CONF-971146 DOE uman ~ ~enome Contact for queries about this publication: Human Genome Program U.S. Department of Energy Office of Biological and Environmental Research ER-72GTN Washington, DC 20585 301/903-6488, Fax: 301/903-8521 E-mail: [email protected] A limited number of print copies are available. Contact: Betty K. Mansfield 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, after the November 1997 meeting, at the Human Genome Project Information Web site under Publications (http://www.ornl.gov/hgmis). 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; 5285 Port Royal Road; Springfield, VA 22161. CONF-971146 DOE Human Genome Program Contractor-Grantee Workshop VI November 9-13, 1997 Santa Fe, New Mexico Date Published: October 1997 Prepared for the U.S. Department of Energy Office of Energy Research Office of Biological and Environmental Research Washington, D.C. 20585 under budget and reporting code KP 0404000 Prepared by Hwnan 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 VI .............................. 1 Poster Number Sequencing 1. Large Scale Genomic Sequencing at Washington University Stephanie L. Chissoe . 5 2. The University of Texas Southwestern High Throughput DNA Project Glen A. Evans ....................................................... 5 3. Progress Towards Sequencing Selected Regions of Human Chromosome 19 Jane Lamerdin ...................................................... 6 4. Analysis ofNine Tandem Zinc Finger-Containing Genes Located within a 339kb Region in Human Chromosome 19q13.2 Mark Shannon ....................................................... 6 5. Genomic Sequencing of 16p 13 .3 N.A. Doggett ....................................................... 7 6. The Beginning of the End: Mapping and Sequencing Human Telomeric DNA Robert K. Moyzis .................................................... 8 7. 7q Telomere: Complete Sequencing Han-Chang Chi ...................................................... 8 8. Finished Sequence of7q Telomere Region: Features, Validation and Polymorphism Detection P. Scott White ....................................................... 9 9. Large-scale High-quality Genomic Sequencing of Human Chromosome 7 Shawn Iadonato . 10 I 0. Sequencing Progress at Lawrence Berkeley National Lab and the Formation of JGI Chris Martin . I 0 II. Comparative Analysis of Human and Mouse Orthologous DNA to Identify Conserved Regulatory Regions Kelly A. Frazer . II 12. Comparative Genomic Sequencing of the Human and Mouse Fibroblast Growth Factor Receptor Type III Gene Michael R. Altherr . 11 13. Comparative Genomic Sequencing of the Murine Syntenic Segments Corresponding to Human Chromosome 16p13.3 Michael R. Altherr .................................................. 12 14. High-Throughput Sequencing of Eubacterial and Archeal Genomes Owen White . 12 15. High-Throughput Transposon Mapping and Sequencing Robert B. Weiss ..................................................... 13 iii Poster Number ~ 16. Complete Sequencing of the 2.3Mbp Genome of the Hypertbermophilic Archaean Pyrobaculum aerophilum Ung-Jin Kim . 13 I 7. Microbial Genome Sequencing and Comparative Analysis D.R. Smith ......................................................... 14 18. Sequencing the Borrelia burgdorferi Genome John J. Dunn and F. William Studier .................................... 15 19. Sequence Analysis of the Plasmids of Bacillus anthracis R.T. Okinaka ....................................................... 16 Sequencing Technologies 20. Rhodobacter capsulatus Genome Sequencing Project: DENS Technology Testing Ground Mugasimangalam Raja . 17 21. Cosmid Sized Templates for DENS Sequencing Teclmique Mugasimangalam Raja ............................................... 17 22. Sequencing of Human Telomeric Region DNA by Differential Extension with Nucleotide Subsets (DENS) Dina Zevin-Sonkin . 18 23. Primer Walking Through Alu Repeats Using DENS Sequencing Teclmique Dina Zevin-Sonkin . 18 24. Structural Insights into the Properties of DNA Polymerases Important for DNA Sequencing Stanley Tabor ...................................................... 19 25. Semiautomated Mutagenesis and Screening of T7 RNA Polymerases Mark W. Knuth .................................................... 20 26. Vectors and Biochemistry for Sequencing by Nested Deletions John J. Dunn ....................................................... 20 27. Trapping of DNA in Non-Uniform Oscillating Electric Fields Ger van den Engh ................................................... 21 28. Energy Transfer Fluorescent Primers Optimized for DNA Sequencing and Diagnostics Alexander N. Glazer ................................................. 21 29. Direct PCR Sequencing with Boronated Nucleotides Barbara Ramsay Shaw . 22 30. Advances in DNA Analysis Using Capillary Array Electrophoresis Richard A. Mathies . 23 31. Development of a Low Cost, High Throughput, Four Color DNA Sequencer MichaelS. Westphall ................................................ 24 32. Multiplexed Integrated On-line System for DNA Sequencing by Capillary Electrophoresis: From Template to Called Bases Edward S. Yeung . 24 33. Production Sequencing Evaluation of a Nearly Automated 96-Capillary Array DNA Sequencer Developed at LBNL Jian Jin ........................................................... 25 iv Poster Number ~ 34. DNA Sequencing by Capillary Electrophoresis from Sample Preparation to Resulting Sequence: A Robust High Throughput Procedure with Long Read Length B.L. Karger ....................................................... 26 35. A Fully Automated 96-Capillary DNA Sequencer Qingbo Li ......................................................... 26 36. Development of a Microchannel Based DNA Sequencer Courtney Davidson . 27 37. Microchannel Process Development and Fabrication for DNA Sequencing Steve Swierkowski . 28 38. An Optical Trigger for Locating Microchanhel Position Laurence R. Brewer ................................................. 29 39. Multiple Capillary DNA Sequencer Illuminated by a Waveguide Mark A. Quesada . 29 40. Technology Development and Informatics Tools for Genome Sequencing E.R. Mardis . 30 41. Single Molecule DNA Sequencing Richard A. Keller ................................................... 30 42. On the Road to Rapid Exonuclease Screening for DNA Sequencing Richard A. Keller . 30 43. Sizing of Individual DNA Fragments Yongseong Kim . 31 44. Single Molecule DNA Detection in Microfabricated Capillary Electrophoresis Chips Richard A. Mathies . 31 45. Sizing Megadalton DNA by Mass Spectrometry W. Henry Benner ................................................... 32 46. Evaluation of New Membrane Surfaces for Chemiluminescent Assays Christopher S. Martin . 33 4 7. Advances in Microfabricated Integrated DNA Analysis Systems Richard A. Mathies .................................................. 33 48. The Flowthrough Genosensor Program at Oak Ridge National Laboratory Kenneth Beattie ..................................................... 34 49. Technical Aspects of Fabrication and Quantitative Analysis of DNA Micro-Arrays for Comparative Genomic Hybridization. Damir Sudar ....................................................... 35 50. Multilabel SERS Gene Probes for DNA Sequencing T. Vo-Dinh ........................................................ 36 51. MicroArray of Gel Immobilized Compounds A. Mirzabekov ...................................................... 37 52. Flow Cytometry-Based Polymorphism Detection and Analysis John P. Nolan ...................................................... 37 53. DNA Characterization by Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Richard D. Smith ............................................... 38 v Poster Number Page 54. Improved Mass Spectrometric Resolution for PCR Product Size Measurement Gregory B. Hurst ................................................... 39 55. Laser Desorption Mass Spectrometry for Quick DNA Sequencing and Analysis C.H. Winston Chen .................................................. 39 56. Genome Analysis Technologies George Church ..................................................... 40 57. 2'-Fluoro Modified Nucleic Acids: Polymerase-Directed Syothesis, Properties, and Stability to Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Tetsuyoshi Ono ..................................................... 41 Mapping and Resources 58. Development and Application of Subtractive Hybridization Strategies to Facilitate Gene Discovery Marcelo Bento Soares . 45 59. EURO-IMAGE: the European IMAGE Consortium for Iotegrated Molecular Analysis of Human Gene Transcripts C. Auffray . 45 60. The Functional Genomics Initiative at Oak Ridge National Laboratory Reinhold Mann . 46 61. Defining the Function of the Human DNA Repair Protein XPF by Comparative Genomics and Protein Chemistry Sandra L. McCutchen-Maloney .......................................