Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening

Prenatal detection and molecular cytogenetic characterization of Xp deletion and Xq duplication: a case report and literature review

BACKGROUND

Copy number variation (CNV) of X chromosome can lead to a variety of neonatal abnormalities, especially for male fetuses. In recent years, due to the high sensitivity and high specificity of NIPS, its application has gradually expanded from chromosome aneuploidy to CNV. Few prenatal cases involving the detection of Xq duplication and deletion by NIPS have been reported, but it is of great significance for genetic counseling.

CASE PRESENTATION

A 36-year-old woman was referred for prenatal diagnosis and genetic counseling at 17 weeks of gestation because of abnormal result of noninvasive prenatal screening (NIPS). Multiple congenital malformations, hydrocephalus, and enlarged gallbladder were observed by prenatal ultrasound. Amniocentesis revealed the karyotype of the fetus as 46, XN, add(X) (p22.2) and the result of chromosomal microarray analysis was arr[hg19] Xq27.1q28(138,506,454-154896094) × 2 and arr[hg19] Xp22.33p22.32(168,551-5,616,964) × 1. CNV-seq showed that the mother shares a 16.42 Mb duplication in the Xq27.1-q28 region and a 2.97 Mb deletion in the Xp22.33-p22.32 region. After genetic counseling, the couple chose to terminate the pregnancy.

CONCLUSION

The combination of NIPS and CMA would be of values in detection of subchromosomal duplications and/or deletions at fetal stage. The detection of X chromosome aberration in a male fetus should give suspicion of the possibility of maternal inheritance.

Klinefelter Syndrome: What should we tell prospective parents?

Klinefelter syndrome (KS) or 47,XXY is the most common sex chromosome aneuploidy (SCA), occurring at a prevalence of 1 in 600 male pregnancies. Historically, only 25% of individuals with KS came to medical attention, for a range of issues across the life course including under-virilisation at birth, developmental and social concerns in childhood, absence, delay or arrest of puberty in adolescence or infertility in adulthood. Our understanding of the phenotypic spectrum of KS has been largely influenced by this ascertainment bias. With increasing uptake of antenatal noninvasive prenatal testing (NIPT), a corresponding increase in identification of KS has been documented. Population-based longitudinal data from infancy to adulthood on these individuals is lacking, which impedes balanced antenatal genetic counselling and raises issues for prospective parents and clinicians alike.

Cell-free DNA screening positive for monosomy X: clinical evaluation and management of suspected maternal or fetal Turner syndrome

Initially provided as an alternative to evaluation of serum analytes and nuchal translucency for the assessment of pregnancies at high risk of trisomy 21, cell-free DNA screening for fetal aneuploidy, also referred to as noninvasive prenatal screening, can now also screen for fetal sex chromosome anomalies such as monosomy X as early as 9 to 10 weeks of gestation. Early identification of Turner syndrome, a sex chromosome anomaly resulting from the complete or partial absence of the second X chromosome, allows medical interventions such as optimizing obstetrical outcomes, hormone replacement therapy, fertility preservation and support, and improved neurocognitive outcomes. However, cell-free DNA screening for sex chromosome anomalies and monosomy X in particular is associated with high false-positive rates and low positive predictive value. A cell-free DNA result positive for monosomy X may represent fetal Turner syndrome, maternal Turner syndrome, or confined placental mosaicism. A positive screen for monosomy X with discordant results of diagnostic fetal karyotype presents unique interpretation and management challenges because of potential implications for previously unrecognized maternal Turner syndrome. The current international consensus clinical practice guidelines for the care of individuals with Turner syndrome throughout the lifespan do not specifically address management of individuals with a cell-free DNA screen positive for monosomy X. This study aimed to provide context and expert-driven recommendations for maternal and/or fetal evaluation and management when cell-free DNA screening is positive for monosomy X. We highlight unique challenges of cell-free DNA screening that is incidentally positive for monosomy X, present recommendations for determining if the result is a true-positive, and discuss when diagnosis of Turner syndrome is applicable to the fetus vs the mother. Whereas we defer the subsequent management of confirmed Turner syndrome to the clinical practice guidelines, we highlight unique considerations for individuals initially identified through cell-free DNA screening.

The Largest Germline Heterozygous Deletion Encompassing Potocki-Shaffer and WAGR Syndromes Loci to Date: A Case Report

Potocki-Schaffer syndrome includes multiple exostoses, parietal foramina, and variable developmental delay/intellectual disability. It is associated with a heterozygous deletion of the 11p12p11.2 region. In some cases, the deletion extends to the WAGR locus (11p13p12). We describe here a 9-month-old girl harboring the largest germline heterozygous deletion characterized so far. Oligohydramnios and parietal foramina were noticed during pregnancy. No patient has been diagnosed before with concomitance of these two syndromes during the prenatal period. Cytogenetic diagnosis was anticipated on basis of clinical and radiological signs. Postnatal conventional karyotype confirmed an interstitial 11p deletion: 46,XX,del(11)(p11.2p15.1). Array-comparative genomic hybridization characterized a 29.6 Mb deletion. Our case illustrates the interest of high-resolution genomic approaches to correlate adequately clinical phenotypes with specific genes in suspected contiguous gene deletion syndromes.

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.

Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35-100.00%); 100.00% sensitivity for T18 (71.51-100.00%); and 100.00% sensitivity for T13 analyses (66.37-100.00%). The specificities were >99% for each trisomy (99.7% (99.01-99.97%) for T21; 99.5% (98.62-99.85%) for T18; 99.7% (99.03-99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.

Interdisciplinary care of children with trisomy 13 and 18

Children with trisomy 13 and 18 (previously deemed "incompatible with life") are living longer, warranting a comprehensive overview of their unique comorbidities and complex care needs. This Review Article provides a summation of the recent literature, informed by the study team's Interdisciplinary Trisomy Translational Program consisting of representatives from: cardiology, cardiothoracic surgery, neonatology, otolaryngology, intensive care, neurology, social work, chaplaincy, nursing, and palliative care. Medical interventions are discussed in the context of decisional-paradigms and whole-family considerations. The communication format, educational endeavors, and lessons learned from the study team's interdisciplinary care processes are shared with recognition of the potential for replication and implementation in other care settings.

Why public funding for non-invasive prenatal testing (NIPT) might still be wrong: a response to Bunnik and colleagues

Bunnik and colleagues argued that financial barriers do not promote informed decision-making prior to prenatal screening and raise justice concerns. If public funding is provided, however, it would seem to be important to clarify its intentions and avoid any unwarranted appearance of a medical utility of the testing.

Effect of education and attitude on health professionals' knowledge on prenatal screening

INTRODUCTION

Ongoing developments in prenatal anomaly screening necessitate continuous updating of counsellors’ knowledge. We explored the effect of a refresher counselling course on participants’ knowledge of prenatal screening.

METHODS

We investigated the association between knowledge and counsellors’ working experience. Also, the association between knowledge and counsellors’ attitude towards prenatal screening was determined. All counsellors in the North-West region of the Netherlands were invited to attend a refresher counselling course and fill in both a pre-course and a post-course questionnaire. The participants consisted of midwifes, sonographers and gynaecologists. A 55-item questionnaire assessed pre-course (T0) and post-course (T1) knowledge. At T0, counsellors’ attitude towards the prenatal screening program was assessed and its association with knowledge analysed.

RESULTS

Of 387 counsellors, 68 (18%) attended the course and completed both questionnaires. Knowledge increased significantly from 77.7% to 84.6% (p<0.01). Scores were lowest regarding congenital heart diseases. Participants with ultrasound experience scored higher on T0, but improvement was seen in participants with and without ultrasound experience. Participants with a positive attitude towards a free-of-charge first trimester combined test had higher knowledge scores than participants with a negative attitude (62% vs 46%; p=0.002).

CONCLUSIONS

A refresher course improved counsellors’ knowledge on prenatal screening. Ultrasound experience and a positive attitude towards free screening may be associated with higher knowledge levels. Participating in a mandatory refresher counselling course is useful for the continuous improvement of healthcare practitioners’ knowledge. More research on the effect of knowledge and attitude on the quality of prenatal screening is necessary.

A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center

OBJECTIVE

To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center.

METHODS

A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings.

RESULTS

Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs.

CONCLUSIONS

NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.

Assessment of a change of protocol of prenatal screening by inclusion of non-invasive prenatal diagnosis

Objectives

Non-invasive prenatal screening (NIPS) is a test for the detection of major fetal chromosomal abnormalities in maternal blood during pregnancy. The purpose of this study was to assess the performance of NIPS implemented within the framework of the Screening Program for Congenital Abnormalities of the Andalusian Health System.

Methods

A retrospective observational study was undertaken to determine the number of NIPS tests performed since its introduction. The number of invasive diagnostic tests done after the implementation of NIPS in the patients included in the program between March 2016 and August 2017 was also quantified.

Results

A total of 6,258 combined first- and second trimester screening tests were performed, covering 95% of the population. In total, 250 subjects were identified as high risk, of whom 200 underwent NIPS after loss to follow-up. NIPS showed a sensitivity of 100% (95% CI: 76.84-100%) and a specificity of 99.46% (95% CI: 97.04-99.99%).

Conclusions

This test has proven to have a very high sensitivity and specificity. The results obtained demonstrate that the incorporation of NIPS in clinical practice minimizes the rate of miscarriages and reduces the frequency of invasive procedures by 70%.

Non-invasive prenatal rhesus D genotyping using cell-free foetal DNA

Background & objectives:

Non-invasive prenatal diagnosis (NIPD) of rhesus D (RHD) genotype using cell-free foetal DNA is extensively used in many developed countries. Studies on NIPD from India are scarce. The aim of the present study was to evaluate the performance of non-invasive foetal RHD genotyping by targeting exon 10 of the RHD gene using cell-free DNA.

Methods:

DNA was extracted from the maternal plasma of alloimmunized and non-alloimmunized women between 7 and 34 wk of gestation. RHD sequence was determined by quantitative real time polymerase chain reaction (PCR). Results were compared with RhD phenotype obtained from cord blood samples of neonates.

Results:

A total of 135 samples from RhD-negative pregnant women were collected. The foetal RHD status was conclusive in all 135 (100%) cases. The highest number of cases reported for RHD genotyping were from Punjab (38.5%) followed by Haryana (24.4%), Himachal Pradesh (17.0%) and Chandigarh Union Territory (13.3%). The non-invasive test correctly predicted the foetal RhD phenotype in 133 of 135 cases, making the accuracy of the test as 98.51 per cent [95% confidence interval (CI): 97.90-99.50%]. The overall sensitivity and specificity of the test were 99.18 per cent (95% CI: 95.52-99.98%) and 92.31 per cent (95% CI: 63.97-99.81%), respectively, with negative and positive predictive values of 99.80 per cent (95% CI: 94.85-99.87%) and 96.31 per cent (95% CI: 62.87-98.84%), respectively.

Interpretation & conclusions:

Non-invasive foetal RHD determination by single-exon quantitative PCR exhibited high accuracy and could be used in routine clinical practice after confirmatory studies are done.

Prenatal detection and evaluation of differences of sex development

INTRODUCTION

Differences/disorders of sex development (DSD) can be detected at different ages, including prenatally. The recent implementation of prenatal genetic testing (including cell-free DNA) may affect the frequency and impact of prenatal diagnosis of DSD. Our aims were to (1) describe prenatal detection and evaluation of differences of sex development presenting to a multidisciplinary DSD clinic and (2) explore possible parental distress accompanying this evaluation.

MATERIALS AND METHODS

A retrospective chart review of mothers presenting prenatally, and patients presenting during infancy, to a multidisciplinary DSD clinic from 2013 to 2017 was conducted. Data extracted included demographics, final diagnoses, prenatal screening, prenatal evaluation, postnatal endocrine, genetic and radiologic testing, and clinician's notes on parent/patient distress.

RESULTS

Sixty-seven patients were identified; ten (15%) had prenatal detection of a suspected DSD. Of those, 4/10 were detected prenatally in the last study year alone. Within the prenatal group, 6/10 had cell-free DNA results discordant with ultrasound, 2/10 were detected by atypical genitalia on ultrasound, and 2/10 were detected through karyotyping performed for other indications. After birth, 3/10 patients were found to not have a DSD. Final diagnoses for the full study cohort are shown in the Summary Table, comparing prenatal versus postnatal presentation to our DSD clinic. Clinicians noted distress for most parents during the prenatal evaluation of a possible DSD, including one mother who reported suicidal thoughts.

DISCUSSION AND CONCLUSIONS

Prenatal suspicion of DSD can occur through discordant prenatal testing and has been observed at our clinic in recent years, in line with other recent studies. Contributing factors to these prenatal presentations could be increased referrals to the clinic, and increased use of non-invasive prenatal testing, which can lead to inaccurate or discordant sex identification. The prenatal suspicion of a potential DSD can be associated with parental distress, underscoring the need for adequate counseling for tests that determine fetal sex, including cell-free DNA.

Management of 46,XY Differences/Disorders of Sex Development (DSD) Throughout Life

Differences/disorders of sex development (DSD) are a heterogeneous group of congenital conditions that result in discordance between an individual's sex chromosomes, gonads, and/or anatomic sex. Advances in the clinical care of patients and families affected by 46,XY DSD have been achieved since publication of the original Consensus meeting in 2006. The aims of this paper are to review what is known about morbidity and mortality, diagnostic tools and timing, sex of rearing, endocrine and surgical treatment, fertility and sexual function, and quality of life in people with 46,XY DSD. The role for interdisciplinary health care teams, importance of establishing a molecular diagnosis, and need for research collaborations using patient registries to better understand long-term outcomes of specific medical and surgical interventions are acknowledged and accepted. Topics that require further study include prevalence and incidence, understanding morbidity and mortality as these relate to specific etiologies underlying 46,XY DSD, appropriate and optimal options for genitoplasty, long-term quality of life, sexual function, involvement with intimate partners, and optimizing fertility potential.

Attitudes of Israeli parents of children with Down syndrome toward non-invasive prenatal screening and the scope of prenatal testing

Due to its early utilization and increasing ability to provide genetic information, non-invasive prenatal screening (NIPS) has reinforced social and bioethical quandaries concerning prenatal genetics. This paper presents exploratory findings based on 20 semi-structured interviews conducted in 2017-2019 with Israeli parents of children with Down syndrome (DS), four of whom also serving as representatives of DS organizations. Their views are presented regarding the pros and cons of NIPS; the social context of decision-making about NIPS; and views on life with DS and termination of pregnancies on that ground. While illustrating the large heterogeneity of views concerning NIPS and prenatal diagnosis (PND) amongst parents of children with DS, our respondents commonly criticized the imbalanced information provided by professionals regarding DS, seen as sending a discriminating message in line with the public ignorance surrounding DS. These views are further discussed in the multi-cultural, ableist and pro-natal context of Israeli society. We conclude by offering practical implications concerning NIPS, parental autonomy, and informed choice.

Placental studies elucidate discrepancies between NIPT showing a structural chromosome aberration and a differently abnormal fetal karyotype

Objective

Placental cytogenetic studies may reveal the origin of discordant noninvasive prenatal testing (NIPT). We performed placental studies to elucidate discordances between NIPT showing a structural chromosome aberration and the fetus having a different chromosome aberration in three cases.

Method

Diagnostic testing with genomic SNP microarray was performed in three cases with NIPT showing a duplication on 4q (case 1), a terminal deletion of 13q (case 2), and a terminal deletion of 15q (case 3). Placental studies involved SNP array analysis of cytotrophoblast and mesenchymal core of chorionic villi of four placental quadrants. Clinical follow‐up was performed as well.

Results

Amniotic fluid revealed a different structural chromosome aberration than predicted by NIPT: a terminal 2q deletion (case 1), a segmental uniparental isodisomy of 13q (case 2), and a terminal duplication of 15q and of 13q (case 3). Placental studies revealed the aberration detected with NIPT in the cytotrophoblast, whereas the fetal karyotype was confirmed in the placental mesenchymal core.

Conclusion

Our study shows that targeted cytogenetic investigations for confirmation of NIPT showing a microscopically visible structural chromosome aberration should be avoided, since another aberration, even a submicroscopic one or one involving another chromosome, may be present in the fetus.

The Prevalence of Y-chromosome Microdeletions in Oligozoospermic Men: A Systematic Review and Meta-analysis of European and North American Studies

CONTEXT

European and North American guidelines recommend Y-chromosome microdeletion (YCM) screening in azoospermic and oligozoospermic men with sperm concentrations of <5 million sperm/ml; however, numerous studies have suggested that YCMs are rare when sperm concentrations are >1 million sperm/ml.

OBJECTIVE

We systematically reviewed and meta-analyzed European and North American studies to determine the prevalence of a complete YCM in oligozoospermic men with sperm concentrations of >0-1, >1-5, and >5-20 million sperm/ml, and to determine whether 1 or 5 million sperm/ml is the most appropriate sperm concentration threshold for YCM screening.

EVIDENCE ACQUISITION

A systematic review of MEDLINE, EMBASE, Cochrane Library, and ClinicalTrials.gov was performed for studies assessing the prevalence of a complete YCM in oligozoospermic men in European and North American studies.

EVIDENCE SYNTHESIS

Thirty-seven studies were identified during a systematic review (n = 12 492 oligozoospermic men). All complete YCMs in oligozoospermic men were AZFc microdeletions. Eighteen studies contained data conducive to meta-analysis (n = 10 866 men). Comparing the pooled estimated prevalence by sperm concentration, complete YCMs were significantly more common in men with sperm concentrations of >0-1 million sperm/ml (5.0% [95% confidence interval {CI}: 3.6-6.8%]) versus >1-5 million sperm/ml (0.8% [95% CI: 0.5-1.3%], p < 0.001). YCMs were similar in men with sperm concentrations of >1-5 and >5-20 million sperm/ml (0.8% [95% CI: 0.5-1.3%] vs 0.5% [95% CI: 0.2-0.9%], p = 0.14).

CONCLUSIONS

In Europe and North America, the majority of YCMs occur in men with sperm concentrations of ≤1 million sperm/ml, with <1% identified in men with >1 million sperm/ml. Male infertility guidelines for North America and Europe should reconsider the sperm concentration screening thresholds to recommend testing for YCMs only for men with sperm concentrations of <1 million sperm/ml.

PATIENT SUMMARY

Complete Y-chromosome microdeletions (YCMs) are rare in men with >1 million sperm/ml. Routine screening for YCMs should occur only if sperm concentration is ≤1 million sperm/ml.

A method for improving the accuracy of non-invasive prenatal screening by cell-free foetal DNA size selection

Background Non-invasive prenatal screening (NIPS) using cell-free foetal DNA (cfDNA) has been widely used for identifying common foetal aneuploidies (e.g. trisomy 21 (T21), trisomy (T18) and trisomy 13 (T13)) in clinical practice. The sensitivity and specificity of NIPS exceeds 99%, but the positive prediction value (PPV) is approximately 70% (combined T21, T18 and T13). Thus, some 30% of pregnant women who have positive NIPS results are eventually identified as normal by amniocentesis. These women therefore must undertake needless invasive tests and risk miscarrying healthy babies because of false positive NIPS results. Methods In order to achieve higher accuracy, we amended the standard NIPS (s-NIPS) protocol with an additional cfDNA size selecting step in agarose-electrophoresis. The advantage of the new method (named e-NIPS) was validated by comparing the results of e-NIPS and s-NIPS using 114 retrospective cases selected from 15,930 cases. Results Our results showed that the foetal cfDNA fraction can be enriched significantly by a size selection step. With this modification, all 98 negative cases and 9 of 11 false positive cases of s-NIPS were correctly identified by e-NIPS, resulting in an increased PPV from 71% to 77%. Additionally, a simulation test showed that e-NIPS is more reliable than s-NIPS, especially when the foetal cfDNA concentration and sequencing coverage are low. Conclusion cfDNA size selection is an important step in improving the accuracy of non-invasive prenatal screening for chromosomal abnormalities.

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.

Guidelines for the Preanalytical Conditions for Analyzing Circulating Cell-Free DNA

Circulating cell-free DNA (cfDNA) isolated from blood has been identified as a potential biomarker in numerous fields, and has been the object of intensive research over the past decade, although its original discovery dates back 60 years. While it is already used routinely in commercial and clinical practice in oncology and prenatal testing, other potential applications have emerged, including for diabetes, cardiovascular diseases, organ transplantation, autoimmune diseases, sepsis, trauma, and sport management. As with the discovery and development of any biomarker, preanalytical requirements and documentation are as important as analytical requirements. Except for the case of noninvasive prenatal testing and prenatal diagnosis, the implementation of cfDNA in a clinical setting remains limited because of the lack of standardization of cfDNA analysis. In particular, only a few attempts have been made to collect and pool scientific data on the relevant preanalytical factors, and no standard operating procedure has yet been set. For this report, we have performed a thorough and systematic search via MEDLINE® for relevant preanalytical variables and patient factors. These form the basis of the guidelines we propose for analyzing nuclear cfDNA.

Development of Reference Materials for Noninvasive Prenatal Aneuploidy Testing by Massively Parallel Sequencing: A Proof-of-Concept Study

BACKGROUND

Noninvasive prenatal aneuploidy testing (NIPT) represents the first large-scale clinical application of massively parallel sequencing technology. However, no NIPT reference material (RM) has yet been widely adopted, impeding the development of quality management systems and standardization. Developing an NIPT RM from a biological sample is complicated by the low concentration of cell-free DNA (cfDNA), which implies pooling specimens and frequent resampling.

METHODS

We tested the feasibility of using DNA from immortalized cell lines of a woman and her aneuploid offspring to spike an artificial plasma matrix. Enzymatic fragmentation of extracted DNA was optimized to achieve fragment size profiles with a mode of 150 to 200 bp, similar to biological cfDNA. This synthetic material was compared with routine biological samples from pregnant women by a targeted NIPT assay in a multiplex sequencing run on a Proton platform.

RESULTS

Sequencing statistics were similar between artificially prepared material and routine biological samples, as well as relative chromosomal representation, and no matrix effects could be detected. Estimate of fetal fraction (FF) was within the range of expected value, and aneuploidy detection statistic (z-score) was also comparable between both types of samples.

CONCLUSIONS

Artificial plasma spiked with DNA from cell lines of mother and offspring is a promising strategy for developing NIPT RM. This type of material would offer the advantage of a constant and stable composition, allowing for greater standardization of NIPT assays. Moreover, it preserves the parental relatedness used by targeted assay to estimate FF by identification of paternal alleles in single-nucleotide polymorphisms or other variable regions.

Prenatal diagnosis by chromosomal microarray analysis

Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae. Not all microdeletions/duplications are associated with adverse clinical phenotypes and in many cases, their presence is benign. In other cases, they are associated with a spectrum of clinical phenotypes that may range from benign to severe, while in some situations, the clinical significance may simply be unknown. These scenarios present a challenge for prenatal diagnosis, and genetic counseling prior to prenatal CMA greatly facilitates delivery of complex results. In prenatal diagnostic samples with a normal karyotype, chromosomal microarray will diagnose a clinically significant subchromosomal deletion or duplication in approximately 1% of structurally normal pregnancies and 6% with a structural anomaly. Pre-test counseling is also necessary to distinguish the primary differences between the benefits, limitations and diagnostic scope of CMA versus the powerful but limited screening nature of non-invasive prenatal diagnosis using cell-free fetal DNA.

Benefits, challenges and ethical principles associated with implementing noninvasive prenatal testing: a Delphi study

BACKGROUND

Noninvasive prenatal testing is a recent technology that provides some genetic information about the fetus through the analysis of cell-free fetal DNA circulating in maternal blood. We aimed to identify the benefits, challenges and guiding ethical principles most relevant to the clinical integration of noninvasive prenatal testing in Canada, according to experts throughout the country.

METHODS

We conducted a 3-round Delphi study involving Canadian experts of contemporary discussions about the ethical and societal implications of prenatal testing and genomic technologies. In round 1, we asked participants to identify clinical benefits and challenges related to the implementation of noninvasive prenatal testing in Canada, and the ethical principles they think should guide it. In round 2, we asked participants to select the most important elements stated by their peers. In round 3, participants were informed of the aggregated results from round 2, and invited to revise or confirm their selection.

RESULTS

Round 1 had a participation rate of 20.2%, and involved 61 participants. Subsequent rounds 2 and 3 had retention rates of 95.1% (n = 58) and 84.5% (n = 49), respectively. Through these discussions, we identified 3 lists of benefits (n = 10), challenges (n = 27), and ethical principles (n = 16) prioritized by Canadian experts as being most relevant to the implementation of noninvasive prenatal testing in Canada.

INTERPRETATION

Although multiple and diverse potential issues were identified, Canadian experts agreed on 2 sets of requirements for the responsible implementation of noninvasive prenatal testing in Canada. Interdisciplinary appraisals may be instrumental to responsible policy-making related to the implementation of noninvasive prenatal testing in Canada.

Identification of a de novo fetal variant in osteogenesis imperfecta by targeted sequencing-based noninvasive prenatal testing

Noninvasive prenatal testing (NIPT), which involves analysis of circulating cell-free fetal DNA (cffDNA) from maternal plasma, is highly effective for detecting feto-placental chromosome aneuploidy. However, recent studies suggested that coverage-based shallow-depth NIPT cannot accurately detect smaller single or multi-loci genetic variants. To assess the fetal genotype of any locus using maternal plasma, we developed a novel genotyping algorithm named pseudo tetraploid genotyping (PTG). We performed paired-end captured sequencing of the plasma cell-free DNA (cfDNA), in which case a phenotypically healthy woman is suspected to be carrying a fetus with genetic defect. After a series of independent filtering of 111,407 SNPs, we found one variant in COL1A1 graded with high pathogenic potential which might cause osteogenesis imperfecta (OI). Then, we verified this mutation by Sanger sequencing of fetal and parental blood cells. In addition, we evaluated the accuracy and detection rate of the PTG algorithm through direct sequencing of the genomic DNA from maternal and fetal blood cells. Collectively, our study developed an intuitive and cost-effective method for the noninvasive detection of pathogenic mutations, and successfully identified a de novo variant in COL1A1 (c.2596 G > A, p.Gly866Ser) in the fetus implicated in OI.

Genetic counselling, patient education, and informed decision-making in the genomic era

Genomic technologies are now being applied to reproductive genetic screening. Circulating cell-free DNA testing in pregnancy for fetal chromosomal abnormalities is becoming more widely used as a screening test, and expanded carrier screening for autosomal and X-linked recessive conditions for more than a hundred conditions is available to couples for testing before and during pregnancy. These are most typically available as a commercial test. The purpose of reproductive genetic screening is to facilitate autonomous reproductive choices. Previous studies would suggest that many women do not make informed decisions about prenatal genetic screening, and the introduction of genomic technologies has generally added to the ethical debate. Appropriate pre-test genetic counselling is recommended, and healthcare providers should include information that is balanced, accurate and up-to-date, comprising written and/or e-learning tools, as well as providing psychosocial support so that couples consider the pros and cons of being tested and can make informed decisions.

Recent developments in genetics and medically assisted reproduction: from research to clinical applications

Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.

Recent developments in genetics and medically-assisted reproduction: from research to clinical applications†‡

Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively-parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.

Offering non-invasive prenatal testing as part of routine clinical service. Can high levels of informed choice be maintained?

Objectives

To assess rates of informed choice among women offered non‐invasive prenatal testing (NIPT) for aneuploidy as part of routine clinical care.

Methods

A cross‐sectional survey was conducted across 6 antenatal clinics in England. Women with a high risk (≥1/150) Down syndrome screening result were offered NIPT, invasive testing, or no further testing. Pretest counselling was delivered as part of routine care by the local maternity team. Women were given a questionnaire containing a measure of informed choice immediately after pretest counselling.

Results

In total, 220 of 247 women completed the questionnaire. Seventy‐six percent were judged to have made an informed choice, a significant decline from our previous study (89.0% vs 75.6%; χ²(2) = 20.2, P < .001). Of those making an uninformed choice, 46% had insufficient knowledge, 19% had not deliberated, and 13% had made a value‐inconsistent decision. Multivariate analysis showed women who were highly educated (OR, 4.33; 95% CI, 1.08‐17.36) or had had screening in a previous pregnancy (OR, 0.24; 95% CI, 0.90‐0.65) were significantly more likely to make an informed choice.

Conclusions

The findings highlight the challenges of ensuring informed choice in routine prenatal care where NIPT is not discussed at multiple points, less time is available for counselling, and written consent is not required.

What's already known about this topic?

Non‐invasive prenatal testing for aneuploidy is a highly accurate screening test, but concerns exist around potential routinisation.

Previous evidence indicated high levels of informed choice are possible, but this was a tightly controlled research setting.

What does this study add?

Non‐invasive prenatal testing can be offered within routine prenatal care in a way that facilitates high levels of informed choice.

However, the decline in rates of informed choice compared with those in the research setting highlight the challenges of offering non‐invasive prenatal testing in routine prenatal care.

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.

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.

Newborn screening for spinal muscular atrophy: The views of affected families and adults

Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant death worldwide. However, due to a lack of treatments, SMA has historically fallen short of Wilson‐Jungner criteria. While studies have explored the acceptability of expanded newborn screening to the general public, the views of affected families have been largely overlooked. This is in spite of the potential for direct impacts on them and their unique positioning to consider the value of early diagnosis. We have previously reported data on attitudes toward pre‐conception and prenatal genetic screening for SMA among affected families (adults with SMA [n = 82] and family members [n = 255]). Here, using qualitative interview [n = 36] and survey data [n = 337], we report the views of this same cohort toward newborn screening. The majority (70%) of participants were in favor, however, all subgroups (except adults with type II) preferred pre‐conception and/or prenatal screening to newborn screening. Key reasons for newborn screening support were: (1) the potential for improved support; (2) the possibility of enrolling pre‐symptomatic children on clinical trials. Key reasons for non‐support were: (1) concerns about impact on the early experiences of the family; (2) inability to treat. Importantly, participants did not view the potential for inaccurate typing as a significant obstacle to the launch of a population‐wide screening program. This study underscores the need to include families affected by genetic diseases within consultations on screening. This is particularly important for conditions such as SMA which challenge traditional screening criteria, and for which new therapeutics are emerging.

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.

The clinical utility of DNA-based screening for fetal aneuploidy by primary obstetrical care providers in the general pregnancy population

Objective:

To assess the clinical utility of cell-free DNA (cfDNA)-based screening for aneuploidies offered through primary obstetrical care providers to a general pregnancy population.

Methods:

Patient educational materials were developed and validated and providers were trained. Serum was collected for reflexive testing of cfDNA failures. Providers and patients were surveyed concerning knowledge, decision making, and satisfaction. Pregnancy outcome was determined by active or passive ascertainment.

Results:

Between September 2014 and July 2015, 72 providers screened 2,691 women. The five largest participating practices increased uptake by 8 to 40%. Among 2,681 reports, 16 women (0.6%) were screen-positive for trisomy 21, 18, or 13; all saw genetic professionals. Twelve were confirmed (positive predictive value (PPV), 75%; 95% CI, 48–93%) and four were false-positives (0.15%). Of 150 failures (5.6%), 79% had a negative serum or subsequent cfDNA test; no aneuploidies were identified. Of 100 women surveyed, 99 understood that testing was optional, 96 had their questions answered, and 95 received sufficient information. Pretest information was provided by the physician/certified nurse midwife (55) or office nurse/educator (40); none was provided by genetic professionals.

Conclusion:

This first clinical utility study of cfDNA screening found higher uptake rates, patient understanding of basic concepts, and easy incorporation into routine obstetrical practices. There were no reported cases of aneuploidy among cfDNA test failures.

Genet Med advance online publication 12 January 2017

Using Targeted Sequencing of Paralogous Sequences for Noninvasive Detection of Selected Fetal Aneuploidies

BACKGROUND

Current methods for noninvasive prenatal testing (NIPT) ascertain fetal aneuploidies using either direct counting measures of DNA fragments from specific genomic regions or relative measures of single nucleotide polymorphism frequencies. Alternatively, the ratios of paralogous sequence pairs were predicted to reflect fetal aneuploidy. We developed a NIPT assay that uses paralog sequences to enable noninvasive detection of fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA (cfDNA) from maternal plasma.

METHODS

A total of 1060 primer pairs were designed to determine fetal aneuploidy status, fetal sex, and fetal fraction. Each library was prepared from cfDNA by coamplifying all 1060 target pairs together in a single reaction well. Products were measured using massively parallel sequencing and deviations from expected paralog ratios were determined based on the read depth from each paralog.

RESULTS

We evaluated this assay in a blinded set of 480 cfDNA samples with fetal aneuploidy status determined by the MaterniT21^® PLUS assay. Samples were sequenced (mean = 2.3 million reads) with 432 samples returning a result. Using the MaterniT21 PLUS assay for paired plasma aliquots from the same individuals as a reference, all 385 euploid samples, all 31 T21 samples, and 14 of 16 T18 samples were detected with no false positive results observed.

CONCLUSIONS

This study introduces a novel NIPT aneuploidy detection approach using targeted sequencing of paralog motifs and establishes proof-of-concept for a potentially low-cost, highly scalable method for the identification of selected fetal aneuploidies with performance and nonreportable rate similar to other published methods.

Informed decision-making about prenatal cfDNA screening: An assessment of written materials

OBJECTIVES

The introduction of prenatal cfDNA screening for fetal aneuploidy and other genetic conditions has exacerbated concerns about informed decision-making in clinical prenatal testing. To assess the information provided to patients to facilitate decisions about cfDNA screening, we collected written patient education and consent documents created by laboratories and clinics.

METHODS

Informed consent documents (IC) were coded by two independent coders. Each IC was assessed for readability, attention to elements of informed consent, and completeness of information about the test and the screened conditions.

RESULTS

We found variance between IC produced by commercial laboratories versus those provided by local clinics or health care systems, and considerable variance among materials from all sources. "Commercial" IC were longer and written at a more difficult reading level than "non-commercial" IC, and were less likely to state explicitly that cfDNA only screens for certain conditions. About one-third of IC were combined with laboratory order forms. Though most IC recommended confirmatory testing for positive results, only about half clearly stated that results could be incorrect-including mentions of false positives or false negatives. About one-third of IC explicitly stated that cfDNA screening was optional. While nearly all IC from any source listed the conditions screened by the test, only about half of the IC included any phenotypic descriptions of these conditions. Few IC mentioned psychosocial considerations, and only one IC mentioned the availability of support groups for families of children with genetic conditions.

CONCLUSIONS

Based on our findings, we recommend that written and well-informed consent be sought before performing cfDNA screening, and we offer minimal and recommended standards for patient education and consent materials.

Prenatal pharmacogenomics: a promising area for research

Clinical applications of prenatal genetic screening currently focus on detection of aneuploidy and other genetic diseases in the developing fetus. Growing evidence suggests that the fetal genome may also be informative about fetal exposures, through contributions to placental transport as well as placental and fetal metabolism. Possible clinical applications of prenatal pharmacogenomic screening include prospective optimization of medication selection and dosage, as well as retrospective assessment of whether a fetus was previously exposed to significant risk. Newly available non-invasive methods of prenatal genetic screening mean that relevant fetal genotypes could be made available to obstetricians for use in management of a current pregnancy. This promising area for research merits more attention than it has thus far received.

Chromosomal Microarrays for the Prenatal Detection of Microdeletions and Microduplications

Chromosomal microarray analysis has replaced conventional G-banded karyotype in prenatal diagnosis as the first-tier test for the cytogenetic detection of copy number imbalances in fetuses with/without major structural abnormalities. This article reviews the basic technology of microarray; the value and clinical significance of the detection of microdeletions, microduplications, and other copy number variants; as well as the importance of genetic counseling for prenatal diagnosis. It also discusses the current status of noninvasive screening for some of these microdeletion and microduplication syndromes.

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.

Preferences for prenatal tests for Down syndrome: an international comparison of the views of pregnant women and health professionals

Non-invasive prenatal testing is increasingly available worldwide and stakeholder viewpoints are essential to guide implementation. Here we compare the preferences of women and health professionals from nine different countries towards attributes of non-invasive and invasive prenatal tests for Down syndrome. A discrete choice experiment was used to obtain participants' stated preference for prenatal tests that varied according to four attributes: accuracy, time of test, risk of miscarriage, and type of information. Pregnant women and health professionals were recruited from Canada, Denmark, Iceland, Israel, Italy, the Netherlands, Portugal, Singapore, and the United Kingdom. A total of 2666 women's and 1245 health professionals' questionnaires were included in the analysis. Differences in preferences were seen between women and health professionals within and between countries. Overall, women placed greater emphasis on test safety and comprehensive information than health professionals, who emphasised accuracy and early testing. Differences between women's and health professionals' preferences are marked between countries. Varied approaches to implementation and service delivery are therefore needed and individual countries should develop guidelines appropriate for their own social and screening contexts.

Changing to NIPT as a first-tier screening test and future perspectives: opinions of health professionals

OBJECTIVE

The aim of this study was to investigate health professionals' opinions toward offering noninvasive prenatal testing (NIPT) as first-tier screening test regardless of pregnant women's risk, and toward a potential broader range of disorders.

METHODS

A questionnaire completed by obstetric health professionals (n = 240) after an in-service NIPT training in the West and North of the Netherlands.

RESULTS

The majority (72%) of respondents favored replacing first-trimester combined test (FCT) by NIPT, although 43% preferred to maintain nuchal translucency measurement. Many respondents believed that replacing FCT by NIPT would only have advantages (57%), would lead to more pregnant women opting for prenatal testing (69%), and would simplify counseling (47%). Differences in attitudes toward counseling between health professionals were observed. When considering NIPT to screen for broader range of disorders, the majority (92%) thought that this should include disorders characterized by neonatal death, whereas 52% of the respondents favored testing for fetomaternal risk factors. Overall, 46% thought screening should be offered as a fixed list of disorders.

CONCLUSION

Most health professionals favor NIPT instead of FCT but prefer to maintain nuchal translucency measurement. If NIPT becomes available as a first-tier screening test, attention remains necessary to ensure that pregnant women make well-informed decisions in line with the aim of prenatal screening.

Screening for Down syndrome in the second trimester of pregnancy

Antenatal screening for fetal anomalies has provided women and their partners with information to make reproductive choices based on the risk of serious chromosomal or structural defects since the 1990s. Alternative tests include first-trimester screening (combined ultrasound and maternal serum markers), second-trimester maternal serum markers and noninvasive cell-free DNA testing. The recent recommendations by the Royal Australian and New Zealand College of Obstetrics and Gynaecology and the Human Genetics Society of Australasia against second-trimester triple testing are based on unsound performance criteria, raise several contestable issues around access and equity and challenge the principles of governments providing affordable options.