2.2.4.2.3 Array-CGH data

The following four tags are mandatory for describing array-CGH clones:

<X> :

genome position (integer)

<Y> :

ratio or log2-ratio value (real), consistently with the value of the array-level tag <Ratio>: M for ratio or L for log2-ratio.

<Chr> :

chromosome name (1, 2, . . X, Y)

<Name> :

clone name (e.g. RP11-84M16)

The remaining tags are not mandatory, but they are required to activate some of the VAMP functions, related to DNA copy number analysis:

• functions related to DNA copy number analysis:

  <Smt> :

  smoothing value (smoothed value of signal for a Clone)

  <Bkp> :

  breakpoint (a DNA breakpoint has been detected after this clone)

  <Out> :

  outlier (clone with signal significantly different from its neighbors: values are either -1 or 1)

  <Gnl> :

  clone status : amplicon, gain, normal, loss, and double loss (values are -10 for double loss, -1 for loss, 0 for normal, 1 for gain, 2 for amplicon)

  These values may be calculated for example with the GLAD algorithm (Hupé et al., 2004)

The clone size (tag <Size>, value in bp) is required for X-zooming in up to the clone scale (not available in the public data sets provided with this distribution).

Any other tags may be added in the <Obj> description. They will be listed in the Info Panel of the bottom-left frame (figure 3.3), and will be taken into account by the Search Elements function (section 3.2.3).

A sample XML file for CGH array data is given in the Annexes (see 8.4).