Since the discovery of a small fraction of circulating cell-free fetal DNA (ccffDNA) in the blood of the mother, non-invasive prenatal diagnosis (NIPD) techniques using a simple blood sample have been developed to 1) screen for chromosomal abnormalities, 2) diagnose fetal sex, and 3) detect variants not carried by the mother (exclusion NIPD by PCR).

Exclusion NIPD by PCR is currently available for certain common variants, but developing it for each variant takes 3-6 weeks per center. The development process for PCR NIPD is lengthy and costly for each variant tested, thereby restricting access to this technique. In practice, this technique is not widely available to couples at risk of transmitting a severe monogenic disease in France, due to the large number of different genes and multiple variants of a given gene.

Next-generation sequencing (NGS) is based on the simultaneous, parallel execution of millions of sequencing reactions, enabling the same nucleotide sequence to be sequenced hundreds of times. It provides qualitative information on the nature of the sequenced base, as well as quantitative information on the number of times the base has been sequenced (reads). Although it only allows for the analysis of around 2% of the entire genome, NGS sequencing of the exome corresponds to almost all the exons of the 22,000 or so genes in our genome. However, this generates a large amount of data, leading to additional costs.

Since its widespread adoption by diagnostic laboratories, some teams have developed an NGS-based NIPD for the exclusion of a pathogenic variant. It allows the analysis of multiple pathogenic variants without requiring an additional development phase. They have demonstrated that NGS-based NIPD is a robust and reliable technology, but one that incurs additional reagent costs.

In France, 1,700 to 1,800 prenatal diagnostic tests (PND) for monogenic diseases are performed each year due to family history. Between 35 and 40% of couples undergoing invasive PND could benefit from NIPD by NGS, as proposed in the PrenatSafe project. The increased availability of NIPD, whether by PCR or NGS, could also affect couples' demand in the long term. In France, the introduction of NIPD by NGS is likely to lead to an increase in requests for NIPD, as many couples with a low risk of recurrence (in the case of de novo mutations) will probably opt for it due to its lack of iatrogenicity.

The rapid and widespread rise of NIPD by NGS, made possible by the use of a standardized, generalizable technique such as NGS, will transform our practices throughout the country. The PrenatSafe project therefore aims to evaluate the cost/benefit ratio of NIPD by NGS compared to the current standard procedure: NIPD by PCR when performed in clinical practice or PND by invasive sampling (trophoblast biopsy or amniocentesis), using an automated, standardized NGS technique involving exome sequencing, which covers almost all indications for exclusion NIPD.

This project is the first cost-consequence analysis of prospective exome-based NIPD, using a single standardized technique. The aim is to translate this innovative technology into routine practice if it proves beneficial and economically viable. Exome-based NIPD for exclusion can be fully automated, from ccfDNA extraction to sequencing. This reduces the risk of human error and brings turnaround times in line with the requirements of prenatal diagnosis. If successful, exome-based NIPD would become an earlier alternative to invasive PND without increasing the risk of fetal loss. It would be available for a very large number of indications and could easily be transferred to other prenatal diagnosis centers in France.

The study will be proposed to couples undergoing prenatal diagnosis following genetic counseling or during a pregnancy follow-up consultation. The NIPD results obtained via NGS within the PRENATSAFE study will not be disclosed to the couple or their prescribing physician, and they will not impact clinical management.

No additional conditions will be diagnosed through NGS-based NIPD. However, the analysis will be conducted under real-life conditions, with a turnaround time of less than ten working days, in order to provide an accurate estimate of NIPD costs.

Informed consent will be obtained from the pregnant woman, her partner, and , if applicable both legal guardians by a physician or trained genetic personnel (e.g., a genetic counselor or another investigator).

Two additional blood samples (20 ml total, Streck tubes) will be collected from the pregnant woman during routine pregnancy monitoring, prior to any invasive prenatal diagnosis if indicated. These tubes will enable the automated extraction of circulating cell-free fetal DNA (cffDNA).

NIPD by NGS will be performed in a trio or quartet format, involving exome sequencing of ccffDNA and genomic DNA from the father, mother and from a previous affected child/fetus, if applicable. Genomic DNA samples will either be collected and stored as part of routine clinical care or transferred to the molecular genetics laboratory at Necker-Enfants Malades Hospital (AP-HP) if necessary. Library preparation for sequencing will be automated using the Magnis Dx system (Agilent Technologies), and data analysis will be conducted using a dedicated bioinformatics algorithm.

For the study, results from prenatal diagnoses performed as part of routine care (invasive PND or PCR-based NIPD) and occurrences of fetal loss and pregnancy outcomes will be recorded.

Pregnancy will be monitored according to standard clinical practice, with no additional visits required for research purposes. Follow-up for the PRENATSAFE study will conclude one month after the expected end of pregnancy or following the post-termination consultation, which occurs three months after medical termination if applicable.

Inclusion Criteria:

• Couple aged over 18 years
• Ongoing pregnancy of at least 7 weeks gestational age
• Requesting, within clinical care, invasive prenatal diagnosis or PCR-based NIPD for a particularly severe monogenic disorder, with indication confirmed by a Multidisciplinary Prenatal Diagnosis Center (CPDPN)
• Eligible for exclusion diagnosis
• Causative gene covered by the Agilent V8 exome capture kit
• Affiliated with the national general social security system
• Informed consent obtained from the pregnant woman and her partner

Exclusion Criteria:

• Prenatal diagnosis request not approved by a Multidisciplinary Prenatal Diagnosis Center (CPDPN)
• Disorder not analyzable by next-generation sequencing (e.g., triplet repeat expansions, sequence homology)
• Woman carrying the pathogenic variant
• Woman or partner deprived of liberty, under guardianship or curatorship
• Index case other than the father, a child, or a fetus from a previous pregnancy within the couple.

Couples undergoing prenatal diagnosis are at high risk of transmitting a severe incurable condition due to a monogenic defect.