DOE Human Genome Program Contractor-Grantee
1. Sequence Analysis of Human Chromosome 19
Anne Olsen1, Paul Predki2, Ken Frankel2, Laurie Gordon1, Astrid Terry1, Matt Nolan1, Mark Wagner1, Amy Brower1, Andrea Aerts2, Marnel Bondoc2, Kristen Kadner2, Manesh Shah3, Richard Mural3, Miriam Land3, Denise Schmoyer3, Sergey Petrov3, Doug Hyatt3, Morey Parang3, Jay Snoddy3, Ed Uberbacher3, and the JGI Production Sequencing Team
1Lawrence Livermore National Laboratory and 2Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Production Sequencing Facility, Walnut Creek, CA; 3Genome Annotation Consortium, Oak Ridge National Laboratory, Oak Ridge, TN
Chromosome 19 has an estimated size of ~65 Mb and is the most GC-rich human chromosome. The higher than expected proportion of genes and ESTs mapped to this chromosome suggests that it is exceptionally gene-rich, consistent with its high GC content. Sequencing of chromosome 19 will thus be especially rewarding in terms of gene discovery and elucidation of higher order gene organization. The sequence-ready BAC/cosmid map of chromosome 19 constructed at Lawrence Livermore National Laboratory currently consists of 17 ordered, restriction mapped BAC/cosmid contigs of average size 3.3 Mb spanning 56.3 Mb, or approximately 97% of the estimated 58 Mb comprising the p- and q-arms. A minimally overlapping set of clones (468 cosmids and 290 BACs) spanning the chromosome has been selected for sequencing. About 15 Mb of unique sequence has been finished and submitted to Genbank. Draft sequence (minimum coverage 3X) has been generated for about 68% of the remaining territory with an average depth of 7.7X. Sequence contigs have been ordered and oriented for about 5.2 Mb of the draft sequence. Updated map and sequence data is available from the LLNL web site and the JGI web site. Sequence is being analyzed through the Genome Annotation Pipeline at Oak Ridge National Laboratory. The analysis of 15 Mb of finished genomic sequence yielded 719 gene models predicted by Genscan, and 766 gene models predicted by GRAIL-EXP. About two-thirds of the gene models predicted by GRAIL-EXP were aligned with one or more ESTs. 500 of the Genscan predicted proteins and 456 GRAIL-EXP predicted proteins had homologs with BLAST E-values <1.0e-5. Annotation summaries are available from the ORNL Genome Catalog and Genome Channel at http://genome.ornl.gov. Detailed analyses of specific chromosomal regions will be presented.
Supported by USDOE under Contracts W-7405-Eng-48 (LLNL), DE AC0376SF00098 (LBNL) and DE-AC05-96OR22464 (ORNL).
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