A POSITIVE DETECTING ALGORITHM FOR DNA LIBRARY SCREENING BASED ON CCCP

Abstract

We describe an algorithm for extracting as much information as possible from pooling experiments for library screening based on the concave-convex procedure (CCCP). Called the CCCP pool result decoder (CCPD), it is a positive clone de- tecting algorithm. Its performance is compared, by simulation, with the Bayesian network pool result decoder (BNPD) proposed by Uehara and Jimbo and the Markov chain pool result decoder (MCPD) proposed by Knill et al. in 1996. To find a few positives among a large number of items, one can use group testing. In group testing, multiple items are assayed in groups. If a group has a negative outcome, all items contained in it are negative. This can reduce the total number of tests. On the other hand, if a group is positive, we know that the group contains at least one positive item. By designing many kinds of groups and by testing each of them, we obtain the results for all groups. After knowing the group results, we may be able to estimate which items are likely to be positive. For each of such items, we apply individual tests to determine whether it is positive or negative. Group testing has been used in medical, chemical, and electrical testing; drug screening; pollution control; multiaccess channel communication; and recently in gene assays like clone library screening, protein-protein interaction tests, and other subjects. See for example Du and Hwang (1999), Schliep and Rahmann (2006), Thierry-Mieg (2006), Klau et al. (2007), Thierry-Mieg and Bailly (2008). In this paper we restrict ourselves to group testing for DNA library screening to give a concrete image of testing and to consider a specialized problem in clone library screening. However, the algorithm given in this paper can be applied to any other fields of group testing. In DNA library screening experiments there are a large number of clones, which are short strings of nucleotides A, T, G and C. Through the use of high-quality gene libraries, the study of gene functions has been developed into a very important research field. The gene libraries are obtained from extensive testing and screening of DNA clones. For each clone,