linkstream2 microblog

http://www.research.va.gov/MVP/

Principal Investigators :

John Concato, M.D., M.S., M.P.H.
Yale

J. Michael Gaziano, M.D., M.P.H.
Harvard

QT:{{”

It’s Launch Time for the Million Veteran Program…

The VA Office of Research and Development is launching its
unprecedented partnership between VA and Veterans who volunteer to help build one of the largest databases of genetic, military exposure and health information. The Million Veteran Program (MVP) promises to reshape the field of genomics—a sophisticated science poised to revolutionize health care for Veterans and others throughout the U.S. and around the world.

“}}

From Schmidt’s talk: The Million Veteran Program is building a DB of genetic, military exposure & health info
http://www.research.va.gov/MVP #1000gb

Science. 2008 Nov 28;322(5906):1377-80. doi: 10.1126/science.1164266.

Mullighan CG1, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing JR.

Interesting older paper

Genomic analysis of the clonal origins of relapsed ALL
http://www.sciencemag.org/content/322/5906/1377.abs Older paper, describing relapse as arising from minor subclone

we can play in meetings, and tell people we are working on cancer research.
http://scienceblog.cancerresearchuk.org/2014/02/04/download-our-revolutionary-mobile-game-to-help-speed-up-cancer-research

Brain-Mapping Milestones: 1st mention of the BrainSpan.org project in
the Times! http://www.nytimes.com/2014/04/22/science/brain-mapping-milestones.html #Neuroscience & #Genomics

http://www.nature.com/ncomms/2014/140409/ncomms4644/full/ncomms4644.html

QT:"We show that many translocation-prone pairs of regions genome-wide, including the cancer translocation partners BCR-ABL and MYC-IGH, display elevated Hi-C contact frequencies in normal human cells."

Overlap of Hi-C & gene fusions

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044196

http://ac.els-cdn.com/S0092867414001457/1-s2.0-S0092867414001457-main.pdf?_tid=82c57e74-c01a-11e3-95b3-00000aacb35e&acdnat=1397070764_5c441e4c90a317cc7642b6873f888eb6

http://www.sciencedirect.com/science/article/pii/S0092867414001457

http://genome.cshlp.org/content/early/2014/03/11/gr.164822.113.abstract

“We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.”

Similar to conclusion positive-section section in FunSeq paper

paper from RECOMB 2014 might be interesting to you, which uses
hitting time in random walk to identify cancer drivers.

http://link.springer.com/chapter/10.1007%2F978-3-319-05269-4_23

HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time

Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas
Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin,
Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp.

Looks like 88 freely available liver cancer genome datasets
http://gigadb.org/dataset/100034