Maternal Mosaicism Challenges in Non-Invasive Prenatal Diagnosis.

To report the incidental detection of maternal somatic mosaicism during the development of exclusion-based non-invasive prenatal diagnosis for monogenic disorders (NIPD-MD) initially indicated for apparently de novo pathogenic or likely pathogenic variants. A droplet digital PCR (ddPCR)-based exclusion NIPD_MD assay was developed for four couples, each with a prior pregnancy affected by a rare autosomal dominant or X-linked condition due to a de novo pathogenic or likely pathogenic variant. Assays were designed to detect fetal-specific variants in maternal plasma, with validation performed on parental and proband samples. In four cases, maternal somatic mosaicism (3%-9%) among 70 personalized NIPD_MD (5.7%) was identified during assay validation, rendering NIPD_MD infeasible due to interference from maternal alleles. Each couple was informed of the elevated recurrence risk. Depending on their preferences, invasive prenatal testing or intensive ultrasound follow-up was undertaken. Retrospective analysis of maternal sequencing data confirmed low-level mosaicism that had been filtered out during routine analysis. These cases underscore a key limitation of exclusion NIPD_MD when maternal mosaicism is present. Its identification is essential for accurate recurrence risk estimation and genetic counseling. Sensitive detection methods, careful pre-test evaluation, and transparent communication are critical to ensure informed reproductive decision-making.