Fetal Fraction Methodologies and Their Clinical Use: Results of a College of American Pathologists Exercise.

Background: Noninvasive prenatal screening for common autosomal trisomies, sex chromosome aneuploidies and microdeletions vary by methodology and laboratory practice. The fetal portion of all cell-free DNA in the maternal circulation defines the fetal fraction (FF). The minimum specimen FF levels for reporting results vary between laboratories as well as the screening target (e.g., common trisomies vs select microdeletions). This variability can lead to confusion for both healthcare providers and patients.

Methods: Participants in the College of American Pathologists Non-Invasive Prenatal Testing 2021-B Exercise provided FF estimates for 3 manufactured samples. Responses to supplemental questions were also collected and analyzed.

Results: Overall, 72 of 77 participants responded. FF was measured by 66 participants using sequence counts (40), single nucleotide polymorphisms (15), fragment length (24), and Y chromosome sequences (24). Nearly half (48%) used multiple methods. For common trisomies, minimum FFs were none or <1% (n = 7), 1.0% to 3.9% (n = 35), 4.0% to 6.9% (n = 23), and ≥7.0% (n = 1); 4 participants did not measure FF. Challenge-specific FFs were variable with CVs of 13%, 15%, and 36%; the latter rate appears due to that sample's fetal karyotype of 47,XYY. Comparing adjusted FF results for the 3 samples shows that 85% of participant results were within 20% of the consensus.

Conclusions: Using multiple methods to estimate FF was common, and cutoff levels for sample suitability varied widely. Within-laboratory FFs were less variable than between laboratories. Current FF estimates from clinical laboratories are not standardized and should be considered laboratory-specific.