COSMIC

In March 2015 the COSMIC (Catalogue of Somatic Mutations in Cancer) team implemented a new licensing strategy (see COSMIC Licensing). Interactive Biosoftware has contracted with the Sanger Institute to provide Alamut users with COSMIC data for free and without any additional subscription.

Data from COSMIC are available in a dedicated track. COSMIC track can be activated into the Options dialog box (menu 'Tools' > 'Options' > 'Display' tab) by ticking the appropriate box.

COSMIC track

Clicking right on a mutation opens a detailed report including sample size and allelic frequencies for each tissue.

The "Ever somatic status confirmed" field of the "Variant Report" is determined according to the mutation somatic status provided by COSMIC.
The status "Not specified" and "Variant of unknown origin" are considered as "N/A".
The status "Reported in another sample as germline" and "Confirmed germline variant" are considered as "No".
The status "Reported in another cancer sample as somatic" and "Confirmed somatic variant" are considered as "Yes".

"Cosmic Report" links to COSMIC website (on GRCh38 COSMIC variants). So some variants only described on GRCh37 may not be found on this link but are available on GRCh37 COSMIC archive website.

Displaying COSMIC mutations for a limited number of tissues

The COSMIC track holds a feature for selecting mutations that are present only in certain tissues for the current gene.

The COSMIC track holds also a feature for defining a permanent set of preferred tissues that may apply for any gene.

References

Forbes et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008 Apr;Chapter 10:Unit 10.11.

Forbes et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50