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.
Highlights
It is widely understood that incidence of structural genomic alterations (GAs) is frequently associated with cancer and has been posed as a prominent cause for acquisition of hallmarks of cancer initiation/progression [1,2]
The raw breakpoints were mapped at single nucleotide resolution in cancer genome deep sequencing data using Meerkat software [26], which were further filtered using GAs from corresponding cancer type pooled normal data and Database of Genomic variants [27]
This data set included three cancer types already present in our analysis viz. breast invasive carcinoma (BRCA; n = 35), glioblastoma multiforme (GBM; n = 16) and ovarian serous cystadenocarcinoma (OV; n = 9); beyond these it included seven other cancer types viz. colorectal adenocarcinoma (CRC; n = 14), multiple myeloma (MM; n = 7), prostrate adenocarcinoma (PR; n = 7), hepatocellular carcinoma (HCC; n = 19), lung squamous cell carcinoma (LUSC; n = 18), uterine corpus endometrioid carcinoma (UCEC; n = 10) and kidney renal clear cell carcinoma (KIRC; n = 3)
Summary
It is widely understood that incidence of structural genomic alterations (GAs) is frequently associated with cancer and has been posed as a prominent cause for acquisition of hallmarks of cancer initiation/progression [1,2]. Most studies so far have focused mainly upon association of mutations, especially nonsynonymous point mutations present in the coding regions of the genome Results from such studies have shown that though certain point mutation events in cancer are more associated with specific genes like BRCA1 in breast cancer [8], TP53 in glioblastoma multiforme [9], such mutations are present in only a small percentage of disease cases [10]. This has led to an increased interest in large-sized GAs (that may span from tens of bases to few megabases of genome) to better understand cancer etiology
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