Copy Number Variant Detection by NIPT: Biological Constraints and the Limits of Prenatal Genomic Inference

Background: Non-invasive prenatal testing (NIPT) based on analysis of Cell-Free Fetal DNA has transformed screening for common aneuploidies and is increasingly extended to genome-wide detection of copy number variants (CNVs). However, CNV detection remains constrained by analytical limitations and biological signal complexity. Methods: This review evaluates the analytical validity, biological constraints, and clinical interpretation challenges of CNV detection by NIPT, framing it as a probabilistic genomic inference rather than a direct measure of fetal copy number. Results: Performance depends on sequencing depth, bin resolution, fetal fraction, guanine–cytosine correction, and reference modeling, leading to variable detection thresholds. The predominantly placental origin of cfDNA introduces discordance through Confined Placental Mosaicism, post-zygotic events, and clonal variation. Maternal CNVs, mosaicism, vanishing twin, and occult malignancy further complicate interpretation and may cause false positives. Clinical validity is heterogeneous, with positive predictive value dependent on CNV size, genomic context, and prevalence. Reporting practices remain inconsistent. Conclusions: CNV detection by NIPT is fundamentally limited by interpretation of a composite maternal–placental signal. Progress requires improved tissue-of-origin discrimination, multi-omic integration, and standardized reporting to ensure responsible clinical implementation.