linkstream2 microblog

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3332.html

Hendrickson cites: Structural insights into mis-regulation of PKA in…tumorshttp://www.pnas.org/content/112/5/1374 SNV stops reg. domain binding #ICSG2015

In other case showed recurring DnaJ–PKA fusion didn’t have coding effect but non-coding effect on promotor

vol. 112 no. 5
1374–1379, doi: 10.1073/pnas.1424206112
Structural insights into mis-regulation of protein kinase A in human tumors

Jonah Cheunga,1,
Christopher Gintera,
Michael Cassidya,
Matthew C. Franklina,
Michael J. Rudolpha,
Nicolas Robineb,
Robert B. Darnellb,c,d, and
Wayne A. Hendricksona,e,1

Similarity #network fusion for aggregating data types http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2810.html Combines mRNA, miRNA & gene fusions to classify cancer subtypes
http://compbio.cs.toronto.edu/SNF/SNF

ALK Mutations Confer Differential Oncogenic Activation
http://www.cell.com/cancer-cell/abstract/S1535-6108%2814%2900393-6 MD modeling better assessing #SNV impact than stats, ie sift

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma

Scott C. Bresler
Daniel A. Weiser
Peter J. Huwe
…
Ravi Radhakrishnan
Mark A. Lemmon
Yaël P. Mossé

DOI: http://dx.doi.org/10.1016/j.ccell.2014.09.019

The evolutionary history of…metastatic prostate #cancer http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14347.html Unexpected: polyclonal "seeding" w/ much met-to-met spread

Transmissible Dog #Cancer #Genome Reveals…History of…Cell Lineage http://www.sciencemag.org/content/343/6169/437.abstract 1.9M somatic mutations from origin ~11K yrs ago

AACR 2015
http://www.aacr.org/Meetings/Pages/MeetingDetail.aspx?EventItemID=25#.VT8JXa1Viko http://linkstream2.gerstein.info/tag/i0pcawg15/

ISEV/ERCC Education Day – ISEV – International Society for
Extracellular Vesicles
http://www.isevmeeting.org/isevercc-education-day.html
http://linkstream2.gerstein.info/tag/i0isev/

2015 Bio-IT World Conference & Expo
http://www.bio-itworldexpo.com/
http://linkstream2.gerstein.info/tag/i0bioit15/
http://lectures.gersteinlab.org/summary/Progressive-summarization-large-scale-data-interpret-cancer–20150423-i0bioIT15/

8th International Conference on Ethics in Biology, Engineering & Medicine (ICEBEM 2015)
http://www.downstate.edu/orthopaedics/bioethics/
http://lectures.gersteinlab.org/summary/Soc-n-Tech-Soln-to-Privacy-in-Personal-Genomics–20150424-i0icebem15/

Tweets for all of them
https://storify.com/markgerstein/favorite-tweets-from-bioit-15-aacr-15-and-isev-15-16

The Race to Clone #BRCA1 http://www.sciencemag.org/content/343/6178/1462.abstract
Lessons on #LOF mutations, synthetic lethality, silly gene names & the 2-hit hypothesis

synthetic lethality (PARP inhibitors), gene names (RING fingers)

Make #precisionmedicine work for cancer http://www.nature.com/news/health-make-precision-medicine-work-for-cancer-care-1.17301 @MarkARubin1: >90% of…patients carry a mutation that may be drug-responsive

QT:{{"
“Hugely complicated genomic reports are rarely available in electronic form and are seldom tied to basic information about the patient. Whole-genome sequencing on tumour samples from nearly 14,000 people by the International Cancer Genome Consortium (ICGC), for instance, has revealed nearly 13 million mutations across the genome.

…
Since 2013, working with a team of computational biologists from Weill Cornell and the Centre for Integrative Biology at the University of Trento in Italy, my colleagues and I have conducted a pilot programme to determine the feasibility of tying genomic to clinical data in real time. So far, we have created easy-to-read reports for 250 people with cancer.
…
We have discovered that more than

"more than 90% of our patients carry a mutation that may be responsive to a known drug — although less than 10% of the patients may be eligible for a clinical trial either for logistical reasons or because there is insufficient evidence to warrant trying a non-approved drug.”
"}}

BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]
http://www.cell.com/cell/abstract/S0092-8674(15)00244-5

Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.

Karreth FA1, Reschke M1, Ruocco A1, Ng C1, Chapuy B2, Léopold V1, Sjoberg M3, Keane TM3, Verma A4, Ala U1, Tay Y1, Wu D5, Seitzer N1, Velasco-Herrera Mdel C3, Bothmer A1, Fung J1, Langellotto F6, Rodig SJ7, Elemento O4, Shipp MA2, Adams DJ3, Chiarle R8, Pandolfi PP9.

Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments
demonstrated that pseudogenes contribute….