Towards optimally multiplexed applications of universal DNA tag systems

We study a design and optimization problem that occurs, for example, when single nucleotide polymorphisms (SNPs) are to be genotyped using a universal DNA tag array. The problem of optimizing the universal array to avoid disruptive cross-hybridization between universal components of the system was addressed in a previous work. However, cross-hybridization can also occur assay-specifically, due to unwanted complementarity involving assay-specific components. Here we examine the problem of identifying the most economic experimental configuration of the assay-specific components that avoids cross-hybridization. Our formalization translates this problem into the problem of covering the vertices of one side of a bipartite graph by a minimum

• Type: Conference
• Year: 2003
• Where: RECOMB
• Authors: Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini
• Keywords: Assay-specific Components, Computational Biology, DNA Tag Array, RECOMB 2003, Single Nucleotide Polymorphisms