Posts Tagged ‘pcawg’

ncdriver and ENCODE

March 17, 2018

Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017 https://www.nature.com/articles/s41525-017-0040-5.pdf

Recurrent somatic mutations in regulatory regions of human cancer genomes

June 10, 2015

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3332.html

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 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, 2014

i0biods14 => #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

http://lectures.gersteinlab.org/summary/Framework-to-prioritize-Regulatory-variants-Progressive-summarization-of-large-scale-data–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

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”

http://www.ncbi.nlm.nih.gov/pubmed/24390350

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

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, 2014

Nice heatmap tool
http://www.gitools.org/home

Diverse mechanisms of somatic structural variations in human cancer genomes

November 11, 2014

contains a mechanisms pipeline, similar to breakseq

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704973/#!po=42.5926

Cell. Author manuscript; available in PMC May 9, 2014.
Cell. May 9, 2013; 153(4): 919–929.
doi: 10.1016/j.cell.2013.04.010
PMCID: PMC3704973
NIHMSID: NIHMS475485

Diverse mechanisms of somatic structural variations in human cancer genomes Lixing Yang,1 Lovelace J. Luquette,1 Nils Gehlenborg,1,2 Ruibin Xi,1 Psalm S. Haseley,1,3 Chih-Heng Hsieh,4Chengsheng Zhang,4 Xiaojia Ren,3 Alexei Protopopov,5 Lynda Chin,5 Raju Kucherlapati,3,6 Charles Lee,4 and Peter J. Park1,3,7,*

BMC Bioinformatics | Full text | Comparing somatic mutation-callers: beyond Venn diagrams

August 19, 2014

Comparing #somatic mutation-callers: beyond Venn
diagramshttp://www.biomedcentral.com/1471-2105/14/189 Moving from poor overlap of existing methods to metacallers

Meta caller developed based on multiple mutation callers calibrated by validation