Fetal Y chromosome abnormalities cause false-low fetal fraction in NIPT: a retrospective analysis of 24,101 pregnant women

Background Low fetal fraction is a common cause of NIPT no-call results, leading to repeat sampling and delayed clinical decisions. In cases of fetal sex chromosome abnormalities (SCAs), the standard Y chromosome-based method for estimating fetal fraction (FF) may be unreliable, potentially leading to misinterpretation of low-FF results. Methods We retrospectively analyzed 24,101 pregnant women who underwent NIPT between January 2023 and January 2025. FF was estimated using the Y chromosome-based method for male fetuses and FF-QuantSC for female fetuses. Confirmatory invasive testing was performed for high-risk or failed cases. Results The SCA prevalence was significantly higher in the low-FF group (FF<3.5%, n = 70) than in the adequate-FF group (FF ≥ 3.5%, n = 24,020), representing a ∼78-fold increased risk (11.43% versus 0.21%; OR = 78.227, P < 0.001). All eight SCAs in the low-FF group involved Y-chromosome abnormalities. Re-estimation using FF-QuantSC corrected the FF to a reportable level in all eight cases, confirming “false-low” FF, estimation using the Y chromosome-based method. Subsequent NIPT analysis, enabled by the qualified FF, successfully reported high-risk results for SCAs (45,X or Y deletions). Moreover, analysis of Y-chromosome read distribution profiles in these eight low-FF cases provided visual clues suggestive of these Y-chromosome abnormalities. Conclusion Low FF in NIPT is strongly associated with fetal Y-chromosome abnormalities, suggesting that Y chromosome-based FF estimation may produce a “false-low” FF in some cases with fetal Y-chromosome abnormalities. We suggest that re-estimating FF using FF-QuantSC combined with Y-chromosome read distribution analysis may be considered before reporting test failure.