Marc Vidal2,6, Charles Boone1,6 and Nicolas Thierry-Mieg3,4,6
E-mail Nicolas.Thierry-Mieg@imag.fr;
E-mail marc_vidal@dfci.harvard.edu;
Abstract
“Smart-pooling,” in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level projects. However, previous applications relied on low redundancy designs that do not leverage the full potential of smart-pooling, and more powerful theoretical constructions, such as the Shifted Transversal Design (STD), lack experimental validation. Here we evaluate STD smart-pooling in yeast two-hybrid (Y2H) interactome mapping. We employed two STD designs and two established methods to perform ORFeome-wide Y2H screens with 12 baits. We found that STD pooling achieves similar levels of sensitivity and specificity as one-on-one array-based Y2H, while the costs and workloads are divided by three. The screening-sequencing approach is the most cost- and labor-efficient, yet STD identifies about twofold more interactions. Screening-sequencing remains an appropriate method for quickly producing low-coverage interactomes, while STD pooling appears as the method of choice for obtaining maps with higher coverage.
Supplemental material is available online at www.genome.org. The protein interactions from this publication have been submitted to the IMEx (http://imex.sf.net) Consortium through IntAct (PMID 17145710) and assigned the identifier IM-11695.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.090019.108.
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- Received December 12, 2008.
- Accepted April 14, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
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