Noninvasive Approaches to Prenatal Diagnosis: Historical Perspective and Future Directions

Potential efficacy of digital polymerase chain reaction for non-invasive prenatal screening of autosomal aneuploidies: a systematic review and meta-analysis

BACKGROUND

Digital Polymerase Chain Reaction (dPCR) presents a promising approach for quantifying DNA and analyzing copy number variants, particularly in non-invasive prenatal testing. This method offers a streamlined and time-efficient procedure in contrast to the widely used next-generation sequencing for non-invasive prenatal testing. Studies have reported encouraging results for dPCR in detecting fetal autosomal aneuploidies. Consequently, this systematic review aimed to evaluate the effectiveness of dPCR in screening for trisomy 21, 18, and 13.

METHODS

A systematic search was conducted in PubMed, Web of Sciences, and Embase for relevant articles published up to December 30, 2023. The Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was utilized for the quality assessment of the included articles. Furthermore, a bivariate random-effect regression model was used to conduct a meta-analysis on the utility of dPCR for trisomy 21 screening.

RESULTS

A total of 9 articles were included in this review, with all of them assessing the utility of dPCR in trisomy 21 screening, and 2 and 1 studies conducting additional analysis on the screening abilities of dPCR for trisomy 18 and 13, respectively. A bivariate random-effects model calculated pooled sensitivity and specificity with a 95% confidence interval (CI). Meta-analysis of 6 studies comparing trisomy-21 screening with karyotyping demonstrated dPCR's pooled sensitivity of 98% [95% CI: 94 -100] and specificity of 99% [95% CI: 99 -100]. While conducting a meta-analysis for trisomy 13 and 18 proved impractical, reported values for sensitivity and specificity were favorable.

CONCLUSIONS

These findings suggest that dPCR holds promise as an effective tool for non-invasive prenatal testing, presenting a less time-consuming and intricate alternative to next-generation sequencing. However, further research is necessary to evaluate dPCR's applicability in clinical settings and to delineate its specific advantages over next-generation sequencing. This study contributes valuable insights into the potential of dPCR for enhancing prenatal screening methodologies.

TRIAL REGISTRATION

The protocol of this study was registered in the International Prospective Register of Systematic Reviews (PROSPERO) on 7/3/2024, with a registration code of CRD42024517523.

Congenital Duodenal Obstruction: National Trends in Management and Outcomes during the Last Quarter of a Century in Norway

INTRODUCTION

 During the last quarter of a century, new surgical techniques in neonates have been introduced, and neonatal intensive care has developed. Few studies have explored the implementation of new techniques and if outcomes in neonates undergoing gastrointestinal surgery have improved in the last decades. Therefore, this study aimed to investigate possible changes in postoperative outcomes and surgical techniques in all neonates operated for congenital duodenal obstruction (CDO) 1995 to 2020 in Norway.

MATERIAL AND METHODS

 This is a national multicenter retrospective study of all neonates undergoing surgery for CDO in Norway from 1995 to 2020. Results from three periods (1995-2003, 2004-2012, and 2013-2020) were compared. The study was approved by the local data protection officers (2020/13386) and (2020/15125).

RESULTS

 We included 186 patients: 41 in period 1 (1995-2003), 83 in period 2 (2004-2012), and 62 in period 3 (2013-2020). Seventy (38%) neonates had Down syndrome and 104 (62%) had additional malformations/disorders. Birth weight, gender, frequency of Down syndrome, and other malformations/disorders did not differ between the three periods. We observed an increased rate of prenatal diagnosis throughout the study period (p < 0.001). The only change in surgical technique was the increased use of transanastomotic feeding tubes (p < 0.001). Length of stay, postoperative complication rate, days with parenteral nutrition, and 30-day mortality rate were stable over time.

CONCLUSION

 Perioperative treatment and postoperative outcomes in neonates with CDO have been surprisingly unchanged during the last quarter of a century. Only an increased rate of prenatal diagnosis and more frequent use of transanastomotic feeding tubes were observed.

Perinatal Palliative Care: Additional Costs of an Interprofessional Service and Outcome of Pregnancies in a Cohort of 115 Referrals

Background: An increasing number of life-limiting conditions (LLCs) is diagnosed prenatally, presenting providers with the ability to present perinatal palliative care (PnPC) services as an option. Objective: To (1) determine the profile characteristics of patients referred for prenatal palliative care counseling to Charité Universitätsmedizin Berlin, Germany; (2) evaluate pregnancy outcome; and (3) analyze the additional human resources per family required to provide specialized PnPC. Methods: Retrospective chart review of pregnant women and infants with potentially LLCs referred for prenatal palliative care counseling between 2016 and 2020. Results: A total of 115 women were referred for prenatal palliative care counseling. Most cases (57.6%) comprised trisomy 13 or 18 (n = 36) and complex congenital conditions (n = 32). Other life-limiting diagnoses included renal agenesis/severe dysplasia (n = 19), congenital heart diseases (n = 18), neurological anomalies (n = 8), and others (n = 5). In 72.0% of cases (n = 85) parents decided to continue pregnancy and plan for palliative birth. Fifty deliveries resulted in a liveborn infant: 33 of these died in the delivery room, 9 neonates died after admission to rooming-in on one of our neonatal wards, and 8 were discharged home or to a hospice. Total human resources (median, range) provided were 563 (0-2940) minutes for psychosocial and 300 (0-720) minutes for medical specialized PnPC per referral. Conclusions: Our data confirm previously observed characteristics of diagnoses, referrals, and outcomes. The provision of specialized and interprofessional PnPC services accounted for ∼14 hours per case of additional human resources.

Maternal prenatal screening programs that predict trisomy 21, trisomy 18, and neural tube defects in offspring

OBJECTIVE

To determine the efficacy of three different maternal screening programs (first-trimester screening [FTS], individual second-trimester screening [ISTS], and first- and second-trimester combined screening [FSTCS]) in predicting offspring with trisomy 21, trisomy 18, and neural tube defects (NTDs).

METHODS

A retrospective cohort involving 108,118 pregnant women who received prenatal screening tests during the first (9-13+6 weeks) and second trimester (15-20+6 weeks) in Hangzhou, China from January-December 2019, as follows: FTS, 72,096; ISTS, 36,022; and FSTCS, 67,631 gravidas.

RESULT

The high and intermediate risk positivity rates for trisomy 21 screening with FSTCS (2.40% and 5.57%) were lower than ISTS (9.02% and 16.14%) and FTS (2.71% and 7.19%); there were statistically significant differences in the positivity rates among the screening programs (all P < 0.05). Detection of trisomy 21 was as follows: ISTS, 68.75%; FSTCS, 63.64%; and FTS, 48.57%. Detection of trisomy 18 was as follows; FTS and FSTCS, 66.67%; and ISTS, 60.00%. There were no statistical differences in the detection rates for trisomy 21 and 18 among the 3 screening programs (all P > 0.05). The positive predictive values (PPVs) for trisomy 21 and 18 were highest with FTS, while the false positive rate (FPR) was lowest with FSTCS.

CONCLUSION

FSTCS was superior to FTS and ISTS screening and substantially reduced the number of high risk pregnancies for trisomy 21 and 18; however, FSTCS was not significantly different in detecting fetal trisomy 21 and 18 and other confirmed cases with chromosomal abnormalities.

Retrospective analysis of 2054 cases from 24 hospitals underwent ultrasonic consultation in a tertiary prenatal diagnosis center in Beijing, China

OBJECTIVES

To investigate the practices of prenatal ultrasound consultation in a region of the China and to describe the rate of concordance between the suspected anomaly and the final diagnosis of the referral examination.

METHODS

Retrospective study with all cases referred from 24 hospitals (Beijing, China) to a tertiary prenatal diagnosis center for ultrasonic consultation in 2018. The concordance between the suspected ultrasonic signs of fetal abnormalities of the referrer and the ultrasonic consultation results were evaluated and divided into full concordance, partial concordance, and discordance.

RESULTS

From 1938 patients with suspected ultrasonic signs, 2054 ultrasound consultation records were obtained. The most frequent anomalies for consultation in the first trimester (348, 91.3%) were cystic hygroma (CH), nuchal translucency (NT), or nuchal fold (NF) thickening, followed by signs of brain abnormalities in the second (173, 22.4%) and the third (182, 34.1%) trimester. The discordant rates of the first single signs were 19.8% for the first trimester, 41.6% for the second trimester, and 37.4% for the third trimester, respectively.

CONCLUSIONS

Our study demonstrated that the discordance of the first single signs was relatively low in the first trimester and higher in the second and third trimesters. The number of sonographers could be increased to ensure timeliness, strengthen training for those with poor concordance rates by referring to appropriate guidelines, and reduce ultrasonic consultation for those with high consistency after further research to save medical resources.

Palliative Care in the Delivery Room: Challenges and Recommendations

Palliative care in the delivery room is an interprofessional and interdisciplinary challenge addressing the dying newborn and parents as well as the caregivers. It differs in some significant aspects from palliative care in the neonatal intensive care unit. Clinical experience suggests that many details regarding this unique specialized palliative care environment are not well known, which may result in some degree of insecurity and emotional distress for health care providers. This article presents basic background information regarding the provision of palliative care to newborns within the delivery room. It offers orientation along with a preliminary set of practical recommendations regarding the following central issues: (i) the basic elements of perinatal palliative care, (ii) the range of non-pharmacological and pharmacological interventions available for infant symptom control near the end of life, (iii) meeting the personal psychological, emotional, and spiritual needs of the parents, and (iv) care and self-care for medical personnel.

The rising tide of cell-free DNA profiling: from snapshot to temporal genome analysis

Genomes of diverse origins are continuously shed into human body fluids in the form of fragmented cell-free DNA (cfDNA). These molecules maintain the genetic and epigenetic codes of their originating source, and often carry additional layers of unique information in newly discovered physico-chemical features. Characterization of cfDNA thus presents the opportunity to non-invasively reconstruct major parts of the host- and metagenome in silico. Data from a single specimen can be leveraged to detect a broad range of disease-specific signatures and has already enabled the development of many pioneering diagnostic tests. Moreover, data from serial sampling may allow unparalleled mapping of the scantily explored landscape of temporal genomic changes as it relates to various changes in different physiological and pathological states of individuals. In this review, we explore how this vast dimension of biological information accessible through cfDNA analysis is being tapped towards the development of increasingly powerful molecular assays and how it is shaping emerging technologies. We also discuss how this departure from traditional paradigms of snapshot genetic testing may pave the way for an onrush of new and exciting discoveries in human biology.

Digital PCR and its applications in noninvasive prenatal testing

In the past decade, digital PCR (dPCR), as a new nucleic acid absolute quantification technology, has been widely used in clinical research. dPCR does not rely on the standard curve and has a higher tolerance to inhibitors. Therefore, it is more accurate than quantitative real-time PCR (qPCR) for the absolute quantification of target sequences. In this article, we aim to review the application of dPCR in noninvasive prenatal testing (NIPT). We focused on the progress of dPCR in screening and identifying fetal chromosome aneuploidies and monogenic mutations. We introduced some common strategies for dPCR in NIPT and analyzed the advantages and disadvantages of different methods. In addition, we compared dPCR with qPCR and next-generation sequencing, respectively, and described their superiority and shortcomings in clinical applications. Finally, we envisaged what the future of dPCR might be in NIPT. Although dPCR can provide reproducible results with improved accuracy due to the digital detection system, it is essential to combine the merits of dPCR and other molecular techniques to achieve more effective and accurate prenatal diagnostic strategies.

Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach

The field of noninvasive prenatal diagnosis (NIPD) has undergone significant progress over the last decade. Direct haplotyping has been successfully applied for NIPD of few single-gene disorders. However, technical issues remain for triplet-repeat expansions. The objective of this study was to develop an NIPD approach for couples at risk of transmitting dynamic mutations. This method includes targeted enrichment for linked-read libraries and targeted maternal plasma DNA sequencing. We also developed an innovative Bayesian procedure to integrate the Hoobari fetal genotyping model for inferring the fetal haplotype and the targeted gene variant status. Our method of directly resolving parental haplotypes through targeted linked-read sequencing was smoothly performed using blood samples from families with Huntington’s disease or myotonic dystrophy type 1. The Bayesian analysis of transmission of parental haplotypes allowed defining the genotype of five fetuses. The predicted variant status of four of these fetuses was in agreement with the invasive prenatal diagnosis findings. Conversely, no conclusive result was obtained for the NIPD of fragile X syndrome. Although improvements should be made to achieve clinically acceptable accuracy, our study shows that linked-read sequencing and parental haplotype phasing can be successfully used for NIPD of triplet-repeat expansion diseases.

Trial registration: NCT04698551_date of first registration: 07/01/2021.

Maternal serum Lamin A is a potential biomarker that can predict adverse pregnancy outcomes

Background

Maternal serum Lamin A (LMNA) was reported to have potential diagnostic value in the prenatal diagnosis of congenital heart disease (CHD). In this study, we aimed to further assess the prognostic value of maternal serum LMNA in predicting adverse pregnancy outcomes.

Methods

A prospective screening study was performed on singleton pregnancies at 15–18 weeks of gestation. After a routine test for alpha fetoprotein (AFP), chorionic gonadotropin (hCG), and unconjugated estriol (uE3), serum LMNA levels were measured. Serum LMNA levels were then converted into multiples of the median (MoM). The median MoM values for adverse pregnancy outcomes were compared with those in normal pregnancies. For diseases with differential LMNA expression in the prospective study, another case-control cohort was recruited. The diagnostic value of LMNA in these diseases was further evaluated.

Findings

Between January 1, 2017 and June 30, 2018, a total of 2906 singleton pregnancies were recruited. Of the 2,906 cases, 2711 had data available for analysis. Congenital structural abnormalities, chromosomal abnormalities, and obstetric complications were observed in 152 (5·6%), 15 (0·6%), and 278 (10·3%) patients, respectively. LMNA was downregulated in pregnancies with fetal CHD, fetal neural tube defects (NTD), and preeclampsia (PE). The case-control study cohort included 256 CHD, 60 NTD, 67 PE, and 400 normal pregnancies. The areas under the curve for the prenatal diagnoses of CHD, NTD, and PE were 0·875, 0·871, and 0·816, respectively.

Interpretation

Maternal serum LMNA was found to be a potential biomarker for the prenatal diagnosis of fetal CHD, NTD, and PE.

Funding

National Key Research and Development Program, National Natural Science Foundation of China, LiaoNing Revitalization Talents Program, National Natural Science Foundation of Liaoning, and 345 Talent Project of Shengjing Hospital.

Clinical Application of Noninvasive Prenatal Testing for Sex Chromosome Aneuploidies in Central China

BACKGROUND

The relatively high incidence and the clinical symptoms of sex chromosome aneuploidies (SCAs) make prenatal screening of SCAs an attractive option for pregnant women. However, limited studies have assessed the clinical performance of noninvasive prenatal testing (NIPT) for screening SCAs. This study was performed to evaluate the clinical performance of NIPT for SCAs in singleton pregnancies in central China.

METHODS

Noninvasive prenatal testing was performed using next-generation sequencing. Standard Z-score analysis was used to identify fetal SCAs. NIPT-positive results were confirmed by invasive prenatal diagnosis (IPD).

RESULTS

A total of 42,164 pregnant women with singleton pregnancies were recruited in this study. They were divided into the following five groups with different clinical indications: with ultrasound soft index abnormalities (9.23%, 3,892/42,164); with advanced maternal age (22.14%, 9,336/42,164); with high risk for maternal serum screening (MSS) (18.35%, 7,738/42,164); with an intermediate risk for MSS (26.6%, 11,215/42,164); and with low risk (23.68%, 9,983/42,164). In all, 223 women had a high risk for SCAs by NIPT with a positive rate of 0.53%. There was no significant difference associated with the five groups in the positive rate. Of all of the positive results, 89 were 45,X (39.91%), 38 were 47,XXX (17.04%), 31 were 46,XY,del(X) (13.90%), 50 were 47,XXY (22.42%,), and 15 were 47,XYY (6.73%). Finally, 147 participants (65.92%) chose to undergo IPD, and 47 cases were confirmed. The combined positive predictive value (PPV) of NIPT for SCA was 31.97% (47/147). PPV was high for 47,XYY (100%, 11/11), moderate for 47,XXX (42.86%, 9/21) and 47,XXY (45.45%, 15/33), but low for 45,X (16.13%, 10/62) and 46,XY,del(X) (10%, 2/20). The termination rates of Turner syndrome and 47,XXY syndrome were higher than 47,XXX and 47,XYY syndromes.

CONCLUSION

In this relatively large cohort, we evaluated the value of NIPT for SCAs. Our data showed that with informed consent and subsequent professional genetical consulting, NIPT can be a useful method to screen SCAs.

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

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

Towards systematic nomenclature for cell-free DNA

Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other clinical scenarios. However, among the obstacles that currently challenge the general progression of the research field, there remains an unmet need for unambiguous universal cfDNA nomenclature. To address this shortcoming, we classify in this report the different types of cfDNA molecules that occur in the human body based on its origin, genetic traits, and locality. We proceed by assigning existing terms to each of these cfDNA subtypes, while proposing new terms and abbreviations where clarity is lacking and more precise stratification would be beneficial. We then suggest the proper usage of these terms within different contexts and scenarios, focusing mainly on the nomenclature as it relates to the domains of oncology, prenatal testing, and post-transplant surgery surveillance. We hope that these recommendations will serve as useful considerations towards the establishment of universal cfDNA nomenclature in the future. In addition, it is conceivable that many of these recommendations can be transposed to cell-free RNA nomenclature by simply exchanging “DNA” with “RNA” in each acronym/abbreviation. Similarly, when describing DNA and RNA collectively, the suffix can be replaced with “NAs” to indicate nucleic acids.

Reference values for ductus venosus doppler indices of normal gestation at 22-37 weeks: A Vietnamese cohort study

Prenatal doppler ultrasound of the ductus venosus plays an important role in the evaluation of fetal circulation and fetal heart function. We aimed to establish the percentile of Resistivity Index (RI) and Pulsatility Index (PI) of the Ductus Venosus (DV) among normal Vietnamese fetuses with a gestation from 22 to 37 weeks in a cohort study. Normal Vietnamese fetuses with a gestation ranging from 22 to 37 weeks were examined in a cohort study. The PI and RI were recorded from the DV. We analyzed 640 participants who all fulfilled the inclusion and exclusion criteria of our study. Results: There was a significant correlation between RI, PI and gestational age as shown with the equations y = 0.077x - 0.003x² + 3.493e - 5x³ (r=0.97) and y = 0.106x - 0.004x² + 4.5e - 5x³ (r=0.94), respectively. A centile module was constructed for the DV RI and PI indices among normal Vietnamese fetuses with gestation from 22 to 37 weeks.

Single Circulating Fetal Trophoblastic Cells Eligible for Non Invasive Prenatal Diagnosis: the Exception Rather than the Rule

Non-Invasive Prenatal Diagnosis (NIPD), based on the analysis of circulating cell-free fetal DNA (cff-DNA), is successfully implemented for an increasing number of monogenic diseases. However, technical issues related to cff-DNA characteristics remain, and not all mutations can be screened with this method, particularly triplet expansion mutations that frequently concern prenatal diagnosis requests. The objective of this study was to develop an approach to isolate and analyze Circulating Trophoblastic Fetal Cells (CFTCs) for NIPD of monogenic diseases caused by triplet repeat expansion or point mutations. We developed a method for CFTC isolation based on DEPArray sorting and used Huntington’s disease as the clinical model for CFTC-based NIPD. Then, we investigated whether CFTC isolation and Whole Genome Amplification (WGA) could be used for NIPD in couples at risk of transmitting different monogenic diseases. Our data show that the allele drop-out rate was 3-fold higher in CFTCs than in maternal cells processed in the same way. Moreover, we give new insights into CFTCs by compiling data obtained by extensive molecular testing by microsatellite multiplex PCR genotyping and by WGA followed by mini-exome sequencing. CFTCs appear to be often characterized by a random state of genomic degradation.

Non-invasive cell-free fetal DNA testing for aneuploidy: multicenter study of 31 515 singleton pregnancies in southeastern China

OBJECTIVE

To analyze the non-invasive prenatal testing (NIPT) for aneuploidy results of 31 515 singleton pregnancies in Fujian province, southeastern China, and assess its performance in low-, moderate- and high-risk pregnancies.

METHODS

Women were categorized into groups according to whether their risk for fetal abnormality was low, moderate or high. Cell-free plasma DNA extracted from peripheral blood samples was subjected to low-coverage whole-genome sequencing. Standard Z-score analysis of the mapped sequencing reads was used to identify fetal aneuploidy, including the three main trisomies (T21, T18 and T13) and sex chromosome aneuploidy (SCA). NIPT-positive results were confirmed by amniocentesis and karyotyping. The performance of NIPT for detection of T21, T18, T13 and SCA was assessed by calculating the sensitivity and specificity.

RESULTS

The rate of chromosomal abnormality detected by NIPT in the study population was 1.38%. A higher rate of chromosomal abnormality was found in the high-risk group (1.57%) compared to the moderate-risk (1.05%) and low-risk (1.18%) groups (P < 0.05). Sensitivity and specificity, respectively, were 98.96% (95/96) and 99.94% (31 274/31 292) for detection of T21, 100% (25/25) and 99.96% (31 352/31 363) for T18, 100% (7/7) and 99.97% (31 373/31 381) for T13 and 100% (61/61) and 99.74% (31 245/31 327) for SCA. Positive predictive values were high for T21 (84.07%) and T18 (69.44%) and moderate for T13 (46.67%) and SCA (42.66%).

CONCLUSION

Our findings support the application of NIPT for reliable and accurate testing of the general population of reproductive-age women for clinically significant fetal aneuploidy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.