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. 2007 Jan 26:8:33.
doi: 10.1186/1471-2164-8-33.

TICdb: a collection of gene-mapped translocation breakpoints in cancer

Francisco J Novo  1 , Iñigo Ortiz de Mendíbil, José L Vizmanos
Affiliations

TICdb: a collection of gene-mapped translocation breakpoints in cancer

Francisco J Novo et al. BMC Genomics. .

Abstract

Background: Despite the importance of chromosomal translocations in the initiation and/or progression of cancer, a comprehensive catalog of translocation breakpoints in which these are precisely located on the reference sequence of the human genome is not available at present.

Description: We have created a database that describes the genomic location of 1,225 translocation breakpoints in human tumors, corresponding to 247 different genes, using information from publicly available sources. Junction sequences from reciprocal translocations were obtained from 655 different references (either from the literature or from nucleotide databases), and were mapped onto the reference sequence of the human genome using BLAST. All translocation breakpoints were thus referred to precise nucleotide positions (949 breakpoints) or gene fragments (introns or exons, 276 breakpoints) within specific Ensembl transcripts.

Conclusion: TICdb is a comprehensive collection of finely mapped translocation breakpoints, freely available at http://www.unav.es/genetica/TICdb/. It should facilitate the analysis of sequences encompassing translocation breakpoints and the identification of factors driving translocation events in human tumors.

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Figures

Figure 1
Figure 1
Outline of the process of mapping translocation breakpoints. Each junction sequence obtained from the literature or nucleotide database (A) was blasted against a database (B) comprising the genomic sequence of all genes known to be involved in reciprocal translocations in human tumors. Inspection of the BLAST output (C) identifies the specific region of each gene involved in the translocation. In the case of genomic fusion sequences, like the one shown in A, BLAST also identifies the nucleotide position of the breakpoint on both translocation partner genes (C, right panels). In this example the breakpoints are located in nucleotide 8654 of intron 4 of ENST00000266427 (ETV6) and in nucleotide 230 of intron 15 of ENST00000381652 (JAK2).
Figure 2
Figure 2
Schema of TICdb, showing the field-names and field-types for each table; underlined field names indicate primary keys.
See this image and copyright information in PMC

References

    1. Mitelman Database of Chromosome Aberrations in Cancer http://cgap.nci.nih.gov/Chromosomes/Mitelman
    1. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer. 2004;4:177–183. doi: 10.1038/nrc1299. - DOI - PMC - PubMed
    1. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet. 2004;36:331–334. doi: 10.1038/ng1335. - DOI - PubMed
    1. IMGT®, the international ImMunoGeneTics information system http://imgt.cines.fr
    1. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M. The Ensembl genome database project. Nucleic Acids Res. 2002;30:38–41. doi: 10.1093/nar/30.1.38. - DOI - PMC - PubMed

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