Stephen Finn University of Dublin Trinity College and St. James s Hospital, Dublin, Ireland
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1 Evaluation of NGS and other methods for ALK translocation detection in NSCLC patients in Europe: results of the European Thoracic Oncology Platform (ETOP) Lungscape Project Stephen Finn University of Dublin Trinity College and St. James s Hospital, Dublin, Ireland
2 Disclosures Commercial research support: Janssen and Astellas Honoraria: Merck, Pfizer, Astra Zeneca, Roche, Boehringer Ingelheim, BMS
3 Current ALK testing ALK translocation: 2 7% inversion or translocation of chromosome 2p resulting in transforming fusion gene targetable by TKI Reported prevalence varies across studies as a consequence of patient-selection criteria and detection methodology FISH and, now, IHC are widely used However, RT-PCR is possible, and NGS is the emerging major testing platform because of the possibility to detect multiple biomarkers using both DNA and RNA (EGFR, KRAS, BRAF, HER2 mutation, ALK, ROS1, RET, NTRK1 3) Question of LDTs vs CE-IVD also in the mix for laboratories to consider ALK, anaplastic lymphoma kinase; BRAF, B-Raf proto-oncogene; CE-IVD, Conformité Européene in vitro diagnostics; DNA, deoxyribonucleic acid; EGFR, epidermal growth factor receptor; FISH, fluorescent in-situ hybridization; HER2, human epidermal growth factor receptor 2; IHC, immunohistochemistry; KRAS, Kirsten rat sarcoma viral oncogene homologue; LDTs, laboratory developed tests; NGS, next generation sequencing; NTRK1 3, neurotrophic receptor tyrosine kinase 1 3; RET, rearranged during transfection; RNA, ribonucleic acid; ROS1, reactive oxygen species 1; RT-PCR, reverse transcription-polymerase chain reaction; TKI, tyrosine kinase inhibitor. Soda M et al. Nature. 2007;448: Wojas-Krawczyk K, et al. Contemp Oncol. 2013;17:
4 Lungscape Translational research program Designed, implemented, and conducted by ETOP Involving leading hospitals across Europe and beyond Multiple decentralized biobanks Virtual central ibiobank EQA Follow-up EQA, external quality assessment; ETOP, European Thoracic Oncology Platform. Available from: view=article&id=115523&itemid=197. Accessed August 2017.
5 Prevalence and clinical outcomes for patients with ALK-positive resected stage 1 to 3 adenocarcinoma: results from the European Thoracic Oncology Platform Lungscape Project Retrospective surgical cohort 16 European centers 1,281 patients screened (adenocarcinoma only) 6.2% positive by IHC 2.2% (at least) positive by FISH IHC is proposed as a screening tool for further FISH assessment H-score cut-off of 120 for 5A4 clone Blackhall FH, et al. J Clin Oncol. 2014;32:
6 Current study A comparison of multiple technologies for assessment of ALK status in the cohort published in 2014 A unique opportunity to assess in a large European cohort Refine and optimize diagnostic strategies
7 Methods 96 cases selected from ETOP Lungscape ibiobank 1,772 screened by IHC stage 1 3 based on any degree of IHC staining 5A4 (Novocastra, UK) decentralized, EQA-controlled FISH on all cases with positive staining decentralized, EQA-controlled RT-PCR for most frequent fusions centralized Targeted NGS centralized Oncomine Solid Tumour Fusion Transcript kit* screens for 70 ALK, RET, and ROS1-specific fusion transcripts novel ALK translocations using 3 5 ALK gene expression assay Macro-dissection for enrichment The same RNA used for both NGS and RT-PCR NSCLC, non-small-cell lung cancer. *IVD.For In vitro Diagnostc Use
8 3 5 assay for targeted NGS The assay measures the difference in expression between the 5 assay and the 3 assay of the ALK gene Samples that do not contain a fusion are expected to have similar expression of the 5 assay compared with the 3 assay of the driver gene Samples that contain a fusion are often expected to have elevated expression of the 3 assay compared with the 5 assay The 3 5 assay is therefore included for 2 alternate purposes to confirm a specific fusion to screen for a fusion other than those specifically sequenced No evidence Uncertain Strong evidence ALK
9 Results 1 IHC screen primary selection criterion (n = 96) IHC H-score 120 positive (n = 23) FISH 88 cases: 24 positive, 64 negative Tumour cellularity median 70% (range 10 90) RNA yield: median 47 ng/μl (range 9 300) RT-PCR successful in 77 of 96 cases (80.2%) B-actin-amplified ALK rearrangement detected in 16 cases RT-PCR Negative: 61 (79.2%) Positive: 16 (20.8%) Not available: 19 (19.8% of 96) Negative: 64 (72.7%) Positive: 24 (27.3%) Not available: 8 (8.3% of 96) 96 ETOP Lungscape cases Negative: 67 (74.4%) Positive: 23 (25.6%) 1+: 58 (60.4%) 2+: 16 (16.7%) 3+: 22 (22.9%) NGS Not available: 6 (6.3% of 96) FISH IHC level H-score < 120: 69 (75.0%) 120: 23 (25.0%) Not available: 4 (4.2% of 96) 70 cases with available results for all 4 methods
10 Results 2 Targeted NGS 95 cases analysed and passed initial QC Specific ALK rearrangement detected in 15 cases Imbalance assay performed on remaining cases 6 cases: strong evidence of imbalance 11 cases: uncertain (considered failed assays) 63 cases: no evidence finally 77 cases accepted 21 positive and 56 negative 3 5 Assay Specific ALK assay Positive For imbalance No evidence Uncertain Strong evidence QC, quality control.
11 Box-plots of 3 5 assay scores by ALK status assay scores Negative Positive Note 1: ALK status is defined by the concordant result of at least 2 of the 3 other methods: RT-PCR, FISH, IHC H-scoring. Note 2: 4 extreme outliers (with values of 1.96, 0.82, 0.71, 0.21) are excluded from the display of negative group.
12 Concordance of methodologies H-score not tested NGS-positive NGS-positive (strong imb. only) NGS-negative NGS failed (uncertain imb.) NGS failed NGS not tested for imb. FISH-positive FISH-negative FISH not tested RT-PCR-positive RT-PCR-negative RT-PCR not tested 200 H-score FISH RT-PCR IHC
13 Variants detected E13A20 4 E20A20 1 E6aA20 3 E6bA20 1 E6(a/b)A20 E6(a/b/b)A Strong imbalance
14 Summary: defining a gold standard Joint concordance of all 4 methods evaluable in 60 cases 55 cases showed full agreement Gold standard to determine sensitivity and specificity gold standard positivity was defined as positive using both IHC-positive threshold (H-score > 120) and FISH positivity evaluable in 82 cases Gold standard positive Sensitivity (%) Specificity (%) NGS RT-PCR 70 79
15 Conclusions NGS is a useful screening tool for ALK rearrangement status, superior to RT-PCR when RNA yield is limited When using NGS, it is critically important to integrate the 3 5 assay and to confirm with one or more additional methods in the imbalance cases These data further highlight the possibility of missing actionable rearrangements when only one screening methodology is available
16 Conclusions (cont.) If maximal sensitivity and specificity for ALK rearrangement detection are sought, confirmation of ALK status using 2 techniques or more in discordant cases is mandatory Accepted and recommended IHC should be the first step (inexpensive and easy technique for screening out negative cases); further confirmation by a molecular technique FISH (cytogenetics) or RT-PCR vs NGS (RNA-based techniques) should ideally follow In discordant cases, a third type of assay could be applied
17 Proposal ALK assessment 2 techniques of: NGS, IHC, and/or FISH Concordant Concordant+ Discordant No ALK rearrangement ALK rearrangement present Third technique
18 Panel testing More information DNA BRAF, HER2 exon 20, MET exon 14, KRAS, EGFR RNA RET, ROS1, NTRK, MET exon 14 Quality assurance Optimal use of scant material Access to clinical trials
19 ETOP NGS ALK I. Letovanec 1 *, S. Finn 2 *, P. Zygoura 3, P. Smyth 2, A. Soltermann 4, L. Bubendorf 5, E.-J. Speel 6, A. Marchetti 7, D. Nonaka 8, K. Monkhorst 9, H. Hager 10, M. Martorell 11, A. Sejda 12, R. Cheney 13, J. Hernandez-Losa 14, E. Verbeken 15, W. Weder 4, S. Savic 5, A. Di Lorito 7, A. Navarro 11, E. Felip 16, A. Warth 17, P. Baas 18, P. Meldgaard 10, F. Blackhall 19, A.-M. Dingemans 6, H. Dienemann 17, R. Dziadziuszko 20, J. Vansteenkiste 15, Cathal O'Brien 2, T. Geiger 21, J. Sherlock 22, J. Schageman 23, U. Dafni 24, R. Kammler 21, K.M. Kerr 25, E. Thunnissen 26, R. Stahel 27, S. Peters 1 on behalf of the ETOP Lungscape Consortium 21 1 Centre Hospitalier Universitaire Vaudois CHUV, Lausanne/Switzerland, 2 St James's Hospital and Trinity College, Dublin/Ireland, 3 Frontier Science Foundation-Hellas, Athens/Greece, 4 University Hospital Zurich, Zurich/Switzerland, 5 University Hospital Basel, Basel/Switzerland, 6 Maastricht University Medical Center, Maastricht/Netherlands, 7 Ospedale Clinicizzato, Chieti/Italy, 8 The Christie NHS Foundation Trust, Manchester/United Kingdom, 9 The Netherlands Cancer Institute, Amsterdam/Netherlands, 10 Aarhus University Hospital, Aarhus/Denmark, 11 Consorcio Hospital General Universitario de Valencia, Valencia/Spain, 12 Medical University Gdansk, Gdansk/Poland, 13 Roswell Park Cancer Institute, Buffalo, NY/United States of America, 14 Vall d'hebron University Hospital, Barcelona/Spain, 15 University Hospital KU Leuven, Leuven/Belgium, 16 Vall D'Hebron University Hospital, Barcelona/Spain, 17 Heidelberg University Hospital, Heidelberg/Germany, 18 The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam/Netherlands, 19 Christie Hospital NHS Foundation Trust, Manchester/United Kingdom, 20 Medical University of Gdansk, Gdansk/Poland, 21 European Thoracic Oncology Platform, Bern/Switzerland, 22 Thermo Fisher Scientific, Paisley/United Kingdom, 23 Thermo Fisher Scientific, Austin, TX/United States of America, 24 Frontier Science Foundation-Hellas & University of Athens, Athens/Greece, 25 Aberdeen University Medical School, Aberdeen/United Kingdom, 26 VU University Medical Center, Amsterdam/Netherlands, 27 University Hospital Zurich, Zurich/Switzerland.
20 Thank you for your attention!
21 Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or application of Thermo Fisher Scientific products presented by third parties during this seminar. Information and materials presented or provided by third parties are provided as-is and without warranty of any kind, including regarding intellectual property rights and reported results. Parties presenting images, text and material represent they have the rights to do so.
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