Table 1.

The summary of current approaches for estimating fetal DNA fraction.

Approaches	Advantages	Limitations
Y Chromosome [3,22]	Simple and accurate	NOT applicable for pregnancies with female fetuses
Maternal plasma DNA sequencing data with parental genotypes [9,30]	Direct and accurate	Paternal DNA may not be available
Targeted sequencing of maternal plasma DNA (FetalQuant) [31]	Sequencing maternal plasma DNA only; accurate	High sequencing depth is required
Shallow-depth sequencing of maternal plasma DNA coupled with maternal genotypes (FetalQuantSD) [32]	Shallow-depth sequencing of maternal plasma DNA; accurate	Maternal genotype requirement will add additional costs; the recalibration curve is required to be rebuilt for different sequencing and genotyping platforms
Shallow-depth maternal plasma DNA sequencing data (SeqFF) [33]	Only shallow-depth sequencing of maternal plasma DNA; single-end sequencing; easy to be integrated into the routine noninvasive prenatal testing (NIPT)	Large-scale samples are needed to train the neutral network; need to improve the accuracy when the fetal DNA fraction is below 5%
Differantial methylation [17,26,34,35]	Accurate	Either bisulfite conversion or digestion with methylation-sensitive restriction enzymes may affect the accuracy; genome-wide bisulfite sequencing is too expensive and prohibitive for the routine NIPT
cfDNA fragment size [36]	Only shallow-depth sequencing of maternal plasma DNA; easy to be integrated into the routine NIPT	Moderate accuracy; paired-end sequencing would increase the costs
Nucleosome track [37]	Only shallow-depth sequencing of maternal plasma DNA	Lower accuracy; high-depth sequencing data is required during the training step