Human Genome Prozram U.S. Department of Energy Office of Biological and Environmental Research SC-72 GTN Germantown, MD 20874-1290 301/903-6488, Fax: 3011903-8521 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 865/576-6669, Fax: 865/574-9888 E-mail: [email protected] An electronic version of this document will be available on February 27, 2000, at the Human Genome Project Infonnation Web site under Publications (http:llwww.ornl.gov/hgmis). Abstracts for this publication were submitted via the web. DOE/SC-0002 DOE Human Genome Program Contractor-Grantee Workshop VIII February 27-March 2, 2000 Santa Fe, New Mexico Date Published: February 2000 Prepared for the U.S. Department ofEnergy Office of Science Office of Biological and Environmental Research Washington, DC 20874-1290 Prepa.-ed by Human Genome Management Information System Oak Ridge National Labomtory Oak Ridge, 1N 37830 Managed by LOCKHEED MARTIN ENERGY RESEARCH CORP. for the U.S. DEPAR1MENT OF ENERGY UNDER CONI'RACT DE-AC05-960R22464 Contents1 Introduction to Contractor-Grantee Workshop VIII . 1 Sequencing . 3 1. Sequence Analysis of HUman Chromosome 19 Anne Olsen, Paul Predki, Ken Frankel, Laurie Gordon, Astrid Terry, Matt Nolan, Mark Wagner, Amy Brower, Andrea Aerts, Marne! Bondoc, Kristen Kadner, Manesh Shah, Richard Mural, Miriam Land, Denise Schmoyer, Sergey Petrov, Doug Hyatt, Morey Parang, Jay Snoddy, Ed Uberbacher, and the JGI Production Sequencing Team . 3 2. Draft Sequencing Procedures for Chromosome 16 Sequencing Mark 0. Mundt, David C. Bruce, Leslie Chasteen, Judith Cohn, Lynne Goodwin, Kristina Kommander, Chris Munk, Robert Sutherland, Norman Doggett, and Larry Deaven . 3 3. Large-Scale Finishing of Human and Mouse Genomic Sequences Richard M. Myers, Jeremy Schmutz, Jane Grimwood, the Sequencing Group at Stanford Human Genome Center, and the Joint Genome Institute . 4 4. A Tale of Three Loci Lee Rowen, Anup Madan, Shizhen Qin, and Lee Hood . 4 5. Human Telomere Mapping and Sequencing Robert K. Moyzis, Deborah L. Grady, Han-Chang Chi, and Harold C. Riethman 5 6. Targeted eDNA Sequencing Kimberly Prichard, Susi Wachocki, Mira Dimitrijevic-Bussod, Mark Mundt, Judith Cohn, David Bruce, Cliff Han, Norman Doggett, Christa Prange, and Michael R. Altherr . 6 7. Determining Quality of Oligonucleo-tides Synthesized in a High Throughput Process Linda S. Thompson, David C. Bruce, Norman A. Doggett, Mark 0. Mundt, and Larry L. Deaven . 6 8. Progress of Concatenation eDNA Sequencing at the BCM-Human Genome Sequencing Center Richard Gibbs . 7 9. Full-Length eDNA Sequencing Using Differential Extension with Nucleotide Subsets (DENS) 0. Chertkov, C. Naranjo, D. Zevin-Sonkin, H. Hovhanissyan, A. Ghochikyan, L. Lvovsky, A. Liberzon, M.C. Raja, and L.E. Ulanovsky . 8 10. pZil': A Versatile Vector for Sequencing by Nested Deletions John J. Dunn . 8 11. pUC-SV: A New Double Adaptor Plasmid System for Sequencing Complex Genomes Jonathan L. Longmire, Nancy C. Brown, Larry L. Deaven, and Norman A. Doggett . 9 12. A Fluorescent Sequencing Vector for High-Throughput Clone Selection by Cell Sorting Juno Choe and Ger van den Engh . 10 13. An Isothermal Amplification System for the Production of DNA Templates for DNA Sequencing Stanley Tabor and Charles Richardson . 10 'Contact authors are balded. iii Poster Number 14. Universal Energy-Transfer Cassettes for Facile Construction of Energy-Transfer Fluorescent Labels Jin Xie, Lorenzo Berti, Richard A. Mathies, and Alexander N. Glazer . II 15. Fimer Chemistry for Sequencing offBAC and Genomic DNA Templates S. Kozyavkin, N. Polouchine, A. Malykh, 0. Malykh, and A. Slesarev ............ 11 16. Chemical Conversion ofBoronated PCR Products into Bidirectional Sequencing Fragments Barbara Ramsay Shaw, Kenneth W. Porter, Ahmad Hasan, Kaizhang He, and Jack Summers . 12 17. Human and Mouse BAC Libraries for Genome Sequencing, Mapping, and Functional Analysis Kazutoyo Osoegawa, Chung Li Shu, Aaron Marnmoser, Joe Catanese, and Pieter J. De Jong . 13 18. Human and Mouse BAC Ends Shaying Zhao, Mark D. Adams, Joel Malek, Lily Fu, Bola Akinretoye, Sofiya Shatsman, Maureen Levins, Stephany McGann, Keita Geer, Getahun Tsegaye, Margaret Krol, Peter Choi, Tamara Feldblyum, William Nierman, and Claire Fraser ............................................. 14 19. Library Strategy for Genome Sequencing Projects William C. Nierman . 15 Instrumentation ................................................................... 17 20. New Technologies for Genome Sequencing and Expression Analysis Wayne P. Rindone, John Aach, Martha Bulyk, George M. Church, Jason Hughes, Abby Mcguire, Pam Ralston, Martin Steffen, and Saeed Tavazoie . 17 21. High-Performance DNA Sequencing and Analysis Richard A. Mathies . 17 22. Radial Capillary Array Electrophoresis Microplate and Scanner for High-Performance DNA Sequencing and Analysis Yining Shi, Brian M. Paegel, James R. Scherer, Peter C. Simpson, David Wexler, Christine Ski bola, Martyn T. Smith, and Richard A. Mathies . 18 23. Turn Geometries for Minimizing Band Broadening in Microfabricated Capillary Electrophoresis Channels Brian M. Paegel, Lester D. Hutt, Peter C. Simpson, and Richard A. Mathies ....... 19 24. Integrated Microfluidic DNA Amplification and Analysis Systems Eric T. Lagally, Daojing Wang, Charles Emrich, and Richard A. Mathies ......... 19 25. High-Speed High-Throughput Mutation Detection Qiufeng Gao, Ho-Ming Pang, and EdwardS. Yeung ......................... 20 26. Micro-Fabricated Devices for Concentrating DNA by Induced-Dipole Trapping Charles Asbury and Ger Van Den Engh .................................. 21 27. Fully Automated Multiplexed Capillary Systems for DNA Sample Analysis Qingbo Li, Thomas E. Kane, Changsheng Liu, Harry Zhao, Gary W. Loge, John Kernan, Songsan Zhou, Kevin Levan, Heidi Monroe, and David Fisk . 21 28. Development and Evaluation of a PCR-Based Sequencing Routine for Use on the ABI 3700 Capillary Machine Lynne Goodwin, Owatha Tatum, Olga Chertkov, Judith Cohn, and P. Scott White . 22 iv Poster Number 29. Rapid and Accurate Detection of Human Functional SNPs Using a Base Stacking Microelectronic DNA Chip Glen Evans, David Canter, Purita Ramos, Ray Radtkey, Ron Sosnowski, Gene Tu, James O'Connell, and Michael Nerenberg . 23 30. DNA Sequencing by Single Molecule Detection Peter M. Goodwin, Hong Cai, James H. Werner, James H. Jett, and Richard A. Keller . 23 31. New Optical Methods for Sequencing Individual Molecules of DNA Jonas Korlach, Michael Levene, Stephen W. Turner, Mathieu Foquet, Harold G. Craighead, and Watt W. Webb . 24 32. High Throughput Multiplexed mtDNA SNP Scoring Using Microsphere-Based Flow Cytometry P. Scott White, Alina Deshpande, Lance Green, Yolanda Valdez, David C. Tomey, andJohnP.Nolan ............................................. 24 33. Mass Spectrometric Analysis of Genetic Variations Lloyd M. Smith . 25 34. Affinity Capture and Mass Spectrometry of Targeted Proteins in Mice Stephen J. Kennel, Gregory B. Hurst, Linda J. Foote, and Michelle V. Buchanan 25 35. Rapid Quantitative Measurements ofProteomes Richard D. Smith, Ljiljana Pasa Tolic, Mary S. Lipton, Pamela K. Jensen, Gordon A. Anderson, and Timothy D. Veenstra ...................... 26 36. DNA Characterization by Electrospray lonization-FTICR Mass Spectrometry DavidS. Wunschel, Bingbing Feng, Ljiljana Pasa Tolic, Mary S. Lipton, and Richard D. Smith . 26 37. DNA Sequencing via Electrospray and Ion/Ion Chemistry in an Electrodyoamic Ion Trap Scott A. McLuckey, James L. Stephenson, Jr., and Gregory B. Hurst . 27 38. DNA and Protein Analyses on Microfabricated Devices R. S. Foote, Y. Khandurina, I. M. Lazar, Y. Liu, T. McKnight, L. C. Waters, S.C. Jacobson, R. S. Ramsey, and J. M. Ramsey ..................... 28 39. Stable Isotope Assisted Mass Spectrometry Allows Accurate Detennination of Nucleotide Compositions of PCR Products Xian Chen, Zhengdong Fei, Lloyd M. Smith, E. Morton Bradbury, and Vahid Majidi . 28 40. Hybridization Detection Tom J. Whitaker and Kenneth F. Willey .................................. 29 41. Automation Using Packard Multiprobe Robots for Finishlng Christine Munk, Judy Buckingham, Marie Krawczyk, Elizabeth Saunders, David Bruce, and Mark Mundt . 29 42. Automated, Low Cost Isolation of Blood or Bacterial Genomic DNA Brian Bauman, Tuyen Nguyen, Zuxu Yao, Tony Zucca, Dan Langhoff, and William MacConnell . 30 43. The Use of Electrode Arrays for the Syothesis ofBiomolecular Affinity Probes Francis Rossi, Christopher Ashfield, Karl Maurer, and Donald Montgomery . 30 44. Development of a High Throughput Peptide Nucleic Acid Syothesizer J. Shawn Roach, Simon Rayoer, Lynn Mayfield, David R. Corey, and Harold "Skip" Garner . 31 v Poster Number 45. MicroArray of Gel Immobilized Compounds on Chip V. Vasiliskov, A. Stomakhin, B. Strizhkov, S. Tillib, V. Mikbailovich, A. Sobo1ev, A. Kuhktin, and A. Mirzabekov . 31 Mapping ........................................................................... 33 46. Analysis ofWUSTL's Human BAC Fingerprint Database R. Sutherland, M. Mundt, and N. Doggett . 33 47. Human Chromosome 16 Mapping Update CliffS. Han, Robert D. Sutherland, Phillip B. Jewett, Mary L. Campbell, Linda J. Meincke, Judy G. Tesmer, Mark 0. Mundt, Larry L. Deaven, and Norman A. Doggett . 33 48. Annotation and Analysis of the Draft Sequence of 16Q12 Jung-Rung Wu, Mark 0. Mundt, CliffS. Han, Kristina Kommander, Robert D. Sutherland,