Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA

BACKGROUND: Noninvasive prenatal screening for aneuploidies and microdeletion/microduplication syndromes (MMS) has gained widespread clinical application. However, the development of noninvasive prenatal diagnosis for monogenic disorders (NIPT-M) has progressed slower. Existing NIPT-M approaches often require specialized designs, are limited to a narrow range of genes, or are expensive and impractical for clinical implementation. METHODS: We present HaploNIPD, a universal haplotype-based approach for NIPT-M, utilizing a targeted capture panel that includes 120,000 selected single-nucleotide polymorphisms. Maternal cell-free DNA (cfDNA) and genomic DNA (gDNA) from family members were targeted captured and massively parallel sequenced. Parental haplotypes were phased, and fetal genome-wide haplotypes and copy number profiles were determined. The clinical efficacy of HaploNIPD was assessed in 70 families with monogenic disorders and 152 samples with known fetal karyotypes. RESULTS: Fetal haplotypes were accurately determined in 69 of 70 families (98.57%), with perfect concordance to invasive prenatal diagnosis results. One case was classified as "no call" due to a recombination event within the target region. Compared to fetal haplotypes derived from chorionic villus or amniotic fluid, the deduced fetal haplotypes in maternal plasma by HaploNIPD had an average genome-wide accuracy of 99.74% and 98.23% for paternal and maternal inheritance, respectively. All common aneuploidies (trisomies 13, 18 and 21, monosomy X, XXX, XXY, and XYY) and MMS were accurately identified. CONCLUSIONS: Our findings demonstrate the potential of HaploNIPD as a robust and versatile platform for NIPT-M capable of noninvasive genome-wide fetal haplotyping and simultaneous detection of aneuploidies and MMS, offering a scalable solution for comprehensive prenatal genetic diagnosis.