Noninvasive prenatal sequencing for multiple Mendelian monogenic disorders among fetuses with skeletal dysplasia or increased nuchal translucency

Is It Feasible to Screen for Fetal De Novo or Paternally Inherited Pathogenic Single Nucleotide Variants in Maternal Plasma Cell-Free DNA? A Systematic Literature Review

OBJECTIVE

Monogenic disorders (MDs), often associated with developmental delay, intellectual disability, hypotonia, or dysmorphic facial features, typically go undetected during pregnancy. These disorders are frequently caused by de novo single nucleotide variants (SNVs), which are not currently covered by routine non-invasive prenatal testing (NIPT). This screening gap limits informed decision-making in pregnancy and can lead to the unexpected birth of neonates with severe conditions. The aim of this study was to look for evidence of whether de novo SNVs can be detected through NIPT and to assess the possibility of screening for autosomal dominant MDs in cell-free DNA in maternal plasma.

METHODS

A systematic literature review conducted on the 27th of February 2024 identified 12 studies examining NIPT of multiple genes associated with MDs. An additional citation analysis for the four most recent studies that were included in the systematic review was conducted on 10th of April 2025. Four additional studies met our inclusion criteria and were incorporated in the final analysis.

RESULTS

The studies demonstrated that next-generation sequencing of a gene panel or whole exome could detect pathogenic single nucleotide variants in fetuses with high positive predictive values 98.9% (66.7%-100%).

CONCLUSION

This review confirms that performing NIPT for de novo and paternally inherited pathogenic variants associated with MDs is technically possible. Ethical considerations, including disorder selection, variant disclosure, and the need for large-scale implementation studies must be addressed to assess the potential risks and ensure effective and responsible implementation.

Advances in Prenatal Cell-Free DNA Screening for Dominant Monogenic Conditions: A Review of Current Progress and Future Directions in Clinical Implementation

Prenatal cell-free DNA (cfDNA) screening has advanced significantly, extending beyond detecting aneuploidies to sub-chromosomal copy number variations. However, its application for screening dominant single-gene conditions, often caused by de novo variants, remains underutilized in the general obstetric population. This study reviews recent data and experience on prenatal cfDNA screening for dominant monogenic conditions using multiple-gene panels, highlighting its potential to enhance early detection and management of genetic disorders. Integrating comprehensive cfDNA screening into routine prenatal care could complement current imaging techniques and standard prenatal cfDNA screening, which may overlook pre-symptomatic fetuses with dominant monogenic conditions in early gestation. Despite promising initial results, further research is needed to confirm the clinical validity and utility of cfDNA screening for these conditions. Larger and more diverse studies are necessary to assess the broader applicability of this technology. In addition, key challenges such as access, genetic counseling, ethical considerations, and policy development need to be addressed. A comprehensive approach, including rigorous test design, informed consent, and robust counseling, is essential for the successful adoption of expanded cfDNA screening, ultimately improving clinical outcomes.

Routine Prenatal cfDNA Screening for Autosomal Dominant Single-Gene Conditions

BACKGROUND

Genetic screening has advanced from prenatal cell-free DNA (cfDNA) screening for aneuploidies (cfDNA-ANP) to single-gene disorders (cfDNA-SGD). Clinical validation studies have been promising in pregnancies with anomalies but are limited in the general population.

METHODS

Chart review and laboratory data identified pregnancies with cfDNA-SGD screening for 25 autosomal dominant conditions at our academic center. Screening was identified as routine by International Classification of Diseases (ICD) 10 codes and chart review. Ultrasound anomalies or known family history of a condition on the panel were excluded. Retrospective chart review investigated test concordance, outcomes, and phenotypes.

RESULTS

cfDNA-SGD was completed for 3480/37 050 (9.4%) pregnancies, of which 2745 (78.9%) were for routine screening. Fourteen (0.51%, 14/2745) had high-risk results defined as pathogenic/likely pathogenic (P/LP) variants: 6 (0.22%) likely fetal variants, and 8 (0.29%) maternal variants with 50% risk for fetal inheritance. Diagnostic testing detected 6/6 fetal and 6/8 maternal cfDNA-SGD variants (2/8 pregnant individuals declined testing but had clinical features on physical exam). Variants were detected in 11/14 pregnancies/newborns and in 9/14 (64.3%) parents/gamete donors. There were no false positives identified by cfDNA-SGD; however, 2 variants were discrepantly classified between the cfDNA-SGD and diagnostic testing laboratories. All pregnancies had normal imaging and 9 had mild postnatal phenotypes. Three terminated pregnancy following diagnostic testing.

CONCLUSIONS

Our study demonstrated that 0.51% of routine cfDNA-SGD was high risk, prompting comprehensive evaluation for pregnancies and parents. Routine cfDNA-SGD allowed for early identification and intervention, but raises counseling challenges due to variable expressivity, limited genotype-phenotype correlations, and discrepant variant classification.

Non-invasive prenatal detection of dominant single-gene disorders in fetal structural abnormalities: a clinical feasibility study

OBJECTIVE

This study evaluated the accuracy of non-invasive prenatal testing (NIPT-SGDs) for dominant monogenic genetic diseases associated with fetal structural abnormalities and to assess the feasibility of clinical application.

METHODS

Pregnant women requiring prenatal diagnosis due to fetal structural abnormalities were enrolled. Maternal peripheral blood was analyzed for cell-free DNA (cfDNA) using coordinative allele-aware target enrichment sequencing (COATE-seq). This assessed fetal allele depth distribution, fraction and variation ratio. The variation's origin was then determined to obtain fetal variation information. Finally, NIPT-SGDs results were confirmed via invasive prenatal diagnosis (IPD).

RESULTS

Upon examination of 113 samples using NIPT-SGDs, COATE-seq successfully analyzed 112 for fetal variation, excluding one due to hemolysis. The study detected six positive cases, yielding a 5.36% detection rate. These disorders included tuberous sclerosis complex (TSC1 and TSC2 being its causative genes), Noonan syndrome (PTPN11), polycystic kidney disease (PKD1), and Kabuki syndrome (KMT2D), occurring twice each, except for Noonan and polycystic kidney disease. Two false positives were due to the mother being a genetic mosaicism. Compared to invasive whole-exome sequencing (WES), NIPT-SGDs did not detect nine positive cases of IPD dominant monogenic diseases, accurately identifying 90.18% (101/112) of the actual positive and negative cases.

CONCLUSION

Our findings demonstrate the clinical utility of NIPT-SGDs using COATE-seq in effectively identifying fetuses with dominant single-gene disorders. Furthermore, this method can be applied to all fetuses.

Beyond blood: Advancing the frontiers of liquid biopsy in oncology and personalized medicine

Liquid biopsy is emerging as a pivotal tool in precision oncology, offering a noninvasive and comprehensive approach to cancer diagnostics and management. By harnessing biofluids such as blood, urine, saliva, cerebrospinal fluid, and pleural effusions, this technique profiles key biomarkers including circulating tumor DNA, circulating tumor cells, microRNAs, and extracellular vesicles. This review discusses the extended scope of liquid biopsy, highlighting its indispensable role in enhancing patient outcomes through early detection, continuous monitoring, and tailored therapy. While the advantages are notable, we also address the challenges, emphasizing the necessity for precision, cost-effectiveness, and standardized methodologies in its broader application. The future trajectory of liquid biopsy is set to expand its reach in personalized medicine, fueled by technological advancements and collaborative research.

Current controversy in prenatal diagnosis: The use of cfDNA to screen for monogenic conditions in low risk populations is ready for clinical use

Noninvasive cfDNA testing for monogenic disorders (sgNIPT) has become integrated into the care of pregnant women at increased risk based on carrier status, known family history, or ultrasound anomalies. The availability of commercial tests for common autosomal recessive and de novo autosomal dominant conditions has led to the use of these tests in low-risk pregnancies. However, is the technology ready for use in this low-risk population? This report is a summary of the debate on this topic at the 27th International Conference on Prenatal Diagnosis and Therapy. Both expert debaters provided strong arguments in favor and against the use of sgNIPT in low-risk pregnancies. The argument in favor of sgNIPT for autosomal recessive conditions is that it allows the identification of affected pregnancies without the need for involving the partner in testing. Arguments for sgNIPT for autosomal dominant conditions include identification of affected fetuses that would have either presented later in pregnancy with fetal anomalies or not been detected prenatally given normal ultrasounds, respect for patient autonomy and patient desire for information. Strong arguments were made against offering sgNIPT screening. Given that traditional carrier screening for recessive conditions can be carried out in many jurisdictions, the added value of sgNIPT has not been clearly demonstrated. Arguments against sgNIPT for autosomal dominant conditions included the total lack of clinical validation studies and the risk of false reassurance in cases of negative results and unnecessary invasive procedures in cases of false positive results. Although there is a desire to take advantage of new technologies to improve the detection of monogenic disorders in low-risk populations, based on the discussion and the audience vote, it appears premature to offer sgNIPT to all low risk pregnant women. Further clinical validation studies are needed prior to broad implementation.

Chorionic Villous Testing Versus Amniocentesis After Abnormal Noninvasive Prenatal Testing

In the setting of a normal first-trimester ultrasound, an amniocentesis may be a better option than chorionic villous sampling for invasive diagnostic testing after a cell-free DNA high risk for trisomy 13, given the high rates of confined placental mosaicism. In unaffected fetuses, other evaluations should be considered depending on the cell-free DNA results, including maternal karyotyping for monosomy X, uniparental disomy testing for chromosomes with imprinted genes, serial growth scans for trisomy 16, and a workup for maternal malignancy for multiple aneuploidies or autosomal monosomy.

Single gene non-invasive prenatal screening for autosomal dominant conditions in a high-risk cohort

PURPOSE

To determine the utility of single gene non-invasive prenatal screening (NIPS-SGD) in a high-risk reproductive genetics clinic.

METHODS

A clinical pilot for NIPS-SGD was conducted from March 2020 to November 2021. A NIPS-SGD panel assessing pathogenic variants in 30 genes was offered to pregnant individuals for the following indications: (1) advanced sperm age ≥40 years, (2) nuchal translucency (NT) ≥ 3.5 mm, (3) fetal anomaly, or (4) family history of a condition covered by the panel. Diagnostic testing was offered concurrently.

RESULTS

NIPS-SGD was ordered for 253 individuals: 88 (34.8%) for fetal anomalies, 96 (37.9%) for advanced sperm age, 37 (14.6%) for increased NT, and 5 (2.0%) for family history. Among 228 (90.1%) completed tests, 8 (3.5%) were positive. Diagnostic testing for 78 individuals revealed no false positive or negative results. Of 41 (25.9%) individuals who received a molecular diagnosis, 34 (82.9%) were outside the scope of NIPS-SGD. Positive NIPS-SGD altered medical management in five cases.

CONCLUSIONS

NIPS-SGD in a high-risk population can lead to earlier prenatal diagnosis, enhanced surveillance, and targeted genetic analysis, but should not replace clinically indicated diagnostic testing. Potential incidental findings include parental diagnoses and misattributed parentage.

Application of whole exome sequencing in fetal cases with skeletal abnormalities

Objectives

To investigate the role of whole exome sequencing (WES) technology in fetuses with skeletal abnormalities (SKA) for establishing an appropriate clinical diagnosis and treatment path.

Methods

From April 2019 to August 2020, eight special families were enrolled into the study. Their fetuses showed abnormal SKA by ultrasonic testing during pregnancy, but it is inconsistent with the normal results identified by chromosomal microarray analysis (CMA) of amniotic fluid or abortion. For further diagnosis, WES was performed to detect the causative genes mutations followed by Sanger sequencing.

Results

Among of these eight fetuses with SKA, we found more than half of pathogenic mutations were in COL1A1/2 gene, except for a known hotspot mutation in FGFR3 gene (c.1138G>A). Three heterozygous mutations of COL1A1 gene, c.2885G>A p (Gly962Asp), c.994G>A p (Gly332Arg) and c.1002 + 5G>T, were de novo mutations. The c.1002 + 5G>T mutation in COL1A1 was firstly reported. In addition, one fetus carried a novel heterozygous mutation of COL1A1 c.644G>A p (Gly215Asp), which was inherited from the mother. Another novel heterozygous mutation c.2482G>T p (Val828Phe) in the COL1A2 gene was identified in another fetus and was inherited from the father. Among of these COL1A1 mutations, these results might involve in two novel splicing mutations.

Conclusion

Our study reported several novel heterozygous mutations which expands the COL1A1/2 mutation spectrum for prenatal diagnosis of SKA. Most importantly, WES technology is necessary as a routine step of the SKA diagnosis before or during pregnancy, combining with the detection of chromosome level.

Chromosomal microarray analysis versus noninvasive prenatal testing in fetuses with increased nuchal translucency

OBJECTIVE

To evaluate if the NT value of 2.5 mm ≤ NT < 3.0 mm is an appropriate indication for CMA tests among fetuses with isolated increased NT and NIPT is more suitable instead.

METHODS

A total of 442 fetuses with NT ≥ 2.5 mm were included, in which 241 fetuses underwent karyotype. CMA tests were then carried out when cytogenic analysis showed normal chromosomes and CNV status was compared between 2.5 mm ≤ NT < 3.0 mm and ≥3.0 mm subgroups. For the NIPT evaluation, 201 of 442 fetuses with smaller increased NT (2.5 mm ≤ NT < 3.0 mm) was examined by either NIPT or karyotype.

RESULTS

Of the 241 fetuses with NT ≥ 2.5 mm, 47(19.50%) were identified by karyotype with chromosomal abnormalities. Among 194 cases with normal karyotype, CMA unraveled additional CNVs in 16(8.25%) cases, including 3(1.55%) pathogenic CNVs, 2(1.03%) likely pathogenic CNVs and 11(5.67%) VOUS. After the subgroup analysis, however, only one case (1.16%) of likely pathogenic was identified by CMA among 86 fetuses with NT between 2.5 mm and 3.0 mm, whereas the rest of 15 CNV cases were all presented in fetuses with NT ≥ 3.0 mm. For the NIPT evaluation, the detection rate of 201 fetuses with isolated increased NT between 2.5 and 3.0 mm was 3.98%, which was indifferent to karyotype with the rate of 5%. In comparison with fetuses with 2.5-3.0 mm combined with other risks, the detection rate of karyotype was 26.92%.

CONCLUSION

While no pathogenic CNVs were detected in fetuses, chromosomal aneuploidies and genomic imbalance were found to be the major type of abnormalities when NT was 2.5-3.0 mm. Therefore, our data suggested that CMA should not be recommended when fetuses with an NT value less than 3.0 mm. Instead, NIPT with similar rate of detection as karyotype was recommended for fetuses with isolated increased NT between 2.5 and 3.0 mm.

Clinical experience with non-invasive prenatal screening for single-gene disorders

OBJECTIVE

To assess the performance of a non-invasive prenatal screening test (NIPT) for a panel of dominant single-gene disorders (SGD) with a combined population incidence of 1 in 600.

METHODS

Cell-free fetal DNA isolated from maternal plasma samples accessioned from 14 April 2017 to 27 November 2019 was analyzed by next-generation sequencing, targeting 30 genes, to look for pathogenic or likely pathogenic variants implicated in 25 dominant conditions. The conditions included Noonan spectrum disorders, skeletal disorders, craniosynostosis syndromes, Cornelia de Lange syndrome, Alagille syndrome, tuberous sclerosis, epileptic encephalopathy, SYNGAP1-related intellectual disability, CHARGE syndrome, Sotos syndrome and Rett syndrome. NIPT-SGD was made available as a clinical service to women with a singleton pregnancy at ≥ 9 weeks' gestation, with testing on maternal and paternal genomic DNA to assist in interpretation. A minimum of 4.5% fetal fraction was required for test interpretation. Variants identified in the mother were deemed inconclusive with respect to fetal carrier status. Confirmatory prenatal or postnatal diagnostic testing was recommended for all screen-positive patients and follow-up information was requested. The screen-positive rates with respect to the clinical indication for testing were evaluated.

RESULTS

A NIPT-SGD result was available for 2208 women, of which 125 (5.7%) were positive. Elevated test-positive rates were observed for referrals with a family history of a disorder on the panel (20/132 (15.2%)) or a primary indication of fetal long-bone abnormality (60/178 (33.7%)), fetal craniofacial abnormality (6/21 (28.6%)), fetal lymphatic abnormality (20/150 (13.3%)) or major fetal cardiac defect (4/31 (12.9%)). For paternal age ≥ 40 years as a sole risk factor, the test-positive rate was 2/912 (0.2%). Of the 125 positive cases, follow-up information was available for 67 (53.6%), with none classified as false-positive. No false-negative cases were identified.

CONCLUSIONS

NIPT can assist in the early detection of a set of SGD, particularly when either abnormal ultrasound findings or a family history is present. Additional clinical studies are needed to evaluate the optimal design of the gene panel, define target populations and assess patient acceptability. NIPT-SGD offers a safe and early prenatal screening option. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Comprehensive non-invasive prenatal screening for pregnancies with elevated risks of genetic disorders: protocol for a prospective, multicentre study

INTRODUCTION

Chromosomal abnormalities and monogenic disorders account for ~15%-25% of recognisable birth defects. With limited treatment options, preconception and prenatal screening were developed to reduce the incidence of such disorders. Currently, non-invasive prenatal screening (NIPS) for common aneuploidies is implemented worldwide with superiority over conventional serum or sonographic screening approaches. However, the clinical validity for the screening of frequent chromosome segmental copy number variations and monogenic disorders still awaits to be proved.

METHODS AND ANALYSIS

This study is a multicentre, prospective study. The participants were recruited from three tertiary hospitals in China starting from 10 April 2021. The study is expected to conclude before 10 October 2022. Pregnant women with abnormal prenatal screening results indicated for invasive prenatal diagnosis or those who decide to terminate their pregnancies due to abnormal ultrasound findings will be evaluated for enrolment. Cell-free DNA extracted from the maternal plasma will be used for an analytically validated comprehensive NIPS test developed by Beijing BioBiggen Technology Co. (Beijing, China). The diagnostic results from prenatal or postnatal specimens as well as the pregnancy outcome data will be collected to examine the clinical sensitivity, specificity, positive and negative predictive values of the test.

ETHICS AND DISSEMINATION

This study was approved by the Obstetrics and Gynecology Hospital of Fudan University (2020-178). Results of this study will be disseminated to public through scientific conferences and a peer-reviewed journal. Written informed consents will be obtained from participants.

TRIAL REGISTRATION NUMBER

ChiCTR2100045739.

Diagnostic testing after positive results on cell free DNA screening: CVS or Amnio?

OBJECTIVE

The positive predictive values of cell free DNA (cfDNA) and rates of confined placental mosaicism (CPM), imprinting and other factors vary by chromosome.

METHODS

We sought to review the literature for each of these features for each chromosome and provide recommendations on chorionic villus sampling (CVS) versus amniocentesis after an abnormal cfDNA result.

RESULTS

For chromosomes with high rates of CPM (trisomy 13, monosomy X and rare autosomal trisomies [RATs]), an amniocentesis should be considered if the first trimester ultrasound is normal. For monosomy X on cfDNA with an unaffected fetus, maternal karyotyping should be considered after normal fetal diagnostic testing. In cfDNA cases with a trisomy involving a chromosome with imprinted genes (6, 7, 11, 14, 15 and 20), CVS should be considered, followed by amniocentesis if abnormal. If the fetus is unaffected, methylation studies should be considered given the risk of uniparental disomy. A third trimester growth ultrasound should be considered for patients with a positive cfDNA screen for a RAT and an unaffected fetus, especially in the case of trisomy 16. For patients with multiple aneuploidy results on cfDNA, a work-up for maternal malignancy should be considered.

CONCLUSIONS

Clinicians should consider rates of CPM, imprinting, ultrasound findings and maternal factors when considering whether to recommend amniocentesis or CVS after an abnormal cfDNA result.

The role of chromosomal microarray and exome sequencing in prenatal diagnosis

PURPOSE OF REVIEW

Advancements in technologies have revolutionized prenatal diagnosis. Chromosomal microarray analysis (CMA) became a proven method and was implemented to detect gains and losses of DNA and absence of heterozygosity across the genome. Next-generation sequencing technologies have brought opportunities and challenges to genetic testing. Exome sequencing detects single-nucleotide variants (SNVs) across the exome and its prenatal application is an emerging field. We reviewed the literature to define the role of CMA and exome sequencing in prenatal diagnosis.

RECENT FINDING

The application of exome sequencing in genetic diagnosis shows increased diagnostic yield and could be potentially implemented for prenatal diagnosis of fetuses with one or more ultrasound structural abnormalities or suspected monogenetic conditions. Although CMA is a gold standard for copy number variant (CNV) detection, large clinical cohort studies emphasized integrated CNV and SNV analyses for precise molecular diagnosis. Recent studies also suggest low-pass genome sequencing-based CNV detection can identify genome-wide imbalances at higher resolutions.

SUMMARY

Data suggest exome sequencing for SNVs and CMA for CNV detection are the most effective approach for prenatal genetic diagnosis. Emerging evidences show genome sequencing has the potential to replace CMA and even exome sequencing to become a comprehensive genetic test in the clinical diagnostic laboratory.