The cell‐free DNA virome of 108,349 Dutch pregnant women

Persistent Uninterpretable or Failed Prenatal Cell-Free DNA Screening Indicates a High-Risk Pregnancy and is Associated With Biological Factors Interfering With cfDNA-Analysis: A Prospective Cohort Study

OBJECTIVE

To investigate maternal characteristics, underlying factors and perinatal outcome in pregnancies with persistent uninterpretable prenatal cfDNA screening in a general obstetric population (GOP).

METHODS

This study included pregnant individuals with persistent uninterpretable prenatal cfDNA screening results from December 2020 to December 2022. Prenatal cfDNA screening results were classified as uninterpretable due to low quality score (LQS) or low fetal fraction (LFF). Maternal autoimmune screening and a third prenatal cfDNA screening were performed later in pregnancy. Data on maternal characteristics and perinatal outcome were analyzed.

RESULTS

Among 123 pregnant individuals with failed prenatal cfDNA screening, 68% were due to LFF and 32% to LQS. Obesity and autoimmune diseases were significantly overrepresented. A third prenatal cfDNA screening at 24 weeks was informative in 77.1% cases, with a higher success-rate in the LFF group (87.8%). Maternal autoimmune screening revealed unknown triple positivity for antiphospholipid antibodies in 2.4%. Abnormal perinatal outcome was registered in 69.9% of patients, with higher rates of adverse perinatal outcome in the LFF group.

CONCLUSION

Persistent uninterpretable prenatal cfDNA screening indicates a higher risk for adverse perinatal outcomes, especially in cases with LFF. Maternal autoimmune screening should be considered to identify high-risk pregnancies. A third prenatal cfDNA screening later in pregnancy can help stratify truly high-risk pregnancies and allows patients with initially uninterpretable results to make an informed decision about diagnostic testing.

Detection of human cytomegalovirus cell-free DNA in pregnant women with symptomatically infected fetuses: proof-of-concept study

OBJECTIVE

To evaluate the presence and levels of cytomegalovirus (CMV) cell-free DNA (cfDNA) fragments in women pregnant with a fetus with symptomatic congenital CMV (cCMV).

METHODS

The study comprised nine women whose fetuses were diagnosed with cCMV between June 2019 and July 2024 at 20 + 4 to 34 + 1 weeks' gestation (n = 8) or neonatally (n = 1) after primary or non-primary maternal infection. In eight women, cfDNA sequencing data from a single timepoint were analyzed, either retrospectively, on data generated from 11-13 weeks' gestation (n = 5) or prospectively, on data generated from 20-26 weeks' gestation (n = 3), upon the diagnosis of cCMV. In one woman (Case 6), CMV-cfDNA analysis was performed at four timepoints: at 12 + 5 weeks (routine non-invasive prenatal testing); 23 + 3 weeks (cCMV diagnosis); and 30 min and 12 h after termination of pregnancy (TOP) at 23 + 6 weeks.

RESULTS

CMV-cfDNA was detectable in all cases. Mostly low levels of CMV-cfDNA were observed in samples obtained at 11-13 weeks' gestation and consistently high levels of CMV-cfDNA were present in samples obtained at cCMV diagnosis. In Case 6, the level of maternal CMV-cfDNA decreased substantially in the samples tested after TOP, compared with samples obtained before TOP.

CONCLUSIONS

Low levels of CMV-cfDNA detected between 11 and 13 weeks may be a biomarker for severe fetal cCMV. CMV-cfDNA analysis in the first trimester could be of added value in CMV screening, particularly for non-primary maternal infections that cannot be identified using other methods. However, as CMV-cfDNA is detectable in many pregnant women in the first trimester, further studies are needed to determine the predictive value of CMV-cfDNA as a biomarker for the development of severe fetal cCMV. High levels of CMV-cfDNA at fetal cCMV diagnosis and low levels directly after TOP suggest that the level of CMV-cfDNA in maternal plasma may not necessarily reflect an active maternal infection, but could indicate a placental infection. © 2025 The Author(s). Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Cell-free DNA from clinical testing as a resource of population genetic analysis

As a noninvasive biomarker, cell-free DNA (cfDNA) has achieved remarkable success in clinical applications. Notably, cfDNA is essentially DNA, and conducting whole-genome sequencing (WGS) can yield a wealth of genetic information. These invaluable data should not be confined to one-time use; instead, they should be leveraged for more comprehensive population genetic analysis, including genetic variation spectrum, population structure and genetic selection, and genome-wide association studies (GWASs), among others. Such research findings can, in turn, facilitate clinical practice, enabling more advanced and accurate disease predictions. This review explores the advantages, challenges, and current research areas of cfDNA in population genetics. We hope that this review can serve as a new chapter in the repurposing of cfDNA sequence data generated from clinical testing in population genetics.

Novel biomarkers of fetal and neonatal environmental exposure, effect and susceptibility

Rapid advancements in science and technology have allowed medical providers to treat wider ranges of diseases with safer and more effective therapies than ever before. One of the areas of health that has been consistently understudied, however, is one that affects us all: environmental health or the effects that the chemicals we are exposed to every day have on our acute and chronic health. This effect can be exacerbated during and shortly after pregnancy, as an individual exposure is often shared by both the mother and the fetus/neonate. The diagnosis and monitoring of chemical exposure can be quite challenging, and improving our understanding of the effects of exposure will therefore require effective use of an expanding set of biomarker tests and biological matrices. This review covers the background and history of neonatal biomarkers of exposure, effect, and susceptibility, focusing on the potential uses for the non-invasive matrix of exhaled breath for the detection and monitoring of chemical exposures. IMPACT: Provides a brief overview of Food and Drug Administration and National Institutes of Health Joint Leadership Council BEST (Biomarkers, EndpointS, and other Tools) Resource. Summarizes new and potential biomarkers for fetal exposure. Collates studies using breath as a matrix for environmental exposures.

Implementing non-invasive prenatal testing in a national screening program: Lessons learned from the TRIDENT studies

The Dutch NIPT Consortium, a multidisciplinary collaboration of stakeholders in prenatal care initiated and launched the TRIDENT studies. The goal of the TRIDENT studies was to implement non-invasive prenatal testing (NIPT), first as a contingent (second-tier) and later as a first-tier test, and to evaluate this implementation. This paper describes how NIPT can be successfully implemented in a country or state. Important factors include the significance of forming a consortium and encouraging cooperation among relevant stakeholders, appropriate training for obstetric care professionals, and taking into account the perspectives of pregnant women when implementing prenatal tests. We describe the advantages of high sensitivity and specificity when comparing contingent NIPT with first-tier NIPT. This paper emphasizes the value of pre- and post-test counselling and the requirement for a standardized method of information delivery and value clarification, to assist couples in decision making for prenatal screening.

Unexpected Findings of Duchenne Muscular Dystrophy in Prenatal Screening of Chromosome Abnormality Based on Cell-Free Fetal DNA

OBJECTIVE

 This study aims to assess the feasibility of detecting and diagnosing Duchenne muscular dystrophy (DMD) during prenatal screening for chromosome abnormalities using cell-free fetal DNA extracted from peripheral blood samples of pregnant women.

STUDY DESIGN

 Two pregnant women identified as high risk through noninvasive prenatal testing (NIPT) underwent amniocentesis to obtain fetal cells. Subsequent fetal chromosomal karyotyping was conducted, and genomic DNA from fetal cells was extracted for copy number variation sequencing (CNV-Seq) analysis, complemented by multiplex ligation-dependent probe amplification (MLPA) to detect deletions or duplications within the DMD gene.

RESULTS

 NIPT results for the two samples indicated potential abnormalities involving chromosomes 21 and 18. However, karyotype analysis of the fetuses revealed no abnormalities. CNV-Seq identified deletions of 0.28 and 0.18 Mb within chromosome Xp21.1, encompassing the DMD gene, in each fetus. In family 1, MLPA results indicated a maternal heterozygous deletion spanning exons 12 to 41 in the DMD gene, while the fetus exhibited deletions in exons 12 to 41. In family 2, MLPA results confirmed normal DMD gene status in the pregnant woman's peripheral blood genomic DNA but revealed a fetal deletion spanning exons 48 to 52. Both fetuses were diagnosed with DMD and subsequently underwent termination.

CONCLUSION

 Abnormalities identified through NIPT necessitate further invasive prenatal diagnostic procedures. For cases involving chromosomal microdeletions or microduplications, a combination of karyotyping and CNV-Seq testing is essential for comprehensive diagnosis. NIPT followed by CNV-Seq may offer insights into large exon deletions within the DMD gene in specific instances.

KEY POINTS

· NIPT results can offer valuable insights into the deletion and duplication of DMD gene for the fetus.. · It's crucial to notice unexpected findings in NIPT.. · A combination of karyotyping and CNV-Seq testing is essential for comprehensive diagnosis..

Utilizing non-invasive prenatal test sequencing data for human genetic investigation

Non-invasive prenatal testing (NIPT) employs ultra-low-pass sequencing of maternal plasma cell-free DNA to detect fetal trisomy. Its global adoption has established NIPT as a large human genetic resource for exploring genetic variations and their associations with phenotypes. Here, we present methods for analyzing large-scale, low-depth NIPT data, including customized algorithms and software for genetic variant detection, genotype imputation, family relatedness, population structure inference, and genome-wide association analysis of maternal genomes. Our results demonstrate accurate allele frequency estimation and high genotype imputation accuracy (R2>0.84) for NIPT sequencing depths from 0.1× to 0.3×. We also achieve effective classification of duplicates and first-degree relatives, along with robust principal-component analysis. Additionally, we obtain an R2>0.81 for estimating genetic effect sizes across genotyping and sequencing platforms with adequate sample sizes. These methods offer a robust theoretical and practical foundation for utilizing NIPT data in medical genetic research.

From shells to sequences: A proof-of-concept study for on-site analysis of hemolymphatic circulating cell-free DNA from sentinel mussels using Nanopore technology

Blue mussels are often abundant and widely distributed in polar marine coastal ecosystems. Because of their wide distribution, ecological importance, and relatively stationary lifestyle, bivalves have long been considered suitable indicators of ecosystem health and changes. Monitoring the population dynamics of blue mussels can provide information on the overall biodiversity, species interactions, and ecosystem functioning. In the present work, we combined the concept of liquid biopsy (LB), an emerging concept in medicine based on the sequencing of free circulating DNA, with the Oxford Nanopore Technologies (ONT) platform using a portable laboratory in a remote area. Our results demonstrate that this platform is ideally suited for sequencing hemolymphatic circulating cell-free DNA (ccfDNA) fragments found in blue mussels. The percentage of non-self ccfDNA accounted for >50 % of ccfDNA at certain sampling Sites, allowing the quick, on-site acquisition of a global view of the biodiversity of a coastal marine ecosystem. These ccfDNA fragments originated from viruses, bacteria, plants, arthropods, algae, and multiple Chordata. Aside from non-self ccfDNA, we found DNA fragments from all 14 blue mussel chromosomes, as well as those originating from the mitochondrial genomes. However, the distribution of nuclear and mitochondrial DNA was significantly different between Sites. Similarly, analyses between various sampling Sites showed that the biodiversity varied significantly within microhabitats. Our work shows that the ONT platform is well-suited for LB in sentinel blue mussels in remote and challenging conditions, enabling faster fieldwork for conservation strategies and resource management in diverse settings.

Cell-Free Nucleic Acids for Early Prediction of Preeclampsia

PURPOSE OF REVIEW

This review summarizes the potential of cell-free nucleic acids for predicting preeclampsia, contrasts them with other methods, and discusses these findings' relevance to preeclampsia's pathogenesis and care.

RECENT FINDINGS

Recent studies have demonstrated the utility of cell-free nucleic acids in early preeclampsia risk prediction. Encouragingly, nucleic acid measurement exhibits similar or better sensitivity as compared to standard screening assays and furthermore sheds light on preeclampsia's underlying placental biology. Over the past decade, liquid biopsies measuring cell-free nucleic acids have found diverse applications, including in prenatal care. Recent advances have extended their utility to predict preeclampsia, a major cause of maternal mortality. These assays assess methylation patterns in cell-free DNA (cfDNA) or gene levels in cell-free RNA (cfRNA). Currently, preeclampsia care focuses on blood pressure control, seizure prevention, and delivery. If validated, early prediction of preeclampsia through liquid biopsies can improve maternal health and deepen our understanding of its causes.

Counseling in fetal medicine: Congenital cytomegalovirus infection

Although the clinical work-up of CMV in pregnancy has gradually become more accurate, counseling for CMV is still challenging. Despite the potential feasibility of universal prenatal serological screening, its introduction in prenatal diagnosis continues to raise concerns related to its real cost-effectiveness. Contextually, anticipating the confirmation of fetal infection earlier in pregnancy is one of the most pressing issues to reduce the parental psychological burden. Amniocentesis is still the gold standard and recent data have demonstrated that it could be performed before 20 weeks of gestation, provided that at least 8 weeks have elapsed from the presumed date of maternal seroconversion. New approaches, such as chorionic villus sampling (CVS) and virome DNA, even if not yet validated as confirmation of fetal infection, have been studied alternatively to amniocentesis to reduce the time-interval from maternal seroconversion and the amniocentesis results. Risk stratification for sensorineural hearing loss (SNHL) and long-term sequelae should be provided according to the prognostic predictors. Nevertheless, in the era of valacyclovir, maternal high-dose therapy, mainly for first trimester infections, can reduce the risk of vertical transmission and increase the likelihood of asymptomatic newborns, but it is still unclear whether valacyclovir continues to exert a beneficial effect on fetuses with positive amniocentesis. This review provides updated evidence-based key counseling points with GRADE recommendations.

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

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

Position statement from the International Society for Prenatal Diagnosis on the use of non-invasive prenatal testing for the detection of fetal chromosomal conditions in singleton pregnancies

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Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

Noninvasive sampling of an individual's body fluids is an easy means to capture circulating cell-free DNA (cfDNA). These small fragments of DNA carry information on the contributing cell's genome, epigenome, and nuclease content. Analysis of cfDNA for the assessment of genetic risk has already revolutionized clinical practice, and a compendium of increasingly higher-resolution approaches based on epigenetic and fragmentomic cfDNA signatures continues to expand. Profiling cfDNA has unlocked a wealth of molecular information that can be translated to the clinic. This review covers the biological characteristics of cfDNA, recent advances in liquid biopsy and the clinical utility of cfDNA.