Posts Tagged ‘pcawg’

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.

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

Pseudogene expression in TCGA data

July 11, 2014

http://www.nature.com/ncomms/2014/140707/ncomms4963/full/ncomms4963.html

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

Leng Han
Yuan Yuan
Siyuan Zheng
Yang Yang
Jun Li
Mary E. Edgerton
Lixia Diao
Yanxun Xu
Roeland G. W. Verhaak
Han Liang

PAWG-WGL Links for PCAWG upload status

July 4, 2014

PanCancer.info has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project