ISPD Annual Meeting 2022

Hi, thank you for your interest in our prenatal genotyping work. You can find our poster from the ISPD Conference on Prenatal Diagnosis and Therapy HERE. Please feel free to contact me regarding the work or potential collaborations.

Objective: Congenital abnormalities affect 3-4% of pregnancies and cause 20-30% of neonatal deaths worldwide. Non-invasive prenatal screening (NIPS) leverages the existence of cell-free fetal DNA with next-generation sequencing to predict fetal presence of large chromosomal abnormalities and, more recently, a select number of single-gene disorders. Here we present a novel sequencing-based approach to detect single-gene conditions in the fetus using maternal blood.

Method: In theory, given the proportion of fetal to maternal DNA (fetal fraction), a true estimate of the allele frequency defines the maternal and fetal genotypes at that locus. We employed two genotyping panels using dual-indexed adapters with unique molecular identifiers (UMIs) to interrogate selectively specific genetic variants: (1) a 9,610-variant panel with even density throughout the genome to estimate the fetal fraction; (2) an 80-variant panel covering common variants across diverse populations to test maternal-fetal genotyping accuracy. We have collected a cohort of 60 mother/newborn duos with genomic DNA and maternal cell-free DNA collected at 24-28 weeks gestation. We completed sequencing on the first 20 duos and will sequence the remaining duos by March 2022.

Results: From the first 20 duos, our fetal fraction estimates correlated to estimates using known genotypes (R2 = 0.95). For the genotyping panel, we obtained a median molecular count of 1,884 with sample-specific medians ranging from 486 to 6,536. We achieved a fetal genotyping accuracy of 84% (992/1,182) and a maternal genotyping accuracy of 97% (1,151/1,187); sample-specific fetal and maternal genotyping accuracies ranged from 75% to 94% and 90% to 100%, respectively.

Conclusions: Using dual-index sequencing adapters with UMIs allowed us to obtain molecular counts from maternal cell-free DNA. Using molecular counts, we estimated accurately the fetal fraction. On the first 20 duos, we realized mixed genotyping accuracies resulting from the limitations of cell-free DNA yield.