Posts Tagged ‘pcawg’
economist story on pcawg
February 5, 2020Tobacco smoking and somatic mutations in human bronchial epithelium
February 1, 2020https://www.nature.com/articles/s41586-020-1961-1
Tobacco smoking and somatic mutations in human bronchial epithelium
Kenichi Yoshida, Kate H. C. Gowers, Henry Lee-Six, Deepak P. Chandrasekharan, Tim Coorens, Elizabeth F. Maughan, Kathryn Beal, Andrew Menzies, Fraser R. Millar, Elizabeth Anderson, Sarah E. Clarke, Adam Pennycuick, Ricky M. Thakrar, Colin R. Butler, Nobuyuki Kakiuchi, Tomonori Hirano, Robert E. Hynds, Michael R. Stratton, Iñigo Martincorena, Sam M. Janes & Peter J. Campbell
ncdriver and ENCODE
March 17, 2018Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017 https://www.nature.com/articles/s41525-017-0040-5.pdf
Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types : Nature Genetics : Nature Publishing Group
January 8, 2015Analysis of noncoding somatic mutations &…expression alterations http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html 505 WGS variants w. RNAseq, #TCGA as of Mar ’14
all of what’s in TCGA as of spring ’14
505 TCGA WGS Somatic mutations, Expression Calls, CNA
via
https://www.synapse.org/#!Synapse:syn2882200
Orthogonal to PCAWG-607 (Alexandrov et al + 100 "public" stomach cancers)
My notes from a meeting whirlwind in early Nov. – CSHL Biological Data Science, PCAWG & exRNA (i0biods14,i0pcawg14)
November 11, 2014i0biods14 => #biodata14
i0pcawg14 => i0pcawg14+exrna
https://storify.com/markgerstein/favorite-tweets-from-biological-data-science-i0bio
https://linkstream2.gerstein.info/tag/i0pcawg14
https://linkstream2.gerstein.info/tag/i0biods14
http://lectures.gersteinlab.org/summary/nc-annotation-sect-from–PAWG-2-5-9-14_prep_for_Boston_mtg
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Ori gin — ScienceDirect
November 11, 2014– how to expand beyond 12 tumors?
– reclassification of lung squam. lung adeno. & subdivisions of breast cancer
Hoadley et al. … Stuart
http://www.sciencedirect.com/science/article/pii/S0092867414008769?via=ihub
Discovery and saturation analysis of cancer genes across 21 tumour … – PubMed – NCBI
November 11, 2014“mutsig2CV”
Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”
November 11, 2014MutSig – 1.0 – Getz et al. Science 2007
MutSigCV – CV – covariates
mutations need to cluster at hotspots & in functional regions
http://www.sciencemag.org/content/317/5844/1500.2
Science 14 September 2007:
Vol. 317 no. 5844 p. 1500
DOI: 10.1126/science.1138764
TECHNICAL COMMENTS
Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”
Gad Getz1,*,†,
Holger Höfling2,*,
Jill P. Mesirov1,
Todd R. Golub1,3,4,5,6,
Matthew Meyerson1,3,
Robert Tibshirani2,7,
Eric S. Lander1,6,8
Gitools – A framework for analysis and visualization of genomic data
November 11, 2014Nice heatmap tool
http://www.gitools.org/home
linkstream2 microblog 