Shifted Transversal Design smart-pooling for high coverage interactome mapping
Shifted Transversal Design smart-pooling for high coverage interactome mapping
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DOI：
10.1101/gr.090019.108
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发表时间：
2009-07-01
期刊：
影响因子：
7
通讯作者：
Thierry-Mieg, Nicolas
中科院分区：
文献类型：
--
作者：
Xin, Xiaofeng;Rual, Jean-Francois;Thierry-Mieg, Nicolas
“智能池”，其中测试试剂以高度冗余的方式多重化，是在系统级项目中实现高效率、灵敏度和特异性的有前途的策略。然而，以前的应用程序依赖于低冗余设计，不充分利用智能池的全部潜力，更强大的理论结构，如移位transmitted设计（STD），缺乏实验验证。在这里，我们评估STD智能池在酵母双杂交（Y2H）相互作用组映射。我们采用两种STD设计和两种已建立的方法，用12种诱饵进行ORFeome范围的Y2H筛选。我们发现，STD池实现了与基于一对一阵列的Y2H相似的灵敏度和特异性水平，而成本和工作负载被三分。筛选测序方法是最具成本效益和劳动力效率的，但STD确定了大约两倍的相互作用。筛选测序仍然是一个适当的方法，快速产生低覆盖率的相互作用组，而STD池出现作为方法的选择，以获得较高的覆盖率的地图。
"Smart-pooling,'' in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level projects. However, previous applications relied on low redundancy designs that do not leverage the full potential of smart-pooling, and more powerful theoretical constructions, such as the Shifted Transversal Design (STD), lack experimental validation. Here we evaluate STD smart-pooling in yeast two-hybrid (Y2H) interactome mapping. We employed two STD designs and two established methods to perform ORFeome-wide Y2H screens with 12 baits. We found that STD pooling achieves similar levels of sensitivity and specificity as one-on-one array-based Y2H, while the costs and workloads are divided by three. The screening-sequencing approach is the most cost- and labor-efficient, yet STD identifies about twofold more interactions. Screening-sequencing remains an appropriate method for quickly producing low-coverage interactomes, while STD pooling appears as the method of choice for obtaining maps with higher coverage.