Non-Invasive Fetal Sequencing (NIFS) as a Transformative Prenatal Genetic Screening Test

Over the past two decades, advances in prenatal diagnostics have improved clinical outcomes by transitioning from low-resolution karyotyping and chromosomal microarray (CMA) to more recent methods like exome sequencing (ES) and genome sequencing (GS). However, diagnostic testing requires invasive procedures, such as amniocentesis, which carry risks to both maternal and fetal health and contribute to high healthcare costs. Non-invasive prenatal testing (NIPT) has mitigated these risks by allowing the detection of chromosomal aneuploidies from maternal blood plasma using cell-free fetal DNA (cffDNA). Despite its widespread adoption—screening 25-50% of pregnancies in the US — NIPT remains limited to low-resolution testing, primarily detecting aneuploidies and changes in a few targeted loci. We propose to validate and optimize our recently published high-resolution non-invasive fetal sequencing (NIFS) technology that is capable of unbiased fetal exome screening at high coverage from a maternal blood draw alone. This innovation could transform maternal-fetal medicine (MFM) and significantly reduce healthcare costs by obviating the need for invasive procedures in fetal genetic testing. Our preliminary studies have demonstrated feasibility of NIFS, with 95.7% sensitivity and 94% precision in surveying fetal genomes across gestational ages relevant to prenatal testing. This project aims to implement and further validate NIFS for potential clinical application through three main objectives. First, we will conduct a comprehensive validation study of anomalous pregnancies (AIM 1) through analysis of 650 retrospective pregnancies with fetal structural anomalies (FSAs) and matched GS from invasive testing to validate pathogenic variant prediction. These analyses will benchmark the efficiency of NIFS in the detection of single-nucleotide variants (SNVs), indels, and copy number variants (CNVs). Second, we will focus on optimization (AIM 2) by developing robust analytic pipelines to discover, interpret, and validate variants at all gestational ages relevant to prenatal testing, conducting stress testing for scalability and estimating unbiased specificity and sensitivity for NIFS as a potential replacement for invasive genetic testing and next step in high-resolution screening for all pregnancies. Third, we will explore the performance of NIFS in non-anomalous pregnancies (AIM 3) by evaluating 500 pregnancies that underwent invasive testing and subsequent GS without an FSA or indication for testing, and 100 pregnancies with aneuploidies or CNVs detected by NIPT. We will estimate NIFS performance metrics and added diagnostic yield over NIPT from these data. This research unites interdisciplinary experts from technological innovation, computational genomics, clinical genetics, and MFM. Our team will rigorously assess NIFS as a non-invasive prenatal screening method that could transform pregnancy care by providing unprecedented access to genetic data and guiding treatment strategies for expectant women. Project Number: 1R01HD119060-01 | Fiscal Year: 2025 | NIH Institute/Center: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | Principal Investigator: MICHAEL TALKOWSKI | Institution: MASSACHUSETTS GENERAL HOSPITAL, BOSTON, MA | Award Amount: $584,317 | Activity Code: R01 | Study Section: Genetics of Health and Disease Study Section[GHD] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R01HD11906001