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Use of a Next Generation Sequencing (NGS)-based test as a clinical trial assay requires that the test be analytically validated to CLIA/CAP regulations. During the course of analytically validating NGS cancer panels for use as patient enrollment assays, we assessed the repeatability, reproducibility and accuracy of commercially available Cancer Panels (Illumina TruSeq Cancer Panel on MiSeq and Life Technologies AmpliSeq v2 Cancer Panel on Ion Torrent PGM). We measured the repeatability and reproducibility by evaluating all variant calls among technical replicates and found in both platforms that variants with higher variant frequency (VF >30%) were called with much higher repeatability and reproducibility than those with lower VF (between 5 and 25%), a level at which many somatic mutations are found.
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