Signalmap v 1

For each sample having sufficient quality and quantity, 700 to 1000 ng of tumor DNA and reference DNA were labeled, purified, and co-hybridized in equal quantity either to the NimbleGen Arrays (Roche, Basel, Switzerland) or Agilent Microarrays (Agilent Technologies, Santa Clara, CA, USA), during 12 to 24 h. Male and female human reference DNA were extracted from human blood for those analyzed on a NimbleGen support, whereas references were provided in the Agilent Kit for those analyzed on an Agilent support. Arrays were washed and scanned according to the technique-specific guidelines.
For samples processed with the Nimblegen technology, images were acquired on a GenePix 4000B scanner with the GenePix V.6.6 software (Molecular Devices, San Jose, CA, USA), and data was extracted using the NimbleScan V.2.5 software. Files produced by the NimbleScan software were then analyzed on SignalMap V.1.9 (Roche, Basel, Switzerland).
For samples processed with the Agilent technology, images were acquired on a SureScan Microarray Scanner using CytoScan software V.2.7, and then analyzed on CytoGenomics software V.3.0.2.11 (Thermo Fisher Scientific, Waltham, MA, USA).
For each sample, the quality of the analysis was evaluated subjectively based on the cytogenetic profile dynamism, the sex mismatch, and the degree of dispersion.