CNV ChromoView - CNV Plot

This tab shows a plot of the copy number variants (CNVs) across the specified chromosome of the sample. Please note that this is not a full coverage copy number plot - only variants are shown. Depending on where the CNV ChromoView page was linked from, a green bar at the top of the plot indicates the genomic location of any region of interest (eg a gene, genomic region or a specific CNV)

If copy number and minor allele values are known, these are plotted (see key below). The values are absolute copy numbers which have been predicted by the PICNIC or ASCAT algorithms.

  • Minor Allele - number of copies of the least frequent allele
    Copy Number - sum of the minor and major allele counts
    CNV, gene or genomic region of interest (depending on where the page was linked from).

Where copy number data has been imported from the ICGC this may consist of only the variant type (Gain or Loss) with no copy number or minor allele values. In such cases the variants are shown in a 'gain and loss' plot (see key below) which shows the location of each variant on the genome

  • Copy Number Gain
    Copy Number Loss
    CNV, gene or genomic region of interest (depending on where the page was linked from).

CNV ChromoView - CNV Table

This tab lists all the CNVs across the chromosome of the sample.

  • Column 1, 'Chr' : The Chromosome of the CNV
  • Column 2, 'Start' : The genomic start position of the CNV
  • Column 3, 'Stop' : The genomic stop position of the CNV
  • Column 4, 'Minor Allele' : The number of copies of the least frequent allele
  • Column 5, 'Copy Number' : The sum of the minor and major allele counts
  • Column 6, 'Type' : The type of variant (Gain or Loss)
  • Column 7, 'CNV' : Links to the CNV Overview page showing summary information for the CNV
  • Column 8, 'Gene|Region|Cnv of Interest' : Indicates ('Yes/No) if the CNV overlaps the region of interest

CNV ChromoView - Gene Expression

This tab lists genes with aberrant gene expression across the chromosome of the sample.

  • Column 1, 'Gene' : Gene name
  • Column 2, 'Position' : The genomic coordinates of the gene (chr:start..end)
  • Column 3, 'Expression' : Either 'Over' or 'Under' gene expression
  • Column 8, 'Expr Level' : The Z-score value for gene expression. Normal range -2 to 2. Over > 2. Under < -2.

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