NDLI: Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology

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Gefitinib induces cytoplasmic translocation of the CDK inhibitor p27 and its binding to a cleaved intermediate of caspase 8 in non-small cell lung cancer cells

Cellular Oncology : Volume 37, Issue 4, August 2014

Cellular Oncology : Volume 37, Issue 3, June 2014

Cellular Oncology : Volume 37, Issue 2, April 2014

Cellular Oncology : Volume 37, Issue 1, February 2014

Cellular Oncology : Volume 36

Cellular Oncology : Volume 35

Cellular Oncology : Volume 34

Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology

Content Provider	Springer Nature Link
Author	Sie, Daoud Snijders, Peter J.F. Meijer, Gerrit A. Doeleman, Marije W. Moorsel, Marinda I. H. Essen, Hendrik F. Eijk, Paul P. Grünberg, Katrien Grieken, Nicole C. T. Thunnissen, Erik Verheul, Henk M. Smit, Egbert F. Ylstra, Bauke Heideman, Daniëlle A. M.
Copyright Year	2014
Abstract	Next generation DNA sequencing (NGS) holds promise for diagnostic applications, yet implementation in routine molecular pathology practice requires performance evaluation on DNA derived from routine formalin-fixed paraffin-embedded (FFPE) tissue specimens. The current study presents a comprehensive analysis of TruSeq Amplicon Cancer Panel-based NGS using a MiSeq Personal sequencer (TSACP-MiSeq-NGS) for somatic mutation profiling.TSACP-MiSeq-NGS (testing 212 hotspot mutation amplicons of 48 genes) and a data analysis pipeline were evaluated in a retrospective learning/test set approach (n = 58/n = 45 FFPE-tumor DNA samples) against ‘gold standard’ high-resolution-melting (HRM)-sequencing for the genes KRAS, EGFR, BRAF and PIK3CA. Next, the performance of the validated test algorithm was assessed in an independent, prospective cohort of FFPE-tumor DNA samples (n = 75).In the learning set, a number of minimum parameter settings was defined to decide whether a FFPE-DNA sample is qualified for TSACP-MiSeq-NGS and for calling mutations. The resulting test algorithm revealed 82 % (37/45) compliance to the quality criteria and 95 % (35/37) concordant assay findings for KRAS, EGFR, BRAF and PIK3CA with HRM-sequencing (kappa = 0.92; 95 % CI = 0.81–1.03) in the test set. Subsequent application of the validated test algorithm to the prospective cohort yielded a success rate of 84 % (63/75), and a high concordance with HRM-sequencing (95 % (60/63); kappa = 0.92; 95 % CI = 0.84–1.01). TSACP-MiSeq-NGS detected 77 mutations in 29 additional genes.TSACP-MiSeq-NGS is suitable for diagnostic gene mutation profiling in oncopathology.
Starting Page	353
Ending Page	361
Page Count	9
File Format	PDF
ISSN	22113428
Journal	Cellular Oncology
Volume Number	37
Issue Number	5
e-ISSN	22113436
Language	English
Publisher	Springer Netherlands
Publisher Date	2014-09-11
Publisher Institution	International Society for Cellular Oncology
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Molecular pathology FFPE Cancer Somatic mutation Validation MPS Cancer Research Biomedicine general Pathology Oncology
Content Type	Text
Resource Type	Article
Subject	Cancer Research Molecular Medicine Oncology

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