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Accurately discovering specific EGFR mutations, especially uncovering the mutation information from a small amount of mutated cells, which could be covered by the noises from other un-mutated cells, is currently becoming an urgent clinical requirement, since several key mutations have proven playing critical roles influencing drug responses of targeted cancer therapies.
The De novo Driver Exclusivity (Dendrix) algorithm [ 113] is a tool for discovery of mutated driver pathways in cancer using only mutation information from the cancer samples.
There are nine other kinases with mutation information from kinase binding assay data, i.e., BRAF, FGFR3, FLT3, KIT, MET, PIK3CA, RET, MET, and LRRK2.
Therefore, it makes it possible for us to standardize all mutation information from different articles.
We investigated this relationship using mutation information from Swiss-Prot dataset.
This is a high-confidence list of manually curated cancer genes with orthogonal layers of evidence, including but not limited to mutation information from COSMIC [ 46].
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COSMICMart allows users to query genes, tissues and mutations information from the samples available in the COSMIC database and to federate these with other datasets such as Ensembl.
The portal integrates mutation information for the analyzed cell lines from CCLE [ 4] and Klijn et al. [ 5].
First, from the literature, we obtained mutation information for 816 LoF and 474 GoF mutations.
We used version v62 (from 29th of November 2012) available from COSMIC's FTP site (ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/), including mutation information curated from 9,950 unique PubMed articles, as well as Cancer Genome Project (CGP) (http://www.sanger.ac.uk/genetics/CGP) studies and international system screens (e.g. International Cancer Genome Consortium (ICGC) (http://dcc.icgc.org/web)).
(i) The RGS protein mutation information is extracted from literature surveys.
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