Novel Haplotype‐Based Noninvasive Prenatal Diagnosis for Recessive Single‐Gene Disorders: A Proof‐of‐Concept Study

Accurate parental haplotype information is crucial for noninvasive prenatal diagnosis (NIPD) of recessive single‐gene disorders (SGD) (NIPD‐SGD). However, conventional approaches rely on complex experimental techniques or trio‐based SNP linkage analysis requiring family members, which limit clinical application. Here, we present a novel direct haplotyping based NIPD approach termed DiHNIPD, utilizing single‐tube long fragment read (stLFR) sequencing. First, parental genome‐wide haplotypes were reconstructed by stLFR‐based whole genome sequencing (WGS). Second, SNPs within and surrounding the target gene in maternal plasma were identified by WGS. Finally, fetal haplotypes were determined by implementing a parental haplotype‐assisted hidden Markov model combined with the Viterbi algorithm. The DiHNIPD results were further confirmed by invasive prenatal diagnosis. This study recruited 23 couples at risk of having a fetus with SGD. DiHNIPD directly phased all parental haplotypes of the target gene and accurately deduced 23 fetal genotypes, achieving 100% concordance with diagnostic results. These results demonstrate that DiHNIPD is a sensitive, user‐friendly and inexpensive strategy for NIPD‐SGD. It eliminates the need for expensive devices and complex procedures and does not rely on family members. This method shows significant promise for clinical use in high‐risk pregnancies without prior offspring.