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  1. Select or enter data for the copy number query fields shown in the following figure and described below.
    Fields for identifying copy number search criteria.
    • Segment Mean <= – Enter the value equal to or less than the higher limit of change.
    • Segment Mean >= – Enter the value equal to or greater than the lower limit of change.
    • Genome Interval > Gene Name – See #Gene Name Search
    • Genome Interval > Chromosome Number – In the text box that opens, enter the chromosome number you want the query to search against.
    • Genome Interval > Chromosome Coordinates – In the From and To text boxes that open, enter the range on the chromosome you want to search. This defines the chromosomal boundaries of the region with the suspected copy number variations.
      Fields for identifying copy number chromosome coordinates values
      The Bioconductor DNAcopy algorithm (see Copy Number Data) identifies the location of the amplification or deletion and then reports it as the base pair at the start and stop of the segment. Each segment is then catalogued with chromosome number, start coordinate, stop coordinate, genes in the segment, and the segment mean value.
    • To search for Gene Symbols, see Choosing Genes.
  2. Continue with step 6 in Searching a caIntegrator Study.

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  1. Select or enter data for the copy number query fields shown in the following figure and described below.
    Fields for identifying CGHCalls search options
    • Copy Number values: Select one or more of the Calls values. Values are -1 (loss), 0 (normal) or 1, (gain). If four levels were used for calling, a value of 2 represents an amplification.
    • Genome Interval > Gene Name – See #Gene Names Search.
    • Genome Interval > Chromosome Number – In the text box that opens, enter the chromosome number you want the query to search against.
    • Genome Interval > Chromosome Coordinates – In the From and To text boxes that open, enter the range on the chromosome you want to search. This defines the chromosomal boundaries of the region with the suspected copy number variations.
      For more information about CGHCalls, see CGHcalls.
    • To search for Gene Symbols, see Choosing Genes.
  2. Continue with step 6 in Searching a caIntegrator Study.

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