Oncomine Solid Tumor DNA Sequencing

The Oncomine™ Solid Tumour DNA kit (OST, Thermo Fisher Scientific), a CE-IVD-marked version of the Ion Ampliseq Colon and Lung Cancer Research Panel v2 (referred to as the Colon and Lung panel), was used to prepare sequencing libraries from cfDNA (1.1-10 ng). Sample preparation was performed using the Ion Chef™ Instrument, and sequencing was conducted on the Ion Personal Genome Machine® (PGM™) System (both Thermo Fisher Scientific, Watham, MA; USA). Each Ion 316™ v2 BC chip was loaded with eight samples. If samples did not meet the criteria of mean depth ≥ 2000, they were disqualified. Variants were called if they were exonic, previously observed, reported to COSMIC, and if the allele frequency ≥ 1% [14 (link)]. Benign SNPs were not reported. All variants were visualized and manually inspected using the Integrative Genomics Viewer [31 (link)]. The data analysis is described in Supplementary File 1.
The performances of each of the 92 amplicons were evaluated by investigating the mean coverage over the 36 patient samples successfully sequenced. Five amplicons generally performed poorly and did not meet the defined mean coverage (CHP2_ERBB4_1, CHP2_PTEN_2, ON_DDR2_3, CHP2_AKT1_1, CHP2_NOTCH1_1). These were excluded from further analyses. The majority of the sequence data has been previously published [9 (link)].