Humancnv610 quad v1

Illumina SNP arrays were used to analyse the DNA samples from 161 tumour samples (74 Illumina HumanCNV610-Quad v1.0, 52 HumanCNV370, 34 HumanOmniExpress-12v1 and 1 HumanCore-12v1). Integragen SA (Evry, France) carried out hybridization, according to the manufacturer’s recommendations. The BeadStudio software (Illumina) was used to normalize raw fluorescent signals and to obtain log R ratio (LRR) and B allele frequency (BAF) values. Asymmetry in BAF signals due to bias between the two dyes used in Illumina assays was corrected using the tQN normalization procedure.39 (link) We used the circular binary segmentation algorithm40 to segment genomic profiles and assign corresponding smoothed values of log R ratio and B allele frequency. The Genome Alteration Print method was used to determine the ploidy of each sample, the level of contamination with normal cells and the allele-specific copy number of each segment41 (link).

DNA samples from 150 PCC/PGL (145 primary tumours and 5 relapses) were analysed with Illumina HumanCNV610-Quad v1.0. Hybridization was carried out by Integragen SA (Evry, France), following the manufacturer’s recommendations. Raw fluorescent signals were launched into BeadStudio software (Illumina) and normalized54 (link) to obtain log R ratio and B allele frequency values. Genomic profiles were divided into homogeneous segments by applying the circular binary segmentation algorithm55 (link) to both log R ratio and B allele frequency values. The ploidy of each sample, the level of contamination with normal cells and the allele-specific copy number of each segment was determined using the Genome Alteration Print method56 (link). The overall genomic instability of each sample was quantified as the fraction of aberrant arm score57 (link). When several samples were available from the same patient, tumour progression trees were reconstructed using the TuMult algorithm24 (link).