ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors

• Published in: Oncogene Vol. 26; no. 46; pp. 6641 - 6652
• Main Authors: HUPE, P, LA ROSA, P, LIVA, S, LAIR, S, SERVANT, N, BARILLOT, E
• Format: Journal Article
• Language: English
• Published: Basingstoke Nature Publishing 11.10.2007; Nature Publishing Group
• Subjects: Bioinformatics; Biological and medical sciences; Breast; Cancer; Cancer research; Cell physiology; Cell transformation and carcinogenesis. Action of oncogenes and antioncogenes; Copy number; Data Interpretation, Statistical; Databases, Genetic; DNA microarrays; Fundamental and applied biological sciences. Psychology; Gene Dosage; Gene Expression Profiling; Gene mapping; Genetic aspects; Genomes; Genomics; Heterozygosity; Humans; Hybridization; Integration; Interfaces; Loss of heterozygosity; Lymphoma; Medical research; Molecular and cellular biology; Neoplasms - diagnosis; Neoplasms - genetics; Neuroblastoma; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Oncogenes; Oncology; Online databases; Physiological aspects; Polymorphism; Single-nucleotide polymorphism; Transcriptomes; Tumors; France; tumors; Copy number; DNA; DNA copy number; Database; Tumor; bioinformatics platform; Bioinformatics; Carcinogenesis; molecular profiles; clinical data
• ISSN: 0950-9232; 1476-5594
• DOI: 10.1038/sj.onc.1210488

In recent years, an increasing number of projects have investigated tumor genome structure, using microarray-based techniques like array comparative genomic hybridization (array-CGH) or single nucleotide polymorphism (SNP) arrays. The forthcoming studies have to integrate these former results and compare their findings to the existing sets of copy number data for validation. These sets also form the basis from which many comparative retrospective analyses can be carried out. Nevertheless, exploitation of this mass of data relies on a homogeneous preparation of copy number data, which will make it possible to compare them together, and their integration into a unified bioinformatics environment with ad hoc analysis tools and interfaces. To our knowledge, no such data integration has been proposed yet. Therefore the biologists and clinicians involved in cancer research urgently need such an integrative tool, which motivated us to undertake the construction of a database for array-CGH and other DNA copy number data for tumors (ACTuDB). When available, the associated clinical, transcriptome and loss of heterozygosity data were also integrated into ACTuDB. ACTuDB contains currently about 1500 genomic profiles for tumors and cell lines for the bladder, brain, breast, colon, liver, lymphoma, neuroblastoma, mouth and pancreas, together with data for replication timing experiments. The CGH array data were processed, using ad hoc algorithms (probe mapping, breakpoint detection, gain or loss status assignment and visualization) developed at Institut Curie. The database is available from http://bioinfo.curie.fr/actudb/ and can be browsed with a user-friendly interface. This database will be a useful resource for the genomic profiling of tumors, a field of highly active research. We invite research groups involved in tumor genome profiling to submit their data to ACTuDB.