Table 2.

Gene copy number alterations: technical aspects and interpretation of the Comparative Genomic Hybridization array analyses

Alteration	Proposed technical considerations		Proposed interpretation depending on the type of gene
Type of alteration	Fold change*	Size of amplicon	Oncogene	Tumor suppressor gene
DNA copy number gain	DNA copy number >2 and <6 for diploid tumors	No specific size to be considered	Not considered	Not considered
Focal amplification	DNA copy number ≥ 6 for diploid tumors	≤10 Mb†	Considered only if: known in the literature/ databases to be of theranostic interest Potentially validated by IHC	Not considered
Heterozygous deletion	1 copy for diploid tumors	No specific size to be considered	Not considered	Considered only if associated to an inactivating mutation of the second allele or loss of the tumor suppressor protein validated by IHC
Homozygous deletion	0 copy for diploid tumors	No specific size to be considered	Not considered	Considered
Somatic uniparental isodisomy	2 identical copies for diploid tumors	No specific size to be considered	Not considered	Considered only if associated to an inactivating mutation of the remaining allele or loss of the tumor suppressor protein validated by IHC

* Fold change to be interpreted by taking into account tumor cellularity and ploidy. IHC = immunohistochemistry.

†10Mb locus size include an average of 100 genes (1 gene per 100 Kb).