Abstract
Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was robust and accurate (r2= 0.994, p-value < 2.2e-16). For samples with FF > 0.04, T21 detection had 100% sensitivity (95% CI: 63.06 to 100%) and 98.53% specificity (95% CI: 92.08 to 99.96%). Fetal sex was determined with 100% accuracy. We later performed a proof of concept for monogenic disease diagnosis of 5/7 skeletal dysplasia cases. In conclusion, it is feasible to perform a comprehensive NIPT by using only data from high coverage targeted sequencing, which, in addition to detecting trisomies, also make it possible to identify pathogenic variants of the candidate genes for monogenic diseases.
Highlights
The discovery of cell-free fetal DNA in the maternal bloodstream (Lo et al, 1997) has revolutionized prenatal diagnosis
We propose the implementation of an in-house noninvasive prenatal test (NIPT) by using high-coverage targeted NGS in order to estimate Fetal fraction (FF), determine fetal sex, and detect trisomy and monogenic disease without the need for parental genotypes
We have developed an NIPT for genetic diseases by using NGS that incorporates the following analysis: FF estimation, fetal sex determination, trisomy detection, and monogenic disease detection
Summary
The discovery of cell-free fetal DNA (cffDNA) in the maternal bloodstream (Lo et al, 1997) has revolutionized prenatal diagnosis. In addition to aneuploidy detection, this strategy enabled the identification of variants associated with monogenic diseases, especially de novo variants (Lam et al, 2012; New et al, 2014; Chitty et al, 2015). This method enabled the development of methods for FF estimation by using single nucleotide polymorphisms (SNPs) from sequencing analysis of maternal plasma cfDNA, avoiding the need of parental genotyping, and reducing laboratory steps and turnaround time (Jiang et al, 2012; Sparks et al, 2012b; Koumbaris et al, 2016). The development of parameters to perform all these analyses simultaneously by using only maternal plasma sequencing data may further reduce cost and turnaround time
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
