Collaborating on
public cancer data

   The Cancer Genome Anatomy Project (CGAP) is an interdisciplinary program established and administered by the National Cancer Institute (NCI) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
   From CGAP's inception in 1996, NCBI been a key participant in bioinformatics planning, data tracking, data archiving, and analytical tool development and implementation. NCBI's role in CGAP has been constantly evolving to meet the demands of changing and expanding raw data sources, as well as the needs of the scientific community.
   The information below highlights NCBI's contributions to CGAP.

   NCBI collaborates closely with NCI as the CGAP pipeline generates large numbers of expressed sequence tags (EST), all of which are deposited into dbEST, and subsequently incorporated into UniGene and HomoloGene. Gene-based, manual annotations may also be added via an interface to LocusLink. A weekly library report is posted on the NCBI web site and provides important feedback information about EST library diversity and future gene discovery prospects. This information is used by CGAP to guide decisions about future library production and sequencing efforts.

   NCBI created the first public CGAP website and designed all analytical tools for the CGAP Tumor Gene Index during the first four years of the project. NCBI developed the online tool, Digital Differential Display to compare computed gene expression profiles between selected cDNA libraries. The CGAP website provides other similar tools under Tissues.

   Serial analysis of gene expression (SAGE) is a more cost-efficient method of producing gene expression data (compared to EST data). CGAP supports the production of SAGE libraries and their sequencing while NCBI has created a repository for the sequence data, developed data processing algorithms, and developed and maintains the SAGEmap website at NCBI. This SAGE data is also accessioned into NCBI's Gene Expression Omnibus resource and are thence indexed, linked and queriable through Entrez ProbeSet.

   NCBI designed and continues to maintain an internal database that tracks CGAP samples, libraries and clones used in the generation of EST and SAGE data.
   The wealth of data produced by CGAP has lead NCBI and NCI staff to develop an ad hoc classification system of hierarchically related keywords. Both NCBI and NCI staff are responsible for the classification of all new human and mouse EST libraries and SAGE libraries on a routine basis.

   NCBI is collaborating closely with a component of CGAP called the Cancer Chromosome Aberration Project (CCAP).
   Using fluorescent in situ hybridization (FISH), CCAP is generating clones that are spaced 1-2 Mb across the human genome. Once mapped, these sequence-ready DNA BAC clones are then made available to the research community. NCBI is involved in identifying candidate BAC clones to be FISH-mapped, archiving the results, and localizing these clones onto draft sequence contigs. This data can be viewed through NCBI's Map Viewer, is linked to NCBI's Clone Registry and UniSTS sites and can also be displayed synoptically on NCI's CGAP Chromosome and NCBI's Human BAC Resource websites.
   CCAP is also characterizing chromosome aberrations in selected tumor types through the use of spectral karyotyping (SKY) and comparative genomic hybridization (CGH). SKY facilitates identification of chromosomal aberrations and CGH can be used to generate a map of DNA copy number changes in tumor genomes. The SKY/CGH database has been designed to house this data, and is publicly accessible.
   Drs. Mitelman, Mertens and Johansson have been systematically summarizing recurrent neoplasia-associated chromosomal aberrations from the Mitelman Database of Chromosome Aberrations in Cancer. This work, which originally appeared in the April 1997 Special Issue of Nature Genetics, entitled "A genome-wide map of chromosomal breakpoints in human cancer", is continuously updated and a summary of the latest data can be viewed with NCBI´s Map Viewer. All recurrent aberrations can be interactively queried at NCI's CGAP website at Recurrent Chromosome Aberrations in Cancer.