The Characterized Cell Line core (CCLC) was established in 2008 with the purpose of preserving and distributing cell lines developed at MD Anderson. The initial focus was on providing well-characterized cell lines so that researchers could choose the correct cell line for their research. Services were expanded almost immediately to include human cell line validation and Mycoplasma testing. Cell line validation is done by short tandem repeats (STR) profiling. To avoid duplicating equipment and effort, the polymerase chain reaction (PCR) fragmentation reactions are run by the Sequencing and Microarray Facility on an Applied Biosystems 3730 XL genetic analyzer. The CCLC has developed a novel STR matching algorithm that can take into account variations due to cell line cross-contamination and to genomic instability. CCLC has also established a proprietary database with STR profiles from over 1000 unique cell lines as well as over 2000 public STR profiles. The CCLC also offers mutational analysis of human cell lines as another method to ensure cell line authenticity. Mutational analysis is done using a Sequenom MassARRAY, which runs a primer extension based method to determine sequence information on a single base. The CCLC has developed a custom somatic mutation panel enabling incorporation of new somatic mutations as they are published in the literature, rather than waiting for a new somatic mutational panel from Sequenom. The CCLC also offers custom-designed panels. Since 2008, the CCLC has been used by 128 Center members, representing all 19 CCSG programs. The institution has supported this core with funding of $99,692 for capital equipment, including incubators, a -80? C freezer, PCR machines, a plate reader, and a Qiacube robot. The CCLC has facilitated publication of 53 reports since 2008, with 58% in journals with an impact score >5 and 15% in journals with an impact factor >10. Publications cited using the CCLC have appeared in several high impact journals such as Nat Gen, Cell, Cancer Cell and J Natl Cancer Inst. Peer-reviewed investigators account for 91% of the utilization, and 34% of the total costs are requested from the CCSG. This will enable expansion of services and additional testing of cell lines to identify cross-contamination between species as well as to test for potential virus contamination. Future work will focus on expanding the number of cell lines available to MD Anderson researchers, expanding characterization of cell lines to include whole genome/exome sequencing approaches, and improving methods to detected cross contamination especially intra-species cross-contamination.
Cell line authentication is now a requirement at MD Anderson for all research using cell lines. This requirement is in place so that data generated here can be of the highest quality. The CCLC not only helps ensure that MD Anderson researchers have the tools to test their cell lines but also assists in characterizing any newly established cell lines.
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