Biological screens from linear codes: theory and tools

 

Biological screens from linear codes: theory and tools by Yaniv Erlich, Anna Gilbert, Hung Ngo, Atri Rudra, Nicolas Thierry-Mieg, Mary Wootters, Dina Zielinski, Or Zuk

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-Solomon-based biological experiments. We provide general purpose tools for experimentalists to construct and carry out practical pooling designs with rigorous guarantees for large screens.

  A free web tool to design and guide experiments will eventually be at: http://pooling.teamerlich.org/

Previous posts of interest:

• Non-adaptive pooling strategies for detection of rare faulty items / Improved Constructions for Non-adaptive Threshold Group Testing
• Group Testing and Its Connection to Compressed Sensing.
• CS: Rare-Allele Detection Using Compressed Se(que)nsing, Shifted Transversal Design smart-pooling for high coverage interactome mapping

 

Also if you want some elements of coding theory here are some free books from Springer:

•  Introduction to Coding Theory ,J. H. van Lint in Graduate Texts in Mathematics (1999)  
• Asymptotic Combinatorial Coding Theory , Volodia Blinovsky in The Springer International Series in Engineering and Computer Science (1997)  

 

 

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