Appropriate prenatal diagnosis of hearing loss could give carrier couples more options for future family planning and probably the preparation for the health and educational needs of the affected neonates(17). In our study, as research for NIPD of NSHL, the earliest testing week is 7 weeks. Among the sixteen singleton pregnant women, NIPD was successfully applied in 93.75% (15/16) of families and the coincidence rate with invasive prenatal diagnosis was 100% (15/15). Only one NIPD result is no call because the imbalance distribution of SNP sites makes it difficult to estimate recombination events. Most (13/15) of pregnant women were in the first trimester and the earliest gestation week was the 7th week.
Besides, due to the wide application of reproductive technology, the probability of multiple pregnancies is increasing. The singleton NIPD algorithms may lead to inaccurate results in dizygotic twins since the fetal fraction of the affected fetus could be lower and result in a dosage change not as considerable as expected. In this case, we proposed a two-step Bayes factor with the first step to distinguish whether the twins inherit different haplotypes. The second step could indicate whether the pathogenic haplotype was inherited for every fetus. Furthermore, if the first step indicates the twin inherited an identical haplotype, the invasive procedure could just need one puncture operation, which reduces the risk of miscarriage.
Whether singleton or twin pregnancy, genomic DNA target sequencing requires no complicated experimental procedure, such as the previously reported haplotype-assisted methods, and is cost-effective if the appropriate array is designed. Moreover, the turnaround time, including the sampling process and sequencing on the Ion Proton platform, can be as short as 1 week. Then the bioinformatics analysis can be accomplished within 1 day, which lends this type of procedure to large-scale clinical applications.
However, there were several shortcomings, and the relevant solution was made to secure NIPD accuracy. First, the traditional proband-based haplotype needs a complete trio family to construct the parent haplotype. However, no proband is also available in our study design. Families with a previous reproductive history, whether normal patients or carriers, can be used to construct haplotypes(9). Families with no reproductive history can also construct haplotypes through grandparents. Second, the NIPD results might be disturbed by recombination events. The CBS algorithm could predict the recombination event, which is used to estimate copy number variation (CNV) data and identify the reasonable breakpoint(18). Then the researchers determined whether the recombinational break point affected the identification of pathogenic variants. Third, for consanguineous marriage, homozygous regions of the gene will increase and result in an insufficient number of informative SNPs, which is not suitable for this method.
For the twin pregnancy with GJB2 gene mutation, the twin’s fetal fraction is coincidentally almost identical. Luckily, the GJB2 gene mutation inheritance is diagnosed clearly in this case. However, if the family was carriers with SLC26A4 gene mutation, the result would be ambiguous. For the SLC26A4 gene, the fraternal twins inherited four parents’ haplotypes (Fig. 3). In this circumstance, the two fetal fractions were identical, and the four haplotypes were inherited, there are two possible inheritance situations. One, it could be two pathogenic mutation carriers. Two, it could be an affected fetus and an unaffected fetus. Invasive prenatal diagnosis is essential in this situation.