Factors affecting low fetal fraction in fetal screening with cell-free DNA in pregnant women: a systematic review and meta-analysis

Abstract

Background Cell-Free DNA (cfDNA) is a non-invasive perinatal test (NIPT) used to assess fetal anomalies. The ability to detect fetal chromosomal aneuploidies is directly related to a sample’s fetal to total DNA fraction, known as the fetal fraction (FF). The minimum FF is considered 4%, and the test result below 4% is uncertain due to low fetal fraction (LFF). This study aimed to conduct a systematic review and a meta-analysis to determine the possible factors affecting LFF in cfDNA testing for fetal screening. Methods PubMed, Web of Science, Google Scholar, Since Direct, Scopus, CINHAL, Cochrane Library, and Persian databases, including Scientific Information Database, Irandoc, and Magiran were searched for studies investigating factors affecting LFF in cfDNA testing from 2000 until the end of 2021. Gathered data were analyzed using Comprehensive Meta-Analysis (CMA) software version 3.3.070. The quality of the included studies was assessed using the Joanna Briggs Institute Critical Appraisal of Cohort Studies tool. Results Thirteen articles related to the topic were included, and seven related articles were reviewed for meta-analysis. The other six were reviewed qualitatively. Four factors were identified that might have a potential effect on the LFF, of which only gestational age had a significant association with LFF (Pooled mean difference= -1.111, SE = 0.515, 95% CI= -2.121, -0.101, (P-value < 0.05)). Maternal age (P-value = 0.573), maternal weight (P-value = 0.113), and Body Mass Index (P-value = 0.104) had no statically significant effect. The effect size was pooled by mean difference and 95% confidence interval. Conclusion Lower gestational age is significantly associated with LFF. Thus, this factor can be considered when interpreting prenatal cfDNA screening tests.

Insights into non-informative results from non-invasive prenatal screening through gestational age, maternal BMI, and age analyses

“…The cutoff requirement for FF is dependent on the test provider. However, most testing laboratories require that the minimum FF is 4% [ 4 ]. Future improvements in technology may make it possible to obtain results at lower FFs.…”

“…Compared to traditional aneuploidy screening methods (serum- and ultrasound-based test), cfDNA sequencing can detect chromosomal aneuploidies with a high sensitivity of 97.45% to 100% and a specificity of 99.94% to 99.96% [ 3 ]. Compared to standard invasive techniques such as Chorionic Villus Sampling (CVS) and amniocentesis, cfDNA testing is non-invasive, easy to perform and poses no direct threat to either the mother or the fetus [ 4 ]. For these reasons NIPT has rapidly gained popularity in many countries worldwide as a routine part of health care for pregnant women [ 5 , 6 ].…”

Haplotype‐based noninvasive prenatal diagnosis of methylmalonic acidemia and the discovery of a recurrent pathogenic haplotype associated with c.609G>A

“…Among the 41 studied pregnancies, four produced indeterminate maternal results from the initial blood collection due to relatively low FF (0.38%–1.72%), which is generally associated with the earlier gestational ages of the studied families. As FF typically increases with gestational age, 28 resampling after 1–3 weeks can often address such cases 14 . Despite this, case F23 failed to deliver a clear maternal result even after blood recollection, presumably due to the inadequate increase in FF (from 0.38% to 1.65%).…”

“…The TCS network (Figure 3C) also demonstrated the exclusive presence of PHAP in hap_2. There were notable differences between hap_2 and other common core haplotypes in NHAP and GHAP (27,15,28 SNPs vs. hap_0, hap_1, hap_3, respectively, Table 3), indicating that carriers of c.609G>A are more likely to find multiple heterozygous SNPs in core haplotypes. The average number of heterozygous SNPs was 21.63 (IQR 15-28) in the 30 carriers from the 40 MMA families, 23.74 (IQR 22-28) in simulated carriers using random combinations of PHAP and NHAP, and 22.38 (IQR 15-27) in simulated carriers using random combinations of PHAP and GHAP (Figure 3B).…”