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Cancer Genome Characterization Initiative

Visit the database of genomic characterization data for multiple tumor types.


All About FISH-mapped BACs

Overview

CGAP is generating a set of cytogenetically FISH-mapped BAC clones at a resolution of 1-2 MB across the human genome and have also been physically mapped to the genome based on STS data. The BAC clones have been linked to a parallel database of cancer-associated chromosome aberrations to provide a wealth of clinical, histopathologic and genetic information and to several relevant NCBI databases.

All CCAP BAC clones can be ordered from Open BioSystems

Finding BACs

  • Click on one of the hyperlinked chromosome numbers in the "Select a chromosome" box to view a specific chromosome. (A chromosome number will be hyperlinked only if there is FISH data available.)
  • The results screen displays a current reference ideogram with links to:
    • Cytogenetic map coordinates that take you to cancer-associated chromosome aberrations
    • BAC id (NCBI)
    • STS id (NCBI)
    • BAC end (NCBI)
    • Insert sequence( NCBI)
    • Contig (NCBI)
  • As new BAC clones are FISH mapped by chromosome, the data is updated. All chromosomes are expected to be FISH-mapped by end of summer, 2001.

The Coordinate System

Since this BAC map is constructed at a higher resolution than that used in the traditional ISCN (1978) G-stain 850-band nomenclature system, it was necessary to derive a method for referencing this data. We chose to add a lowercase letter (beginning with 'a') to the ISCN nomenclature to indicate separate, resolvable divisions within each band. For example:

  • The large band 7p22.23 contains seven resolvable divisions (7p22.23a, 7p22.23b, ..., 7p22.23g, centomeric to telomeric.
  • The small band 7p32.1 has one resolvable division (7p32.1a).

Map Information and Links

Information is provided in one table per chromosome, in which each row contains information related to a single BAC clone. Each table has four columns, containing the following information and links:

Column HeadingDescription
Reference ideogram:Provides a spatial reference for the additional letter designations on top of the traditional G-stain 850-band nomenclature system.
Map coordinateGives a band or range of bands for the location of the FISH-mapped BAC clone. The link leads you to the human neoplasm recurrent chromosomal aberration data for this location.
BAC clone idGives the bacterial artificial chromosome id (used to order the clone from Research Genetics). The link takes you to NCBI's BAC clone registry where additional BAC information is found.
STS idGives the sequence tag site (STS) identifier that is linked to additional STS mapping information, including GenBank accession and NHGRI contigs.
BAC EndGives the identifier for one or both of the end sequences of the BAC and links you to the NCBI GenBank entry.
Insert SequenceProvides the GenBank accession number of the BAC clone and links to the GenBank entry.
ContigLinks to NCBI's Human Map View

Return to the FISH-mapped BACs.