Development of ESP: Structural & Functional Oncogenomics

Summary

Principal Investigator: Colin C Collins
Affiliation: University of California
Country: USA
Abstract: The long-term objective of this proposal is to gain an enhanced understanding of the structural genomics of solid tumors through development of a novel, sequence-based method capable of identifying all types of structural rearrangements that occur in tumor genomes. Genome rearrangements can promote cancer development, progression and/or resistance to therapy by altering gene regulation and/or function, and the involved genes are potential therapeutic targets. This is well established in leukemia and lymphoma, but less so in solid tumors, in part because of the difficulty of identifying the genes involved in complex structural rearrangements. We describe here a powerful and high resolution, sequence-based analytical approach called End Sequence Profiling (ESP). ESP maps copy number aberrations and directly identifies and clones en masse genome breakpoints associated with genome rearrangements such as inversions, translocations, deletions and amplifications. ESP is accomplished by constructing a BAC library of a tumor genome, end sequencing a larger number of BAC clones, and mapping the BAC end sequences (BES) onto the normal genome sequence. Paired BES that map to different parts of the normal genome span structural rearrangements. Sequencing these clones will reveal exact breakpoints and involved genes. In Specific Aim 1 we will: Implement ESP as a cost effective sequence-based technology for determining the structural organization of tumor genomes and clone rearrangement breakpoints en masse. Determine the minimum sequencing depth needed to yield the maximum structural information. Determine if ESP can reproducibly identify recurrent rearrangements between tumors, and if so, whether specific sequence elements are associated with these rearrangements. In Specific Aim 2 we will: Develop robust computational methods for the analysis, visual representation, and integration of ESP data with the human reference sequence, making possible comparison of ESP data from independent tumors. Knowledge of how genome rearrangements such as inversions and translocations impact local gene expression is critical. Thus, we will integrate ESP-based structure data with expression microarray data and co-localize aberrantly expressed genes with genome rearrangement breakpoints. In Specific Aim 3: We will biologically and clinically validate key ESP findings. We believe ESP provides a rational framework for sequencing tumor genomes. In fact, ( 100 tumor genomes can be analyzed at ( 10 kb resolution for less than sequencing a single 3000 Mb genome yielding hundreds of novel biomarkers and therapeutic targets associated with translocations, inversions, and complex rearrangements. This is important because, just as a comprehensive systems-based knowledge of human biology is predicated on the structural organization and sequence of the human genome, a structure-based view of tumor genomes is essential for a comprehensive understanding of tumor biology.
Funding Period: 2003-08-01 - 2007-07-31
more information: NIH RePORT

Top Publications

  1. pmc Decoding the fine-scale structure of a breast cancer genome and transcriptome
    Stanislav Volik
    Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
    Genome Res 16:394-404. 2006
  2. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
  3. pmc Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer
    Ali Bashir
    Bioinformatics Graduate Program, University of California San Diego, San Diego, California, United States of America
    PLoS Comput Biol 4:e1000051. 2008

Scientific Experts

  • Benjamin J Raphael
  • Ali Bashir
  • Stanislav Volik
  • John H Brebner
  • Irina A Shagina
  • Dmitri A Shagin
  • Anna Lapuk
  • Michael R Stratton
  • Pieter J de Jong
  • Krystyna Bajsarowicz
  • Joe W Gray
  • Quanzhou Tao
  • Jan Fang Cheng
  • John Murnane
  • Guiqing Huang
  • Colin Collins
  • Graham Bignel
  • Pamela L Paris
  • David Kowbel
  • Pavel Pevzner

Detail Information

Publications3

  1. pmc Decoding the fine-scale structure of a breast cancer genome and transcriptome
    Stanislav Volik
    Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
    Genome Res 16:394-404. 2006
    ..Given these properties, ESP could play an important role in a tumor genome project...
  2. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
    ..The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes...
  3. pmc Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer
    Ali Bashir
    Bioinformatics Graduate Program, University of California San Diego, San Diego, California, United States of America
    PLoS Comput Biol 4:e1000051. 2008
    ..These results will be useful in calibrating future cancer sequencing efforts, particularly large-scale studies of many cancer genomes that are enabled by next-generation sequencing technologies...