Description
The Cancer Gene Drug Knowledge Database by Rodrigo Dienstmann is a curated
list of cancer genes/variants and drugs that were shown to influence these.
Variants are mapped to the genomic location, unless no RefSeq transcript
matches the reference amino acid of the variant. Gene-level data is mapped to
the location of the RefSeq transcript of the gene.
Display conventions
Each entry in the knowledge database is represented by an individual feature.
Clicks on the features show the disease, the description of the mutation of
expression change and the effect of the gene or mutation. Separated from this
summary are then blocks of rows, where each block characterizes one drug
("Therapeutic context"), it's effect ("Association"), how well established the
drug is and where it has been reported (Pubmed link).
This is very "sparse" track, with only 600 features and a total genome coverage
of 14Mbp. The ten most annotated genes in this track are the typical cancer
genes (number of annotations in parentheses): EGFR (36), ERBB2 (27), MAP2K1
(26), ALK (23), KIT (20), MET (19), KRAS (14), ABL1 (14), FGFR2 (13), PTEN
(12).
The last field "Mapped to genome via" was added by the mapping pipeline and is
not part of the database. It shows, using HGVS, how the variant was mapped to
the genome. The mapping first checks the amino acid on all RefSeq Protein
sequences at the indicated position, maps this to the corresponding RefSeq cDNA
sequence and then uses pslMap to find the correct hg19 position.
Fusion genes are mapped to both gene locations.
Data access
The full database can be downloaded from Synapse.
Version 15 was used for this track.
The mapped locations on hg19 are available as a bigBed file.
Credits
Thanks to Hoifung Poon and Rodrigo Dienstmann for feedback on the data.
References
Dienstmann R, Dong F, Borger D, Dias-Santagata D, Ellisen LW, Le LP, Iafrate AJ.
"Standardized decision support in next generation sequencing reports of somatic cancer variants."
Mol Oncol, 8(5)859, 2014
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US Server