Cgh analytics v4

DNA was hybridized to 8 Â 60 K whole-genome Agilent arrays (G4450A; Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's protocol. The ADM-2 algorithm of the CGH Analytics v4.0.76 software (Agilent Technologies) was used to identify DNA copy number anomalies at the probe level. A low-level copy number gain was defined as a log 2 ratio 40.25 and a copy number loss was defined as a log 2 ratio o0.25. A high-level gain or amplification was defined as a log 2 ratio41.5 and a homozygous deletion was suspected when the ratio was o À 1.
The genomic index was calculated for each profile as follows: genomic index ¼ A 2 /C, where A is the total number of alterations (segmental gains and losses) and C is the number of involved chromosomes.

Genomic DNA was extracted from formalin fixed paraffin embedded tissues using QIAmp®DSP DNA formalin fixed paraffin embedded tissue kit according to the manufacturer's protocol for DNA isolation (Qiagen®) after RNAse digestion. A cutoff of 50% of cellularity in tumor samples was set for the analysis. DNA was hybridized onto 8 × 60 K whole-genome arrays (G4450A; Agilent® Technologies) according to the manufacturer's protocol. Microarray Scanner and images were analyzed by Feature Extraction V10.7.3.1 followed by Agilent® Cytogenomic software 4.0.3.12. The ADM-2 algorithm of the CGH Analytics v4.0.76 software (Agilent® Technologies) was used to identify the DNA copy number abnormalities at the probe level. A low-level copy number gain was defined as a log 2 ratio > 0.25 and a copy number loss was defined as a log 2 ratio < -0.25. A high-level gain or amplification was defined as a log 2 ratio > 1.5 and a homozygous deletion was suspected when the ratio was <-1.5. The range for Derivative Log ratio spread cutoff was fixed to 0.50.
The genomic index was calculated for each profile as follows: Genomic Index = A²/C, where A is the total number of alterations (segmental gains and losses) and C is the number of involved chromosomes [8, 9] .