Shifted Transversal Design smart-pooling for high coverage interactome mapping
- Xiaofeng Xin1,4,
- Jean-François Rual2,5,
- Tomoko Hirozane-Kishikawa2,
- David E. Hill2,
- Marc Vidal2,6,
- Charles Boone1,6 and
- Nicolas Thierry-Mieg3,4,6
- 1 Banting and Best Department of Medical Research and Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada;
- 2 Center for Cancer Systems Biology (CCSB), and Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 3 Laboratoire TIMC-IMAG, TIMB, CNRS UMR5525, Faculte de Medecine, 38706 La Tronche Cedex, France
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↵4 These authors contributed equally to this work.
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.
Footnotes
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↵5 Present address: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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↵6 Corresponding authors.
E-mail Nicolas.Thierry-Mieg{at}imag.fr; fax +33-456-520-055.
E-mail charlie.boone{at}utoronto.ca; fax (416) 978-8287.
E-mail marc_vidal{at}dfci.harvard.edu; fax (617) 632-5739.
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[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
