Simple searches can also be performed for tissue types (primary locations such as “pancreas,” or subspecializations such as “uterus,” classified in COSMIC as Soft Tissue: Striated Muscle: Uterus), tumor morphology (e.g., “glioma”), sample name (e.g., “HCC38”), or a mutation description (e.g., the common KRAS mutation “c.35G>A” “p.G12D”). It is possible to search COSMIC for gene names and their HUGO synonyms. Most searches in COSMIC are performed simply through the Text Search box. The search results window is displayed, with each option providing a small description. In this example, enter KRAS into the search box to perform a search by gene (searching is not case-sensitive). To perform a simple search, enter the search term of choice in the Text Search box. Also on this page are links to recent announcements from COSMIC, and a running total of the system's current contents.Ģ. Finally, the Genes from Literature Curation describes those genes which have received complete literature curation, as distinct from those which are from CGP sources only. The Quick Search allows the overview of the genotype information for tumors from a chosen tissue site (e.g., “lung”) in one step. Alternatively, the Detailed Search allows navigation to a gene name or precise cancer phenotype, offering lists of options from which to choose. The easiest method is to type a gene name, tissue type, or cancer morphology into the Text Search box. ĬOSMIC can be searched in a number of different ways, requiring different parameters.
The statistics are regenerated every release in this case, the numbers relate to the October 2007 release. The main COSMIC home page detailing current content statistics and top-level search options. Some examples are provided to illustrate how easily and precisely the data can be investigated. The Commentary section discusses the context within which COSMIC exists, some of the issues it resolves, and some that may be encountered. Two alternate protocols briefly describe accessing the data at a more basic level, using exported datasheets or by obtaining a copy of the database itself.
#Cosmic view deep down how to
In this unit, the Basic Protocol describes how to examine the data in COSMIC using the graphical Web system. COSMIC now contains details of most of the genes known to have tumor-promoting point mutations, and curation of fusion events between multiple genes has commenced, since these are also common occurrences in cancer. The system is regularly updated, receiving new data once every two months. Since its initial release in 2004, COSMIC has grown to include data from nearly 4800 genes investigated for somatic mutations in cancer almost 250000 tumor samples have been investigated, resulting in over 50000 mutations.
It has been further extended to include tumor resequencing results from the Cancer Genome Project (CGP) at the Wellcome Trust Sanger Institute.
#Cosmic view deep down full
The system is designed to preserve and improve the usefulness of published somatic mutation data by full curation of the scientific literature for genes known to be involved in cancer, as defined in the Cancer Gene Census ( Futreal et al., 2004). The Catalogue of Somatic Mutations in Cancer (COSMIC) is currently the most comprehensive global resource accessing the world literature on somatic mutations in human cancer.
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