Extended Non-Invasive Prenatal Testing for Chromosomal and Monogenic Disorders by Cell-Free DNA Sequencing: A Blinded Comparison With Amniocentesis.

Clinical exome sequencing of cell-free fetal DNA in a parent-fetus trio design, combined with low-pass genome sequencing for aneuploidies and CNVs

This prospective, blinded, single-centre diagnostic accuracy study compares integrated non-invasive fetal exome sequencing of cell-free DNA (iNIFS) with paired amniocentesis in 641 consecutive pregnancies referred for amniocentesis at 16-18 weeks. Plasma cell-free DNA underwent low-pass genome sequencing for aneuploidies and CNVs and, after short-fragment enrichment, clinical exome sequencing in a parent-fetus trio design; the reference standard combined QF-PCR, karyotyping, array-CGH and, where indicated, trio exome sequencing on amniotic fluid. The test was reportable in 624 of 641 pregnancies (97.3%), 612 formed the analysis population, and the reference found a pathogenic or likely pathogenic finding in 107 of them (17.5%). Sensitivity was 99.1% (95% CI 94.9-99.8), specificity 99.6%, PPV 98.1% and NPV 99.8%; the only false negative was a maternally inherited variant, the situation in which the fetal contribution is hardest to distinguish.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

An impressive result for non-invasive testing extended to monogenic disorders, but obtained in a high-risk population (17.5% abnormal findings) at a single centre: predictive values will not transfer as such to a low-risk population. The false negative on a maternally inherited variant illustrates the structural limit of the approach, and the authors maintain that invasive confirmation of positive findings and multicentre validation are needed. At this stage it complements invasive sampling rather than replacing it.

Analysis by Dr Thibaut Benquey