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Cellular fingerprint: This electropherogram demonstrates the STR (short tandem repeat) technique NIST will use to identify human cell lines. The chart shows (in grey) specific locations, or loci, on the DNA chain of a human chromosome that are known to harbor short repeating sequences of DNA bases of varying lengths. The peaks count the actual number of such repeats at each locus. If the STRs at a sufficient number of loci are counted this way NIST uses eight loci the chances of a random match are approximately 100 million to one.
The National Institute of Standards and Technology (NIST) has announced that it is launching a project to collect and catalog DNA identification data for up to 1,500 human cell lines used in biological and medical research. In a notice posted in the Feb. 3, 2012, Federal Register, NIST called for voluntary contributions of cell lines to be cataloged in the project.
The data will be collected in a publically accessible database hosted by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine of the National Institutes of Health.
"Immortalized" human cell lines are laboratory cultures of cells that have been induced to continue growing and replicating. They are widely used in pharmaceutical, biomedical and biotechnology research, multiplied and divided, passing from lab to lab and country to country. The oldest such cell line is the so-called HeLa line, originally derived from cervical cancer cells. That line dates to 1951.
The biomedical research community has become increasingly concerned about mix-ups, cross contamination and misidentification in widely used cell lines—problems that potentially could invalidate research results. The problem was highlighted by the work of University of California researcher Walter Nelson-Rees, who in a series of papers in the 1970s documented extensive misidentification of cell cultures contaminated with cells from the HeLa line. Studies since then have demonstrated that the problem is, if anything, getting worse. In one survey, the German cell line repository Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) found that 18 percent of human cancer cell lines sampled were misidentified.
A key problem to date has been the lack of a convenient, reliable method by which research groups can validate the identity of their lines. The NIST project seeks to remedy that by building a database of cell lines that are reliably identified by profiling DNA markers called short tandem repeats (STRs)—the same technique used in criminal forensics to match DNA samples. The profile analyzes nuclear DNA from the cells for STRs—short sequences of DNA bases that are repeated from two to six times in row—at eight specific sites on the molecule. It also checks a gene to determine cell gender. The probability that two unrelated cells will have matching profiles is approximately 1 in 100 million.
STR profiling offers several advantages for identifying cell lines, in addition to being highly discriminating, according to NIST experts. It's a relatively simple procedure for a cell biology lab to run; the costs are low, particularly because STR profiling kits developed for the forensic community are readily available; and the results can be summarized as numeric values and made widely available through a public-access database such as the one hosted by NCBI.
Information on cell lines in the database will include various descriptors such as the cell line name, the tissue of origin, morphology, pathologic or disease-state and details of the growth culture; the STR markers and procedures used in identification and the STR profile of the cell line.
NIST will accept up to 15 candidate cell lines from submitters on a first-come, first-served basis. No cell lines grown on nonhuman feeder cells will be accepted due to the possibility of cross-species contamination. Submitters must bear the cost of shipping the cell samples or DNA extracts to NIST. NIST will pay for the STR profiling, subject to the availability of funds.
Full details of the program are available in the NIST Federal Register notice, "Identification of Human Cell Lines Project" [Docket No. 120104006–2006–01], available at http://www.gpo.gov/fdsys/pkg/FR-2012-02-03/pdf/2012-2459.pdf. Information on the project as it progresses will be available on the website of the NIST Applied Genetics Group.