Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases

Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemo-philia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases.

Automated summary

Monogenic inherited diseases are a common cause of congenital disabilities, resulting in significant burdens on affected families. This study demonstrates the feasibility of using cell-based noninvasive prenatal testing (cbNIPT) with single-cell whole-genome sequencing (WGS) and haplotype analysis to diagnose various monogenic diseases prenatally. The results show that WGS performs better than targeted sequencing in terms of genome coverage, allele dropout, and false-positive rates. This research highlights the potential of cbNIPT by WGS and haplotype analysis in the prenatal diagnosis of monogenic diseases.