Collections of Simultaneously Altered Genes as Biomarkers of Cancer Cell Drug Response
Monday, May 6th, 2013http://cancerres.aacrjournals.org/content/73/6/1699.long
Nice use of CCLE dataset which is an improvement over NCI-60
Posts Tagged ‘i0cmu13’
Some interesting mutation assessor tools featured at Automated Personal Genome Analysis
Monday, May 6th, 2013CRAVAT
Cancer-Related Analysis of VAriants Toolkit
http://www.cravat.us/
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
VAAST
http://www.yandell-lab.org/software/vaast.html
(explicit acknowledgement of VAT)
CHASM and SNVBox:
toolkit for detecting biologically important single nucleotide mutations in cancer.
http://www.ncbi.nlm.nih.gov/pubmed/21685053
http://www.chasmsoftware.org
Vogelstein v. Lander, Round 1
Monday, May 6th, 2013http://ecerami.github.io/vogelstein-v-lander-round1.html
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
http://www.cell.com/abstract/S0092-8674(13)00288-2
QT:”
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. “