Every year, 4-6 million pregnant women undergo noninvasive prenatal testing (NIPT),
which is used world-wide for fetal aneuploidy screening. Adequate fetal cell-free
DNA (cfDNA) is the critically important factor to ensure high sensitivity and specificity.
In this study, we sought to increase the fetal fraction by adjusting experimental
factors in the size selection for NIPT. CfDNA was extracted from 1495 pregnant women
at 12-26 weeks of gestation for sequencing of shorter cfDNA NIPT (< 140 bp). Multivariable
linear regression models were used to evaluate the association between experimental
factors and fetal fraction. Nomograms for the likelihood of high fetal fraction (>
20%) were constructed according to significant factors in multivariable regression
models. Our results suggested that cfDNA and library concentrations were negatively
correlated with fetal fraction, and uniquely mapped reads were positively correlated
with fetal fraction. Lower cfDNA and library concentrations, shorter cfDNA fragments,
and higher uniquely mapped reads may be more conducive to obtaining higher fetal fractions.
Furthermore, we constructed easy-to-use nomograms incorporating the maternal, fetal
characteristics and experimental factors to precisely predict the probability of high
fetal fraction with an area under the curve (AUC) of 0.773 (95% confidence interval:
0.749-0.797). Collectively, our maternal plasma cfDNA-based nomograms consider experimental
factors that can be adjusted and may improve a laboratory's ability to obtain higher
fetal cfDNA concentrations.