#+title: Prioritization of structural variants based on known biological information
#+author: Brad Chapman \\ Bioinformatics Core, Harvard Chan School \\ http://j.mp/bcbiolinks
#+date: 10 July 2015

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* bcbio prioritization

** Validated, community developed tools

#+ATTR_LATEX: :width 1.0\textwidth
[[./images/bcbio_nextgen_highlevel.png]]

\vspace{1cm}
https://github.com/chapmanb/bcbio-nextgen

** Structural variants critical in cancer

#+ATTR_LATEX: :width 1.0\textwidth
[[./images/nature14169-sf2.jpg]]

\scriptsize
http://www.nature.com/nature/journal/v518/n7540/full/nature14169.html

** Structural variants hard to detect

#+ATTR_LATEX: :width 0.9\textwidth
[[./images/sv-dup-val.png]]

\footnotesize
http://bcb.io/2015/03/05/cancerval/

** Prioritize in previously known regions

#+ATTR_LATEX: :width 1.0\textwidth
[[./images/prioritize-overview.png]]

** Public cancer variant databases

- CIViC: https://civic.genome.wustl.edu
- IntOGen: http://www.intogen.org

#+BEGIN_CENTER
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[[./images/biology-of-cancer.jpg]]
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\vspace{0.01cm}
\scriptsize
http://www.amazon.com/The-Biology-Cancer-Robert-Weinberg/dp/0815340761
\normalsize

** Prioritization -- summary

- Structural variants critical but hard
- Use known biological information
- Support community databases
- bcbio.prioritize \\
  \small
  https://github.com/chapmanb/bcbio.prioritize
  \normalsize
- bcbio \\
  \small
  https://github.com/chapmanb/bcbio-nextgen
