Affymetric SNP Array Data of 45 liver metastasis samples from colorectal cancer patients

To investigate genomic plasticity over time associated with response to standard chemotherapy, we collected longitudinal liver metastasis (LM) samples from 155 patients and characterized the copy number aberration (CNA) landscape and its effect on the transcriptome. CNA profiles of lesions exhibiting different treatment response were compared and focal genomic divergences reported. By investigating genomic-phenotype associations of the largest reported LM cohort to date, we identified novel molecular features associated with drug response supporting the relevance of collecting clinical metastatic samples. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen liver metastasis samples at baseline (pre-treatment) and at the time of clinical progression (post-treatment) In this study, 45 liver metastasis samples (35 pre-treatment and 10 post treatment) were analyzed using Affimetrix CytoScan HD platform and 149 liver metastasis samples (97 pre-treatment and 52 post-treatment) were analyzed by whole exome sequencing (WES) for copy number abberation assessment. 45 samples were analyzed using both platforms. We evaluated and compared the performance of WES and the CytoScan HD platforms for CNA inference