Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing

Abstract

The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

“…So far, several characteristics with different separation capabilities have been described. The combination of these complementing characteristics into a single meta-predictor has great promise for improving overall accuracy and detecting new useful patterns in the sequenced fragments [ 332 , 333 ].…”

Validation of Copy Number Variants Detection from Pregnant Plasma Using Low-Pass Whole-Genome Sequencing in Noninvasive Prenatal Testing-Like Settings

“…Sequencing reads were aligned to the reference genome hg19 (NCBI build 37) using the Bowtie2 algorithm [ 16 ]. Fetal fractions were calculated from the Y chromosome [ 17 ] in pregnancies carrying a male fetus and using the “combined” method as previously published [ 18 ] for female fetuses. To identify microaberrations, we grouped the reads per bin (20 kb bin size).…”

Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions

“…In an ideal case, the deletion/duplication of fetal chromosome will mean a decrease/increase by a factor mb � ff/2, where ff is the fetal fraction and mb is mean bin count. Since this is a crude simplification and there are uncertainties in the fetal fraction estimation [17,20], and the non-uniform distribution of fetal fraction across the genome [17], we mark as significant all segments that overstep 75% of this theoretical increase/decrease. This percentage can be varied and represents a trade-off between sensitivity and specificity of prediction.…”