Posts Tagged ‘pcawg’

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

Oncotator

August 4, 2014

http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator

Useful listing of data sources, viz:

QT:{{”

Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

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
https://www.atlassian.com/software/bamboo