COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

By S. Forbes, Nidhi Bindal, S. Bamford, C. Cole, C. Kok, D. Beare, Mingming Jia, Rebecca Shepherd, Kenric Leung, A. Menzies and 4 more. 2010

2,389 citations recorded by the source corpus.

COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136 000 coding mutations in almost 542 000 tumour samples; of the 18 490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. Key amongst these is TP53, now available through a collaboration with the IARC p53 database. In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated. Major website upgrades now make these data much more mineable, with many new selection filters and graphics. A Biomart is now available allowing more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

Subfields: Cancer Research, Molecular Biology

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Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, neutral): “In turn, this would be likely to block dynamic sampling of the V U conformation and explains why the S411L mutant cannot signal upon stimulation with p3dsRNA ligands.”
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma (2013, positive): “Mutations in homologous codons in FGFR2 and FGFR3 are commonly found in other tumor types, particularly bladder, skin and endometrial cancers (see the Catalogue of Somatic Mutations in Cancer (COSMIC) database 34 ).”
Oncotator: cancer variant annotation tool (2015, methodology): “With the emergence of large databases of germline (Sherry et al., 2001; Landrum et al., 2013; NHLBI GO Exome Sequencing Project, 2014) and somatic (Forbes et al., 2010) variation, synthesis of all available clinical and biological information for single variants greatly empowers researchers to…”
Ensembl 2013 (2012, methodology): “A new human somatic structural variation dataset has been added containing data from COSMIC (28).”
A Landscape of Driver Mutations in Melanoma (2012, methodology): “For example, RAC1 P29S mutation has been reported in a head and neck tumor (Stransky et al., 2011) and in a breast tumor (Forbes et al., 2011); furthermore, homologous P29 mutations in other Rho family members were observed in melanoma (Figure 3).”
Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation (2011, background): “Identification of frequently mutated genes The genes found to be mutated by the aforementioned ap proach include 32 genes listed in the Catalogue of Somatic Mutations in Cancer database and previously found to be mutated in other cancer genomes (Table S3; Forbes et al., 2011).”
Panitumumab-FOLFOX4 treatment and RAS mutations in colorectal cancer. (2013, neutral): “Not serious 48 (19) 28 (11) 76 (15) 50 (19) 24 (9) 74 (14)”
Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding (2016, background): “Using the UCSC Genome Browser (42), we found two observations of a serine 411 mutation to leucine (S411L) in large intestine and malignant melanoma tumor samples, annotated in the COSMIC and NCBI ClinVar databases (43,44).”
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants (2011, background): “Cancer-causing variants are selected from breast, colorectal, pancreatic tumor resequencing studies [43– 45] and COSMIC database [46] that are provided with CHASM package.”