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A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome

Nature Genetics volume 24, pages 339–340 (2000)Cite this article

The Cancer Chromosome Aberration Project (CCAP) aims to integrate systematically the cytogenetic and physical maps of the human genome. This will be achieved by high-resolution fluorescence-in-situ-hybridization (FISH) mapping of colony-purified, STS-tagged, single-site hybridizing BAC clones spaced at 1–2-Mb intervals across the entire genome. In the opening phase of the CCAP initiative, we have generated the BAC clone sets that link the cytogenetic and physical maps of chromosomes 7 and 22. We have established a publicly accessible repository of CCAP clones and developed a web site (http://www.ncbi.nlm.nih.gov/CCAP) for data retrieval and cross-referencing of CCAP clones with other cytogenetic and genomic databases relevant to cancer.

The collection of mapped BAC clones described here is offered as a shared resource to the scientific community for study of chromosome aberrations. CCAP BACs can be purchased through a separate repository (specify the BAC ID, chromosome number and catalogue #MB11200, http://www.resgen.com). With the availability of the genomic sequence of chromosome 7 and the sequence of the euchromatic part of human chromosome 22, several long, contiguous sequence segments (contigs) can be constructed6,7. BACs mapped by CCAP can often be localized within these contigs by alignment of BAC end sequences to the finished contig or because they are among the clones that actually contributed to the contig. Thus sequence data and pointers to additional clones will often be available for fine-scale analysis of genomic regions associated with chromosome aberrations. For example, for the first seven listed BACs beginning at the chromosome 22 centromere with bK115F6 and ending with bk992D9, the availability of sequence information allows us to delineate the distances between them to the nearest 5 kb as 1,195 kb, 1,120 kb, 1,420 kb, 1,800 kb, 1,085 kb and 1,745 kb, confirming the 1–2 Mb spacing we sought. We have made available a demonstration of the use of these seven BAC clones in the characterization of a translocation into the Igλ region in a malignant cell line derived from a patient with multiple myeloma (see Fig. 3, http://genetics.nature.com/supplementary_info/).

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Figure 1: Two-colour, high-resolution FISH mapping of chromosome 22 BACs.
Figure 2: Cytogenetic coordinate system for chromosomes 7 and 22 and localization of mapped BAC clones.

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Authors and Affiliations

  1. Genetics Department, Medicine Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA

    Ilan R. Kirsch, Raluca Yonescu, Eva Hilgenfeld, Maria Martelli, W. Michael Kuehl & Thomas Ried

  2. Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA

    Eric D. Green & Valerie V. Braden

  3. Office of the Director, National Cancer Institute, NIH, Bethesda, Maryland, USA

    Robert Strausberg & Richard D. Klausner

  4. National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA

    Greg Schuler & Alex E. Lash

  5. Cancer Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA

    Grace L. Shen

  6. Sanger Centre, Cambridge, UK

    Nigel Carter, David Bentley, Margaret A. Leversha & Ian Dunham

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  1. Ilan R. Kirsch
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Correspondence to Ilan R. Kirsch.

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Kirsch, I., Green, E., Yonescu, R. et al. A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome. Nat Genet 24, 339–340 (2000). https://doi.org/10.1038/74149

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