Targeted DNA Sequencing of Circulating Tumor Cell-Enriched Samples from Stage II/III NSCLC Patients

Targeted DNA sequencing of circulating tumor cell (CTC) enriched blood samples from stage II/III non-small cell lung cancer (NSCLC) patients prior to undergoing chemoradiation and immunotherapy treatment. The CTC samples were enriched using a label-free microfluidic platform, the Labyrinth. Following enrichment, the samples were fixed in 80% methanol or ethanol and stored at -80C or -20C, respectively. DNA was extracted from the samples using Qiagen's DNA/RNA AllPrep kit and submitted to the Univeristy of Michigan's Advanced Genomics Core (AGC) to perform targeted DNA sequencing using Illumina's TruSight Oncology (TSO) 500 assay. The TSO 500 assay consists of a 523 gene panel of specific oncogenes. Following sequecing, the pair-end fastq files were locally processed through the TSO 500 analysis pipeline (version: ruo-2.2.0.12) to produce the CombinedVariantOutput files per patient. Each file contains a list of all variants detected within the patient. For each variant, the following information is provided: gene name, chromosome, genomic position, reference call, alternative call, allele frequency, depth, p-dot notation, c-dot notation, consequence of variant, and the number of affected exons.