It has been estimated that ~18-36% of cell lines utilized in biomedical research are contaminated and/or are completely misidentified1. Consequently, verification of human cell line identity is of critical significance since the validity of data obtained depends on the authenticity of the cell line. TRIP offers Short Tandem Repeat (STR) analysis to verify the authenticity of human cell lines. Some funding organizations, along with major publishers, such as those affiliated with the American Association for Cancer Research (AACR), have established requirements for cell line authentication prior to publication.
When you submit samples for authentication, you will receive a report indicating STR and Amelogenin genotypes for all loci. The report includes an interpretative comment regarding any indication of possible sample contamination (2% sensitivity) and evaluation (identification or authentication of cell line identity) relative to a publication, repository database, or baseline specimen.
For questions or inquiries, please contact Rebecca Baus at rmbaus@wisc.edu or trip@pathology.wisc.edu.
For pricing, please see our TRIP Fee Schedule. To request STR services, go to our iLab webpage.
1 “The costs of using unauthenticated, over-passaged cell lines: how much more data do we need?” Hughes, P., et al. BioTechniques 43: 575-586, 2007.
Cell Line Authentication
FAQ
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What are your sample requirements for Cell Line Authentication?
Samples can be submitted as either DNA or cell pellet. All samples should be in a 1.5mL microfuge tube.
DNA: A minimum concentration of 10ng/µL genomic DNA is required however, around 50ng/µL is ideal. A minimum volume of 20µL is required regardless of concentration. Contact us if you are having difficulty meeting this volume requirement.
Cells: Cells should be counted in order to provide approximately 2 million cells. Counts excessively higher than 2 million will create technical difficulties. Two million cells pelleted will look like <5µL if it were a liquid volume.
Cells should be pelleted and washed. Pipette off as much media/wash buffer as possible leaving only the cell pellet. You may store your cell pellet at 4°Celcius until you are ready to drop them off. Cells must be transported in double containment packaging to comply with UW-Madison Biosafety guidelines. Contact us if you are having difficulty meeting the cell count requirement. This is only an estimated count and fewer cells will be feasible.
DNA should be extracted from Virus Cell Lines prior to submission. We do not accept virus cells as cell pellets.
What are STRs?
Short Tandem Repeats, or STRs, are repeats in our DNA sequence that are 1-6 base pairs in length, generally repeated 5-50 times. Because of the variation of repeat numbers between individuals, these are useful for identification. Much like forensic DNA typing of evidence at a crime scene used to compare profiles of individuals, we can use STRs to create a genetic profile for cell lines allowing us to compare to a known profile and “authenticate” the line.
How often should I authenticate my cell lines?
-Upon receiving a cell line from another source to confirm identity and establish a baseline
-Prior to freezing
-Every other month while growing in culture
-Prior to publication
Dunham JH and Guthmiller P. Doing Good Science: Authenticating Cell Line Identity. [Internet] 2012. Available from: http://www.promega.com/resources/pubhub/cell-line-authentication-with-strs-2012-update/
Do you authenticate non-human cell lines?
We only perform Human Cell Line Authentication. The Promega PowerPlex ® 16 HS kit consists of 15 human STR markers in addition to the sex determinant marker, Amelogenin.
What will this service provide for me?
When performing Cell Line Authentication through the TRIP lab we will provide you with a report detailing the genetic profile of your cell line. This genetic profile will be compared to a known profile, when available, detail any signs of ploidy, microvariants, or contamination. Your initial baseline submissions will be kept on file to compare to future samples. You may request a copy of the electropherogram at any time.
This report is put together by TRIP personnel who have authenticated over 4500 samples since we began this service in 2014. It is affirmed by William Rehrauer, Ph.D., co-Director of TRIP – Molecular and Director of the Clinical Molecular Diagnostics lab at the University of Wisconsin Hospital and Clinics.
If, at any time, you have questions about your results we are available to answer questions via email or appointment.
What if my cell line doesn’t match the comparison profile 100%?
Standards for cell line authentication have been promoted with suggested algorithms to determine degrees of “relatedness” and have been recommended as a way to interpret results from STR profiling of human cell lines. In general, >80% allelic match is common between related samples, whereas < 50% allelic match is unrelated (Capes-Davis A, et al., Match criteria for human cell line authentication: Where do we draw the line? Int. J. Cancer. 132, 2510-2519. 2013).
Do I have to authenticate my cell lines?
Many journals request cell lines to be authenticated prior to publication. This list is continually growing as the scientific community becomes more aware of the effects misidentification can have on research.
AACR Journals:
Cancer Discovery
Cancer Research
Clinical Cancer Research
Cancer Epidemiology, Biomarkers & Prevention
Molecular Cancer Research
Molecular Cancer Therapeutics
Cancer Prevention Research
Carcinogenesis
Cell Biochemistry and Biophysics
Cell Biology International
Endocrine Society Journals:
Endocrinology
Endocrine Reviews
Journal of Clinical Endocrinology & Metabolism
Molecular Endocrinology
Hormones and Cancer
International Journal of Cancer
In Vitro Cellular & Developmental Biology – Animal
Journal of Molecular Biology
Journal of the National Cancer Institute
Molecular Vision
Nature Publishing Group:
Nature
Nature Reviews Molecular Cell Biology
Nature Genetics
Nature Reviews Immunology
Nature Reviews Cancer
Nature Reviews Neuroscience
Nature Biotechnology
Nature Methods
Neuro-Oncology
Placenta
PLoS ONE
Society for Endocrinology journals:
Journal of Endocrinology
Journal of Molecular Endocrinology
Endocrine-Related Cancer
What are the chances my cell line is misidentified or contaminated?
Many researchers feel a false sense of security that their cell lines are identified correctly and are clean/not contaminated. TRIP has performed Human Cell Line Authentication on well over 4500 samples since it began this service in 2014. Data from samples submitted to TRIP by Academic Researchers in 2017, revealed 28.8% of submissions were not a 100% allelic match, 2.5% of submissions were contaminated, and 26.3% were misidentified lines. We continued to see that trend in 2018 with contamination on the rise (13.2% as of September 2018). When a cell line is misidentified months or years of research time and dollars are spent working with a cell line that is not the line you thought it was. This can easily be prevented by regularly submitting your samples for testing.
The good news is, with continued testing of cell lines and labs disposing of misidentified lines, these numbers have improved. We found in 2019, samples submitted to TRIP by Academic Researchers had a decreased percentage in those cell lines that did not match 100% (28.8% down to 3.8%) and misidentified lines (26.3% down to 3.8%). We have made great progress in our goal of assisting researchers in putting out reproducible results using authenticated human cell lines.
Do you perform mycoplasma testing?
Currently, we do not perform mycoplasma testing.
What STR markers do you test?
The Promega PowerPlex® HS System tests 13 CODIS STR markers (FGA, TPOX, D8S1179, vWA, CSF1PO, D16S539, D7S820, D13S317, D5S818, D18S51, D21S11, TH01 and D3S1358) along with Penta D and Penta E and the sex determinant marker, Amelogenin.
How do I find a comparison profile?
Commercial vendors will often provide a genetic profile on their website for the lines they sell. For example, ATCC profiles can be found under the “Specifications” tab when viewing a cell line.
Other places to obtain a comparison profile:
Publications
Cellosaurus database: https://web.expasy.org/cellosaurus/
The lab you received the cells from
How is a genetic profile created from my cell sample?
DNA is extracted from a cell pellet using our automated Promega Maxwell® 16 Instrument along with the Maxwell® 16 LEV Blood DNA kit. Once DNA is obtained and quantified, a multiplex PCR reaction is performed using the PowerPlex® 16 HS System to co-amplify 15 STR loci and the sex determinant marker, Amelogenin, each labeled with fluorescein, TMR, or JOE. The amplicon is then capillary electrophoresed on the ABI 3500xl Genetic Analyzer. GeneMapper software creates an electropherogram that is analyzed in order to establish a genetic profile for your cell line.
What does an electropherogram look like?
This electropherogram is divided into 3 channels. The first channel (blue) includes STR loci D3S1358, Th01, D21S11, D18S51 and Penta E labeled with fluorescein (FL). The second channel (green) includes D5S818, D13S317, D7S820, D16S539, CSF1PO and Penta D labeled with JOE (6-carboxy-4’, 5’-dichloro-2’,7’-dimethoxy-fluorescein). The third channel (black) includes STR loci vWA, D8S1179, TPOX, FGA and the sex determinant marker Amelogenin labeled with TMR (carboxy-tetramethylrhodamine).
The GeneMapper software converts the number of repeats at each of the loci into peaks. The allelic ladder (grey stripes) provides a standard of 209 common alleles. Two peaks at a given locus represent a heterozygous genotype while one peak is homozygous. Each of these repeat numbers are inherited, one maternally and the other paternally. The top number in the small box represents the number of repeats. A decimal in that number would indicate a partial repeat.
