Next Generation Sequencing Gene Panels For Targeted .
KCE REPORT 240NEXT GENERATION SEQUENCING GENE PANELS FOR TARGETEDTHERAPY IN ONCOLOGY AND HAEMATO-ONCOLOGY2015www.kce.fgov.be
KCE REPORT 240HEALTH TECHNOLOGY ASSESSMENTNEXT GENERATION SEQUENCING GENE PANELS FOR TARGETEDTHERAPY IN ONCOLOGY AND HAEMATO-ONCOLOGYMARC VAN DEN BULCKE, LORENA SAN MIGUEL, ROBERTO SALGADO, ELS DE QUECKER, HARLINDE DE SCHUTTER, ANOUK WAEYTENS, PETERVAN DEN BERGHE, SABINE TEJPAR, JEROEN VAN HOUDT, STEVEN VAN LAERE, BRIGITTE MAES, FRANK HULSTAERT2015www.kce.fgov.be
COLOPHONTitle:Next generation sequencing gene panels for targeted therapy in oncology and haemato-oncologyAuthors:Marc Van den Bulcke (Kankercentrum – Centre du Cancer; WIV-ISP), Lorena San Miguel (KCE), Roberto Salgado(Institut Jules Bordet and GasthuisZusters Antwerpen), Els De Quecker (UZ Leuven), Harlinde De Schutter(Stichting Kankerregister – Fondation Registre du Cancer), Anouk Waeytens (RIZIV – INAMI), Peter Van DenBerghe (UZ Leuven), Sabine Tejpar (UZ Leuven), Jeroen Van Houdt (UZ Leuven), Steven Van Laere(GasthuisZusters Antwerpen), Brigitte Maes (Jessa Ziekenhuis Hasselt), Frank Hulstaert (KCE)Project coordinator:Marijke Eyssen (KCE)Reviewers:Geneviève Veereman (KCE), Nancy Thiry (KCE)External experts:Marc Abramowicz (Hôpital Erasme, ULB), Philippe Aftimos (Institut Jules Bordet), Hélène Antoine-Poirel (Cliniquesuniversitaires Saint-Luc), Ahmad Awada (Institut Jules Bordet), Vincent Bours (CHU Liège), Bernard China (WIV– ISP), Kathleen Claes (UZ Gent), Lieven Clement (Universiteit Gent), (Kristof Cokelaere (Jan YpermanZiekenhuis), Sigrid De Keersmaecker (WIV – ISP), Lizzy De Lodel (Universiteit Gent), Hendrik De Raeve (OLVZAalst), Jacques De Grève (UZ Brussel), Franceska Dedeurwaerdere (AZ Delta Roeselare), Dieter Deforce(Universiteit Gent), Sophie Deleyn (BELAC), Els Dequeker (UZ Leuven), Barbara Dewaele (UZ Leuven), NickyD'Haene (Hôpital Erasme, ULB), Hilde Engels (RIZIV – INAMI), Giuseppe Floris (UZ Leuven), Christian Focan(CHC), Tine Geldof (Vlerick Business School), Vanessa Ghislain (WIV – ISP), Els Goetghebeur (Universiteit Gent),Yves Guiot (Cliniques universitaires Saint-Luc), Vassilis Golfinopoulos (EORTC), Geneviève Haucotte (INAMI –RIZIV), Karin Haustermans (KU Leuven), Pierre Heimann (Erasme, ULB), Olga Kholmanskikh (FAGG – AFMPS),Denis Lacombe (EORTC), Frederic Lambert (CHU Liège), Denis Larsimont (Institut Jules Bordet), Erwin Lauwers(Vlaamse Liga tegen Kanker), Marie Le Mercier (Hôpital Erasme, ULB), Tim Leest (FAGG – AFMPS), HenkLouagie (AZ St Lucas), Frederic Maddalena (Cliniques universitaires Saint-Luc), Marion Maetens (Institut JulesBordet), Friedel Nollet (AZ St Jan Brugge), Patrick Pauwels (UZA), Marc Peeters (UZA), Nancy Roosens (WIV –ISP), Michael Rosskamp (Fondation Registre du Cancer – Stichting Kankerregister), Catherine Sibille (InstitutJules Bordet), Christos Sotiriou (Institut Jules Bordet), Christel Van Campenhout (WIV – ISP), Eric Van Cutsem(UZ Leuven), Nancy Van Damme (Stichting Kankerregister – Fondation Registre du Cancer), Philippe Van deWalle (WIV – ISP), Saskia Van Den Bogaert (FOD Volksgezondheid – SPF Santé Publique), Caroline Van DenBroecke (AZ St Lucas), Bernard Van den Heule (Laboratoire CMP), Didier Van der Steichel (Fondation contre leCancer – Stichting tegen Kanker), Jo Van Dorpe (AZ Delta Roeselare), Walter Van Dyck (Vlerick Business School),Liesbeth Van Eycken (Stichting Kankerregister – Fondation Registre du Cancer), Nicole Van Laethem (BELAC),Nadine Van Roy (UZ Gent), Sara Vander Borght (UZ Leuven), Pascal Vannuffel (Institut de Pathologie et deGénétique, Gosselies)External validators:Sandrine Baffert (Institut Curie Paris, France), Jean-Jacques Cassiman (KU Leuven), Leon Van Kempen (McGillUniversity Montreal, Canada)
Acknowledgements:We wish to thank Andrée Mangin (KCE) and Marie-Joëlle Robberechts (Centre du Cancer – Kankercentrum; ISP–WIV) for administrative support. The coded laboratories located in Belgium, the UK and Canada are thanked forsharing with us their detailed NGS panel cost estimations. We wish to extend our gratitude to the companyrepresentatives from Illumina, Life Technologies/Ion Torrent, Multiplicom and Biocartis for providing information onthe technologies and products of relevance for this report.Other reported interests:Membership of a stakeholder group on which the results of this report could have an impact.: Pierre Heimann,Hélène Antoine-Poirel (Centre de Génétique Humain, UCL Saint Luc), Vincent Bours (Laboratoire de diagnosticCHU Liège),Catherine Sibille (Institut Jules Bordet, anatomopathology), Friedel Nollet (Molecular Diagnostics.bevzw), Frederic Lambert (CHU Liège molecular genetics)Holder of intellectual property (patent, product developer, copyrights, trademarks, etc.): Catherine Sibille (inventorscertificate ‘diagnostic application immunogenetics’), Marc Van den Bulcke (patent for Transgenic plant eventdetection)Participation in scientific or experimental research as an initiator, principal investigator or researcher: HélèneAntoine-Poirel (implication in NGS studies), Els Dequeker (promotor PhD longitudinal study about quality controlof onco-biomarkers), Catherine Sibille (project Télévie), Frédéric Lambert (‘Correlation génotypage des tumeurscolorectale et données d’imagerie médicale / PET-CT’ – local study of the CHU de Liège), Leon Van Kempen(implementation of clinical targeted panel sequencing at the Molecular Pathology Centre at Jewish GeneralHospital (Montreal QC))A grant, fees or funds for a member of staff or another form of compensation for the execution of research: ElsDequeker (scientific research credit KULeuven and pharmaceutical industry), Catherine Sibille (grants for MastersResearch for medicine student), Els Goetghebeur (contract WIV-ISP), Lieven Clement (ZAP UGent)Consultancy or employment for a company, an association or an organisation that may gain or lose financially dueto the results of this report: Harlinde De Schutter (Medical Advisor Oncology at Amgen until 1 March 2013), ElsGoetghebeur (ZAP UGent), Lieven Clement (ZAP UGent)Payments to speak, training remuneration, subsidised travel or payment for participation at a conference: ElsDequeker (ECP, ESMP, ESHG), Frédéric Lambert (speaker for several pharmaceutical companies), Brigitte Maes(Pfizer, Novartis)Presidency or accountable function within an institution, association, department or other entity on which the resultsof this report could have an impact: Geneviève Haucotte (INAMI – RIZIV), Pierre Heimann (Erasme, ULB), ElsDequeker (head of department research group biomedical quality control KULeuven), Kristof Cokelaere(Commission of Pathological Anatomy), Christel Van Campenhout (WIV-ISP recognitions and quality medicallaboratories), Catherine Sibille (responsible Molecular Anatomopathologic Biology and responsible NGS Platformrecognized by Institut Jules Bordet), Vassilis Golfinopoulos (medical vice-director EORTC), Frédéric Lambert(head of laboratory for targeted/personalized therapy), Els Goetghebeur (president Centrum voor Statistiek,Ugent), Leon Van Kempen (accountable operation and finance of the Molecular Pathology Centre).
Layout:Ine VerhulstDisclaimer: The external experts were consulted about a (preliminary) version of the scientific report. Theircomments were discussed during meetings. They did not co-author the scientific report and did notnecessarily agree with its content. Subsequently, a (final) version was submitted to the validators. The validation of the report resultsfrom a consensus or a voting process between the validators. The validators did not co-author thescientific report and did not necessarily all three agree with its content. Finally, this report has been approved by common assent by the Executive Board. Only the KCE is responsible for errors or omissions that could persist. The policy recommendationsare also under the full responsibility of the KCE.Publication date:02 February 2017 (2nd edition; 1st edtion: 19 March 2015)Domain:Health Technology Assessment (HTA)MeSH:Molecular Targeted Therapy; High-Throughput Nucleotide Sequencing; Pathology, molecular; Cost-BenefitAnalysis; Neoplasms; Hematologic NeoplasmsNLM Classification:QZ.50 (Molecular Pathology)Language:EnglishFormat:Adobe PDF (A4)Legal depot:D/2015/10.273/26Copyright:KCE reports are published under a “by/nc/nd” Creative Commons -for-kce-reports.How to refer to this document?Van den Bulcke M, San Miguel L, Salgado R, De Quecker E, De Schutter H, Waeytens A, Van Den Berghe P,Tejpar S, Van Houdt J, Van Laere S, Maes B, Hulstaert F. Next generation sequencing gene panels for targetedtherapy in oncology and haemato-oncology. Health Technology Assessment (HTA) Brussels: Belgian Health CareKnowledge Centre (KCE). 2015. KCE Reports 240. D/2015/10.273/26.This document is available on the website of the Belgian Health Care Knowledge Centre.
KCE Report 240Next generation sequencing for targeted therapy in oncology TABLE OF CONTENTSLIST OF TABLES .3LIST OF FIGURES .4LIST OF ABBREVIATIONS .5 SCIENTIFIC REPORT.91INTRODUCTION .91.1BACKGROUND .91.2RESEARCH QUESTIONS .131.3GENERAL APPROACH .141.4EVALUATION OF DIAGNOSTIC TESTS.142TOWARDS NEXT GENERATION SEQUENCING PANEL TESTS IN ONCOLOGY .162.1MOLECULAR DIAGNOSTICS USED IN ONCOLOGY.162.2NEXT GENERATION SEQUENCING, THE TECHNOLOGY .182.3INTRODUCTION TO NEXT GENERATION SEQUENCING PANEL TESTS .202.3.1The sequencing revolution .202.3.2Importance of targeted sequencing for exploratory clinical research in oncology .222.3.3New technologies, more options, new challenges .262.4COMPOSITION OF THE NGS PANELS.262.4.1NGS panels for solid tumours .272.4.2NGS panels for hemato-oncology .282.4.3Other considerations for NGS panel selection .283REGULATORY ASPECTS, QUALITY ASSURANCE AND EDUCATIONAL NEEDS .293.1NEED FOR INFORMED CONSENT AND PRE-TEST COUNSELLING .293.2REGULATORY CONTEXT OF MOLECULAR TESTS FOR SOMATIC MUTATIONS .293.2.1Regulations for diagnostic laboratories in Belgium .293.2.2Regulations for in-house methods and in-vitro diagnostics .303.3EXTERNAL QUALITY ASSURANCE OF MOLECULAR TESTS FOR SOMATIC MUTATIONS .323.3.1EQA schemes for Haematological and Solid Tumours.321
2Next generation sequencing for targeted therapy in oncology3.43.53.644.14.24.34.455.15.25.3KCE Report 2403.3.2Performance of the participating (Belgian) laboratories.33QUALITY ASSURANCE OF NGS PANEL TESTS FOR SOMATIC MUTATIONS .373.4.1General considerations and the importance of quality.373.4.2Quality assurance for the wet and dry lab part of NGS .39REPORTING OF NGS DATA .44NEEDS FOR EDUCATION AND A MULTIDISCIPLINARY EXPERT COMMITTEES.50IMPACT OF TEST ACCURACY ON INCREMENTAL COST-EFFECTIVENESS RATIOS .52INTRODUCTION AND SCOPE .52METHODOLOGY .524.2.1Search strategy .524.2.2Selection procedure .534.2.3Selection criteria.53RESULTS .53ILLUSTRATIVE EXAMPLES FOR BELGIUM .544.4.1Data sources .544.4.2Results and discussion .554.4.3The relevance of test specificity when applied to NGS panels .59FINANCING OF COMPANION DIAGNOSTICS AND TARGETED THERAPY .61THE DISCONNECTION BETWEEN PHARMACEUTICALS AND COMPANION DIAGNOSTIC .615.1.1The need for a companion diagnostic conflicts with traditional drug development.615.1.2Disconnection between reimbursement of companion diagnostics and drugs in Belgium .62BILLING CODES FOR MOLECULAR DIAGNOSTICS IN ONCOLOGY IN BELGIUM .635.2.1Evolution of billing codes, overall expenditures and testing volumes .645.2.2Current issues with billing codes .65MOLECULAR TESTS BILLED BY TYPE OF TUMOUR DIAGNOSED IN BELGIUM (2010-2011) .685.3.1Aims and methods of analysis by tumour type .685.3.2Selection of tumour types.685.3.3IMA/AIM data .685.3.4Results .69
KCE Report 240Next generation sequencing for targeted therapy in oncology5.4CURRENT COST OF NGS PANEL TESTS.736OPTIONS FOR INTRODUCING NGS PANEL TESTS IN THE BELGIAN HEALTHCARE .76 APPENDICES .79APPENDIX 1.GLOSSARY .79APPENDIX 2.COMPOSITION OF NGS PANELS .91APPENDIX 3.SEARCH STRATEGIES - IMPACT OF TEST ACCURACY ON ICERS . 110APPENDIX 3.1. PUBMED . 110APPENDIX 3.2. EMBASE . 110APPENDIX 3.3. ECONLIT . 111APPENDIX 3.4. CRD NHS DATABASES. 112APPENDIX 4.MOLECULAR TESTS BY PATHOLOGY, WITH BILLING CODES . 113APPENDIX 5.SELECTED NOMENCLATURE CODES . 119 REFERENCES . 123LIST OF TABLESTable 1 – Targeted therapies reimbursed in Belgium (December 2014) .12Table 2 – Predictive, diagnostic and prognostic genomic alterations and level of evidence, adapted fromGood et al.11 .21Table 3 – Example of classification of clinical utility of molecular alterations, copied fromAndré et al, 201423 .25Table 4 – EQA KRAS Results 2012-2013 .34Table 5 – EQA haematology-oncology results 2009-2010 .35Table 6 – Overview of participants and results of the ESP Colon EQA schemes .36Table 7 – Type of method used by laboratories in the ESP colon 2013 scheme .37Table 8 – Examples of risk factors that may induce sequencing errors .38Table 9 – Reporting, elements to be included in the summary report (one page) .47Table 10 – Reporting, supplement 1: test characteristics and bio-informatics details .48Table 11 – Reporting, supplement 2: quality issues and test performance data (patient specific) .49Table 12 – Reporting, supplement 3: variants retained after analysis .49Table 13 – Cost effectiveness of different test alternatives for targeting treatment with trastuzumab inbreast cancer .563
4Next generation sequencing for targeted therapy in oncologyKCE Report 240Table 14 – Cost effectiveness of different test alternatives for targeting treatment with crizotinib in NSCLC .58Table 15 – Number of tests per year (year of the activity) and expenditures for selected t
(head of laboratory for targeted/personalized therapy), Els Goetghebeur (president Centrum voor Statistiek, Ugent), Leon Van Kempen (accountable operation and finance of the Molecular Pathology Centre).
Next-Gen Sequencing Workflow Source: Lu and Shen, 2016, Biochemistry, Genetics and Molecular Biology. DOI: 10.5772/61657 Genome Whole genome sequencing Whole exome sequencing Targeted gene panels (cancer, newborns, autism, etc.) Transcriptome Whole RNA sequencing mRNA transcriptome (poly-A selection)
Also referred to as Next-Generation Sequencing Parallelize the sequencing process, producing thousands or millions of sequences concurrently Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing as many as 500,000 sequencing-by-synthesis operations may
limited throughput and the high costs of sequencing remained major barriers. The release of the first truly high-throughput sequencing platform in the mid-2000s heralded a 50,000-fold drop in the cost of human genome sequencing since the Human Genome Project 3 and led to the moniker: next-generation sequencing (NGS).
Next Generation Sequencing (NGS) Impact of NGS. 1st generation sequencing - Sanger sequencing - utilizes chain terminating dideoxynucleotides - slow and laborious, method has been relatively unchanged for 30 years - data mixture of sequences - sequence data can be reviewed manually
the next few years. next-generation sequencing technologies Sequencing technologies include a number of methods that are grouped broadly as template preparation, sequencing and imaging, and data analysis. The unique combination of specific protocols distinguishes one technology from another and determines the type of data produced from each .
For Research Use Only. Not for use in diagnostic procedures. Table of Contents I. Introduction: Genomic Technologies for Cancer Research 3 II. Approaches for Detecting Somatic Mutations 4 Targeted Sequencing Solutions for Somatic Mutation Detection 4 Exome Sequencing 4 Focused Sequencing Panels 4 Custom Targeted Sequencing 4 Whole-Genome Sequencing Solutions 4
Next generation sequencing (NGS) Nature Methods 2011 Sequencing technology defies Moore's law. 2009: Illumina, Helicos 40-50K 4 2010: 5K , a few days Sequencing the Human Genome Year Log 10 (price) 2000 2005 2010 10 8 6 60K , 2 weeks 4 2 2014: 1000 , 24 hrs 2008: ABI SOLiD 2007: 454
Next Generation Sequencing - Whole Exome Sequencing (WES) The exome accounts for only 1.5% of the human genome, and yet includes 85% of all disease-causing mutations (10). Whole exome sequencing (WES) examines all protein-coding regions in the human genome. In this method, DNA fragments are hybridized in solution to sequence-specific capture
