Balding D J, Torney D C
Department of Applied Statistics, University of Reading, England.
Fungal Genet Biol. 1997 Jun;21(3):302-7. doi: 10.1006/fgbi.1997.0985.
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 pool, and if no error tolerance is required. An information theory lower bound requires at least 12 pools to satisfy these minimal criteria, and an "interleaved binary" design can be constructed on 20 pools, with about 380 clones per pool. However, the designs with more pools have important properties of robustness to various possible errors and general applicability to a wider class of pooling experiments.
我们考虑用于构巢曲霉1530个克隆图谱独特序列筛选的非适应性混合设计。该图谱具有以下特性：克隆可能存在少数例外情况，但它们是有序排列的，并且基因组上任意一点被不超过2个克隆覆盖。我们提出了施泰纳系统S(3, 5, 65)的两种子设计，一种有65个混合池，每个混合池约有118个克隆；另一种有54个混合池，每个混合池约有142个克隆。即使存在大量实验误差率，每种设计也能检测到1个或2个阳性克隆。如果利用图谱中的重叠信息、对混合池中克隆数量没有限制且不需要容错能力，那么可以设计出更高效的方案。根据信息论下限，至少需要12个混合池才能满足这些最低标准，并且可以构建一个“交错二进制”设计，该设计有20个混合池，每个混合池约有380个克隆。然而，混合池数量更多的设计具有对各种可能误差的重要稳健性特性，并且对更广泛的一类混合实验具有普遍适用性。
