Figure 2

Technology overview of NGS using the 1052-amplicon targeted sequencing panel. Sample qualification is performed using a real-time PCR assay to determine the percent ‘functional’ DNA copies in FFPE samples using the Quantitative Functional Index (QFI). The library preparation is based on RainDance technologies picodroplet PCR to amplify target sequences with subsequent sequencing on an Illumina platform (GAIIx or HiSeq). The bioinformatics workflow trims adaptors and filters out low-quality reads, then includes genomic alignments, variant calling and result reporting (See Materials and Methods for more details and Additional file 1: Figure S6 for the result visualization).