Dear community, Im in search of a gene fusion database with information linking documented gene fusions (PML-RARA, TMPRSS2-ERG etc) with e.g. Ensembl transcripts + exon annotation. Preferrable also providing the sequences of the joining exons to avoid misunderstandings regarding annotations.
I have tried to find something updated in this domain but I must admit Im a little bit surprised of the lack of updated databases, especially since cancer sequencing has really taken off with mutliple published TCGA papers for various cancers.
Any suggestions are greatly appreciated!
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written
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johan.lindberg.ki •
1 answer
COSMIC has a list of "curated fusion" http://cancer.sanger.ac.uk/cosmic/fusion/overview?fid=74303&gid=55499
Look also at ChimerDB: http://biome.ewha.ac.kr:8080/FusionGene/
and
ConjoinG: http://metasystems.riken.jp/conjoing/
These 3 are included in what I consider as the best tool for fusion gene discovery: FusionCatcher http://code.google.com/p/fusioncatcher
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We are still in fairly preliminary stages, but one of the goals of the CIViC (Clinical Interpretation of Variants in Cancer) database is to help address this problem.