Noninvasive fetal genotyping of single nucleotide variants and linkage analysis for prenatal diagnosis of monogenic disorders

Abstract

Background High-cost, time-consuming and complex processes of several current approaches limit the use of noninvasive prenatal diagnosis (NIPD) for monogenic disorders in clinical application. Thus, a more cost-effective and easily implementable approach is required. Methods We established a low-cost and convenient test to noninvasively deduce fetal genotypes of the mutation and single nucleotide polymorphisms (SNPs) loci by means of targeted amplification combined with deep sequencing of maternal genomic and plasma DNA. The sequential probability ratio test was performed to detect the allelic imbalance in maternal plasma. This method can be employed to directly examine familial pathogenic mutations in the fetal genome, as well as infer the inheritance of parental haplotypes through a group of selected SNPs linked to the pathogenic mutation. Results The fetal mutations in 17 families with different types of monogenic disorders including hemophilia A, von Willebrand disease type 3, Duchenne muscular dystrophy, hyper-IgM type 1, glutaric acidemia type I, Nagashima-type palmoplantar keratosis, and familial exudative vitreoretinopathy were identified in the study. The mutations included various forms: point mutations, gene inversion, deletions/insertions and duplication. The results of 12 families were verified by sequencing of amniotic fluid samples, the accuracy of the approach in fetal genotyping at the mutation and SNPs loci was 98.85% (172/174 loci), and the no-call rate was 28.98% (71/245 loci). The overall accuracy was 12/12 (100%). Moreover, the approach was successfully applied in plasma samples with a fetal fraction as low as 2.3%. Conclusions We have shown in this study that the approach is a cost-effective, less time consuming and accurate method for NIPD of monogenic disorders.

First‐trimester noninvasive prenatal diagnosis of seven facioscapulohumeral muscular dystrophy type 1 families using SNP‐based amplicon sequencing: An earlier, rapid and safer way

“…Furthermore, we adopted amplicon sequencing to construct the DNA library, which reduces the cost to less than half of that of the hybridization capture method. Wu et al demonstrated the feasibility of amplicon sequencing for NIPD by designing 20-30 amplicons flanking related pathogenic variants in seven different diseases (Wu et al, 2022). In consideration of the high recombination rate upstream of the DUX4 gene (Pini et al, 2023), we increased the number of SNPs to 402, which enabled more accurate detection of recombination events.…”

SERPINB7 mutation causes Nagashima‐type palmoplantar keratosis and its spatiotemporal expression in zebrafish

“…We reviewed 32 NPPK relevant studies since 2013, totaling 389 cases (Table S1). 1–5,17,19–43 Twenty‐nine pathogenic mutations in SERPINB7 were summarized. Only eight out of 389 NPPK cases with a single heterozygous mutation were identified as patients due to either clear family history or undetermined second mutation.…”

Population monitoring of trisomy 21: problems and approaches

“…Clearly, for population monitoring of trisomy 21 NIPD offers completely new aspects with respect to population-wide ascertainment in early pregnancy. Moreover, direct haplotyping has been successfully applied for NIPD of monogenic disorders [ 90 – 92 ] including triplet-repeat expansion diseases [ 93 ]. Based on the significant progress of NIPD in the past few years, it is realistic to assume that in the future haplotyping of aneuploidies is possible as well as differentiation between MI and MII errors.…”