Fig 1.
NGS workflow used for different Ion Torrent platforms in a clinical laboratory.
Ion PGM, Ion Proton and Ion S5XL sequencing workflow using cancer hot spot panel v2 (CHPv2), oncomine panel (OCP) and comprehensive cancer panel (CCP) for library prep. Ion one touch 2 and Ion one touch ES was used for PGM and Proton for template preparation and enrichment of ion spheres. Enriched ion spheres were sequenced on Ion PGM and Ion Proton respectively. For Ion S5XL Ion chef was used which automates the template preparation, enrichment and chip loading. Preloaded reagent cartridge and on board Torrent suite software reduces the initialization, sequencing and data analysis time.
Fig 2.
Variant call comparison between Ion Proton and Ion S5XL.
(A) Venn diagram showed variant call comparison between Ion Proton and Ion S5Xl Ion S5XL showed 97% concordance for mutation detection with Ion Proton. Eight variant calls were missed by Ion S5XL due to low coverage in the variant region of the CCP panel compared to Ion Proton (B) Correlation between Variant allelic Fraction (VAF) of mutations detected on protons and Ion S5 XL (R2 = 0.70; p<0.0001) and each point on the graph represents a single variant analyzed by the Ion Proton and S5XL platforms.
Table 1.
Concordance of Ion S5XL with Ion PGM and Ion Proton for variants detected using different Ampliseq panels (CCP; OCP and CHPv2).
Fig 3.
Limit of detection study performed on Ion S5 XL platform using S530 chip.
Sensitivity study using DLD1 cell line serially diluted in wild type HL60 cell line DNA at 50, 25, 12.5, 6.25, 3.12, 1.50, and 0.75%. DLD1 cell line harbors heterozygous mutations in six different genes: PIK3CA, KRAS, KIT, TP53, FGFR1 and SMO.
Fig 4.
Inter-reproducibility studies performed on Ion S5 XL platform using S530 chip.
Reproducibility studies using one normal tumor paired CCP libraries and one OCP libraries across two different sequencing runs on S5XL platform.