A new pooling strategy for high-throughput screening: the Shifted Transversal Design

BackgroundIn binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplication of the individual experiments, thereby correcting for experimental noise. The main difficulty consists in designing the pools in a manner that is both efficient and robust: few pools should be necessary to correct the errors and identify the positives, yet the experiment should not be too vulnerable to biological shakiness. For example, some information should still be obtained even if there are slightly more positives or errors than expected. This is known as the group testing problem, or pooling problem.ResultsIn this paper, we present a new non-adaptive combinatorial pooling design: the "shifted transversal design" (STD). It relies on arithmetics, and rests on two intuitive ideas: minimizing the co-occurrence of objects, and constructing pools of constant-sized intersections. We prove that it allows unambiguous decoding of noisy experimental observations. This design is highly flexible, and can be tailored to function robustly in a wide range of experimental settings (i.e., numbers of objects, fractions of positives, and expected error-rates). Furthermore, we show that our design compares favorably, in terms of efficiency, to the previously described non-adaptive combinatorial pooling designs.ConclusionThis method is currently being validated by field-testing in the context of yeast-two-hybrid interactome mapping, in collaboration with Marc Vidal's lab at the Dana Farber Cancer Institute. Many similar projects could benefit from using the Shifted Transversal Design.

[1]  E. Barillot,et al.  Theoretical analysis of library screening using a N-dimensional pooling strategy. , 1991, Nucleic acids research.

[2]  Ding-Zhu Du,et al.  New constructions of non-adaptive and error-tolerance pooling designs , 2002, Discret. Math..

[3]  Ding-Zhu Du,et al.  A survey on combinatorial group testing algorithms with applications to DNA Library Screening , 1999, Discrete Mathematical Problems with Medical Applications.

[4]  Richard C. Singleton,et al.  Nonrandom binary superimposed codes , 1964, IEEE Trans. Inf. Theory.

[5]  D. Du,et al.  Combinatorial Group Testing and Its Applications , 1993 .

[6]  C. Colbourn,et al.  The CRC handbook of combinatorial designs , edited by Charles J. Colbourn and Jeffrey H. Dinitz. Pp. 784. $89.95. 1996. ISBN 0-8493-8948-8 (CRC). , 1997, The Mathematical Gazette.

[7]  D. Balding,et al.  Efficient pooling designs for library screening. , 1994, Genomics.

[8]  R. Gibbs,et al.  A clone-array pooled shotgun strategy for sequencing large genomes. , 2001, Genome research.

[9]  D J Balding,et al.  The design of pooling experiments for screening a clone map. , 1997, Fungal genetics and biology : FG & B.

[10]  Anthony J. Macula,et al.  A simple construction of d-disjunct matrices with certain constant weights , 1996, Discret. Math..

[11]  H. Hanani,et al.  On steiner systems , 1964 .

[12]  R. Plasterk,et al.  Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Hudson,et al.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression , 2003, Nature Genetics.

[14]  David C. Torney,et al.  Optimal Pooling Designs with Error Detection , 1994, J. Comb. Theory, Ser. A.

[15]  Donald L. Kreher,et al.  Pooling, lattice square, and union jack designs , 1999 .

[16]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[17]  G. Evans,et al.  Physical mapping of complex genomes by cosmid multiplex analysis. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M. Vidal,et al.  A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome , 2001, EMBO reports.

[19]  Emanuel Knill,et al.  A Comparative Survey of Non-Adaptive Pooling Designs , 1996 .

[20]  A. Macula.  Probabilistic nonadaptive group testing in the presence of errors and DNA library screening , 1999 .