Fetal fraction and noninvasive prenatal testing: What clinicians need to know

Abstract

The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.

FIGURE 1

Multiple organ sources of cell-free DNA in maternal plasma

FIGURE 2

Relationship between fetal fraction and chromosome 21 z-score in euploid and pregnancies with Down syndrome. The large open circles indicate chromosome z-scores in first and second trimester pregnancies with Down syndrome. As fetal fraction increases, the average z-score also increases. The line indicates the change in the average z-score by fetal fraction. All but 4 of the 212 cases are above a z-score of 3, and these 4 occur at fetal fractions of 7% or less. Small open circles indicate chromosome 21 z-scores in 1484 euploid pregnancies. The z-scores are centered on zero and generally fall between −3 and +3. Only three euploid pregnancies fall above a z-score of 3 (arrows), and these are not associated with lower fetal fractions. Reproduced from Canick et al (2013) with permissions from Wiley-Blackwell Publishing

FIGURE 3

Normalized chromosomal read count in relation to the fetal fraction. Normalized chromosomal read count in relation to the fetal fraction (SeqFF) for chromosomes 13 (A), 18 (B), 21 (C), and 7 (D). The X-axis depicts the fetal fraction and the Y-axis the normalized chromosomal read count. Horizontal and diagonal lines, respectively, mark the predicted normal and trisomic normalized read counts (full lines) and ±3 SD as measured in the normal cases (X-axis and dashed lines). Values within 3 SD from expected trisomy counts are plotted as blue triangles. Values outside the area delineated by the X-axis and dashed lines represent cases with |Z| > 3 and |TriZ| > 3. These are plotted as red circles and indicate pregnancies at risk for fetoplacental mosaicism. The arrows indicate a set of discordant twins. Reproduced from Brison et al (2019) with permission from Wiley-Blackwell Publishing