Archive for the 'SciLit' Category
A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue
February 10, 2016Dietary modification of the microbiome affects risk for cardiovascular disease. – PubMed – NCBI
February 10, 2016Age-related macular degeneration – Genetics Home Reference
February 10, 2016A 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 on a genomic scale : Nature Methods : Nature Publishing Group
February 9, 2016Similarity #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
The European Bioinformatics Institute in 2016: Data growth and integration
February 9, 2016.@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
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations : Nature Communications : Nature Publishing Group
February 9, 2016http://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
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex : Nature Neuroscience : Nature Publishing Group
February 9, 2016http://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
Boutros PC…., van der Kwast T, Bristow RG* (2015) “Spatial genomic heterogeneity within localized, mult i-focal prostate cancer” Nature Genetics 47(7):736-745 (PMID: 26005866)
January 25, 2016Spatial 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.
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription: Cell
January 23, 2016http://www.cell.com/cell/pdf/S0092-8674(15)01504-4.pdf
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution : Nature : Nature Publishing Group
January 23, 2016Dynamics of genomic clones in breast #cancer PDX at #singlecell resolution http://www.nature.com/nature/journal/v518/n7539/full/nature13952.html Extensive trees of samples & some WGS
Peter Eirew,
Adi Steif,
Jaswinder Khattra,
Gavin Ha,
…
Jazmine Brimhall,
Arusha Oloumi,
Tomo Osako
et al.
Nature 518, 422–426 (19 February 2015) doi:10.1038/nature13952
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