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STR Analysis for Cell Line Authentication Gaining Traction in Research Community

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In 2005, scientists from two Spanish research institutions published a paper in Cancer Research reporting the spontaneous transformation of human adult stem cells to cancer stem cells — the first time, they asserted, that such a phenomenon had been reported.

However, in 2010 a majority of the authors agreed to retract their original paper, citing the inability to reproduce their findings, and surmising that the original findings were the result of cross-contamination between an actual cancer cell line and the stem cell line they thought had transformed.

The problem of misidentified or contaminated cell lines is not uncommon in molecular biology research and, in fact, has been recognized as a potential problem for at least 50 years.

But in recent years, cell line authentication has become much faster, easier, and cheaper primarily due to the application of PCR-based short tandem repeat analysis — already an indispensable technology in applied markets such as human identification and forensics.

As such, a number of companies and research institutions have in recent years begun to market cell line authentication services using STR analysis to help alleviate the problem.

"I would say it is the gold standard right now for cell line authentication," Erin Hall, director of cell line authentication at Genetica DNA Laboratories, a specialty testing company of Laboratory Corporation of America, told PCR Insider this week.

"There are other ways and older methods, but a lot of them [don’t authenticate] down to the individual human level," Hall added. "And obviously you could sequence the entire human genome as an authentication method, but that's extremely expensive … and not practical. STR profiling is probably the most straightforward, simple method."

These days, peer-reviewed journals are more stringent about checking whether study authors have authenticated their cell lines. However, according to Hall, there is still a general lack of awareness of the issue in the broader research community.

"Every year more and more journals are actually requiring it before the researchers can even publish," Hall said. "A lot of researchers are getting to that stage, after five years of research, about to publish, and the journal says to them: 'Did you authenticate your cell lines?' And they will say: 'What is that?' It literally needs to be a quality control check at the beginning, during, and at the end of every experiment using human cell lines or stem cell lines."

According to an editorial in Nature in 2009 calling for increased funding for cell line authentication, various studies and reported experiences from cell-culture repositories around the world have shown that as many as 36 percent of cultures contain a misidentified species or cell type.

In January of this year, cell line repository non-profit American Type Culture Collection released a document setting forth guidelines for unambiguous authentication and identification of human cell lines using STR profiling.

Hall noted that the issuance of those guidelines potentially marked a tipping point for widespread awareness in the molecular biology research community of the need to authenticate cell lines.

LabCorp acquired Cincinnati, Ohio-based Genetica last month for an undisclosed amount. Genetica has been offering a number of DNA testing services — including testing for paternity, ancestry, immigration, human identity, and infectious diseases — for more than 20 years.

It is unclear how exactly Genetica's DNA testing services fit into LabCorp's business — calls and e-mails to the company were not returned — but Hall said that for the purposes of cell line authentication, the combined resources of the companies give them a leg up on competing vendors.

"Between the two of us, there is more than 30 years of experience in human identification, which is basically what cell line authentication is," Hall said. "Genetica basically brings to the table a lot of experience. We've been doing cell line authentication longer than any single private company that has jumped into the cell line authentication business, so we know we've probably tested more samples than any other company."

ATCC also provides cell line authentication services, and regularly tests cells residing in its extensive repositories. Other cell line authentication providers include DNA Diagnostics Center, the European Collection of Cell Cultures of the UK's Health Protection Agency, Identicell, Idexx Radil, and the Johns Hopkins University Genetic Resources Core Facility.

"It's not something that any research lab can just pick up and start doing," Hall said. "Even though the concept is quite straightforward, the analysis and potential problems that you can face really should be left up to an expert."

For its service, Genetica uses Promega STR analysis kits, including the PowerPlex 18D, which tests 18 independent genetic sites specific for human DNA including the 13 CODIS loci, D2S1338, D19S433, PENTA E, PENTA D, and amelogenin; and the StemElite ID, which examines nine independent genetic sites specific for human DNA including amelogenin and one mouse marker.

Genetica can also test additional loci, up to 26 total, using Promega’s PowerPlex ESI 16 and GenePrint FFFL systems.

The company claims on its website a turnaround time of two business days and prices starting at $95 per sample.

Hall said that Genetica uses Promega's STR analysis kits because they are widely accepted and well-vetted in the research community for such applied markets.

"One of the essential things to have for cell line authentication is a … [universal] database of reference samples," she said. "The kits sold by Promega include the genetic sites that are part of that universal database. There are thousands and thousands of STR sites all over the human genome, but if you have nothing to compare it to, you have nothing at all."

Hall added that one of Genetica's major goals is to disseminate information about cell line authentication to the research community.

"Educating the researchers on the need for [cell line authentication] … is probably the number one stumbling block right now," she said. "It's really sort of blindsiding some researchers. We've had clients that had a completely misidentified cell line after years of work. To be a fly in the wall in that lab … I don't know what they do at that point, but I think it's a lesson learned."

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