Table 1. Variant detection performance using reference cell-line cfDNA. High true positive detection rates were demonstrated for short variants (Single Nucleotide Variants - SNVs, and Indels) at low variant allele expected frequencies across all reference cell line samples (2 Seraseq® ctDNA Mutation Mix samples in duplicates). From both input amounts (10 ng and 50 ng) 100% of short variants (SNVs and Indels) were detected at 1% allele frequency using either of the two KAPA HyperPETE Panels. At 0.5% allele frequency from 10 ng input, the true positive detection rate was 94% and 96.9% using the KAPA HyperPETE Hot Spot Panel and the KAPA HyperPETE Pan Cancer Panel, respectively. At 0.5% allele frequency from 50 ng input, the true positive detection rate was 100% and 98.4% using the KAPA HyperPETE Hot Spot Panel and the KAPA HyperPETE Pan Cancer Panel, respectively.
* Variants were present but not included in the true positive rate calculation as read support was lower than the cutoff used in the analysis pipeline.
Table 2 (a, b, c). Variant detection performance using tissue DNA. High, 100% true positive detection rates were demonstrated for short variants (SNVs and Indels, table 2a) at an expected frequency of ~ 5%, CNVs (Copy number variants, table 2b) at an expected copy number of ~4.5 - 6 and MSI (Microsatellite instability, table 2c). The true positive detection rate was assessed across the subset of the tested samples with known variants (cell-lines, FFPET samples, xenografts), from 10 ng, 50 ng and quality adjusted input amounts. MSI detection demonstrated a true positive rate of 100%.
Table 3. Fusion detection performance using tissue RNA (FFPET). All fusions (100%) were detected in the reference cell line samples at both 10 ng and 50 ng RNA input amounts. Two (2) Seraseq® RNA Fusion FFPE samples and one (1) Horizon Discovery RNA Fusion FFPE sample, each run in duplicate, were used to assess fusion detection performance. The EGFR-SEPT14 variant in Seraseq® Fusion RNA Mix v4 was manually curated as the fusion caller in NAVIFY® Mutation Caller identified an EGFR partner that has a homologous sequence to SEPT14. Comparable variant detection results were achieved when down-sampling to 1M read pairs (data not shown).