Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Sequencing by Hybridization: Towards an Efficient Large-Scale DNA Methodology

Radomir Crkvenjakov
Hyseq, Inc., 670 Almanor Ave., Sunnyvale, CA 94086

Hyseq has acquired the patent on SBH, a sequencing method in which computerized sequence assembly by overlap is not preceded by sequential monomer by monomer determination of restricted portions of sequence. Instead, determination of partial to complete lists of constituent oligomers in 1-2 kb DNA fragments by oligonucleotide hybridization provides the shortest possible stretches for sequence assembly.

In a technology transfer from Argonne National Laboratory, Hyseq obtained the rights on DOE sponsored research of an SBH format 1 production line capable of collecting ten million hybridization scores per day and to a novel variant of SBH format 3 or "super chip." The large-scale methodology optimally combining SBH format 1 with automated single pass gel sequencing in a production-line setting can factor out the disadvantages of sequence assembly inherent to SBH while retaining its potential for acceleration of the sequencing process by several orders of magnitude. For example, sequencing a 4.5 Mb bacterial genome requires 10,000 gel sequencing reactions and 25 million hybridization scores with 3,500 heptamer probes; both tasks easily accomplished within a 6 month time-frame with accuracy of 0.001 at an initial cost of 20 cents per base.

Building on format 1 development, Hyseq will also focus on the unique niche in DNA diagnostics: screening a large number of multilocus, multi-patient 200-2000 bp PCR samples by resequencing with a small number of probes in centralized facilities thus providing gene sequencing at a fraction of the present cost.