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Evaluation of Ion Torrent's AmpliSeq Cancer Hotspot Panelv2 on FFPE tissues
Author(s) -
Tunkey Christopher D.,
Amos Christopher I.,
Wells Wendy A.,
Tsongalis Gregory J.
Publication year - 2013
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.27.1_supplement.874.22
Subject(s) - ion semiconductor sequencing , kras , concordance , biology , computational biology , colorectal cancer , medicine , genetics , oncology , bioinformatics , cancer , gene , dna sequencing
Objective We routinely perform clinical molecular genetic testing using PCR‐based methods to detect BRAF, KRAS and EGFR variants in human cancers. Clinically actionable findings are reported to oncologists who can then personalize management strategies for any given patient. In this study we evaluated precision and accuracy of the Ion Torrent AmpliSeq Cancer Hotspot Panelv2 (46 genes). Methods Six known mutation positive FFPE tissues were selected (2 BRAF, 2 KRAS, 2 EGFR mutants). Normal kidney and colon FFPE tissues were used as controls. 10ng of starting material from each sample was used to prepare 8 barcoded libraries. The libraries were multiplexed and run through on 3 separate OneTouch reactions and then processed on 3 separate 316 chips over a period of two weeks. Results There was 100% concordance between previous PCR results and the corresponding variants identified in each of the mutant patient samples using the Ion Torrent panel. The BRAF, EGFR and KRAS mutations were consistently identified in each of the triplicate NGS reactions. Conclusions Samples chosen based on a diversity of important clinical results were selected as a test set to evaluate the performance of the AmpliSeq Cancer Panel Hotspotv2. Every sample included in an Ion Torrent run with a known mutation status has been confirmed when run on the PGM. We also demonstrated the ability of this platform to produce consistent variant calls between runs and offer better coverage of clinically important gene regions.