The design of pooling experiments for screening a clone map

Abstract

We consider nonadaptive pooling designs for unique-sequence screening of a 1530-clone map of Aspergillus nidulans. The map has the properties that the clones are, with possibly a few exceptions, ordered and no more than 2 of them cover any point on the genome. We propose two subdesigns of the Steiner system S(3, 5, 65), one with 65 pools and approximately 118 clones per pool, the other with 54 pools and about 142 clones per pool. Each design allows 1 or 2 positive clones to be detected, even in the presence of substantial experimental error rates. More efficient designs are possible if the overlap information in the map is exploited, if there is no constraint on the number of clones in a poo..