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OE Human Genome Program Contractor-Grantee Workshop IX

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OE Human Genome Program Contractor-Grantee Workshop IX Contents Introduction to Contractor-Grantee Workshop IX ....................................................................... l Genomes to Life Program Overview...................................................................................................... 3 Meeting Abstracts ............................................................................................................................................ 5 Sequencing ............................................................................................................................................................... 5 1. The US DOE Joint Genome Institute's High Throughput Production Sequencing Program Susan Lucas, Tijana Glavina, Jamie Jett, Lyle Probst, Andrea Aerts, Nathan Bunker, Sanjay Israni, Astrid Terry, John C. Detter, Sam Pitluck, Heather Kimball, Yunian Lou, Martin Pollard, Anne Olsen, Chris Elkin, Paul Richardson, Dan Rokhsar, Paul Predki, Elbert Branscomb, Trevor Hawkins, and the JGI Sequencing Team.................................................................................................... 5 2. Leveraging Comparative Sequencing Information to Generate a Complete Functional Map of Human Chromosome 19 Lisa Stubbs, Xiaochen Lu, Sha Hammond, Eddie Wehri, Anne Bergmann, Robin Deis, Angela Kolhoff, and Joomyeong Kim ................................................................................. 5 3. The Finishing of Human Chromosomes 19 and 5 Jane Grimwood, Jeremy Schmutz, Mark Dickson, Richard M. Myers, and all members of the Sequencing Group at the Stanford Human Genome Center...................................... 6 4. Assembly and Analysis of Finished Sequence for Human Chromosome 19 Anne Olsen, Susan Lucas and the JGI Production Sequencing Group; Jane Grimwood, Jeremy Schmutz and the Stanford Finishing Group; Laurie Gordon and the LLNL Mapping Group; Paramvir Dehal, Art Kobayashi, Sam Pitluck and the JGI Informatics Group; and Trevor Hawkins ...................................................................... 6 5. Finishing of Human Chromosome 16 Norman Doggett, Mark Mundt, David Bruce, Cliff Han, Levy Ulanovsky, Larry Deaven, Susan Lucas, Trevor Hawkins, and JGl Staff.. .................................................................... ? 6. An Overview ofthe Finish Sequencing Process at LANL: Design, Automation, and Organization David C. Bruce, Mark 0. Mundt, Levy E. Ulanovsky, Heather A. Blumer, Judy M. Buckingham, Connie S. Campbell, Mary L. Campbell, Olga Chertkov, J. Joe Fawcett, Valentina M. Leyba, Kim K. McMurry, Linda J. Meincke, A. Christine Munk, Beverly A. Parson-Quintana, Donna L. Robinson, Elizabeth H. Saunders, Judith G. Tesmer, Linda S. Thompson, Patti L. Wills, Norman A. Doggett, and Larry L. Deaven............................................................................................................ 7 lll Sequencing Resources .......................................................................................................................................... 9 7. Construction ofBAC Libraries Using Sheared DNA Kazutoyo Osoegawa, Chung Li Shu, and Pieter J. de Jong ........................................................... 9 8. BAC Library End Sequencing in Support of Whole Genome Assemblies David C. Bruce, Mark 0. Mundt, Kim K. McMurry, Linda J. Meincke, Donna L. Robinson, Norman A. Doggett, and Larry L. Deaven ......................................................................... 9 9. An Approach to Filling Gaps in the Sequence of the Human Genome X.-N. Chen, P. Bhattacharyya, S. Y. Zhao, M. Sekhon, J. McPherson, M. Wang, U.-J. Kim, H. Shizuya, M. Simon, and J. R. Korenberg .................................................. 10 10. Isolation of Segments Missing from the Draft Human Genome Sequence Using Yeast N. Kouprina, G. Solomon, S.-H. Leem, A. Ly, E. Pak, J. C. Barrett, and V. Larionov............... 10 11. Recent Segmental Duplications: A Dynamic Source of Gene Innovation and Complex Regions of Sequence Assembly J. A. Bailey, J. E. Horvath, M. E. Johnson, M. Rocchi, and E. E. Eichler ................................... 11 12. Pooling DNA Clones for Shotgun Sequencing Richard Gibbs and the staff of the Baylor College of Medicine-Human Genome Sequencing Center, Wei Wen Cai, and Allan Bradley ..................................................... 11 13. Production Clone Rearraying Using the QBot (Genetix Ltd.) and the LANL Cherrypicldng Program John J. Fawcett, James Colehan, Lyn Honeybome, Bill Stevenson, David C. Bruce, Norman A. Doggett, and Larry L. Deaven ....................................................................... 12 14. Applications oflsothermal Rolling Circle Amplification in a High-Throughput Sequencing Environment John C. Detter, Jamie M. Jett, Andre R. Arellano, Alicia R. Ferguson, K.ristie Tacey, Mei Wang, Heidi C. Turner, Susan M. Lucas, Ken Frankel, Paul Predki, Dan Rokhsar, Paul M. Richardson, and Trevor L. Hawkins ............................................ 12 15. Efficient Isothermal Amplification of Single DNA Molecules Stanley Tabor and Charles llichardson ........................................................................................ 13 16. Amplification ofBAC DNA with Rolling Circular Amplification CliffS. Han, Judy Tesmer, Linda L. Meincke, Donna L. Robinson, Connie S. Campbell, Larry L. Deaven, and Norman A. Doggett.. ..................................................................... 13 17. A Singii}-Copy, Amplifiable Plasmid Vector That Uses Homing Endonuclease Recognition Sites to Facilitate Bidirectional Nested Deletion Sequencing of Difficult Regions John J. Dunn, Laura Praissman, Laura-Li Buder-Loffredo, and Sean McCorkle ....................... 14 18. DENS: Finishing Without Custom Primers Levy ffianovsky, Olga Chertkov, Malinda Stalvey, Marie-Claude Krawczyk, David Hill, David Bruce, Mark Mundt, Larry Deaven, and Norman Doggett .................................... 15 19. High Throughput Synthesis of Oligonucleotides in Support of Finishing L. Sue Thompson, Mark Mundt, David Bruce, Larry Deaven, and Norman Doggett.. ............... 15 20. Automated 384-Well Purification for Terminator Sequencing Products Chris Elkin, Hitesh Kapur, David Humphries, Troy Smith, and Trevor Hawkins ...................... 16 21. Whole Genome Direct Sequencing: Completion of Microbial Genome and Mammalian BAC Projects using ThermoFidelase, Fimer and D-St-rap Technologies S. Kozyavldn, A. Malykh, K. Mezhevaya, A. Morocho, N. Polouchine, V. Shakhova, 0. Shcherbinina, and A. Slesarev ..................................................................................... 16 IV 22. A Tape Conveyer System for Storage and Distribution of Biological Samples Ger van den Engh and Juno Choe ................................................................................................ !? 23. Developing a High Throughput Lox Based Recombinatorial Cloning System Robert Siegel, Raj Jain, Nileena Velappan, Leslie Chasteen, and Andrew Bradbury ................. ! 7 24. Plant Mini-Chromosome Vectors J. Mach and H. Zieler .................................................................................................................... 18 25. Sampling Diversity with Mitochondrial Genomics Jeffrey L. Boore, Nikoletta Danos, David DeGusta, H. Matthew Fourcade, Lisa Gershwin, Alleo Haim, Kevin Helfenbein, Martin Jaekel, Kirsten Lindstrom, J. Robert Macey, Susan Masta, Monica Medina, Rachel Mueller, Marco Passarnonti, Corrie Saux, Renfu Shao, and Yvonne Valles .................................................................. 19 Instrumentation.................................................................................................................................................... 21 26. Method for Fast and Highly Parallel Single Molecule DNA Sequencing Jonas Korlach, Michael Levene, Stephen W. Turner, Harold G. Craighead, and Watt W. Webb ................................................................................................................... 21 27. Fast Detection of Nucleic Acid Hybridization with a Tapered Optical Fiber Sensor Hyunmin Yi, Vildana Hodzic, James J. Sumner, Matthew P. Delisa, Saheed Pilevar, Frank H. Portugal, James B. Gillespie, Christopher C. Davis, and William E. Bentley .................................................................................................... 21 28. High Performance Capillary Electrophoresis in DNA Sequencing and Analysis: Recent Developments Barry L. Karger, Lev Kotler, Arthur Miller, and Hui He ............................................................ 22 29. Microchanncl DNA Sequencing by End-Labeled Free Solution Electrophoresis (ELFSE): Development of Polymeric End-Labels, Wall Coatings, and Electrophoresis Methods Wyatt N. Vreeland, Jong-lu Won, Robert J. Meagher, M. Felicia Bogdan, and Ann elise E. Barron ............................................................................................................ 22 30. Microfabricated Fluidic Devices for the Analysis of Genomic Materials K. A. Swinney, R. S. Foote, C. T. Culbertson, S. C. Jacobson, and J. Michael Ramsey ............. 23 31. Molecular Gates for Improved Sample Cleanup and Handling in Microfabricated Devices Tzu-Chi Kuo, Donald M. Cannon, Mark A. Shannon, Paul W. Bohn, and Jonathan V. Sweedler...................................................................................................... 24 32. Electron Tomography of Whole Cells Grant J. Jensen and Kenneth H. Downing ...................................................................................
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