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Hyperploidy is associated with increased gene expression and with activating mutations in driver oncogenes.
Only two mutations in driver genes significantly changed allele frequencies, both in the same individual (SU35420).
This is consistent with our scoring system that mutations in driver genes will tend to have strong impact on protein functions.
The detection of activating mutations in driver genes encoding protein kinases has led to the development of small-molecule inhibitor drugs targeting those kinases.
Note that here we implicitly assume that all non-synonymous mutations in driver genes are potential driver mutations if they are selected by a method.
Whereas if the selection coefficient was increased, more mutations in driver loci would escape being removed at low frequencies by genetic drift, such that more fixation events would be seen.
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The first one is "high coverage," which means the majority of samples have at least one mutation in driver pathway; the second one is "high exclusivity," which means that lots of samples have no more than one mutation in one driver pathway.
Both truncating – stop gained or lost, frame-shift, splice donor or splice acceptor – and missense mutations in LoF driver TFs were considered LoF driver mutations, while only missense mutations in Act driver TFs were considered Act driver mutations.
The transformed FIS systematically outperforms the original FIS on nine proxy validation sets, each composed of a positive set of mutations enriched in driver nsSNVs and a negative set of mutations enriched in passenger nsSNVs (or polymorphisms).
I retrieved all mutations detected in driver TFs across almost 7,000 tumors sequenced in 48 cohorts representing the 28 aforementioned tumor types from the Integrative Oncogenomics (IntOGen) platform [ 15] (www.intogen.org).org
Fifth, we did not take into account correlations among mutations in identifying driver genes.
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