Table 1. Some commonly used methods applicable for assessing quality of cell lines.
| Quality assurance metric | CO1 Barcode | Karyotype | STR | SNP | Species-specific primers+ | WGS++ |
|---|---|---|---|---|---|---|
| Species identification | X | X% | X | X | X | |
| Identity of donor individual | X | X | X | |||
| Large chromosomal structural changes | X | X | ||||
| Spontaneous mutations/genetic drift | X@ | X@ | X | |||
| Contamination with adventitious agents* | X | X | ||||
| Interspecies contamination | X | X% | X# | X# | X | X |
| Intraspecies contamination | X | X | X | |||
| Phenotypic changes detected with methods other than genomic** | Specialized assays | |||||
+ [22]
++ Whole genome sequencing (WGS) is capable of addressing all of these metrics provided there is sufficient bioinformatics support for the interrogation of genomic sequence databases.
% Chromosome number was the basis of early reports of cell line misidentification [16].
@ These methods will only be able to detect mutations in the regions of DNA that are covered by the probes or amplicons in the specific assay.
* Other tests (including enzymatic) that are specific for mycoplasma are readily available and are strongly recommended to determine this frequent contamination.
# If probes or primers specific for other species are included in the assays.
** Changes due to culture conditions and independent of any genomic changes would have to be carefully controlled for. Quantitative methods for assessing would need to be accompanied by benchmarks that allow comparison of data between laboratories.