Infinium humancode 24 beadchip snp arrays

Illumina Infinium HumanCode-24 BeadChip SNP arrays were used to analyze the DNA samples. 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^{31 (link)}. We used the circular binary segmentation algorithm^{32 (link)} to segment genomic profiles and assign corresponding smoothed values of LRR and BAF. 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 segment^{33 (link)}.

DNA was extracted for 55 PDX samples using the Blood & Cell culture DNA mini kit (Qiagen) following the manufacturer's instructions. Illumina Infinium HumanCode‐24 BeadChip SNP arrays were used to analyze the DNA samples. 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 (Staaf et al, 2008). We used the circular binary segmentation algorithm (Venkatraman & Olshen, 2007) to segment genomic profiles and assign corresponding smoothed values of log R ratio and B allele frequency. The Genome Alteration Print (GAP) 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 segment (Popova et al, 2009). Chromosomal instability index (CIN) was estimated by the mean number of SNP probes with a loss or gained status normalized by chromosomes length. SNP data are available through ArrayExpress (http://www.ebi.ac.uk/arrayexpress) under accession E‐MTAB‐5006.