Help documentation
  • Overview
  • BreCAN-DB v1.0 is a repository of personalized cancer DNA Breakpoint profiles to facilitate understanding the role of genomic variations found in cancer genomes at personalized level. These breakpoints correspond to large-sized genomic alterations such as insertions, deletions, translocations, inversions and tandem duplications. User can browse these breakpoint profiles of personalized cancer genomes in Breakpoint Browser, smoothly drag and zoom in/out at the chromosomal level or basepair level. It also provides ways to submit or compare breakpoint profiles against database.
  • Breakpoints Browser
  • BreCAN-DB allows user to smoothly browse cancer DNA breakpoint profiles using Breakpoint Browser accessible from navigation bar. User can switch on/off the display of any profile, cancer type according to comparison analysis. User can visualize any genomic region using predefined genomic coordinates, select that region and zoom in the main canvas. Moreover, browsing tracks are listed in the "Available Tracks" panel, and user can enable/disable them according to his interests.
  • Tracks description
    • Human Reference Genome
    • This section contains three tracks i.e. Human genome assembly (UCSC build hg19), Chromosome bands and Refseq genes. Users can switch on/off display of any of these tracks.
    • Breakpoint Hotspots
    • One of the main aim of BreCAN-DB is to find genomic regions that are more susceptible to DNA breaks in cancers. This section contains five tracks representing such regions called breakpoint hotspots in five different types of cancers, namely, breast cancer, Glioblastoma, Ling adenocarcinoma, Ovarian cancer, Head and Neck cancer.
    • Personalized DNA breakpoint profiles
    • This sections contains tracks of personalized cancer DNA breakpoint profiles of 99 cancer samples from five different types of cancer mentioned above. All breakpoints were mapped at nucleotide level resolution and it is obvious that breakpoint position or any other feature of length 1 base is not clearly visible at chromosomal level view, therefore for better visibility, each breakpoint is represented by a rectangular bar, a 20Kb region centered at the breakpoiint position. Following table describes the number of profiles for each type of cancer.

      Table representing number of cancer profiles:
      Cancer Type Abbreviation used Number of profiles Source
      Breast invasive carcinoma BRC 15 Mayerson et. al.
      Glioblastoma multiforme GBM 27 TCGA
      Lung adenocarcinoma LUAD 17 TCGA
      Ovarian serous cystadenocarcinoma OV 23 TCGA
      Head and neck squamous cell carcinoma HN 17 TCGA
      TOTAL 99
  • Compare Profiles
  • BreCAN-DB also allows to compare breakpoint profiles against database of 99 cancer genomic breakpoint profiles.
    (1) Enter the breakpoint profiles in bed format or Select a file containing breakpoint profiles in bed format. If you are unaware of format, Click on example "Bed file" provided on corresponding page.
    (2) Choose cancer type against which you want to compare the given breakpoint profile.
    (3) Click "Compare" to compare the breakpoint profile against BreCAN-DB database.
  • Submit profiles
  • BreCAN-DB provides a way to submit breakpoint profiles in BreCAN-DB. If you have breakpoint profiles mapped at the personalized cancer genome level, we request to contribute in pupulating the database and help the scientific community. If you have any query regarding this, send us an email.
  • Map hotspots
  • This module maps breakpoint hotpots in user uploaded breakpoint profiles using BEDTools.
  • Download
  • This module allows one to download 99 whole genome breakpoint profiles from five cancer types.
  • BreCAN-DB Team
  • BreCAN-DB Team welcomes any query/suggestions to improve your experience. For any support, write us using Contact us page

Tips:
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