrates dramatic changes in both the magnitude of changes and the fraction of the proteins involved. Such information is important to understand the physiology of pregnancy and the development of biomarkers to differentiate normal vs abnormal pregnancy and determine the response to interventions.

Prenatal and pre-implantation genetic diagnosis

The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.

Precision wildlife medicine: applications of the human-centred precision medicine revolution to species conservation

The current species extinction crisis is being exacerbated by an increased rate of emergence of epizootic disease. Human-induced factors including habitat degradation, loss of biodiversity and wildlife population reductions resulting in reduced genetic variation are accelerating disease emergence. Novel, efficient and effective approaches are required to combat these epizootic events. Here, we present the case for the application of human precision medicine approaches to wildlife medicine in order to enhance species conservation efforts. We consider how the precision medicine revolution, coupled with the advances made in genomics, may provide a powerful and feasible approach to identifying and treating wildlife diseases in a targeted, effective and streamlined manner. A number of case studies of threatened species are presented which demonstrate the applicability of precision medicine to wildlife conservation, including sea turtles, amphibians and Tasmanian devils. These examples show how species conservation could be improved by using precision medicine techniques to determine novel treatments and management strategies for the specific medical conditions hampering efforts to restore population levels. Additionally, a precision medicine approach to wildlife health has in turn the potential to provide deeper insights into human health and the possibility of stemming and alleviating the impacts of zoonotic diseases. The integration of the currently emerging Precision Medicine Initiative with the concepts of EcoHealth (aiming for sustainable health of people, animals and ecosystems through transdisciplinary action research) and One Health (recognizing the intimate connection of humans, animal and ecosystem health and addressing a wide range of risks at the animal-human-ecosystem interface through a coordinated, collaborative, interdisciplinary approach) has great potential to deliver a deeper and broader interdisciplinary-based understanding of both wildlife and human diseases.

Prenatal DNA Sequencing: Clinical, Counseling, and Diagnostic Laboratory Considerations

Clinical diagnostic laboratories are producing next-generation sequencing-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation, and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history, and the physical examination is only indirectly available via prenatal sonography. Here, we provide an overview of these challenges and highlight the clinical utility, reporting, and counseling issues associated with prenatal DNA sequencing. Future considerations are also discussed. © 2017 John Wiley & Sons, Ltd.

Postnatal and non-invasive prenatal detection of β-thalassemia mutations based on Taqman genotyping assays

The β-thalassemias are genetic disorder caused by more than 200 mutations in the β-globin gene, resulting in a total (β⁰) or partial (β⁺) deficit of the globin chain synthesis. The most frequent Mediterranean mutations for β-thalassemia are: β⁰39, β⁺IVSI-110, β⁺IVSI-6 and β⁰IVSI-1. Several molecular techniques for the detection of point mutations have been developed based on the amplification of the DNA target by polymerase chain reaction (PCR), but they could be labor-intensive and technically demanding. On the contrary, TaqMan^® genotyping assays are a simple, sensitive and versatile method suitable for the single nucleotide polymorphism (SNP) genotyping affecting the human β-globin gene. Four TaqMan^® genotyping assays for the most common β-thalassemia mutations present in the Mediterranean area were designed and validated for the genotype characterization of genomic DNA extracted from 94 subjects comprising 25 healthy donors, 33 healthy carriers and 36 β-thalassemia patients. In addition, 15 specimens at late gestation (21–39 gestational weeks) and 11 at early gestation (5–18 gestational weeks) were collected from pregnant women, and circulating cell-free fetal DNAs were extracted and analyzed with these four genotyping assays. We developed four simple, inexpensive and versatile genotyping assays for the postnatal and prenatal identification of the thalassemia mutations β⁰39, β⁺IVSI-110, β⁺IVSI-6, β⁰IVSI-1. These genotyping assays are able to detect paternally inherited point mutations in the fetus and could be efficiently employed for non-invasive prenatal diagnosis of β-globin gene mutations, starting from the 9^th gestational week.

Fetal therapy for Down syndrome: an ethical exploration

BACKGROUND

Parallel to recent advances in prenatal screening for Down syndrome (DS), therapies for different aspects of the condition have become available. As intellectual disability is a key aspect, this is an active area for research. Several groups have hypothesized that prenatal interventions will give better chances at improving cognitive functioning in persons with DS than postnatal treatment. Clinical trials are being developed.

METHOD

We first discuss the ethical pros and cons of trying to improve cognitive functioning in persons with DS to see if there are categorical objections to the general idea, and then move on to explore ethically relevant aspects of the prospect of developing fetal therapy for DS (FTDS).

RESULTS

Only on the basis of a one-dimensional emphasis on the social model of disability would (fetal) therapy aimed at cognitive improvement be inherently problematic.

CONCLUSIONS

Inviting pregnant women to participate in FTDS-research should be based on adequate pre-clinical trials, as well as information aimed at avoiding the so-called 'therapeutic misconception'. Should FTDS be proven to be effective and safe, women carrying a fetus with trisomy 21 who have decided to continue the pregnancy may have a moral obligation to make use of this option. © 2016 John Wiley & Sons, Ltd.

Noninvasive Prenatal DNA Testing: The Vanguard of Genomic Medicine

Noninvasive prenatal DNA testing is the vanguard of genomic medicine. In only four years, this screening test has revolutionized prenatal care globally and opened up new prospects for personalized medicine for the fetus. There are widespread implications for increasing the scope of human genetic variation that can be detected before birth, and for discovering more about maternofetal and placental biology. These include an urgent need to develop pretest education for all pregnant women and consistent post-test management recommendations for those with discordant test results. The reduction in invasive testing has had downstream effects on specialist training and caused many countries to re-examine their national approaches to prenatal screening. Finally, the accumulating datasets of genomic information on pregnant women and their fetuses raise ethical issues regarding consent for future data mining and intellectual property.

First trimester contingent screening for trisomies 21,18,13: is this model cost efficient and feasible in public health system?

PURPOSE

To evaluate the effectiveness of three different first trimester screening models for trisomies 21, 18 and 13, in terms of detection rate, invasive test rate and final costs.

MATERIAL AND METHODS

We analyzed the distribution of risk for trisomies 21, 18 and 13 in a population of 20,831 singleton pregnancies based on maternal age, fetal heart rate, nuchal translucency, free beta human chorionic gonadotropin and pregnancy-associated plasma protein A (Combined test). On the basis of our data, we estimated the performance and cost of screening for trisomies using three different models at specific cutoffs: Combined test; Cell free DNA test and Contingent screening test.

RESULTS

Using Combined test, DR for major trisomies was estimated to be 94.92%, invasive test rate was 6.3%. cfDNA would result in a DR of 97.92%, with an invasive test rate of 3.64%. Contingent screening approach would result in an overall DR of 97.82, with a rate for invasive procedure of 1.36% and a final cost lower than other screening policies (2,338,433 euro vs 5,796,060 of cfDNA and 2,385,473 of Combined test).

CONCLUSIONS

Contingent screening test could be a cost-efficient and feasible first trimester screening test for aneuploidies in public health system.

A Framework for Unrestricted Prenatal Whole-Genome Sequencing: Respecting and Enhancing the Autonomy of Prospective Parents

Noninvasive, prenatal whole genome sequencing (NIPW) may be a technological reality in the near future, making available a vast array of genetic information early in pregnancy at no risk to the fetus or mother. Many worry that the timing, safety, and ease of the test will lead to informational overload and reproductive consumerism. The prevailing response among commentators has been to restrict conditions eligible for testing based on medical severity, which imposes disputed value judgments and devalues those living with eligible conditions. To avoid these difficulties, we propose an unrestricted testing policy, under which prospective parents could obtain information on any variant of known significance after a careful informed consent process that uses an interactive decision aid to deliver a mandatory presentation on the purposes, techniques, and limitations of genomic testing, as well as optional resources for reflection and consultation. This process would encourage thoughtful, informed deliberation by prospective parents before deciding whether or how to use NIPW.

Antisense oligonucleotides delivered to the amniotic cavity in utero modulate gene expression in the postnatal mouse

Congenital diseases account for a large portion of pediatric illness. Prenatal screening and diagnosis permit early detection of many genetic diseases. Fetal therapeutic strategies to manage disease processes in utero represent a powerful new approach for clinical care. A safe and effective fetal pharmacotherapy designed to modulate gene expression ideally would avoid direct mechanical engagement of the fetus and present an external reservoir of drug. The amniotic cavity surrounding the fetus could serve as an ideal drug reservoir. Antisense oligonucleotides (ASOs) are an established tool for the therapeutic modulation of gene expression. We hypothesize that ASOs administered to the amniotic cavity will gain entry to the fetus and modulate gene expression. Here, we show that an ASO targeting MALAT1 RNA, delivered by transuterine microinjection into the mouse amniotic cavity at embryonic day 13-13.5, reduces target RNA expression for up to 4 weeks after birth. A similarly delivered ASO targeting a causal splice site mutation for Usher syndrome corrects gene expression in the inner ear, a therapeutically relevant target tissue. We conclude that intra-amniotic delivery of ASOs is well tolerated and produces a sustained effect on postnatal gene expression. Transuterine delivery of ASOs is an innovative platform for developing fetal therapeutics to efficaciously treat congenital disease.

Changing Paradigms in Down Syndrome: The First International Conference of the Trisomy 21 Research Society

Down syndrome (DS) is the most common genetic cause of intellectual disability (ID) in humans with an incidence of ∼1:1,000 live births worldwide. It is caused by the presence of an extra copy of all or a segment of the long arm of human chromosome 21 (trisomy 21). People with DS present with a constellation of phenotypic alterations involving most organs and organ systems. ID is present in all people with DS, albeit with variable severity. DS is also the most frequent genetic cause of Alzheimer's disease (AD), and ∼50% of those with DS will develop AD-related dementia. In the last few years, significant progress has been made in understanding the crucial genotype-phenotype relationships in DS, in identifying the alterations in molecular pathways leading to the various clinical conditions present in DS, and in preclinical evaluations of potential therapies to improve the overall health and well-being of individuals with DS. In June 2015, 230 scientists, advocates, patients, and family members met in Paris for the 1st International Conference of the Trisomy 21 Research Society. Here, we report some of the most relevant presentations that took place during the meeting.

A two-layer assay for single-nucleotide variants utilizing strand displacement and selective digestion

Point mutations have emerged as prominent biomarkers for disease diagnosis, particularly in the case of cancer. Discovering single-nucleotide variants (SNVs) is also of great importance for the identification of single-nucleotide polymorphisms within the population. The competing requirements of thermodynamic stability and specificity in conventional nucleic acid hybridization probes make it challenging to achieve highly precise detection of point mutants. Here, we present a fluorescence-based assay for low-abundance mutation detection based on toehold-mediated strand displacement and nuclease-mediated strand digestion that enables highly precise detection of point mutations. We demonstrate that this combined assay provides 50-1000-fold discrimination (mean value: 255) between all possible single-nucleotide mutations and their corresponding wild-type sequence for a model DNA target. Using experiments and kinetic modeling, we investigate probe properties that obtain additive benefits from both strand displacement and nucleolytic digestion, thus providing guidance for the design of enzyme-mediated nucleic acid assays in the future.

Epsilon globin gene expression in developing human fetal tissues

OBJECTIVE

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

STUDY DESIGN

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

RESULTS

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

CONCLUSION

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

Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

The Qubit fluorometer is a DNA quantification device based on the fluorescence intensity of fluorescent dye binding to double-stranded DNA (dsDNA). Qubit is generally considered useful for checking DNA quality before next-generation sequencing because it measures intact dsDNA. To examine the most accurate and suitable methods for quantifying DNA for quality assessment, we compared three quantification methods: NanoDrop, which measures UV absorbance; Qubit; and quantitative PCR (qPCR), which measures the abundance of a target gene. For the comparison, we used three types of DNA: 1) DNA extracted from fresh frozen liver tissues (Frozen-DNA); 2) DNA extracted from formalin-fixed, paraffin-embedded liver tissues comparable to those used for Frozen-DNA (FFPE-DNA); and 3) DNA extracted from the remaining fractions after RNA extraction with Trizol reagent (Trizol-DNA). These DNAs were serially diluted with distilled water and measured using three quantification methods. For Frozen-DNA, the Qubit values were not proportional to the dilution ratio, in contrast with the NanoDrop and qPCR values. This non-proportional decrease in Qubit values was dependent on a lower salt concentration, and over 1 mM NaCl in the DNA solution was required for the Qubit measurement. For FFPE-DNA, the Qubit values were proportional to the dilution ratio and were lower than the NanoDrop values. However, electrophoresis revealed that qPCR reflected the degree of DNA fragmentation more accurately than Qubit. Thus, qPCR is superior to Qubit for checking the quality of FFPE-DNA. For Trizol-DNA, the Qubit values were proportional to the dilution ratio and were consistently lower than the NanoDrop values, similar to FFPE-DNA. However, the qPCR values were higher than the NanoDrop values. Electrophoresis with SYBR Green I and single-stranded DNA (ssDNA) quantification demonstrated that Trizol-DNA consisted mostly of non-fragmented ssDNA. Therefore, Qubit is not always the most accurate method for quantifying DNA available for PCR.

Non-invasive prenatal testing for fetal chromosome abnormalities: review of clinical and ethical issues

Genomics-based non-invasive prenatal screening using cell-free DNA (cfDNA screening) was proposed to reduce the number of invasive procedures in current prenatal diagnosis for fetal aneuploidies. We review here the clinical and ethical issues of cfDNA screening. To date, it is not clear how cfDNA screening is going to impact the performances of clinical prenatal diagnosis and how it could be incorporated in real life. The direct marketing to users may have facilitated the early introduction of cfDNA screening into clinical practice despite limited evidence-based independent research data supporting this rapid shift. There is a need to address the most important ethical, legal, and social issues before its implementation in a mass setting. Its introduction might worsen current tendencies to neglect the reproductive autonomy of pregnant women.