Affymetrix OncoScan SNP arrays for profiling copy-number alterations (CNAs) and loss-of-heterozygosity (LOH) in colon cancer

Intratumor heterogeneity fosters the evolution of the genome leading to metastatic progress and therapy resistance . Here, we investigate the relative contribution of tumor aneuploidy and genomic heterogeneity involving CNAs and mutational events as prognostic and predictive determinants for disease recurrence in early-stage colon cancer patients. We combined SNP arrays, targeted next-generation sequencing, fluorescence in situ hybridization and inmunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. We assessed the subclonality of copy-number alterations (CNAs) and mutations, CD8+ lymphocyte infiltration levels and their association with time to recurrence (TTR). Two hundred nanograms of tumor DNA were processed for hybridization on arrays following the commercial protocol OncoScan FFPE assay kit (Affymetrix, Santa Clara, CA, USA). After hybridization, microarrays were processed and scanned using Affymetrix scanners. Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (Affymetrix, Santa Clara, California). Quality control statistics as well as integrated OSCHP files were generated by OncoScan Console. To then generate whole-genome copy-number and allele-frequency calls, raw SNP-array fluorescence intensity data were processed using SNP-FASST2 segmentation algorithm from Nexus Biodiscovery software.