linkstream2 microblog

contains proteomics on some of the TCGA samples
http://proteomics.cancer.gov/programs/cptacnetwork

metabric consortium

gene expression & copy number data available and survival data (on request) for the 4 main breast cancer types (basal, her2 , luma, lumb)

similar to TCGA but from the UK

Allows construction of discovery & validation sets to compare segregation of survival with mRNA level

compare segreg. of survival with inferred protein activity v mRNA level

#Singlecell #RNAseq highlights intratumoral heterogeneity http://www.sciencemag.org/content/344/6190/1396.abs Subtype classifiers variably expressed across indiv. cells

Patel AP(1), Tirosh I(2), Trombetta JJ(2), Shalek AK(2), Gillespie SM(3),
Wakimoto H(4), Cahill DP(4), Nahed BV(4), Curry WT(4), Martuza RL(4), Louis
DN(5), Rozenblatt-Rosen O(2), Suvà ML(6), Regev A(7), Bernstein BE(8).

Published Online June 12 2014
Science 20 June 2014:
Vol. 344 no. 6190 pp. 1396-1401
DOI: 10.1126/science.1254257

Comparing #somatic mutation-callers: beyond Venn
diagramshttp://www.biomedcentral.com/1471-2105/14/189 Moving from poor overlap of existing methods to metacallers

Meta caller developed based on multiple mutation callers calibrated by validation

Transduction of nonrepetitive DNA mediated by L1 retrotransposition in #cancer #genomes
http://www.sciencemag.org/content/345/6196/1251343.abs associated w/ hypomethylation

Jose M. C. Tubio1,
Yilong Li1,*,
Young Seok Ju1,*,
Inigo Martincorena1,
Susanna L. Cooke1,
…
Adrienne M. Flanagan30,31,
P. Andrew Futreal1,32,
Sam M. Janes3,
G. Steven Bova12,
Michael R. Stratton1,
Ultan McDermott1,
Peter J. Campbell1,10,33,‡

QT:{{”
Retrotransposons are DNA repeat sequences that are constantly on the move. By poaching certain cellular enzymes, they copy and insert themselves at new sites in the genome. Sometimes they carry along adjacent DNA sequences, a process called 3′ transduction. Tubio et al. found that 3′ transduction is a common event in human tumors. Because this process can scatter genes and regulatory sequences across the genome, it may represent yet another mechanism by which tumor cells acquire new mutations that help them survive and grow.
“}}

Activating Mutations Cluster in… Regions of… #Kinases & Do Not Associate with Conserved or Catalytic Residues
http://onlinelibrary.wiley.com/doi/10.1002/humu.22493/abstract

related to Kin-Driver – a database of driver mutations, which can be used as a gold std in driver predictions

http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator

Useful listing of data sources, viz:

QT:{{”

Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.

“}}

Uses bamboo testing software
https://www.atlassian.com/software/bamboo

Doctor’s Quest to Save People by Injecting Them With Scorpion Venom http://www.wired.com/2014/06/scorpion-venom Ethical issues in #funding “tumor paint” research

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759719/

Annotated somatic variants and interactive variant analysis results are available online atwww.ingenuity.com/acrg2012.

Eighty-eight primary HCC tumors and matched adjacent nontumor liver tissues were analyzed by whole-genome DNA sequencing to identify somatic mutations and HBV integration sites. The vast majority (92%,n = 81) of patients in this cohort were HBV carriers (i.e., HBsAg seropositive) suffering from chronic hepatitis B or cirrhosis. None of the patients were hepatitis C virus (HCV) positive

the data:

http://gigadb.org/dataset/100034

The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652

the data:

http://gigadb.org/dataset/100034

The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652