Targeted Next-Generation Sequencing for profiling frequently mutated genes in early-stage colon cancer

Intratumor heterogeneity fosters the evolution of the genome leading to metastatic progress and therapy resistance. Here, we investigate the relative contribution of genomic heterogeneity involving mutations and CNAs as prognostic and predictive determinants for disease recurrence in early-stage colon cancer. We combined targeted next-generation sequencing (NGS) and SNP arrays on a retrospective cohort of untreated stage II colon cancer patients to assess the association of genomic subclonality with time to recurrence (TTR). Enriched libraries were prepared from 50 ng of DNA per tumor sample using the SMARTer ThruPLEX DNA-seq Library Preparation kit (TaKaRa, Japan) and a predesigned gene capture pool of IDT xGen Lockdown probes (IDT, Coralville, Iowa, USA). Paired-end sequencing runs were performed on a MiSeq platform (Illumina, San Diego, CA, USA) following a protocol with 2x130 bp reads.