Oncodrive-fm

[…] n the analysis, conversion of EnsEMBL to UCSC chromosome nomenclature was done using the function mapSeqlevels from the package GenomeInfoDb. Potential driver genes were identified using MutSigCV and Oncodrive-fm. MutSigCV was executed using the default mutation rate covariate after fixing its gene names to current nomenclature with maftools, a hg38-compatible coverage file generated with the CovG […]

[…] tered based on sequence coverage, quality scores and germline variants, and annotated against the Ensembl database as described previously []. Putative driver genes were identified using MutSigCV [], Oncodrive-fm [] and OncodriveCLUST [] as described previously [], except that OncodriveCLUST version 0.4.1 was used. For this analysis, the 172 patients in the diagnostic cohort were divided into five […]

[…] on the significance (P-value) of the FM bias (that is, the bias towards the accumulation of mutations with high functional impact). The significantly mutated signalling pathways (based on the IntOGen Oncodrive-fm functional impact bias, FM bias P<0.05) were further selected (). MutsigCV was also used to detect significant genes with point mutations above the background mutation rate. […]

[…] rporated mutation data from multiple tumour types using Oncodrive-fm implemented within the IntOGen-mutations platform (). The most recurrently mutated genes according to MutSig were also detected by Oncodrive-fm as significantly mutated (Q-value<0.05). Oncodrive-fm also identified a number of other important mutated genes (that is, displaying high FM bias) including SETD2, NOTCH2, RBPJ, ARID1A, A […]

[…] l samples. MutSigCV was run using the standard genomic covariates of (i) global gene expression data, (ii) DNA replication time and (iii) HiC statistic of open versus closed chromatin states. We used Oncodrive-fm as implemented within the IntOGen-mutations platform, using data mutation data from multiple tumour studies (http://bg.upf.edu/group/projects/oncodrive-fm.php; http://www.intogen.org/anal […]

[…] L patients. In addition to KRAS and NOTCH1, we identified KMT2D, KIF1B (MIM# 605995) and ME1 (MIM# 154250) as novel putative driver genes using three complementary tools (MutSigCV, Lawrence et al. () Oncodrive-fm, Gonzalez-Perez, Lopez-Bigas () and OncodriveCLUST, Tamborero et al. ()). To find subtype-specific patterns, we analyzed the T-ALL samples and the largest BCP-ALL subtypes (HeH, t(12;21), […]