Extended Non-Invasive Prenatal Testing for Chromosomal and Monogenic Disorders by Cell-Free DNA Sequencing: A Blinded Comparison With Amniocentesis
In brief
Cell-free DNA sequencing matched amniocentesis in 99.5% of pregnancies
In 612 pregnancies referred for amniocentesis, sequencing maternal blood detected chromosomal and genetic findings with 99.5% overall agreement with amniotic-fluid testing; results were reportable in 97.3% of the 641 pregnancies enrolled. One missed finding was inherited from the mother, a difficult variant type to distinguish, and positive results still need invasive confirmation; multicenter validation is needed.
- Journal
- Prenatal diagnosis (Q1)
- Published
- 20 October 2026
- Study design
- Unclassified
- Evidence level
- Level 5, Expert Opinion (CEBM 5)
- Authors
- Alvaro Mesoraca, Katia Margiotti, Marco Fabiani, Francesco Libotte, Laura D'Emidio, Raffaella Raffio, et al.
- PMID
- 42900896
- DOI
- 10.1002/pd.70285
Why clinicians should know about it
- Picked for Genetics (clinical) (paper of the day, 23 October 2026): Prospective diagnostic accuracy study of prenatal genomic screening
Abstract
OBJECTIVE: To determine whether molecular integrated non-invasive fetal exome sequencing (iNIFS), using clinical exome sequencing of maternal-plasma cell-free DNA, concords per pregnancy with paired amniocentesis. METHOD: Prospective, blinded, single center, paired sample diagnostic accuracy study in 641 consecutive pregnancies referred for clinically indicated amniocentesis at 16-18 weeks. Plasma cell-free DNA underwent low-pass whole-genome sequencing for aneuploidies and CNVs and, after short-fragment enrichment, clinical exome sequencing within a parent fetus trio design. The reference standard comprised QF-PCR, karyotyping, array-comparative genomic hybridization and, where indicated, trio clinical exome sequencing on amniotic-fluid DNA. RESULTS: iNIFS was reportable in 624/641 pregnancies (97.3%); 612 (95.5%) had complete paired data and formed the analysis population. The reference established a pathogenic or likely pathogenic finding in 107/612 (17.5%). NIPT gave 106 true positives, 503 true negatives, 2 discordant positives and 1 discordant negative: sensitivity 99.1% (95% CI 94.9-99.8), specificity 99.6% (98.6-99.9), PPV 98.1% (93.5-99.5), NPV 99.8% (98.9-100.0), agreement 99.5% and Cohen's κ 0.98. The discordant negative was a maternally inherited variant, the class for which distinguishing maternal from fetal contributions is most challenging. CONCLUSION: Molecular iNIFS showed high concordance with paired amniocentesis across chromosomal, copy-number and monogenic findings, while retaining an explicit no call rate. Multicentre validation and invasive confirmation of positive findings remain necessary.
Abstract as published, via PubMed.
For healthcare professionals. The summary is generated by AI from the published abstract, and the evidence level is assigned automatically from the study design on the Oxford CEBM hierarchy. Neither is medical advice. Read the full paper before changing practice.