Abstract
The concentration of cell-free fetal DNA fragments should be detected before noninvasive prenatal testing (NIPT). The fetal DNA molecules have significant clinical potential in determining the overall performance of NIPT and clinical interpretation. It is important to measure fetal DNA fraction before NIPT. However, there is still little research on how to calculate the concentration of female fetuses. Two estimation approaches were proposed to calculate fetal DNA fraction, including the fragments size-based approach, aneuploid-based approach, which are all approaches based on chromosome segments. Based on high-throughput sequencing data, two approaches to calculate the DNA fraction of male fetuses were tested and obtained the experiment values, which were close to the actual values. The correlation coefficient of fragments size-based approach was 0.9243 (P < 0.0001) and the aneuploid-based approach reached 0.9339 (P < 0.0001). We calculated the concentration of female fetuses and obtained remarkable experimental results. We came up with two approaches for calculating the fetal DNA fraction of female fetuses. It provides an important theoretical basis for the detection of female fetal concentration in future clinical diagnosis.
Highlights
Cell-free fetal DNA has been confirmed to be present in the plasma of pregnant women
We found a correlation between size ratios and fetal DNA fractions for the 35 male samples in the training group
We found a positive correlation between the fetal DNA fraction through the fragments size-based approach and the fetal DNA fraction through the aneuploid-based approach (r = 0.9339, P < 0.0001, linear regression)
Summary
Cell-free fetal DNA (cffDNA) has been confirmed to be present in the plasma of pregnant women. Many studies show that the detection of cffDNA in maternal plasma has significant clinical potential for the noninvasive prenatal diagnosis of fetal genetic disorders and pregnancy-associated diseases (Jahr et al, 2001). The cffDNA in the maternal plasma accounts for about 5–20% of the total cell-free DNA fragments (Lo et al, 1999). The cffDNA from maternal plasma accounts for about 3.4% in early gestation and comprises a mean of 6.2% in late gestation (Lo et al, 1998). As the gestation time increases, the concentration of cffDNA rises sharply in the last 8k of pregnancy (Lo et al, 2007). When NIPT is used to detect fetal chromosome aneuploidy, low cffDNA concentration will
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