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
Posts Tagged ‘cancer’
BMC Bioinformatics | Full text | Comparing somatic mutation-callers: beyond Venn diagrams
August 19, 2014Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
August 11, 2014Transduction of nonrepetitive DNA mediated by L1 retrotransposition in #cancer #genomes
http://www.sciencemag.org/content/345/6196/1251343.abs associated w/ hypomethylation
Jose M. C. Tubio1,
Yilong Li1,*,
Young Seok Ju1,*,
Inigo Martincorena1,
Susanna L. Cooke1,
…
Adrienne M. Flanagan30,31,
P. Andrew Futreal1,32,
Sam M. Janes3,
G. Steven Bova12,
Michael R. Stratton1,
Ultan McDermott1,
Peter J. Campbell1,10,33,‡
QT:{{”
Retrotransposons are DNA repeat sequences that are constantly on the move. By poaching certain cellular enzymes, they copy and insert themselves at new sites in the genome. Sometimes they carry along adjacent DNA sequences, a process called 3′ transduction. Tubio et al. found that 3′ transduction is a common event in human tumors. Because this process can scatter genes and regulatory sequences across the genome, it may represent yet another mechanism by which tumor cells acquire new mutations that help them survive and grow.
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Activating Mutations Cluster in the “Molecular Brake” Regions of Protein Kinases and Do Not Associate w ith Conserved or Catalytic Residues
August 7, 2014Activating Mutations Cluster in… Regions of… #Kinases & Do Not Associate with Conserved or Catalytic Residues
http://onlinelibrary.wiley.com/doi/10.1002/humu.22493/abstract
related to Kin-Driver – a database of driver mutations, which can be used as a gold std in driver predictions
Oncotator
August 4, 2014http://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
One Doctor’s Quest to Save People by Injecting Them With Scorpion Venom | Magazine | WIRED
July 22, 2014Doctor’s Quest to Save People by Injecting Them With Scorpion Venom http://www.wired.com/2014/06/scorpion-venom Ethical issues in #funding “tumor paint” research
chinese cancer data
July 18, 2014http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759719/
Annotated somatic variants and interactive variant analysis results are available online atwww.ingenuity.com/acrg2012.
Eighty-eight primary HCC tumors and matched adjacent nontumor liver tissues were analyzed by whole-genome DNA sequencing to identify somatic mutations and HBV integration sites. The vast majority (92%,n = 81) of patients in this cohort were HBV carriers (i.e., HBsAg seropositive) suffering from chronic hepatitis B or cirrhosis. None of the patients were hepatitis C virus (HCV) positive
the data:
http://gigadb.org/dataset/100034
The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652
chinese cancer data
July 17, 2014the data:
http://gigadb.org/dataset/100034
The original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/23788652
PAWG-WGL Links for PCAWG upload status
July 4, 2014PanCancer.info has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project
Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia
June 8, 2014Science. 2008 Nov 28;322(5906):1377-80. doi: 10.1126/science.1164266.
Mullighan CG1, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing JR.
Interesting older paper
Genomic analysis of the clonal origins of relapsed ALL
http://www.sciencemag.org/content/322/5906/1377.abs Older paper, describing relapse as arising from minor subclone
cell free DNA circulating for cancer
May 12, 2014NYT recently ran an article as well:
http://www.nytimes.com/2014/04/08/business/cancer-analysis-tools-circumvent-biopsies.html
http://www.nature.com/nm/journal/v20/n4/abs/nm.3511.html
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
http://www.nature.com/nm/journal/vaop/ncurrent/abs/nm.3519.html
http://stm.sciencemag.org/content/6/224/224ra24
http://www.nejm.org/doi/full/10.1056/NEJMoa1213261
http://stm.sciencemag.org/content/4/162/162ra154.full
DIAGNOSTICS: Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing
linkstream2 microblog 