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. 2014 Nov 14;7:62. doi: 10.1186/s12920-014-0062-0

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© Choudhary et al.; licensee BioMed Central Ltd. 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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).