Simultaneous Prenatal cfDNA Screening of Aneuploidy, Recessive Single-Gene Conditions, and Fetomaternal Blood Compatibility

BACKGROUND: The provision of prenatal genetic screening in 3 core clinical contexts-recessive conditions, aneuploidy, and serological incompatibility-involves multiple tests across reproductive partners. This complexity limits utilization and impairs adherence to guideline-recommended care, particularly in carrier screening, where male partners are frequently not tested when a female carrier is identified. Here, we describe the analytical validation of a fetomaternal integrated recessive, serological, and trisomy genetic screen (FIRSTGENE), a single assay that harnesses in silico fragment-length trajectory analysis to evaluate all 3 contexts simultaneously, identifying clinically relevant variants in both the mother and the fetus without requiring a paternal sample. METHODS: FIRSTGENE screens singleton pregnancies for mutations in 20 recessive genes; RhD compatibility; aneuploidies in chromosomes 13, 18, 21, X, and Y; and 22q11.2 microdeletion. Each part of the test was individually validated using a relevant subset of plasma samples from a curated collection (478 total samples from 456 patients) and 93 cell-line mixtures digested to resemble maternal and fetal cell-free DNA. RESULTS: FIRSTGENE demonstrated ≥98.2% sensitivity and ≥99.0% specificity for fetal alleles in recessive-disease genes in plasma and cell lines; 100% sensitivity and specificity for RhD compatibility in plasma; 100% sensitivity and ≥99.8% specificity for fetal chromosomal abnormalities in plasma; and ≥99.9% sensitivity and specificity for maternal alleles in recessive-disease genes in plasma. CONCLUSIONS: FIRSTGENE demonstrated high analytical sensitivity and analytical specificity for each component of the assay. Its capability to generate multiple prenatal screening results from a single blood draw may improve the efficiency and accessibility of prenatal genetic screening.