Posts Tagged ‘pcawg’

economist story on pcawg

February 5, 2020

Tobacco smoking and somatic mutations in human bronchial epithelium

February 1, 2020

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, 2018

Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017

Recurrent somatic mutations in regulatory regions of human cancer genomes

June 10, 2015

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types : Nature Genetics : Nature Publishing Group

January 8, 2015

Analysis of noncoding somatic mutations &…expression alterations 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

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, 2014

i0biods14 => #biodata14
i0pcawg14 => i0pcawg14+exrna–PAWG-2-5-9-14_prep_for_Boston_mtg–20141108-i0biods14/

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

Discovery and saturation analysis of cancer genes across 21 tumour … – PubMed – NCBI

November 11, 2014


Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”

November 11, 2014

MutSig – 1.0 – Getz et al. Science 2007
MutSigCV – CV – covariates
mutations need to cluster at hotspots & in functional regions

Science 14 September 2007:
Vol. 317 no. 5844 p. 1500
DOI: 10.1126/science.1138764


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, 2014

Nice heatmap tool