Do we need to worry about contamination by circulating fetal DNA?

Circulating fetal cell-free DNA and prenatal molecular diagnostics: are we ready for consensus?

“…Although this technique is gaining ground in different fields of laboratory medicine, concern has been expressed regarding the routine use of cffDNA in laboratory clinical diagnostics. Recently Wu et al [4] highlighted the risk of fetal DNA contaminating whole blood DNA samples, and some questions regarding the safety of using cffDNA, especially when performing molecular diagnostic tests, remain unanswered. In particular, the quantity of cffDNA, which can originate in different fetal tissues, generally increases with gestational age; therefore, for the purposes of clinical diagnostics, there is a need to standardize the best possible timing to obtain maternal blood samples when performing the test to screen maternal rather than fetal DNA mutations.…”

“…The model proposed by Wu et al [4] cannot guarantee the elimination of either contamination or confounding factors, for the following reasons: 1) the spiking of fetal mutant DNA alleles (obtained for example from peripheral blood leukoctyes) in normal DNA samples does not perfectly represent the situation of cffDNA fragments mixed with maternal cfDNA fragments. For routine diagnostics, DNA is obtained through whole blood extraction, yielding a mix of cffDNA and cfDNA; 2) the methods used for CFTR and F5 and F2 factors are not so sensitive as NGS and quantitative PCR methods, which can be strongly affected by contamination from fetal DNA.…”