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

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.

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.

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.

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.