# Single‐cell‐based non‐invasive screening for fetal pathogenic microimbalances using maternal blood: comparison with invasive prenatal diagnosis

## TL;DR

A new non-invasive prenatal test using single-cell sequencing detects fetal chromosomal abnormalities with high accuracy, offering better screening than current methods.

## Contribution

A novel non-invasive prenatal testing method using single-cell sequencing achieves high sensitivity and specificity for detecting fetal microimbalances.

## Key findings

- scsbNIPT detected genome-wide microimbalances ≥300 kb with 92.9% sensitivity and 98.2% specificity.
- The test showed 100% sensitivity for p/lpCNVs ≥300 kb in early pregnancies (11+0 to 14+6 weeks).
- scsbNIPT outperformed existing cfDNA-based methods in detecting chromosomal abnormalities.

## Abstract

Pathogenic or likely pathogenic copy‐number variants (p/lpCNVs) are a significant cause of perinatal morbidity and mortality. Current prenatal screening based on cell‐free DNA (cfDNA) fails to detect the majority of microimbalances (microdeletions/microduplications), leaving a significant residual risk of undetected chromosomal abnormalities. This study evaluated the clinical performance of a novel single‐cell‐sequencing‐based non‐invasive prenatal testing (scsbNIPT) method utilizing circulating extravillous trophoblasts (cEVTs) for the detection of fetal p/lpCNVs, particularly microimbalances < 8 Mb.

This was a prospective, blinded, observational multicenter cohort study of 1390 high‐risk pregnant women undergoing prenatal invasive diagnostic testing between November 2021 and December 2023. A 20‐mL maternal blood sample was collected from each subject between 11 + 0 and 22 + 6 weeks' gestation prior to invasive sampling. cEVTs were isolated and subjected to whole‐genome sequencing, using a proprietary workflow. scsbNIPT results were compared with standard invasive prenatal diagnostic results obtained by karyotyping and/or chromosomal microarray analysis.

scsbNIPT showed a sensitivity of 92.9% (95% CI, 76.5–99.1%) and a specificity of 98.2% (95% CI, 97.0–99.0%) for the detection of genome‐wide microimbalances measuring ≥ 300 kb to < 8 Mb. The sensitivity for p/lpCNVs ≥ 300 kb in pregnancies screened at 11 + 0 to 14 + 6 weeks was 100% (95% CI, 83.9–100%). For trisomy 21, the sensitivity of scsbNIPT was 98.0% (95% CI, 92.9–99.8%) and the specificity was 99.7% (95% CI, 99.0–99.9%).

This study demonstrates the scientific validity and clinical utility of scsbNIPT for the non‐invasive detection of genome‐wide fetal p/lpCNVs, particularly microimbalances, with high sensitivity and a resolution comparable to that of chromosomal microarray analysis. scsbNIPT may offer more complete screening for genome‐wide p/lpCNVs, markedly lowering the residual risk early in pregnancy compared with existing cfDNA‐based methods. © 2026 Menarini Silicon Biosystems. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.