COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines

Genome-wide pooled shRNA screens enable global identification of the genes essential for cancer cell survival and proliferation and provide a 'functional genetic' map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting approximately 16 000 human genes...

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Bibliographic Details
Published in:Nucleic acids research 2012-01, Vol.40 (D1), p.D957-D963
Main Authors: Koh, Judice L. Y., Brown, Kevin R., Sayad, Azin, Kasimer, Dahlia, Ketela, Troy, Moffat, Jason
Format: Article
Language:English
Subjects:
Cell Line, Tumor
Databases, Genetic
Genes, Essential
Genes, Neoplasm
Humans
Neoplasms - genetics
Oligonucleotide Array Sequence Analysis
RNA Interference
RNA, Small Interfering
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Summary:Genome-wide pooled shRNA screens enable global identification of the genes essential for cancer cell survival and proliferation and provide a 'functional genetic' map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting approximately 16 000 human genes and a newly developed scoring approach, we identified essential gene profiles in more than 70 breast, pancreatic and ovarian cancer cell lines. We developed a web-accessible database system for capturing information from each step in our standardized screening pipeline and a gene-centric search tool for exploring shRNA activities within a given cell line or across multiple cell lines. The database consists of a laboratory information and management system for tracking each step of a pooled shRNA screen as well as a web interface for querying and visualization of shRNA and gene-level performance across multiple cancer cell lines. COLT-Cancer Version 1.0 is currently accessible at http://colt.ccbr.utoronto.ca/cancer.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr959