linkstream2 microblog

http://www.sciencecodex.com/first_wgs_of_multiple_pancreatic_cancer_patients_outlined_in_study_by_tgen_mayo_and_shc-99930

http://cen.acs.org/articles/90/i30/Diagnostics-Drugs-Pairings-Advance-Personalized.html
Good article about how companion diagnostics for making personalized med. are taking off

QT:”
Within two weeks last August, the U.S. Food & Drug Administration approved two new cancer drugs: Roche’s Zelboraf, also called vemurafenib, for metastatic melanoma and Pfizer’s Xalkori, or crizotinib, for non-small-cell lung cancer. What sets those drugs apart from other cancer treatments is the requirement that physicians use a diagnostic test to determine whether each one is right for a patient. In the year since their approval, the two drugs have become poster children for personalized medicine and for what the industry calls “companion diagnostics.”
…
Xalkori and Zelboraf are not the first drugs to use companion diagnostics. That honor goes to Herceptin, Genentech’s drug for HER2 (human epidermal growth factor receptor 2)-positive breast cancer, which was approved in 1998.
…
Roche’s path began in 2002, when scientists discovered that mutations in the BRAF gene, which encodes an enzyme involved in cell signaling, are involved in some cases of metastatic melanoma. By 2005, Plexxikon, Roche’s partner in developing Zelboraf, had designed a drug to inhibit the mutated B-Raf kinase expressed by the aberrant gene. Plexxikon contacted Roche Molecular Systems to see whether the diagnostics company could develop a test for the mutation.
…
On July 6, FDA approved a companion diagnostic from Qiagen to identify appropriate patients for a new indication for the cancer drug cetuximab, which is comarketed by Eli Lilly & Co. and Bristol-Myers Squibb as Erbitux.
…
The biopharmaceutical company Endocyte is built on the idea of companion diagnostics, says Ron Ellis, president and chief executive officer.
”

Related to this:

The genesis of Zelboraf: Targeting mutant B-Raf in melanoma
Matthew J. Davis and Joseph Schlessinger
http://jcb.rupress.org/content/199/1/15

http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs

http://www.cell.com/abstract/S0092-8674%2812%2901061-6?utm_source=ECE001&utm_campaign=&utm_content=&utm_medium=email&bid=OV63V3F:KK4SNSD 23 whole genome tumor/normal pairs

This was covered in NYT a few days ago
http://www.nytimes.com/2012/09/10/health/research/for-a-lung-cancer-drug-treatment-may-be-within-reach.html No direct access to ‘vcf’ files.

Here is the link to the 21 Breast Cancer genomes:
http://www.ncbi.nlm.nih.gov/pubmed/22608084
Found hotspots of mutation….

Genome sequence data have been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/ at the EBI) with accession number EGAD00001000138. SNP6 array data have been deposited with ArrayExpress Archive (EBI, accession number E-MTAB-1087).

Seem to have cancer SNV calls all over the genome.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11273.html

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2359.html

http://well.blogs.nytimes.com/2012/07/23/choosing-watchful-waiting-for-prostate-cancer/

http://www.genome.gov/27549451

http://www.cell.com/retrieve/pii/S009286741200640X?cc=y
Transcribed pgenes perhaps acting as ceRNAs very tissue specific, in a variety of cancers
Most less conservative threshold on calling transcription than in encodeprodpgenes