RT Journal Article
SR Electronic
T1 Biological screens from linear codes: theory and tools
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 035352
DO 10.1101/035352
A1 Yaniv Erlich
A1 Anna Gilbert
A1 Hung Ngo
A1 Atri Rudra
A1 Nicolas Thierry-Mieg
A1 Mary Wootters
A1 Dina Zielinski
A1 Or Zuk
YR 2015
UL http://biorxiv.org/content/early/2015/12/25/035352.abstract
AB Molecular biology increasingly relies on large screens where enormous numbers of specimens are systematically assayed in the search for a particular, rare outcome. These screens include the systematic testing of small molecules for potential drugs and testing the association between genetic variation and a phenotype of interest. While these screens are “hypothesis-free,” they can be wasteful; pooling the specimens and then testing the pools is more efficient. We articulate in precise mathematical ways the type of structures useful in combinatorial pooling designs so as to eliminate waste, to provide light weight, flexible, and modular designs. We show that Reed-Solomon codes, and more generally linear codes, satisfy all of these mathematical properties. We further demonstrate the power of this technique with Reed-Solomonbased biological experiments. We provide general purpose tools for experimentalists to construct and carry out practical pooling designs with rigorous guarantees for large screens.