Bioinformatics and Integrated Oncology Program Retreat 2011

Ingenuity Pathway
TargetScan
cytopenias - few cells
Comrad - Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data http://bioinformatics.oxfordjournals.org/content/early/2011/04/09/bioinformatics.btr184.abstract
edge betweeness - edges that occur on many shortest paths between other edges have higher betweenness than those that do not.

triple negative - most aggressive tumour subtype, can't be detected by common markers (ie oestrogen receptor (ER), Her2 - herceptin, progesterone receptor, MUC1, CEA)
  - BRCA1 and BRCA2 are less commonly used because these are found in germ line?

most mutations are found in tp53

http://www.foxnews.com/health/2011/06/02/scientists-testing-new-drug-for-triple-negative-breast-cancer/

The hallmarks of cancer. Hanahan D, Weinberg RA
www.ncbi.nlm.nih.gov/pubmed/10647931


MammaPrint

OncotypeDX

stroma - environment surrounding tumour (can be useful for prediction?)
epithelium - tumor region

PAM50 gene set  - Parker 2009
www.aruplab.com/pam50
Parker JS, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009;27(8):1160–7.

Met: Chris Bajdik
http://www.bccrc.ca/dept/cc/chris-bajdik

keynote: Michael Hallett, McGill Centre for Bioinformatics