linkstream2 microblog

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3687363/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694844/

http://www.ncbi.nlm.nih.gov/pubmed/23656565

A Variant of the HTRA1 Gene Increases Susceptibility to Age-Related Macular Degeneration

Zhenglin Yang1,2,3,*,
Nicola J. Camp4,*,
Hui Sun5,
Zongzhong Tong1,2,
Daniel Gibbs1,2,
D. Joshua Cameron1,2,
Haoyu Chen1,2,
Yu Zhao1,2,
Erik Pearson1,2,
Xi Li1,2,
Jeremy Chien6,
Andrew DeWan7,
Jennifer Harmon1,2,
Paul S. Bernstein1,
Viji Shridhar6,
Norman A. Zabriskie1,
Josephine Hoh7,
Kimberly Howes1,
Kang Zhang1,2,†

http://science.sciencemag.org/content/314/5801/992

QT:{{”
Age-related macular degeneration results in blindness, and one major locus (HTRAX) accounts for approximately one-half of genetic cases. “}}
Should be HTRA1

http://ghr.nlm.nih.gov/condition/age-related-macular-degeneration

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

.@emblEBI in ’16 via @ewanbirney
http://europepmc.org/articles/PMC4702932/ Seq DB growth stable w/ yearly doubling (post ~’08 spike) & EGA now faster than ENA

cite the data growth stats here:
http://europepmc.org/articles/PMC4702932/figure/F2/

Fig 2
– amt prvt data incr as for ncbi + arrays are falling now less than masspec – after a huge incr from ’07 to ’12 , now stab. at12-mo doubling

http://www.nature.com/ncomms/2015/150121/ncomms7033/full/ncomms7033.html

Julie Brind’Amour,
Sheng Liu,
Matthew Hudson,
Carol Chen,
Mohammad M. Karimi
& Matthew C. Lorincz

Nature Communications 6, Article number: 6033 doi:10.1038/ncomms7033

http://www.nature.com/neuro/journal/v19/n1/abs/nn.4181.html

Andrew E Jaffe,
Yuan Gao,
Amy Deep-Soboslay,
Ran Tao,
Thomas M Hyde,
Daniel R Weinberger
& Joel E Kleinman

Nature Neuroscience 19, 40–47 (2016) doi:10.1038/nn.4181

Spatial genomic heterogeneity w/in…prostate #cancer
http://www.nature.com/ng/journal/v47/n7/full/ng.3315.html WGS analysis of many sites suggests divergent tumor evolution

Boutros…, van der Kwast, Bristow (2015) “Spatial genomic
heterogeneity within localized, multi-focal prostate cancer” Nature Genetics 47(7):736-745 (PMID: 26005866)

This work represents the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcomes at the level of whole-genome sequencing (WGS). Five patients, with index tumors of Gleason score 7, were subjected to a WGS protocol with spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity. In their analysis, Boutros et al, discovered recurrent amplification of MYCL, which is associated with TP53 loss. This finding is one of the first clear functional distinctions between MYC family members in prostate cancer and suggests that MYCL amplification may be preferentially localized in the index lesion. Overall, the authors believe their results are useful in the development of prognostic biomarkers that are necessary to achieve personalized prostate cancer medicine. It is important to note that such diagnostic biopsy protocols can miss regions of more aggressive cancers resulting in the patient being under-staged.

http://www.cell.com/cell/pdf/S0092-8674(15)01504-4.pdf