Direct haplotyping enables noninvasive prenatal testing (NIPT) without analyzing proband, which is a promising strategy for pregnancies at risk of an inherited single-gene disorder. Here, we aimed to expand the scope of single-gene disorders that NIPT using linked-read direct haplotyping would be applicable to. Three families at risk of myotonic dystrophy type 1, lipoid congenital adrenal hyperplasia, and Fukuyama congenital muscular dystrophy were recruited. All cases exhibited distinct characteristics that are often encountered as hurdles (i.e., repeat expansion, identical variants in both parents, and novel variants with retrotransposon insertion) in the universal clinical application of NIPT. Direct haplotyping of parental genomes was performed by linked-read sequencing, combined with allele-specific PCR, if necessary. Target DMPK, STAR, and FKTN genes in the maternal plasma DNA were sequenced. Posterior risk calculations and an Anderson–Darling test were performed to deduce the maternal and paternal inheritance, respectively. In all cases, we could predict the inheritance of maternal mutant allele with > 99.9% confidence, while paternal mutant alleles were not predicted to be inherited. Our study indicates that direct haplotyping and posterior risk calculation can be applied with subtle modifications to NIPT for the detection of an expanded range of diseases.

直接单倍型可以在不分析先证者的情况下实现无创产前检测 (NIPT)，这对于有遗传性单基因疾病风险的妊娠来说是一种很有前途的策略。在这里，我们旨在扩大 NIPT 使用连锁阅读直接单倍型分析的单基因疾病范围。招募了三个有患 1 型强直性肌营养不良症、类脂先天性肾上腺增生症和福山先天性肌营养不良症风险的家庭。所有病例都表现出独特的特征，这些特征在 NIPT 的普遍临床应用中经常遇到障碍（即重复扩增、双亲中的相同变体以及具有反转录转座子插入的新变体）。亲本基因组的直接单倍型通过连锁读取测序进行，必要时结合等位基因特异性PCR。目标对母体血浆 DNA 中的DMPK、STAR和FKTN基因进行了测序。进行后风险计算和 Anderson-Darling 检验以分别推断母系和父系遗传。在所有情况下，我们可以以 > 99.9% 的置信度预测母系突变等位基因的遗传，而预测父系突变等位基因不会被遗传。我们的研究表明，直接单倍型分析和后验风险计算可以通过对 NIPT 进行细微修改来应用，以检测更广泛的疾病。