Significance Testing for Aberrant Copy-Number (STAC)
The Problem:
- Genomic copy number aberrations (CNAs) occur in many solid tumors and may drive tumor initiation and/or progression.
- The problem is to determine CNAs which occur significantloy more often than chance across multiple samples in a class of tumors.
- Accurate identification of such significant CNAs across multiple experiments/samples is necessary for prioritizing regions for further study.
- Researchers have traditionally relied on non-statistical methods such as simple frequency cutoffs and manual review to prioritize regions.
- This approach may identify some regions of interest, however, it is subject to investigator bias and lacks statistical power necessary to control the error rates involved.
- Therefore there is a need for unbiased statistical methods which can identify non-random genomic copy number changes from multiple experiments.
We developed STAC to fill this need.
STAC Developers and Programmers:
- Grant, G.R. - Penn Center for Bioinformatics (PCBI), Computational Biology and Informatics Laboratory (CBIL), University of Pennsylvania.
- Diskin, S. - Children’s Hospital of Philadelphia and Penn Center for Bioinformatics (PCBI), University of Pennsylvania
- Eck, T. - Penn Center for Bioinformatics (PCBI), Computational Biology and Informatics Laboratory (CBIL), University of Pennsylvania
- Guttman, M. - Penn Center for Bioinformatics (PCBI), University of Pennsylvania
STAC Consultants:
- Maris, J.M. - Children’s Hospital of Philadelphia and Abramson Family Cancer Research Center, University of Pennsylvania
- Stoeckert, C.J. Jr. - Penn Center for Bioinformatics (PCBI), Computational Biology and Informatics Laboratory (CBIL), University of Pennsylvania
- Weber B.L. - Abramson Family Cancer Research Center, University of Pennsylvania, and Glaxo Smith Kline
- Greshock J. - Abramson Family Cancer Research Center, University of Pennsylvania
Publication:
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments.
Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR. Genome Res. 2006 Sep;16(9):1149-58. doi: 10.1101/gr.5076506. Epub 2006 Aug 9. PMID: 16899652