1Todd Taylor, 1Yasushi Totoki, 1Tadayuki Takeda, 1Hideki Noguchi, 2Robert Baertsch, 3Jonathan Mudge, 3Tim Hubbard, 1Yoshiyuki Sakaki
1RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan, 2UCSC Genome Bioinformatics Group, CBSE/ITI, 501D Engineering II Building, UCSC, 1156 High St, Santa Cruz, CA 95064, 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
As a member of the International Human Genome Sequencing Project, our group led the effort for completion of the sequence of human chromosome 11. As major sequence contributor and coordinator, our center took responsibility for analyzing and annotating the entire chromosome (134Mb).
The current tiling path of chromosome 11 consists of 8 contigs (ranging from 503kb to 49.6Mb) containing 1121 accessions. We reached the centromere on both sides and the telomere on 11q. Only six internal clone gaps remain, totaling about 270kb; continued efforts to close the remaining gaps include long-PCR based on human and chimpanzee whole-genome shotgun data.
Chromosome 11 is relatively gene-dense and harbors genes for several well-known disorders such as: Beckwith Wiedemann syndrome, type 1 diabetes, ataxia telangiectasia, and Long QT syndrome. Over one-third of all human olfactory receptor genes are on chromosome 11. In addition, three medically important regions, the IGF2/H19 locus, the HBB beta-globin cluster, and the APO cluster, have been targeted for study as part of the ENCODE project. Other loci have been implicated in behavioral and psychiatric disease variation.
The chromosome is being manually annotated according to Hawk standards. Genes are categorized as follows: known, novel CDS, novel transcript, putative and pseudogene. Our plan is to experimentally verify all novel and putative genes where cDNA evidence does not already exist. The sequence is analyzed by comparing it to all sequence data from other available species, as well as the rest of the human genome. Full-length cDNA and EST sequences are aligned to the sequence in order to try and identify all transcript variants, for both known and novel genes. Several ab initio and homology-based gene/exon prediction programs were used in addition to other programs that identify CpG islands, promoter sites, etc. Comparison with other available genome assemblies will be made to identify additional genes and conserved regions that may be involved in gene regulation. The most recent gene annotation analysis of the sequence will be presented.
Other abstracts in same session