Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

@article{citeulike:2363021, abstract = {The most widely used method for detecting genome-wide proteinDNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. 10.1101/gr.7080508}, author = {Johnson, David S. and Li, Wei and Gordon, Benjamin D. and Bhattacharjee, Arindam and Curry, Bo and Ghosh, Jayati and Brizuela, Leonardo and Carroll, Jason S. and Brown, Myles and Flicek, Paul and Koch, Christopher M. and Dunham, Ian and Bieda, Mark and Xu, Xiaoqin and Farnham, Peggy J. and Kapranov, Philipp and Nix, David A. and Gingeras, Thomas R. and Zhang, Xinmin and Holster, Heather and Jiang, Nan and Green, Roland and Song, Jun S. and Mccuine, Scott A. and Anton, Elizabeth and Nguyen, Loan and Trinklein, Nathan D. and Ye, Zhen and Ching, Keith and Hawkins, David and Ren, Bing and Scacheri, Peter C. and Rozowsky, Joel and Karpikov, Alexander and Euskirchen, Ghia and Weissman, Sherman and Gerstein, Mark and Snyder, Michael and Yang, Annie and Moqtaderi, Zarmik and Hirsch, Heather and Shulha, Hennady P. and Fu, Yutao and Weng, Zhiping and Struhl, Kevin and Myers, Richard M. and Lieb, Jason D. and Liu, Shirley X. }, citeulike-article-id = {2363021}, doi = {http://dx.doi.org/10.1101/gr.7080508}, journal = {Genome Res.}, keywords = {chip-chip}, month = {February}, pages = {gr.7080508+}, posted-at = {2008-03-17 12:32:23}, priority = {2}, title = {Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets}, url = {http://dx.doi.org/10.1101/gr.7080508}, year = {2008} }

TY - JOUR ID - citeulike:2363021 L3 - citeulike-article-id:2363021 N2 - The most widely used method for detecting genome-wide proteinDNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. 10.1101/gr.7080508 JF - Genome Res. TI - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets SP - gr.7080508 KW - chip-chip AU - Johnson, David AU - Li, Wei AU - Gordon, Benjamin AU - Bhattacharjee, Arindam AU - Curry, Bo AU - Ghosh, Jayati AU - Brizuela, Leonardo AU - Carroll, Jason AU - Brown, Myles AU - Flicek, Paul AU - Koch, Christopher AU - Dunham, Ian AU - Bieda, Mark AU - Xu, Xiaoqin AU - Farnham, Peggy AU - Kapranov, Philipp AU - Nix, David AU - Gingeras, Thomas AU - Zhang, Xinmin AU - Holster, Heather AU - Jiang, Nan AU - Green, Roland AU - Song, Jun AU - Mccuine, Scott AU - Anton, Elizabeth AU - Nguyen, Loan AU - Trinklein, Nathan AU - Ye, Zhen AU - Ching, Keith AU - Hawkins, David AU - Ren, Bing AU - Scacheri, Peter AU - Rozowsky, Joel AU - Karpikov, Alexander AU - Euskirchen, Ghia AU - Weissman, Sherman AU - Gerstein, Mark AU - Snyder, Michael AU - Yang, Annie AU - Moqtaderi, Zarmik AU - Hirsch, Heather AU - Shulha, Hennady AU - Fu, Yutao AU - Weng, Zhiping AU - Struhl, Kevin AU - Myers, Richard AU - Lieb, Jason AU - Liu, Shirley PY - 2008/02/07/ UR - http://dx.doi.org/10.1101/gr.7080508 ER -