Efficient pooling designs for library screening

William J. Bruno; Emanuel Knill; David J. Balding; D. C. Bruce; N. A. Doggett; W. W. Sawhill; R. L. Stallings; Craig C. Whittaker; David C. Torney

arXiv · math/9412222

Efficient pooling designs for library screening

William J. Bruno·Emanuel Knill·David J. Balding·D. C. Bruce·N. A. Doggett·W. W. Sawhill·R. L. Stallings·Craig C. Whittaker·David C. Torney

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Abstract

We describe efficient methods for screening clone libraries, based on pooling schemes which we call ``random $k$-sets designs''. In these designs, the pools in which any clone occurs are equally likely to be any possible selection of $k$ from the $v$ pools. The values of $k$ and $v$ can be chosen to optimize desirable properties. Random $k$-sets designs have substantial advantages over alternative pooling schemes: they are efficient, flexible, easy to specify, require fewer pools, and have error-correcting and error-detecting capabilities. In addition, screening can often be achieved in only one pass, thus facilitating automation. For design comparison, we assume a binomial distribution for the number of ``positive'' clones, with parameters $n$, the number of clones, and $c$, the coverage. We propose the expected number of {\em resolved positive} clones---clones which are definitely positive based upon the pool assays---as a criterion for the efficiency of a pooling design. We determine the value of $k$ which is optimal, with respect to this criterion, as a function of $v$, $n$ and $c$. We also describe superior $k$-sets designs called $k$-sets packing designs. As an illustration, we discuss a robotically implemented design for a 2.5-fold-coverage, human chromosome 16 YAC library of $n=1,298$ clones. We also estimate the probability each clone is positive, given the pool-assay data and a model for experimental errors.

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William J. Bruno, Emanuel Knill, David J. Balding, D. C. Bruce, N. A. Doggett, W. W. Sawhill, R. L. Stallings, Craig C. Whittaker, David C. Torney. 1994-12-04. Efficient pooling designs for library screening. https://arxiv.org/abs/math/9412222

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