Universal DNA tag systems: a combinatorial design scheme

  • Authors:

  • Amir Ben-Dor;Richard Karp;Benno Schwikowski;Zohar Yakhini

  • Affiliations:

  • Department of Computer Science & Engineering, University of Washington;International Computer Science Institute and Mathematical Sciences, Research Institute, University of California at Berkeley;Department of Computer Science & Engineering, University of Washington;Chemical and Biological Systems Department, Agilent Laboratories, a Hewlett-Packard Subsidiary

  • Venue:
  • RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
  • Year:
  • 2000

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Abstract

Custom-designed DNA arrays offer the possibility of simultaneously monitoring thousands of hybridization reactions These arrays show great potential for many medical and scientific applications such as polymorphism analysis and genotyping. Relatively high costs are associated with the need to specifically design and synthesize problem specific arrays. Recently, an alternative approach was suggested that utilizes fixed, universal arrays. This approach presents an interesting design problem—the arrays should contain as many probes as possible, while minimizing experimental errors caused by cross-hybridization. We use a simple thermodynamic model to cast this design problem in a formal mathematical framework. Employing new combinatorial ideas, we derive an efficient construction for the design problem, and prove that our construction is near-optimal.