STR Profiling for Human Cell Line Authentication
In light of the NIH's recommendation that all cell lines be authenticated before publication, we offer a short tandem repeat (STR) profiling service using several commercially available kits. The profile generated can be used to confirm the identity of an acquired line by comparison to a known profile, or to establish an identity profile for a cell line established locally.
General recommendations are to authenticate when a new line is established or acquired to determine an identity for the cell line. Cells should be authenticated again before freezing, once every two months that the culture is actively growing, if the performance of the line is not consistent or results are unexpected, and before publication. If using more than one cell line in the lab, all lines should be initially tested to rule out cross contamination.
The FAF accepts either purified DNA or frozen cell pellets for analysis. Services include DNA isolation and/or STR profiling using one of three commercially available kits: PowerPlex 1.2 System (Promega), StemElite ID System (Promega), and AmpFLSTR Identifiler PCR Amplification Kit (Applied Biosystems). These kits are only suitable for cell lines of human origin. See the below table for STRs included in each kit.
STR markers in each identification kit:
| Marker | Powerplex 1.2 | StemElite | Identifiler |
| Amelogenin | X | X | X |
| CSF1PO | X | X | X |
| D13S317 | X | X | X |
| D16S539 | X | X | X |
| D18S51 | X | ||
| D19S433 | X | ||
| D21S11 | X | X | |
| D2S1338 | X | ||
| D3S1358 | X | ||
| D5S818 | X | X | X |
| D7S820 | X | X | X |
| D8S1179 | X | ||
| FGA | X | ||
| THO1 | X | X | X |
| TPOX | X | X | X |
| vWA | X | X | X | Mouse marker | X | Total | 9 | 10 plus mouse | 16 |
Ordering
Ordering instructions and request forms for STR analysis and DNA isolation are available through the below links. There are two sets, one for Johns Hopkins customers, and the other for external customers.
Instructions and Request Forms- Johns Hopkins/Internal Customers:
- Cell Line Authentication Ordering Instructions: Hopkins (.pdf)
- Cell Line Authentication Order Form: Hopkins (.xls)
- External Customers (outside Johns Hopkins):
Pricing*
DNA isolation: $25 per sample
STR Analysis:
PowerPlex 1.2 System: $50 per sample
StemElite : $70 per sample
Identifiler: $100 per sample
Pricing includes pcr, sizing on an Applied Biosystem 3730XL, allele designation for markers within chosen kit, and repeating once any samples that may fail the initial genotyping.
For payment we accept either an IO number or purchasing card from John Hopkins investigators. We will accept a P.O. or purchasing (credit) card from external customers.
*Listed pricing is for Johns Hopkins investigators; all other customers will have a 16% administrative fee added.
What you will receive
You will receive an Excel document containing allele calls, raw data (size of alleles in base pairs, peak height, peak area) and screen shots of the electropherograms. Two controls, HeLa and K562, are included with all STR analysis.
The STR profile generated by the FAF can be used to confirm the identity of a line by comparison to a known profile, or to establish a profile for a cell line established locally. If you wish to confirm the identity of your line and do not have a reference profile or sample for comparison, we recommend that you check the public databases prior to profiling. Please note that cell lines can be genetically unstable and, therefore, STR profiles can vary with passage.
Turnaround Time
Samples for STR profiling are run once a week on Tuesday, with results emailed usually on Monday of the following week. Samples received in the lab by 11AM Tuesday will be processed that day. Samples received after 11AM Tuesday will be held until the following week for processing. Hopkins customers need to drop off samples in Blalock 1005 by 4PM on Mondays or hand deliver to the FAF in Canton for inclusion in Tuesday processing. Any failed samples from a Tuesday run will be re-run the following Tuesday with all results being emailed by that following Monday.
SNP Karyotying
If you are interested in characterizing your samples further, they can be karyotyped on one of Illumina's dense SNP arrays. These arrays allow for analysis of LOH and copy number, as well as chromosomal loss. They will not easily identify translocations. For more information about these services, please see the JHU SNP Center web-site.
FAF services may only be used for research purposes. Any data or samples generated by the facility may not be used for human diagnostic or therapeutic use.