CNV - Overview

This tab shows an overview of the data for the specified CNV (Copy Number Variant) with links to the COSMIC Genome Browser, Ensembl and ChromoView where all the CNVs on this chromosome can be viewed for the sample.

Definition of Minor Allele and Copy Number in tables:

  • Minor Allele: the number of copies of the least frequent allele eg if ABB, minor allele = A ( 1 copy) and major allele = B ( 2 copies)
  • Copy Number: the sum of the major and minor allele counts eg if ABB, copy number = 3

Definition of Gain and Loss:

We have introduced filtering thresholds to only display CNVs which are high level amplifications, homozygous deletions, or where there has been 'substantial loss' within an otherwise duplicated genome. We also use a higher threshold for amplification if genome duplication has occurred. We use average ploidy > 2.7 to define genome duplication.

  • ICGC: Gain and Loss as defined in the original data.
  • TCGA (reanalysed with ASCAT) and Cell Lines Project Affymetrix SNP6.0 array data analysed with PICNIC
    • Gain:
      • average genome ploidy <= 2.7 AND total copy number >= 5
      • OR average genome ploidy > 2.7 AND total copy number >= 9
    • Loss:
      • average genome ploidy <= 2.7 AND total copy number = 0
      • OR average genome ploidy > 2.7 AND total copy number < ( average genome ploidy - 2.7 )

Data Access

Copy number data for the Cell Line Project can be downloaded from our SFTP site.

This tab lists all the genes which are within or overlap the CNV.

  • Column 1, 'Gene Overview' : Links to summary information for the gene
  • Column 2, 'Gene Analysis' : Links to the gene analysis page showing a detailed view of the mutations and other CNVs at that locus
  • Column 3, 'Gene Position' : Links (click an icon) to CNV ChromoView, the COSMIC Genome Browser and Ensembl
  • Column 4, 'In Cancer Census' : Indicates (y=yes, n=no) if the gene is a known cancer gene, listed in the Census)

This tab lists all the studies associated with this CNV.

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