6 protocols
array scanning and feature extraction protocol
Array were scanned with an Agilent Scanner G2505B. Data were extracted with Agilent Feature Extraction Software
nucleic acid hybridization to array protocol
DNA was hybridized with the Agilent Gene Expression Hybridization kit
nucleic acid labeling protocol
DNA was labelled with the Agilent Genomic DNA Labeling Kit
nucleic acid extraction protocol
DNA was extracted with the NucleoSpin Tissue Kit (Macherey Nagel)
sample collection protocol
Biopsies were immediately snap-frozen in liquid nitrogen and kept at –80°C until used
normalization data transformation protocol
Normalization was performed by subtracting the weighted median from the log- ratios for each array. Duplicated probes were merged by the median. Segmentation was performed using the HaarSeg method [50]. Each segment was assigned a probability of being lost (–1), normal (0), gained (+1) or amplified (+2) using the CGHcall method [51]. Minimal common regions (MCRs) were identified using a permutation method taking into account the frequency of calls in each sample and chromosome to calculate statistically significant MCRs. We used the TuMult algorithm [29] to reconstruct the lineage of tumor samples from the same patient, together with the sequence of chromosomal events occurring during tumorigenesis.