Human Genome Program U.S. Department of Energy Office of Biological and Environmental Research SC-72 GTN Germantown, MD 20874-1290 301/903-6488, Fax: 301/903-8521 E-mail: [email protected] A limited number of print copies are available. Contact: Sheryl Martin Human Genome Management Information System Oak Ridge National Laboratory 1060 Commerce Park, MS 6480 Oak Ridge, TN 37830 423/576-6669, Fax: 423/574-9888 E-mail: [email protected] An electronic version of this document will be available on January 12, 1999 at the Human Genome Project Information Web site under Publications (http://www.ornl.gov/hgmis). Abstracts for this publication were submitted via the web . This report has been reproduced directly from the best obtainable copy. Available to DOE and DOE contractors from the Office of Scientific and Technical Information; P.O. Box 62; Oak Ridge, TN 37831. Price information: 423/576-8401. Available to the public from the National Technical Information Service; U.S. Department of Commerce; 52 85 Port Royal Road; Springfield, VA 22161. CONF-990104 DOE Human Genome Program Contractor-Grantee Workshop VII January 12-16, 1999 Oakland, California Date Published: December 1998 Prepared for the U.S. Department ofEnergy Office of Science Office of Biological and Environmental Research Washington, D.C. 20874-1290 Prepared by Human Genome Management Information System Oak Ridge National Laboratory Oak Ridge, 1N 37830-6480 Managed by LOCKHEED MARTIN ENERGY RESEARCH CORP. for the U.S. DEPARTMENT OF ENERGY UNDER CONTRACT DE-AC05-960R22464 Contents Introduction to Contractor-Grantee Workshop VII ................................... l Poster Number Sequencing l. Uncovering tbe Riches ofHuman Chromosome 19 Through Genomic Sequencing Jane E. Lamerdin . 3 2. Genomic Sequencing of3 Mb ofHuman Chromosome l6pl3.3 Containing 4 Disease Genes N. A. Doggett .............................................................. 4 3. Sequencing Human Chromosome 14 and tbe Mouse Major Histocompatibility Locus: A Progress Report Lee Rowen ................................................................ 4 4. Physical Mapping and Sequencing of Human Chromosome l6p 12.1-11.2 Hyung Lyun Kang . 5 5. Human Telomere Mapping and Sequencing ~~~ ........................................................ 6 6. A Comparison of Sequence Gap Closure Strategies Glenda G. Quan . 6 7. The SaF Finishing Tools MattP. Nolan ............................................................. 7 8. Process Description of a 5 Mb I Year Finish Sequencing Operation Using 100% Plasmid Double End Sequencing David C. Bruce ............................................................ 8 9. Automation of Finishing at JGI-LLNL Stephanie Stilwagen . 8 10. Sequence Validation and Quality Assessment at tbe Joint Genome Institute M. Bussod ................................................................ 9 11. LANL Finishing Team Accomplisluuents in FY98 J. Buckingham ............................................................ 10 12. JGI-LANL Sequencing Cost Reduction and Quality hnprovement: R&D Results Owatha L. "Tootie" Tatum . 11 13. Concatenation eDNA Sequencing and Analysis of500 Human Brain eDNA Clones Richard A. Gibbs . 11 14. Cosmid Finishing and Full Insert eDNA Sequencing Using Differential Extension with Nucleotide Subsets (DENS) L. E. Ulanovsky . 12 Sequencing Technologies and Resources 15. Structural Analysis oftbe T7 DNA Replication System and Further Development of its Use in DNA Sequencing and Amplification Stanley Tabor . 15 16. Mutagenesis and Reaction Condition Studies ofT? RNA Polymerase Variants to Incorporate Deoxynucleotides Mark Knutb .............................................................. 16 111 Poster Number 17. Megabase and Gigabase Templates: Direct Automated Sequencing off Microbial and Eukaryotic Chromosomal DNA S. Kozyavkin . 17 18. PCR Using Branched Modular Primers Levy E. Ulanovsky . 17 19. Synthesis, Characterization, and Potential Applications ofBiotinylated Energy Transfer Oligonucleotides Jin Xie .................................................................. 18 20. Development of a Multilabel DNA Mapping Technique Using SERS Gene Probes Tuan Vo-Dinh . 18 21. Vectors for Using Nested Deletions to Sequence Either Strand of Cloned DNA John J. Dunn . 19 22. Direct Conversion ofPCR Products into Bidirectional Sequencing Fragments Barbara Ramsay Shaw . 20 23. Analysis of Gradients of Polymer Concentration or Ionic Strength Mark A. Quesada .......................................................... 21 24. Design and Assembly of a Turnkey, High Throughput Oligonucleotide Synthesis Facility for Use on the Human Genome Project J. Shawn Roach ........................................................... 22 25. Prep Track I - A Dynamic Approach to Liquid Handing Robotics D. Humphries ............................................................. 22 26. PrepTrack II Design: Lessons Learned from PrepTrack I John Bercovitz . 23 2 7. Adapting the Tecan Genesis 2 Meter Workstation for High Density Agarose Gel Loading Linda Sindelar . 23 28. Technology Development for the Human Genome Project Trevor L. Hawkins . 23 29. Automation for High Throughput Genomic DNA Sequencing Ronald W. Davis . 24 30. Co-Development ofHigh Throughput Sequencing Systems with the Joint Genome Institute Eric Lander . 24 31. Laboratory Automation for Finish Sequencing at LLNL Stephan Trong . 24 32. Sheath-Flow Capillary Array DNA Sequencer Development at JGIILBNL Jian Jin .................................................................. 25 33. Fully Automated DNA Sequencing with a Commercial96-Capillary Array Instrument Qingbo Li . 26 34. Automation and Integration of Multiplexed On-Line Sample Preparation with Capillary Electrophoresis for High-Throughput DNA Sequencing EdwardS. Yeung .......................................................... 26 35. Long-Read DNA Sequencing by Capillary Array Electrophoresis Barry L. Karger . 27 IV Poster Number 36. DNA Sequencing Using Capillary Array Electrophoresis Jndu Kheterpal . 2 7 37. Focused Single Molecule DNA Detection in Microfabricated Capillary Electrophoresis Chips Richard A. Mathies . •. 28 38. Ultra-High Throughput DNA Genotyping and Sequencing on Radial Capillary Array Electrophoresis Microplates Peter C. Simpson . 29 39. Integrated Sequencing Sample Preparation on CE Microplates Yining Shi . 30 40. Integrated Electrochemical Detection with Microfabricated Capillary Electrophoresis Chips Pankaj Singhal . 30 41. Integrated Microchip Devices for DNA Analysis R. S. Foote ............................................................... 31 42. Single Nucleotide Polymorphism Detection and Identification Directly from Human Genomic DNA by Invasive Cleavage of Oligonucleotide Probes Mary Ann D. Brow . 32 43. High Throughput SNP Discovery and Scoring Using Bead-Based Flow Cytometry P. Scott White . 33 44. DNA Characterization by Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Richard D. Smith . 33 45. Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis C. H. Winston Chen ........................................................ 34 46. PCR Product Size Measurement Using MALDI Mass Spectrometry G. B. Hurst . 35 47. Analyzing Genetic Variations by Mass Spectrometry Lloyd M. Smith . 36 48. DNA Sequencing by Single Molecule Detection James H. Jett . 36 49. Manipulation of Single DNA Molecules by Induced-Dipole Forces in Micro-Fabricated Structures Chip Asbury . 36 50. A Quantitative Analytical Tool for Improving DNA-Based Diagnostic Arrays Tom J. Whitaker . 37 51. A Light-Directed DNA/RNA- Microarray Synthesizer Xiaochuan Zhou ........................................................... 38 52. Development ofFlowthrough Genosensor Chips Mitchel J. Doktycz ......................................................... 38 53. Sequence Analysis and Thermodynamic Studies of Short DNA Duplexes on Oligonucleotide Generic Microchip E. Timofeev . 39 v Poster Number Mapping 54. Third-Strand Binding Probes for Duplex DNA in Particles of Varying Size Marion D. Johnson III . 41 55. Optical Mapping: A Complete System For Whole Genome Shotgun Mapping D. C. Schwartz ............................................................ 41 56. Verifying Sequence By Atomic Force Microscopy David P. Allison . 4 2 57. Molecular Cytogenetics Comes of Age: A Resource that Extends From "T" to Shining "T" J. R. Korenberg . 4 3 58. Automated Purification of Blood, or Bacterial Genomic DNA William P. MacConnell ...................................................... 43 59. New Host Strains for Stabilization and Modification ofYAC Clones Vladimir Larionov . 44 60. Direct Isolation of a Centromeric Region from a Human Mini-Chromosome by in Vivo Recombination in Yeast Natalay Kouprina . 45 61. Insert Clone Selection by Sorting GFP-Expressing E. coli Juno Choe . 45 62. A Resource of Mapped BAC Clones for Identifying Cancer Chromosome Aberrations Norma J. Nowak ........................................................... 46 63. Preparation ofNew BAC Vectors for BAC Cloning and Transformation- Associated Recombination ("TAR") Cloning Changjiang Zeng . ..