False-Negative NIPT Result for Trisomy 21

Chaoui, Rabih; Flöter, Martina

doi:10.1055/s-0043-120758

Cited by 1 publication

(1 citation statement)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Factors known to affect the FF in maternal plasma include gestational age, maternal weight, and placental biology (Hestand et al, 2019; Hou et al, 2019; Kinnings et al, 2015; van Beek et al, 2017). It is crucial to perform an efficient quality control of the NIPT test, considering all the possible factors affecting the outcome, in order to eliminate false negative results in prenatal screening; a failure to do so may result in an incorrect diagnosis or chromosomal aberrations, which are left unnoticed (Cao et al, 2016; Heling et al, 2018; Peng & Jiang, 2017).…”

Section: Introductionmentioning

confidence: 99%

Total number of reads affects the accuracy of fetal fraction estimates in NIPT

Miceikaitė

Brasch‐Andersen

Fagerberg

et al. 2021

Molec Gen & Gen Med

View full text Add to dashboard Cite

Background Sufficient fetal fraction (FF) is crucial for quality control of NIPT (Non‐Invasive Prenatal Test) results. Different factors influencing bioinformatic estimation of FF should be considered when implementing NIPT. To what extent the total number of sequencing reads influences FF estimate has been unexplored. In this study, to test the robustness of SeqFF FF estimation and provide additional recommendations for NIPT analysis quality control, we compared the SeqFF FF estimates with two other methods and investigated how the number of sequencing reads and FF level affects the accuracy and precision of FF estimates. Methods WGS data of 516 NIPT samples from a prenatal screening program was obtained. Sample data were randomly downsampled by the read count, and FF was calculated by SeqFF software. Then, the outcome was compared with FF estimates from SNP‐ and chrY‐based methods. FF estimated with different read counts and FF levels were compared with FF at 30 M reads as a reference. Results SeqFF FF highly correlates with SNP‐ and chrY‐based FF estimates. Raising read count from 2 M to 10 M drastically increased the accuracy of FF estimates. After adding more reads, we saw a further improvement in FF accuracy, reaching a plateau at 20 M reads. Precision of SeqFF FF estimate is independent of FF level in the sample. Conclusion SeqFF is a robust method for FF estimation for both genders and for any FF level in range 2–13%. Accuracy of FF estimates highly depends on the read count. We recommend using no less than 10 M reads to achieve accurate FF estimates for NIPT analysis in clinical settings.

show abstract