Abstract
PurposeThe percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%).MethodsA scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)–based NIPS. All samples were tested with and without FFA.ResultsZero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity.ConclusionFFA transforms low-FF samples into high-FF samples. By combining FFA with WGS–based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.
Highlights
Since its introduction into clinical care nearly a decade ago,[1,2,3,4,5] noninvasive prenatal screening (NIPS) based on cell-free DNA has provided millions of pregnant women with information about their risk for fetal chromosomal abnormalities
We present an analytical validation and extended characterization of a fetal fraction amplification (FFA) technology that can be scalably applied to samples undergoing NIPS and yields significantly higher FF levels, thereby increasing sensitivity and specificity for all fetal anomalies arising from copy-number changes of any size across the genome
FFA increases FF an average of 2.3-fold for each sample To directly measure the impact of FFA, we tested 2401 samples from our verification and validation studies with both the standard NIPS and FFA protocols, focusing on the number of samples with FF < 4%, the threshold for low FF suggested by American College of Medical Genetics and Genomics (ACMG).[38]
Summary
Since its introduction into clinical care nearly a decade ago,[1,2,3,4,5] noninvasive prenatal screening (NIPS) based on cell-free DNA (cfDNA) has provided millions of pregnant women with information about their risk for fetal chromosomal abnormalities. A primary driver of NIPS sensitivity for aneuploidy in a given maternal plasma sample is the fetal fraction (FF), which describes the proportion of cfDNA fragments that originate from the placenta.[6] For most samples, FF values are between 4% and 30%.7. Many laboratories fail samples with FF < 4% to diminish the risk of issuing false negative reports. Because the molecular and bioinformatic implementations of NIPS have evolved, diversified, and generally improved over time, sensitivity at progressively lower FF levels is platform- and laboratorydependent.[6,8] a recently published clinical experience study demonstrated that a customized whole-genome sequencing (WGS)–based NIPS, which does not fail low-FF samples, can have comparable accuracy at high FF and low FF for the common aneuploidies on chromosomes 13, 18, and 21.9
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
