Sample Overview - Circos

This tab displays a circular plot (circos) which shows each chromosome of the genome as a segment with each datatype shown as a separate track on the image. Circos gives a clear overview of all the structural variants, aberrant gene expression and copy number, and both coding and non-coding point mutations for the selected sample. Circos is a software package developed by Martin Krzywinski (for more details see Krzywinski, M. et al.). This image is available for whole genome screens only due to the quantity and complexity of the data in these samples.

The tracks are as follows (from the outside).

    Coding Variants

  • Deletions
  • Insertions
  • Nonsense mutations
  • Missense mutations
  • Silent mutations
  • Splice mutations
  • Complex mutations
  • Non-Coding Variants

  • Non coding Variants
  • Methylation (Histogram with light pink and light blue background colour) :

  • Hyper Methylation
  • Hypo Methylation
  • Aberrant Gene Expression (Histogram with red and green circles) :

  • Over Expression
  • Under Expression
  • Copy Number Variants (Pink and Blue histogram) :

  • CNV Gain
  • CNV Loss
  • Chromosomal Rearrangements (Green and Purple ribbons in the innermost circular space) :

  • Intra-chromosomal Rearrangements
  • Inter-chromosomal Rearrangements

Sample Overview

This tab shows a general overview of data for the selected sample. A sample is an instance of a portion of a tumour being examined for mutations. 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. A number of samples can be taken from a single tumour and a number of tumours can be obtained from one individual. A sample id is used to identify a sample within the COSMIC database. There can be multiple ids, if the same sample has been entered into the database multiple times from different papers.

This tab also provodes details on the tissue classification for the sample along with the tumour source details.

If the sample name has many id's associated with it, follow the 'Sample Information/Sample name' link at the top of the page to see a list of all the sample ids.

Sequence Coverage Statistics

 
        READ 0                % of bases not covered by any sequence
        READ 21               % of bases covered by a minimum of 21 reads
        READ 41               % of bases covered by a minimum of 41 reads
        Rpair                 Total number of read pairs
        Gbp Seq               Total sequence
        UM Pairs              % of unmapped reads
        Gbp Map               Total of mapped sequence
        Mapped                Percentage of sequence mapped
        Gbp Uniq              Total of mapped unique reads
        Uniq                  Percentage of mapped reads that are unique
       

Sample Overview - References

This table lists all curated publications reporting this sample. More details of the paper can be found by following the ‘COSMIC link’ or ‘Pubmed Link’. This table also provides the ability to search, sort and export the table in csv or tsv format.

  1. Reference Title - The abbreviated title of the article. Mouseover the title to see the full article title.
  2. Author – First author (s) of the publication, to see all authors of the publication please click the COSMIC or Pubmed link.
  3. Year - The publication year of the journal from which the article was taken.
  4. Journal - An abbreviated title of the journal the article was sourced from, followed by volume and page number.
  5. Status – There are currently three statuses:
    • Curated : The reference has been fully curated in to COSMIC.
    • Listed : The reference have been read, but the data has not been entered into COSMIC for one of many reasons.
    • Reviews : These references are reviews of mutation data from other references. They are not entered into COSMIC as the data has generally been entered via the original papers.
  6. COSMIC – Links to the more detailed reference overview page listing details of the selected publication including samples and genes analysed.
  7. Pubmed - Links to Pubmed for more details on this publication.

Sample Overview - Methylation

This tab shows a table of differential methylation for the sample. The table contains the following Columns -

  1. Gene Name - Gene name which links to the gene analysis page
  2. Probe ID - The unique identifier for the probe which targets a specific CpG.
  3. Probe Posn. - The genomic position od the CpG targeted by the probe with links to the COSMIC Cancer Genome Browser and Ensembl.
  4. Type - The type of methylation variant; High (beta-value >0.8), Low (beta-value <0.2)
  5. Level (Beta-Value) - The beta-value for the probe/sample
  6. Normal Average - average beta-value across the normal samples

Sample Overview - Mutations

This table lists all the mutations that have been found in the selected sample. It shows the gene and transcript that the mutation was identified in and the mutation is described using a syntax for both amino acid and cDNA. Finally, the somatic status, zygosity, validation status and the type of mutation are shown. This table also provides the ability to search, sort and export the table in csv or tsv format.

A 'Mutation Filters' panel is shown on the right hand side of the page. This allows filtering of the mutations listed.

Mutation Impact

Derived from FATHMM (Functional Analysis through Hidden Markov Models), an algorithm which predicts the functional, molecular and phenotypic consequences of protein missense variants using hidden Markov models. The FATHMM descriptors Cancer or Damaging are defined as 'Pathogenic' and Passenger or Tolerated are defined as 'Neutral'.

Genes

To view only mutations in known cancer genes (in the Census), select 'Cancer Gene Census'. Selecting 'All' shows all mutations.

Mutation Type

Use this filter to view only mutations (substitutions) of a particular type(s). Multiple types can be selected.

Sample Overview - Fusions

This table lists all the fusions that have been found in the selected sample, showing the gene pairs and fusion syntax. The gene fusion pairs listed in the first column (labelled 'Gene') link to the gene overview page for each gene. The links in the 'CDS mutation' column point to the Fusion Summary page which shows more details for the fusion including the fusion transcript structure. This table also provides the ability to search, sort and export the table in csv or tsv format.

Sample Overview - Mutation Spectrum

The mutations observed in a sample are presented here in a mutation spectrum graph. The image is available for all samples that have mutations. It shows all substitution nucleotide base pair changes on the Y axis and the frequency on X axis.

The plot shows the frequency of the six mutation classes (C:G>A:T, C:G>G:C, C:G>T:A, T:A>A:T, T:A>C:G & T:A>G:C). In other plots these mutation classes are summarised by mapping the mutation to the pyrimidine base, therefore C:G>T:A mutations are shown as C>T. A seventh class has been included to show the frequency of insertion and deletion mutations (indels).

Each blue bar links to the Mutation Details page, which lists all of the mutations of the selected type detected in the sample.

UV light causes dipyrimidine bases to covalently bond together, during DNA replication this error is seen as an abasic site and can lead to the insertion of adenosine in place of guanine opposite the damaged base. Thymine bases in these covalently bonded photoproducts are less frequently mutated. This therefore leads to C>T transition mutations, therefore UV light results in an elevated frequency of this mutation class.

Ref – Brash, DE. (1997). Trends in Genetics. 13:410-414

Sample Overview - Sequence Context

This Sequence Context image in available only in the Cell Lines Project website.

Summary plot of flanking sequence for all mutations referenced to the pyrimidine base (T>X, T>G, T>C, T>A: C>X, C>T, C>G, C>A). The plot shows the mutated base at position 0 together with the frequency for the 10 bases 5’ and 3’.

Sample Overview - Heatmap

This heatmap image in available only in the Cell Lines Project website.

Genomic heatmap constructed from counts of each mutation-type at each mutation context corrected for the frequency of each trinucleotide in the coding region of the reference genome. Log-transformed values of these ratios have been plotted. The 5′ base to each mutated base is shown on the vertical axis and 3′ base on the horizontal axis.

Sample Overview - Genes Without Mutation

This table lists all the genes, exhibiting no mutations, that have been screened in this sample (non-genome screens only). Clicking on any of the gene names will link to the Gene Overview page for that gene.

Sample Overview - Breakpoints

This table describes the one or more breakpoints which make up a structural variant (whole genome screen samples only).

A breakpoint is defined as a region or point where the sample sequence has altered from the reference sequence. One variant event can consist of one or multiple breakpoints. Each row, gives the start and stop position of the variant along with the Mutation Description linking to the COSMIC Genome Browser and Ensembl.

This table also provides the ability to search, sort and export the table in csv and tsv format.

Sample Overview - Non-Coding Mutations

This table shows the non-coding variants found in this sample (genome screens only), available in exportable csv and tsv formats.The last column in the table shows the FATHMM-MKL score, with values ≥ 0.7 indicating functional significance. Please see http://fathmm.biocompute.org.uk/downloads.html for more information about the FATHMM-MKL algorithm, and the 'Mutation Impact' section of Cancer Genome Annotation for help interpreting the scores.

Sample Overview - CNV & Expression

This tab shows a table of Gene Expression and Copy Number Variation data for the sample with links to CNV, Study, and (icons) to the ChromoView page (to view CNVs), the COSMIC Genome Browser and Ensembl. The table contains the following Columns -

  1. Gene - Gene name which links to the gene analysis page
  2. Expression - classified as 'Under', 'Over', 'Normal' or '-' where there is no data.
  3. Expr Level - The Z-score value for gene expression. Normal range -2 to 2. Over > 2. Under < -2.
  4. CN Type - Type of CNV, either Loss or Gain.
  5. Minor Allele - Minor allele count for the specified CNV
  6. Copy Number - Total Copy Number for the specified CNV (major allele + minor allele counts)
  7. CN Segment Posn. - Genomic position of the CNV and icon links to the ChromoView page (to view CNVs across the whole chromosome), the COSMIC Genome Browser and Ensembl.
  8. Average Ploidy - average ploidy across the whole genome of the sample
  9. Study - Unique Study identifier which links to the study page.
  10. CNV - Unique CNV Identifier which links to CNV overview page.

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