Abstract
BACKGROUND: Non-invasive prenatal testing (NIPT) has emerged as a highly accurate screening modality for fetal aneuploidies. However, its cost-effectiveness in resource-constrained settings remains unclear. This study evaluated the cost-effectiveness of NIPT versus direct amniocentesis for aneuploidy screening in pregnant women with variable risk profiles from the perspective of the Brazilian Private healthcare system. METHODS: A decision tree model with a one-year time horizon compared NIPT-based screening followed by confirmatory amniocentesis versus amniocentesis. The analysis included pregnant women with singleton pregnancies at risk due to abnormal first trimester screening. Clinical parameters were derived from systematic literature review, while costs and resource utilization data were obtained from the UNIMETRICS database. Outcomes included cost per Quality-adjusted life years (QALYs), cost per procedure-related loss avoided and cost per amniocentesis avoided. Deterministic and probabilistic sensitivity analyses assessed parameter uncertainty using 10,000 Monte Carlo simulations. RESULTS: In the base case analysis, NIPT implementation resulted in an incremental cost of IntI $ 4.874,52 (BRL 2,790,99) per patient per year. The strategy reduced amniocenteses by 18.4% and procedure-related losses by 0.06% annually. The incremental cost-effectiveness ratio was IntI $ 34.064,44 (BRL 21.453,96) per QALY. Subgroup analyses demonstrated consistent results across risk strata. Sensitivity analysis revealed that utility values, amniocentesis acceptance rates and procedure-related loss risk were the most influential parameters affecting cost-effectiveness outcomes. CONCLUSIONS: The NIPT-amniocentesis strategy might be cost-effective, because NIPT implementation slightly reduces invasive testing and associated complications, and incurs moderately incremental costs within the Brazilian supplementary healthcare system. These findings provide crucial evidence for healthcare policy decisions regarding NIPT assessment in prenatal screening programs in middle-income healthcare settings. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12962-026-00732-1.