Research abstract

Article abstract

Nature Biotechnology 26, 676 - 684 (2008)
Published online: 25 May 2008 | doi:10.1038/nbt1405

Rapid genome sequencing with short universal tiling probes

Arno Pihlak1,2, Göran Baurén2,3, Ellef Hersoug1,2, Peter Lönnerberg1,2, Ats Metsis1,2 & Sten Linnarsson1,2

The increasing availability of high-quality reference genomic sequences has created a demand for ways to survey the sequence differences present in individual genomes. Here we describe a DNA sequencing method based on hybridization of a universal panel of tiling probes. Millions of shotgun fragments are amplified in situ and subjected to sequential hybridization with short fluorescent probes. Long fragments of 200 bp facilitate unique placement even in large genomes. The sequencing chemistry is simple, enzyme-free and consumes only dilute solutions of the probes, resulting in reduced sequencing cost and substantially increased speed. A prototype instrument based on commonly available equipment was used to resequence the Bacteriophage lambda and Escherichia coli genomes to better than 99.93% accuracy with a raw throughput of 320 Mbp/day, albeit with a significant number of small gaps attributed to losses in sample preparation.

  1. Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 1, SE-171 77 Stockholm, Sweden.
  2. Genizon Svenska AB, Nobels väg 12A, SE-171 77 Stockholm, Sweden.
  3. Present address: GE Healthcare, Björkgatan 30, SE-751 84 Uppsala, Sweden.

Correspondence to: Sten Linnarsson1,2 e-mail:


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