A decade-long retrospective analysis of cell line authentication in China using over 10,000 samples

Since the 1951 establishment of the HeLa cell line, immortalized cell lines have served as indispensable in vitro models for basic and clinical biomedical research. However, misidentification and contamination continue to undermine experimental reproducibility and validity. Here, we authenticate 11,087 cell lines from 6,947 Chinese institutions between 2016 and 2025 using STR profiling. Decade-long analysis reveals steady annual increases in testing volume and accuracy, identifying HeLa, T24, K-562, HEK293T, and A-549 as the most frequent contaminants. We observe that mutation rates at core STR loci are two to three orders of magnitude higher than those of germline mutations. Given the apparent variability in genomic stability across these loci, we develop a novel weighted algorithm based on locus-specific mutation frequencies of the eight core loci. Re-analysis demonstrates that this algorithm outperforms the classical Tanabe method by reducing false positives and negatives while increasing overall stringency. Additionally, the rising use of murine models highlights the urgent need for more comprehensive reference databases. Our large-scale analysis reflects a growing commitment within China's biomedical community to combat misidentification, offering critical insights for preventing contamination and providing conceptual avenues for next-generation authentication strategies.