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

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. © 2007 Novo et al; licensee BioMed Central Ltd.