Cell line identification with DNA replication timing fingerprints

Project Summary Cultured cell lines have been widely used for basic research to study cell functionas models for diseaseand for drug screeningCorrect identification of the cell lines used is necessary to make the right scientific conclusions and replicate experimentsCell lines in culture can be contaminated by foreign cellswhich may rapidly displace the original cellsThe routine verification of the identity of cultured cells should be performedbut a majority of laboratories do not monitor the identity of their cell linesand many cell lines are misidentifiedAnalyses of cells submitted to major repositories such as the DSMZDeutsche Sammlung von Mikroorganismen und Zellkulturenand the ATCCAmerican Type Culture Collectionhave found thatof cell lines submitted by investigators are misidentifiedThe costseffortand time required to confirm the identity of cell lines have been a barrier to adoption of cell line identification as a routine quality control measureCurrent technologies for identifying cultured cells are limitedand their cost is a barrier for small scale useIn this SBIR phase I applicationwe aim to develop a novel tool for cell line and cell type identification using DNA replication timingRTfingerprintswhich are RT values at specific genomic regionsIn our previous studieswe have discovered that DNA RT was highly specific to different cell lines and cell types and this specificity can be exploited for the purpose of cell line type identificationPLoS Comp BiolGenome ResearchGenome ResearchA patent for RT fingerprint identification and use has been issued inRecentlywe have applied this technology to identify common markers between distinct progeroid diseasesPNASA novel segmentation methodcalled iSegfor segmenting genomic and epigenomic data has also been developed in our labBMC BioinformaticsIn Presswhich can be used to further improve the identification of RT fingerprintsWe propose to collect a large number of DNA RT profiles for a diverse set of cell lines and cell types and develop RT fingerprints for their identificationA web server will be built to take usersinput of RT data and output the cell line best matched with the input dataThe web server can also take data of new cell lines from users to allow continually developing our models and databaseRT fingerprints can be measured cost effectively using polymerase chain reactionPCRexperimentSince the total cost for obtaining RT fingerprint for one sample is around $which can be further reduced when scaled upour method makes it possible to routinely check the identity of cultured cells Project narrative This SBIR phase I application aims to develop a novel tool for cell line and cell type identification using DNA replication timing fingerprintswhich can be measured costeffectively using polymerase chain reactionPCRexperimentA web server will be built to take usersinput of replication timing data and output the cell line best matched with the input dataThe web server can also take data of new cell lines from users to allow continually developing our models and database