Stop the swap: SNPTrace genotyping as routine authentication for human organoid biobank lines

Human organoid lines can be expanded long-term and are increasingly shared through centralized biobanks and core facilities, making rigorous identity tracking essential for reproducible research. Mislabeling and cross-contamination remain persistent risks in cell culture, with historical and ongoing evidence that misidentification can go undetected undermining biological conclusions. Here, we describe the implementation of the SNPTrace platform for genetic authentication of human organoid lines within a biobank/core workflow.

Using SNPTrace, we generated 96-SNP genotypes for 108 human organoid lines from 49 individual donors and evaluated performance across core tracking scenarios. We compared organoids derived from multiple regions of the same organ within a donor, organoids generated from different organs from the same donor, and serial passages of the same organoid line. Across these conditions, SNPTrace profiles were stable and concordant within donor, supporting use of SNPTrace as a practical genetic "tag" for donor-level identity and longitudinal line tracking in a core facility. In addition, sex calls from allosomal markers matched recorded metadata, providing an orthogonal check on sample annotation and aiding identification of potential discrepancies. Integrating SNPTrace into routine biobank QC enables standardized authentication of human organoid lines and supports reliable downstream sharing.