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Background  The identification of cell-free fetal DNA (cffDNA) facilitated non-invasive prenatal screening (NIPS) through analysis of cffDNA in maternal plasma. However, challenges regarding its clinical implementation become apparent. Factors affecting fetal fraction should be clarified to guide its clinical application.    Results  A total of 13,661 pregnant subjects with singleton pregnancies who undertook NIPS were included in the study. Relationship of gestational age, maternal BMI, and maternal age with the cffDNA fetal fraction in maternal plasmas for NIPS was investigated. Compared with 13 weeks (12.74%) and 14–18 weeks group (12.73%), the fetal fraction in gestational ages of 19–23 weeks, 24–28 weeks, and more than 29 weeks groups significantly increased to 13.11%, 16.14%, and 21.17%, respectively ( P  < 0.01). Compared with fetal fraction of 14.54% in the maternal BMI group of < 18.5 kg/m 2 , the percentage of fetal fraction in the group of 18.5–24.9 kg/m 2  (13.37%), 25–29.9 kg/m 2  (12.20%), 30–34.9 kg/m 2  (11.32%), and 35–39.9 kg/m 2  (11.57%) decreased significantly ( P  < 0.01). Compared with the fetal fraction of 14.38% in the group of 18–24 years old, the fetal fraction in the maternal age group of 25–29 years old group (13.98%) ( P  < 0.05), 30–34 years old group (13.18%) ( P  < 0.01), 35–39 years old group (12.34%) ( P  < 0.01), and ≥ 40 years old (11.90%) group ( P  < 0.01) decreased significantly.    Conclusions  The percentage of fetal fraction significantly increased with increase of gestational age. Decreased fetal fraction with increasing maternal BMI was found. Maternal age was also negatively related to the fetal fraction.

Factors affecting cell-free DNA fetal fraction: statistical analysis of 13,661 maternal plasmas for non-invasive prenatal screening