rnai, immuno, bact, viruses, nano
Posts Tagged ‘cancer’
The five most promising new cancer treatments – health – 16 October 2012 – New Scientist
February 19, 2013Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
December 18, 2012http://genome.cshlp.org/content/early/2012/11/01/gr.141382.112
analysis of 95 tumor genomes
Article: Predicting cancer drivers: are we there yet?
December 1, 2012http://genomemedicine.com/content/4/11/88
associated with transFIC method
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
November 5, 2012This paper introduces a new method for detecting copy number variants in cancer genomes that addresses deficiencies of previous detection methods. The new method, dubbed HHCRF by the authors, adds the use of sequential correlations in selecting classification features for inferring copy numbers and identifying clinically relevant genes. This improvement results in higher accuracy on noisy data, and the identification of more clinically relevant genes, relative to previous methods. These results were obtained by testing HHCRF on both simulated array-CGH microarray data, and on actual breast cancer, uveal melanoma, and bladder tumor datasets.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677736/
Bioinformatics. 2009 May 15;25(10):1307-13. Epub 2008 Dec 3. Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.
Expressed pseudogenes in the transcriptional landscape of human cancers.
November 2, 2012http://www.ncbi.nlm.nih.gov/pubmed/22726445
Cell. 2012 Jun 22;149(7):1622-34.
Cancer N/S ratio
October 20, 2012From XJM:
A few references about nonsynonymous/synonymous ratio in Cancer: Here is a Nature paper finding nonsynonymous/synonymous ratio to be 3:1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712719/
Here is an article reporting the ratio to be about 4:1
http://www.nature.com/ng/journal/v43/n11/full/ng.950.html
Another one:
http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2012.00976.x/full
An online powerpoint reporting 2:1 ratio:
http://www.genome.gov/Pages/Research/DIR/DIRNewsFeatures/Next-Gen101/Samuels_WholeExomeSequencing.pdf
Spectrum of somatic mitochondrial mutations in five cancers
October 19, 2012http://www.pnas.org/content/109/35/14087.abstract
Allusion to whole genome data, but focus is on coding regions & mitochondrial mutations
First WGS of multiple pancreatic cancer patients outlined in study by TGen, Mayo and SHC | Science Codex
October 14, 2012Diagnostics-Drugs Pairings Advance Personalized Medicine | July 23, 2012 Issue – Vol. 90 Issue 30 | Chemical & Engineering News
October 4, 2012http://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.”
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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.
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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.
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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.
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The biopharmaceutical company Endocyte is built on the idea of companion diagnostics, says Ron Ellis, president and chief executive officer.
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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
Dissecting the genomic complexity underlying medulloblastoma : Nature : Nature Publishing Group
September 26, 2012http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs
linkstream2 microblog 