Nationwide implementation of exclusion non-invasive prenatal diagnosis for single-gene disorders: Nine-year activity...

Non-invasive prenatal diagnosis for single-gene disorders (SGD-NIPD) has progressively emerged as a reliable alternative to invasive prenatal procedures in selected high-risk situations. In France, an exclusion strategy targeting paternal or de novo pathogenic variants has been implemented through a coordinated nationwide public network. We report five-year activity data, key technical performance indicators, and future perspectives of this model.

We conducted a retrospective multicenter study including all exclusion NIPD tests performed within the French public network between January 2017 and January 2026. Variant-specific assays were developed using droplet digital PCR (ddPCR). We analyzed activity trends, indication spectrum, assay availability, diagnostic reliability, and turnaround time.

A total of 2038 exclusion NIPD tests were performed. Annual activity increased elevenfold between 2017 and 2025, reaching 611 tests in 2025. Indications comprised de novo variants (52%), autosomal recessive conditions (34%), and autosomal dominant disorders (13%). Across four centers, 1133 validated variant-specific assays are currently available, covering 478 genes. Assay development success rate reached approximately 94%. No false-positive or false-negative results have been reported. The mean turnaround time was 6 days.

Exclusion NIPD for single-gene disorders has achieved nationwide scalability within a public healthcare framework, combining analytical robustness, rapid result delivery, and broad disease coverage. Ongoing developments, including targeted haplotype-based approaches for maternally inherited variants within the national DANNIgene program, aim to extend the scope of non-invasive prenatal diagnosis. These advances may ultimately pave the way toward broader genomic inference strategies while maintaining structured clinical and ethical oversight.