Health Economic Evaluation of Non-Invasive Prenatal Exclusion Diagnosis

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.