Posts Tagged ‘i0cmu13’

Collections of Simultaneously Altered Genes as Biomarkers of Cancer Cell Drug Response

Monday, May 6th, 2013
Nice use of CCLE dataset which is an improvement over NCI-60

Some interesting mutation assessor tools featured at Automated Personal Genome Analysis

Monday, May 6th, 2013

Cancer-Related Analysis of VAriants Toolkit

Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool
BMC Genomics. In press

(explicit acknowledgement of VAT)

toolkit for detecting biologically important single nucleotide mutations in cancer.


Vogelstein v. Lander, Round 1

Monday, May 6th, 2013
Short list of 140 drivers v an ever growing list

Science. 2013 Mar 29;339(6127):1546-58. doi: 10.1126/science.1235122. Cancer genome landscapes.
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. QT:”
To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance.

Lessons from the Cancer Genome
Systematic studies of the cancer genome have exploded in recent years. These studies have revealed scores of new cancer genes, including many in processes not previously known to be causal targets in cancer. “