Implementation of amplicon parallel sequencing leads to improvement of diagnosis and therapy of lung cancer patients

Journal of Thoracic Oncology

Volumn 10, Issue 7, 2015, Pages 1049-1057

  König, Katharina ^a,b   Peifer, Martin ^b,c   Fassunke, Jana ^a   Ihle, Michaela A ^a   Künstlinger, Helen ^a   Heydt, Carina ^a   Stamm, Katrin ^d   Ueckeroth, Frank ^a   Vollbrecht, Claudia ^a   Bos, Marc ^a   Gardizi, Masyar ^a   Scheffler, Matthias ^a   Nogova, Lucia ^a   Leenders, Frauke ^c   Albus, Kerstin ^a   Meder, Lydia ^a   Becker, Kerstin ^e   Florin, Alexandra ^a   Rommerscheidt Fuss, Ursula ^a   Altmüller, Janine ^c,e   Kloth, Michael ^a   Nürnberg, Peter ^e   Henkel, Thomas ^d   Bikár, Sven Ernö ^f   Sos, Martin L ^a   Geese, William J ^g   Strauss, Lewis ^g   Ko, Yon Dschun ^a,b   Gerigk, Ulrich ^a,c   Odenthal, Margarete ^a   Zander, Thomas ^a   Wolf, Jürgen ^a   Merkelbach Bruse, Sabine ^a   Buettner, Reinhard ^a   Heukamp, Lukas C ^a,c,h   more..

^a UNIVERSITY HOSPITAL OF COLOGNE   (Germany)

^b Labor Dr Quade und Kollegen GmbH   (Germany)

^c UNIVERSITY OF COLOGNE   (Germany)

^d Targos Molecular Pathology GmbH   (Germany)

^e UNIVERSITY OF COLOGNE   (Germany)

^f GENterprise GmbH   (Germany)

^g BRISTOL MYERS SQUIBB   (United States)

^h NEO New Oncology GmbH   (Germany)

Author keywords

Amplicon; Formalin fixed; Lung cancer; Next generation sequencing; Routine diagnostic

Indexed keywords

BIOLOGICAL MARKER; DNA; TUMOR MARKER;

AMPLICON; ARTICLE; CANCER DIAGNOSIS; CANCER PATIENT; CANCER STAGING; CANCER THERAPY; COST EFFECTIVENESS ANALYSIS; DDR2 GENE; DNA SEQUENCE; FEASIBILITY STUDY; GENE MUTATION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HISTOLOGY; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG CANCER; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RECEPTOR GENE; RELIABILITY; SQUAMOUS CELL LUNG CARCINOMA; CARCINOMA, NON-SMALL-CELL LUNG; COHORT ANALYSIS; GENETICS; ISOLATION AND PURIFICATION; LUNG NEOPLASMS; PROCEDURES;

BIOMARKERS, TUMOR; CARCINOMA, NON-SMALL-CELL LUNG; COHORT STUDIES; DNA, NEOPLASM; HUMANS; LUNG NEOPLASMS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84938662240     PISSN: 15560864     EISSN: 15561380     Source Type: Journal    
DOI: 10.1097/JTO.0000000000000570     Document Type: Article

References (49)

1. König K, Meder L, Kröger C, Loss of the keratin cytoskeleton is not sufficient to induce epithelial mesenchymal transition in a novel KRAS driven sporadic lung cancer mouse model. PLoS One 2013 8 e57996
2. Clinical Lung Cancer Genome Project (CLCGP); Network Genomic Medicine (NGM) A genomics-based classification of human lung tumors. Sci Transl Med 2013 5 209ra153
3. Giaccone G., Epidermal growth factor receptor inhibitors in the treatment of non-small-cell lung cancer. J Clin Oncol 2005 23 3235 3242
4. Kwak EL, Bang YJ, Camidge DR, Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med 2010 363 1693 1703
5. Sos ML, Fischer S, Ullrich R, Identifying genotype-dependent efficacy of single and combined PI3K-And MAPK-pathway inhibition in cancer. Proc Natl Acad Sci U S A 2009 106 18351 18356
6. Kim HS, Mitsudomi T, Soo RA, Cho BC., Personalized therapy on the horizon for squamous cell carcinoma of the lung. Lung Cancer 2013 80 249 255
7. Weiss J, Sos ML, Seidel D, Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci Transl Med 2010 2 62ra93
8. Peifer M, Fernández-Cuesta L, Sos ML, Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet 2012 44 1104 1110
9. Sos ML, Dietlein F, Peifer M, A framework for identification of actionable cancer genome dependencies in small cell lung cancer. Proc Natl Acad Sci U S A 2012 109 17034 17039
10. Imielinski M, Berger AH, Hammerman PS, Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012 150 1107 1120
11. Cancer Genome Atlas Research Network Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012 489 519 525
12. Cancer Genome Atlas Research Network Comprehensive molecular profiling of lung adenocarcinoma. Nature 2014 511 543 550
13. Lawrence MS, Stojanov P, Polak P, Mutational heterogeneity in cancer and the search for new cancer-Associated genes. Nature 2013 499 214 218
14. Liao RG, Jung J, Tchaicha J, Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma. Cancer Res 2013 73 5195 5205
15. Doebele RC, Oton AB, Peled N, Camidge DR, Bunn PA Jr, New strategies to overcome limitations of reversible EGFR tyrosine kinase inhibitor therapy in non-small cell lung cancer. Lung Cancer 2010 69 1 12
16. D'Arcangelo M, D'Incecco A, Cappuzzo F., Rare mutations in non-small-cell lung cancer. Future Oncol 2013 9 699 711
17. Oxnard GR, Binder A, Jänne PA., New targetable oncogenes in non-small-cell lung cancer. J Clin Oncol 2013 31 1097 1104
18. Navin N, Krasnitz A, Rodgers L, Inferring tumor progression from genomic heterogeneity. Genome Res 2010 20 68 80
19. Sun JM, Hwang DW, Ahn JS, Ahn MJ, Park K., Prognostic and predictive value of KRAS mutations in advanced non-small cell lung cancer. PLoS One 2013 8 e64816
20. Chang F, Li MM., Clinical application of amplicon-based next-generation sequencing in cancer. Cancer Genet 2013 206 413 419
21. Ney JT, Froehner S, Roesler A, Buettner R, Merkelbach-Bruse S., High-resolution melting analysis as a sensitive prescreening diagnostic tool to detect KRAS, BRAF, PIK3CA, and AKT1 mutations in formalin-fixed, paraffin-embedded tissues. Arch Pathol Lab Med 2012 136 983 992
22. Travis WD, Brambilla E, Noguchi M, International association for the study of lung cancer/American Thoracic Society/European Respiratory Society International Multidisciplinary Classification of Lung Adenocarcinoma. J Thorac Oncol 2011 6 244 285
23. Zimmer S, Kahl P, Buhl TM, Epidermal growth factor receptor mutations in non-small cell lung cancer influence downstream Akt, MAPK and Stat3 signaling. J Cancer Res Clin Oncol 2009 135 723 730
24. Kent WJ., BLAT-The BLAST-like alignment tool. Genome Res 2002 12 656 664
25. Bhagwat M, Young L, Robison RR., Using BLAT to find sequence similarity in closely related genomes. Curr Protoc Bioinformatics 2012 Chapter 10 Unit10.8
26. Robinson JT, Thorvaldsdóttir H, Winckler W, Integrative genomics viewer. Nat Biotechnol 2011 29 24 26
27. Thorvaldsdóttir H, Robinson JT, Mesirov JP., Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013 14 178 192
28. Viglietto G., Activating E17K mutation in the gene encoding the protein kinase AKT1 in a subset of squamous cell carcinoma of the lung. Cell Cycle 2009 8 2869 2870
29. Brose MS, Volpe P, Feldman M, BRAF and RAS mutations in human lung cancer and melanoma. Cancer Res 2002 62 6997 7000
30. Sharma SV, Bell DW, Settleman J, Haber DA., Epidermal growth factor receptor mutations in lung cancer. Nat Rev Cancer 2007 7 169 181
31. Kawano O, Sasaki H, Endo K, PIK3CA mutation status in Japanese lung cancer patients. Lung Cancer 2006 54 209 215
32. Jin G, Kim MJ, Jeon HS, PTEN mutations and relationship to EGFR, ERBB2, KRAS, and TP53 mutations in non-small cell lung cancers. Lung Cancer 2010 69 279 283
33. Kong-Beltran M, Seshagiri S, Zha J, Somatic mutations lead to an oncogenic deletion of met in lung cancer. Cancer Res 2006 66 283 289
34. Kerick M, Isau M, Timmermann B, Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics 2011 4 68
35. Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, Duncavage EJ., Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens. J Mol Diagn 2013 15 623 633
36. Kobayashi S, Boggon TJ, Dayaram T, EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med 2005 352 786 792
37. Mok TS, Wu YL, Thongprasert S, Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. N Engl J Med 2009 361 947 957
38. Pao W, Miller VA, Politi KA, Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med 2005 2 e73
39. Hammerman PS, Sos ML, Ramos AH, Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov 2011 1 78 89
40. Miao L, Wang Y, Zhu S, Identification of novel driver mutations of the discoidin domain receptor 2 (DDR2) gene in squamous cell lung cancer of Chinese patients. BMC Cancer 2014 14 369
41. An SJ, Chen ZH, Su J, Identification of enriched driver gene alterations in subgroups of non-small cell lung cancer patients based on histology and smoking status. PLoS One 2012 7 e40109
42. Travis WD., Classification of lung cancer. Semin Roentgenol 2011 46 178 186
43. Wong SQ, Li J, Tan AY, CANCER 2015 Cohort Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. BMC Med Genomics 2014 7 23
44. Wagle N, Berger MF, Davis MJ, High-Throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2012 2 82 93
45. Loman NJ, Misra RV, Dallman TJ, Performance comparison of benchtop high-Throughput sequencing platforms. Nat Biotechnol 2012 30 434 439
46. Koshimizu E, Miyatake S, Okamoto N, Performance comparison of bench-Top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder. PLoS One 2013 8 e74167
47. Akamatsu H, Koh Y, Kenmotsu H, Multiplexed molecular profiling of lung cancer using pleural effusion. J Thorac Oncol 2014 9 1048 1052
48. Niederst MJ, Engelman JA., Bypass mechanisms of resistance to receptor tyrosine kinase inhibition in lung cancer. Sci Signal 2013 6 re6
49. Govindan R, Ding L, Griffith M, Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012 150 1121 1134