Sample Summary Page

• Welcome to the sample summary page. This page provides an overview of all the information, stored in COSMIC, associated with the selected sample.
   
  
• This page is divided into twelve main sections:
   
  

Sample Name

• The sample name can be derived from a number of sources. In many cases it originates from the cell line name. Other sources include names assigned by the annotators, or an incremented number assigned during an anonymisation process.
   
  

COSMIC Sample id

• This id is used to identify a sample within the COSMIC database. It is assigned as the samples are curated. There can be multiple ids, if the same sample has been entered into the database multiple times. More information on this can be found on the additional information page, which is available from the COSMIC homepage.
   
  

Sample Features

• The sample features table lists details of a tumour sample not applicable to the entire tumour from which the sample was derived.
   
  

Tumor Classification

• This section is composed of a two column table, showing a detailed classification for the sample. The methods used to determine this classification can be found on the additional information page, which is available from the COSMIC homepage.
   
  

Tumour Features

• Another two column table that describes various features of the tumour from which the sample was obtained.
   
  

Genes Tested With Mutations

• This list shows all the genes, exhibiting mutations, that have been screened in this sample. Clicking on any of the gene names will link to the summary for that gene.
   
  

Mutations

• This section consists of two different views:
  - COSMIC Point Mutations.
  - Rearrangement information if the sample has been involved in a whole genome screen.
   
  
• Mutations (COSMIC Point Mutations): This table lists all the mutations that have been found in the selected sample. It shows the sample id to which the mutation has been linked. The mutation is displayed for both amino acid and cDNA transcripts. Finally, the gene that the mutation was identified in is displayed.
   
  

  


 

• Rearrangement Information: This displays an image (CIRCOS developed by Martin Krzywinski) of the rearrangements found in the sample, together with cosmic point mutations and links to the CGHViewer website for copy number. The menu bar allows access to the different data.
   
  
• Menu Options:
  Overview: Selecting this option will display the circos image of rearrangement data. This option is default for samples that have rearrangement data.
  
  COSMIC Point Mutations will link to the Mutations table (see above).
  
  Copy Number: This will link to the CGHViewer (SNP6.0) data, where copy number plots for each chromosome can be seen in more detail. Note: This data is different to the original solexa data that was used to generate the plots on the circos image.
  
  Structural Variants: This will link to a tabulated list of all the mutation ids and annotation data for this sample. Please see Sample Structural Variants help page for more details.
   
  

Mutation Spectrum: This will link to a Graphical view of mutations in a sample that are described through mutation spectrum graph This image is avaialable for all the samples that has got any mutaions. It shows substitution nucleotide base pair changes on y axis and its frequency on x axis Please see :


 



• Circos image:
  
  • Insertions:
    
     
    
  • Deletions:
    
     
    
  • Hetrozygous Somatic substitutions:
    
     
    
  • Homozygous Somatic substitutions:
    
     
    
  • Synonymous Coding:
    
     
    
  • Non Synonymous Coding:
    
     
    
  • Stop Gained:
    
     
    
  • Splice Site:
    
     
    
  • LOH from SNP 6.0:
    
     
    
  • Intra chromosomal rearrangements:
    
     
    
  • Inter chromosomal Rearrangements:
    
     
    

  

  
  Options:
   
  - Click on a Chromosome:
  

  

  
  - Click on a Copy Number Plot
  

  

  
  - Click anywhere in the centre of the plot:
  

  

  
  

External Data Sources

• This section lists other web sites that contain pertinent information on this sample. Each entry is usually followed by a direct link to the sample information.
   
  

References

• The references section shows all the references that have mentioned the selected sample. It shows the title, authors, journal, year, volume, pages and pubmed id for the paper. Clicking on the pubmed id will link directly to pubmed. Clicking on the 'More Details' link will display a complete overview of the reference, including all the samples and genes that are linked to it.
   
  

Studies

• The studies section lists all studies performed by the Cancer Genome Project that have included this sample.
   
  
• Clicking on the [More Details] link will produce an overview of the study.
   
  

Individual

• The final section of this page provides information about the individual from which the sample was obtained. This is often left as 'unknown' because many of the samples are obtained anonymously.
   
  

Genes Tested Without Mutations

• This tabbed table lists all the genes, exhibiting no mutations, that have been screened in this sample. Clicking on any of the gene names will link to the summary for that gene.
   
  

Any More Questions?

• If you can not find the help you need in these pages please contact cosmic@sanger.ac.uk