Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification

Abstract

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line’s species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

Human B-cell cancer cell lines as a preclinical model for studies of drug effect in diffuse large B-cell lymphoma and multiple myeloma

“…As cell lines are continuously cultured, there is a risk of cell-line misidentification or crosscontamination. Crosscontamination can lead to overgrowth by the contaminating cell type within only a few passages, changing the identity of the cell line or leading to unacknowledged heterogeneous mixing of cell lines [44][45][46]. Good cell culture practice can substantially reduce, but cannot entirely eliminate, the risk of cell culture crosscontamination or mislabeling during routine handling.…”

“…Our laboratory group maintains the HBCCL in continuous culture for a maximum of 20 passages. Furthermore, some scientific journals have recently started to require proof of cell line authentication [45]. To ensure the correct identity before data analysis, our HBCCL panel is subjected to barcoding and mycoplasma testing, both before and after individual experiments.…”

Epigenetic Changes During Cell Transformation

“…In our experience, the epigenetic state of the cell line models we have employed does not vary to a significant extent when grown under appropriate and consistent conditions. We routinely verify cell line identity using STR profiling using 13 CODIS markers; reference DNA fingerprinting data for most of the widely used cell lines are available from cell line collections such as the ATCC or from the investigators who developed the models [7, 8]. …”

LRH1 as a driving factor in pancreatic cancer growth

“…All the cell lines have been authenticated by short tandem repeat (STR) profiling to reduce the frequency of cell misidentification. [8] Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO 2 in corresponding medium supplemented with 10% FBS and antibiotics (penicillin and streptomycin). Cells were passaged when they reached 80% confluence.…”