Posts Tagged ‘pcawg’
Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types : Nature Genetics : Nature Publishing GroupJanuary 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
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
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Ori gin — ScienceDirectNovember 11, 2014
– how to expand beyond 12 tumors?
– reclassification of lung squam. lung adeno. & subdivisions of breast cancer
Hoadley et al. … Stuart
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
Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”
Jill P. Mesirov1,
Todd R. Golub1,3,4,5,6,
Eric S. Lander1,6,8
Nice heatmap tool
contains a mechanisms pipeline, similar to breakseq
Cell. Author manuscript; available in PMC May 9, 2014.
Cell. May 9, 2013; 153(4): 919–929.
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,*
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
Useful listing of data sources, viz:
Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.
Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.
Uses bamboo testing software