Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The ONWARDS insulin icodec trials

A round-up of the ONWARDS phase 3 clinical trials evaluating the novel weekly insulin icodec in people with diabetes.
ADVANCED SEARCH
Log in
Top
Cellular Oncology
Published in: Cellular Oncology 5/2014

01-10-2014 | Original Paper

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

Authors: Daoud Sie, Peter J.F. Snijders, Gerrit A. Meijer, Marije W. Doeleman, Marinda I. H. van Moorsel, Hendrik F. van Essen, Paul P. Eijk, Katrien Grünberg, Nicole C. T. van Grieken, Erik Thunnissen, Henk M. Verheul, Egbert F. Smit, Bauke Ylstra, Daniëlle A. M. Heideman

Published in: Cellular Oncology | Issue 5/2014

Login to get access

Abstract

Purpose

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.

Methods

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).

Results

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.

Conclusion

TSACP-MiSeq-NGS is suitable for diagnostic gene mutation profiling in oncopathology.
Literature
1.
C. Ferte, F. Andre, J.C. Soria, Molecular circuits of solid tumors: prognostic and predictive tools for bedside use. Nat Rev Clin Oncol 7, 367–380 (2010)PubMedCrossRef
2.
S.A. Aparicio, D.G. Huntsman, Does massively parallel DNA resequencing signify the end of histopathology as we know it? J Pathol 220, 307–315 (2010)PubMed
3.
R. Rosell, T.G. Bivona, N. Karachaliou, Genetics and biomarkers in personalisation of lung cancer treatment. Lancet 382, 720–731 (2013)PubMedCrossRef
4.
L.A. Garraway, J. Verweij, K.V. Ballman, Precision oncology: an overview. J Clin Oncol 31, 1803–1805 (2013)PubMedCrossRef
5.
P.B. Chapman, A. Hauschild, C. Robert, J.B. Haanen, P. Ascierto, J. Larkin, R. Dummer, C. Garbe, A. Testori, M. Maio, D. Hogg, P. Lorigan, C. Lebbe, T. Jouary, D. Schadendorf, A. Ribas, S.J. O’Day, J.A. Sosman, J.M. Kirkwood, A.M. Eggermont, B. Dreno, K. Nolop, J. Li, B. Nelson, J. Hou, R.J. Lee, K.T. Flaherty, G.A. McArthur, Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 364, 2507–2516 (2011)PubMedCrossRefPubMedCentral
6.
J.Y. Douillard, K.S. Oliner, S. Siena, J. Tabernero, R. Burkes, M. Barugel, Y. Humblet, G. Bodoky, D. Cunningham, J. Jassem, F. Rivera, I. Kocakova, P. Ruff, M. Blasinska-Morawiec, M. Smakal, J.L. Canon, M. Rother, R. Williams, A. Rong, J. Wiezorek, R. Sidhu, S.D. Patterson, Panitumumab-FOLFOX4 treatment and RAS mutations in colorectal cancer. N Engl J Med 369, 1023–1034 (2013)PubMedCrossRef
7.
N.I. Lindeman, P.T. Cagle, M.B. Beasley, D.A. Chitale, S. Dacic, G. Giaccone, R.B. Jenkins, D.J. Kwiatkowski, J.S. Saldivar, J. Squire, E. Thunnissen, M. Ladanyi, College of American pathologists international association for the study of lung cancer and association for molecular pathology, Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the college of American pathologists, international association for the study of lung cancer, and association for molecular pathology. J Mol Diagn 15, 415–453 (2013)PubMedCrossRef
8.
C.D. de Gonzalez, P.A. Clarke, B. Al-Lazikani, P. Workman, Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance. Clin Pharmacol Ther 93, 252–259 (2013)CrossRef
9.
S.D. Boyd, Diagnostic applications of high-throughput DNA sequencing. Annu Rev Pathol 8, 381–410 (2013)PubMedCrossRef
10.
C.L. Corless, P.T. Spellman, Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discov 2, 23–24 (2012)PubMedCrossRef
11.
S.E. Yost, E.N. Smith, R.B. Schwab, L. Bao, H. Jung, X. Wang, E. Voest, J.P. Pierce, K. Messer, B.A. Parker, O. Harismendy, K.A. Frazer, Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res 40, e107 (2012)PubMedCrossRefPubMedCentral
12.
N.J. Loman, R.V. Misra, T.J. Dallman, C. Constantinidou, S.E. Gharbia, J. Wain, M.J. Pallen, Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30, 434–439 (2012)PubMedCrossRef
13.
M.A. Quail, M. Smith, P. Coupland, T.D. Otto, S.R. Harris, T.R. Connor, A. Bertoni, H.P. Swerdlow, Y. Gu, A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012)PubMedCrossRefPubMedCentral
14.
F. Chang, M.M. Li, Clinical application of amplicon-based next-generation sequencing in cancer. Cancer Genet 206, 413–419 (2013)PubMedCrossRef
15.
H.J. Dubbink, Z.C. Deans, B.B. Tops, F.J. van Kemenade, S. Koljenovic, H.J. van Krieken, W.A. Blokx, W.N. Dinjens, P.J. Groenen, Next generation diagnostic molecular pathology: Critical appraisal of quality assurance in Europe. Mol Oncol (2014). doi:10.​1016/​j.​molonc.​2014.​03.​004 PubMed
16.
17.
FDA-approved Next-Generation sequencing system could expand clinical genomic testing: experts predict MiSeqDx system will make genetic testing more affordable for smaller labs. Am. J. Med. Genet. A 164A, x-xi (2014)
18.
V. Endris, R. Penzel, A. Warth, A. Muckenhuber, P. Schirmacher, A. Stenzinger, W. Weichert, Molecular diagnostic profiling of lung cancer specimens with a semiconductor-based massive parallel sequencing approach: feasibility, costs, and performance compared with conventional sequencing. J Mol Diagn 15, 765–775 (2013)PubMedCrossRef
19.
C.E. Cottrell, H. Al-Kateb, A.J. Bredemeyer, E.J. Duncavage, D.H. Spencer, H.J. Abel, C.M. Lockwood, I.S. Hagemann, S.M. O’Guin, L.C. Burcea, C.S. Sawyer, D.M. Oschwald, J.L. Stratman, D.A. Sher, M.R. Johnson, J.T. Brown, P.F. Cliften, B. George, L.D. McIntosh, S. Shrivastava, T.T. Nguyen, J.E. Payton, M.A. Watson, S.D. Crosby, R.D. Head, R.D. Mitra, R. Nagarajan, S. Kulkarni, K. Seibert, H.W. Virgin, J. Milbrandt, J.D. Pfeifer, Validation of a next-generation sequencing assay for clinical molecular oncology. J Mol Diagn 16, 89–105 (2014)PubMedCrossRef
20.
C.M. McCourt, D.G. McArt, K. Mills, M.A. Catherwood, P. Maxwell, D.J. Waugh, P. Hamilton, J.M. O’Sullivan, M. Salto-Tellez, Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One 8, e69604 (2013)PubMedCrossRefPubMedCentral
21.
H. Do, S.Q. Wong, J. Li, A. Dobrovic, Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin Chem 59, 1376–1383 (2013)PubMedCrossRef
22.
L. Lacroix, A. Boichard, F. Andre, J.C. Soria, Genomes in the clinic: the Gustave Roussy cancer center experience. Curr Opin Genet Dev 24C, 99–106 (2014)CrossRef
23.
S.Q. Wong, J. Li, A.Y. Tan, R. Vedururu, J.M. Pang, H. Do, J. Ellul, K. Doig, A. Bell, G.A. MacArthur, S.B. Fox, D.M. Thomas, A. Fellowes, J.P. Parisot, A. Dobrovic, Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. BMC Med Genomics 7, 23 (2014)PubMedCrossRefPubMedCentral
24.
S. Chevrier, L. Arnould, F. Ghiringhelli, B. Coudert, P. Fumoleau, R. Boidot, Next-generation sequencing analysis of lung and colon carcinomas reveals a variety of genetic alterations. Int J Oncol 45, 1167–1174 (2014)PubMed
25.
D. Kramer, F.B. Thunnissen, M.I. Gallegos-Ruiz, E.F. Smit, P.E. Postmus, C.J. Meijer, P.J. Snijders, D.A. Heideman, A fast, sensitive and accurate high resolution melting (HRM) technology-based assay to screen for common K-ras mutations. Cell Oncol 31, 161–167 (2009)PubMed
26.
D.A. Heideman, F.B. Thunnissen, M. Doeleman, D. Kramer, H.M. Verheul, E.F. Smit, P.E. Postmus, C.J. Meijer, G.A. Meijer, P.J. Snijders, A panel of high resolution melting (HRM) technology-based assays with direct sequencing possibility for effective mutation screening of EGFR and K-ras genes. Cell Oncol 31, 329–333 (2009)PubMed
27.
D.A. Heideman, I. Lurkin, M. Doeleman, E.F. Smit, H.M. Verheul, G.A. Meijer, P.J. Snijders, E. Thunnissen, E.C. Zwarthoff, KRAS and BRAF mutation analysis in routine molecular diagnostics: comparison of three testing methods on formalin-fixed, paraffin-embedded tumor-derived DNA. J Mol Diagn 14, 247–255 (2012)PubMedCrossRef
28.
Dutch Federation of Biomedical Scientific Societies, Human Tissue and Medical Research: Code of conduct for responsible use (2011)
29.
P.Fang, Z.Yan, W.Liu, A.Darwanto, K.Pelak, K.Anoe, C.Spittle, S.Sankar, C.Galderisi, J.Li, Validation of Illumina TruSeq Amplicon Cancer Panel with concordance testing using Ion AmpliSeq Cancer Panel and other methods. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6–10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 73, Abstract nr 3229 (2013)
30.
M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal 17, 10–12 (2011)
31.
32.
33.
34.
P. Cingolani, V.M. Patel, M. Coon, T. Nguyen, S.J. Land, D.M. Ruden, X. Lu, Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Front Genet 3, 35 (2012)PubMedCrossRefPubMedCentral
35.
J.T. Robinson, H. Thorvaldsdottir, W. Winckler, M. Guttman, E.S. Lander, G. Getz, J.P. Mesirov, Integrative genomics viewer. Nat Biotechnol 29, 24–26 (2011)PubMedCrossRefPubMedCentral
36.
G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean, A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010)PubMedCrossRef
37.
P.J. Groenen, W.A. Blokx, C. Diepenbroek, L. Burgers, F. Visinoni, P. Wesseling, J.H. van Krieken, Preparing pathology for personalized medicine: possibilities for improvement of the pre-analytical phase. Histopathology 59, 1–7 (2011)PubMedCrossRef
Metadata
Title
Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology
Authors
Daoud Sie
Peter J.F. Snijders
Gerrit A. Meijer
Marije W. Doeleman
Marinda I. H. van Moorsel
Hendrik F. van Essen
Paul P. Eijk
Katrien Grünberg
Nicole C. T. van Grieken
Erik Thunnissen
Henk M. Verheul
Egbert F. Smit
Bauke Ylstra
Daniëlle A. M. Heideman
Publication date
01-10-2014
Publisher
Springer Netherlands
Published in
Cellular Oncology / Issue 5/2014
Print ISSN: 2211-3428
Electronic ISSN: 2211-3436
DOI
https://doi.org/10.1007/s13402-014-0196-2

Other articles of this Issue 5/2014

Cellular Oncology 5/2014 Go to the issue

Original Paper

A novel saliva-based microRNA biomarker panel to detect head and neck cancers

Original Paper

Apoptosis induction and anti-cancer activity of LeciPlex formulations

Original Paper

Robust meta-analysis shows that glioma transcriptional subtyping complements traditional approaches

Original Paper

BMP9 regulates cross-talk between breast cancer cells and bone marrow-derived mesenchymal stem cells

Original Paper

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

Review

Nestin involvement in tissue injury and cancer - a potential tumor marker?
Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras
Prof. Fabrice Barlesi
Developed by: Springer Medicine
Image Credits