Multiplexed Nucleic Acid Programmable Protein Arrays

Yu, Xiaobo; Song, Lusheng; Petritis, Brianne; Bian, Xiaofang; Wang, Haoyu; Viloria, Jennifer; Park, Jin; Bui, Hoang; Li, Han; Wang, Jie; Liu, Lei; Yang, Liuhui; Duan, Hu; McMurray, David N.; Achkar, Jacqueline M.; Magee, Mitch; Qiu, Ji; LaBaer, Joshua

First, we constructed a mathematical model to determine the optimal level of multiplexing, which considers the number of proteins, cost, array size, and hit rate to predict the number of arrays that would be needed for a two-step screening and verification study. A survey of HT unbiased target screening studies that used protein microarrays, both in the literature and our own results using NAPPA, revealed that hits are rare (typically <5%) (Figure 1B) . For 10k proteins and a hit rate of 5%, the mathematical model indicated that multiplexing 5 proteins per spot (Figure 1C) would provide a good balance of maximizing the number of features, minimizing the number of arrays, and yielding the minimum overall workload when compared to using non-multiplexed arrays for both the screening and verification steps.