title: BreCAN-DB: a repository cum browser of personalized DNA breakpoint profiles of cancer genomes.
abstract: BreCAN-DB (http://brecandb.igib.res.in) is a repository cum browser of whole genome somatic DNA breakpoint profiles of cancer genomes, mapped at single nucleotide resolution using deep sequencing data. These breakpoints are associated with deletions, insertions, inversions, tandem duplications, translocations and a combination of these structural genomic alterations. The current release of BreCAN-DB features breakpoint profiles from 99 cancer-normal pairs, comprising five cancer types. We identified DNA breakpoints across genomes using high-coverage next-generation sequencing data obtained from TCGA and dbGaP. Further, in these cancer genomes, we methodically identified breakpoint hotspots which were significantly enriched with somatic structural alterations. To visualize the breakpoint profiles, a next-generation genome browser was integrated with BreCAN-DB. Moreover, we also included previously reported breakpoint profiles from 138 cancer-normal pairs, spanning 10 cancer types into the browser. Additionally, BreCAN-DB allows one to identify breakpoint hotspots in user uploaded data set. We have also included a functionality to query overlap of any breakpoint profile with regions of user's interest. Users can download breakpoint profiles from the database or may submit their data to be integrated in BreCAN-DB. We believe that BreCAN-DB will be useful resource for genomics scientific community and is a step towards personalized cancer genomics.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Narang
authors.affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India.
authors.forename: Parashar
authors.initials: P
authors.lastname: Dhapola
authors.affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India shantanuc@igib.res.in.
authors.forename: Shantanu
authors.initials: S
authors.lastname: Chowdhury
mesh_terms: D056905:Chromosome Breakpoints; D004273:DNA, Neoplasm / Q000737:chemistry; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004273:DNA, Neoplasm