Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA

Current non-invasive prenatal screening is targeted toward the detection of chromosomal abnormalities in the fetus 1 , 2 . However, screening for many dominant monogenic disorders associated with de novo mutations is not available, despite their relatively high incidence 3 . Here we report on the development and validation of, and early clinical experience with, a new approach for non-invasive prenatal sequencing for a panel of causative genes for frequent dominant monogenic diseases. Cell-free DNA (cfDNA) extracted from maternal plasma was barcoded, enriched, and then analyzed by next-generation sequencing (NGS) for targeted regions. Low-level fetal variants were identified by a statistical analysis adjusted for NGS read count and fetal fraction. Pathogenic or likely pathogenic variants were confirmed by a secondary amplicon-based test on cfDNA. Clinical tests were performed on 422 pregnancies with or without abnormal ultrasound findings or family history. Follow-up studies on cases with available outcome results confirmed 20 true-positive, 127 true-negative, zero false-positive, and zero-false negative results. The initial clinical study demonstrated that this non-invasive test can provide valuable molecular information for the detection of a wide spectrum of dominant monogenic diseases, complementing current screening for aneuploidies or carrier screening for recessive disorders. A non-invasive prenatal test utilizing cell-free DNA simultaneously detects mutations in 30 genes frequently associated with dominant monogenic diseases and demonstrates high accuracy in human clinical samples.