Disclosures. Personalized Meds from the molecular onco-pathology s perspective

Transcription

1 1 FIGON DMD Symposium From Protocol towards Personalized Tailored Therapy Ede, October 6th 2015 Personalized Meds from the molecular onco-pathology s perspective Diagnostic in Pathology in Molecular Tumor Profiling Molecular Pathology Next-generation-Pathology Ed Schuuring Head Laboratory Molecular Pathology, UMCG Groningen Coördinator Netwerk for Molecular Pathology North Netherlands KMBP (Clinical Scientist in Molecular Pathology) Professor in Molecular Oncological Pathology Pao, Lancet Oncol 2011; Pao, Nat Med 2012 Kris JAMA 2014 >2015: classification of lung cancer is changing into molecular tumor profiling Disclosures Consultant/Advisory Board: AstraZeneca, Roche, Pfizer, Novartis, Amgen, BioCartis, QCMD, ESP, IQNTH Speaker s fee: Abbott, Novartis, Roche Stock/Royalties: None Molecular diagnostics in Pathology for treatment planning using gene-targeted therapy in NL ( ) Content: Which predictive markers should be tested? Platform? Panel-NGS vs WGS or WES Interpretation of the results and reporting Treatment advice (molecular tumor board) Archiving, exchanging experiences, Organisation of the laboratory (KMBP)

2 2 Molecular diagnostics of lung cancer for treatment planning using gene-targeted therapy in NL dutch guidelines In 2007: starting with EGFR-mutation screening In 2013: Dutch guideline in NSCLC Only EGFR-mutation analysis In 2013: ALK-translocation (Registration crizotinib July 2012) In July 2015: revisited Dutch guideline for NSCLC: (1) EGFR, ALK; (2) HER2, BRAF, RET and ROS1 Landscape of driver mutations in lung adenocarcinoma using whole-genome-sequencing Whole genome/exome sequencing: * >2 (potential) actionable or driver mutations per tumor * >50% of NSCLC: rare mutations only Molecular diagnostics of lung cancer for treatment planning using gene-targeted therapy in NL international guidelines Dutch Oncoline guideline for NSCLC (July 2015): (1) EGFR, ALK; (2) HER2, BRAF, RET and ROS1 New anticancer drugs becoming available for gene-targeted therapy CAP-IASLC-AMP guideline for NSCLC (2013) (Lindeman 2013) (1) EGFR, ALK; (2) HER2, BRAF, RET and ROS1 ESMO guideline for NSCLC (2013) (Kerr, Ann Oncol 2014) EGFR, ALK (recommend KRAS, BRAF, HER2 and ROS1) 2014: 71 FDA-approved anticancer drugs including 52 targeted/ precision medicines Fojo JAMA OtoHN dec 2014

3 3 Driver Druggable Mutation Incidence in Lung Cancers Molecular tumor profiling: the new wave in cancer care molecular medicine in 2015 Molecular status of key analytes in several diseases is already standard of care: Melanoma: Lung cancer: Colon cancer: GIST: BRAF (NRAS, ckit) EGFR, ALK, ROS (RET, KRAS, BRAF, PIK3CA, MET, FGFR1) KRAS, NRAS, BRAF (PIK3CA) ckit, PDGFRA (NRAS) MSK-IMCT platform, Kris, JAMA 2014 Molecular Oncological Pathology at UMCG: De moleculaire diagnostiek van longkanker tbv gen-mutatie-gerichte therapie Nieuwe predicitieve biomarkers in kader van klinische trials Vanaf 2015 e.v. (verwachtte toepassingen): Activerende EGFR mutaties (~10% AC) > next-generation-tki (afatinib) resistente EGFR mutaties (100% AC) > dacomitinib, afatinib/cetuximab, C0-1686, AZD9291, AUY922 ( resistente ) ALK mutaties (100% AC) > next-generation-tki (ceritinib, alectinib) FGFR1-amplificatie (~20% SCC) > nintedanib BRAF-mutatie (< 2% AC) > vemurafinib, dafrafenib KRAS-mutatie (~40% AC) > MET/MEK/RAF inhibitors MET-amplificatie/exon-skipping (4-20% AC) > crizotinib, cabozantinib, capmatinib ROS1-translocatie (1.7% AC) > crizotinib RET/KIF5B-translocatie (<2% AC) > sunitinib, vandetanib, sorafinib HER2-mutatie (2% AC) > herceptin, afatinib, EGFR-amplificatie (10% AC) > cetuximab, erlotinib, PIK3CA-mutatie (<5% AC) > mtor inhibitor, aspirine DDR1-mutatie (~4% SCC) > dasatinib Molecular tumor profiling: the new wave in cancer care molecular pathology in Maximum ~30-40 predictive/diagnostic genes based On current guidelines and ongoing clinical trial Molecular diagnostics in Pathology ( ) > NGS gene-panel detecting CNV and SNV UMCG is longkanker-expertcentrum en participeert in vele (inter)nationale trials

4 4 Molecular diagnostics in Pathology for treatment planning using gene-targeted therapy in NL Content: which predictive markers should be tested? platform? Panel-NGS vs WGS or WES Interpretation of the results and reporting treatment advice (molecular tumor board) archiving, exchanging experiences, Organisation of the laboratory (KMBP) Next generation sequencing how to detect CNV/SNV best? Whole genome sequencing High quality DNA (only frozen), high input (500 ng), 30x coverage, most comprehensive genomic data, high costs, long TAT, qualified expertise Whole exome sequencing High quality DNA (only frozen), high input (500 ng), 100x coverage, complete coding regions, moderate costs, long TAT, qualified expertise Sequencing of defined target genes (gene-panel) Low quality DNA (also FFPE), low input (10-20 ng), x coverage, only selected hotspots, acceptable costs, TAT (<5d) Next generation sequencing how to detect CNV/SNV best? Whole genome sequencing High quality DNA (only frozen), high input (500 ng), 30x coverage, most comprehensive genomic data, high costs, long TAT, qualified expertise Whole exome sequencing High quality DNA (only frozen), high input (500 ng), 100x coverage, complete coding regions, moderate costs, long TAT, qualified expertise Sequencing of defined target genes (gene-panel) Low quality DNA (also FFPE), low input (10-20 ng), x coverage, only selected hotspots, acceptable costs, TAT (<5d) A small biopsy B core-needle biopsy C surgical specimen D cytology E biopsy with very few tumor cells In nowadays clinical practice: >90% = FFPE-blocks (formaline-fixed paraffin-embedded) TISSUE IS THE ISSUE D E Lopes-Rios/Sietsma

5 5 1st last Sufficient DNA for NGS >20% neoplastic cells - Panel-Ion Torrent: 10 ng (~1600 cells) - Panel-Miseq: 50 ng - WES: ~500 ng - WGS: ~500 ng 5% neoplastic cells Not enough tumor DNA <(0.)1% neoplastic cells courtesy of Erik Thunnissen, VUMC >50% neoplastic cells courtesy of Erik Thunnissen, VUMC Next generation sequencing tissue is the issue PS analytical sensitivity of NGS: ~5%!!! Coverage 30x (WGS/WES) vs x (panel-ngs): Lymphangitis carcinomatosa, Sufficient for diagnosis Not enough for prediction Primary goal of molecular tumor profiling: The detection of the common mutation present in all neoplastic cells (tissue should contain >20% neoplastic cells) Secondary goal of molecular tumor profiling: TTF1 p63 courtesy of Erik Thunnissen, VUMC The early detection of low copy targeted-therapy-resistant mutations (tissue should contain >80% neoplastic cells)

6 6 Tissue management = interaction between pulmonologist/oncologist/ surgeon/radiologist and pathologist Next generation sequencing Ethical considerations Sample collector: Sampling more ( 4) biopsies/ tumor tissue Clinical request for diagnosis + prediction? Clinical suspicion of metastases y/n? Pathology : Distribute samples over >1 block Careful initial cut Spare section for reflex analysis Focused diagnostic analysis Molecular tumor profiling in lung cancer standard of care based on guidelines and clinical trials presently restricted to ~30 genes In case of WGS and WES: What to do with information on mutations in disease/cancer genes for which the effect on treatment strategy is unknown? What to do with information the clinician/patient did not ask for (e.g. associated with hereditary diseases)? courtesy of Erik Thunnissen, VUMC Next generation sequencing Patient s right to know Whole genome sequencing High quality DNA (only frozen), high input (500 ng), 30x coverage, most comprehensive genomic data, high costs, long TAT, qualified expertise Whole exome sequencing High quality DNA (only frozen), high input (500 ng), 100x coverage, complete coding regions, moderate costs, long TAT, qualified expertise Sequencing of defined target genes (gene-panel) Low quality DNA (also FFPE), low input (10-20 ng), x coverage, only selected hotspots, acceptable costs, TAT (<5d) The Oncologist 2014

7 7 Patient s right to know Screening for predictive markers to select patients for targeted therapies in routine molecular diagnostic at Pathology ( ): Molecular diagnostics: same single NGS-platform used in Pathology with only relevant targeted gene-panel: All routine tissues (including FFPE) can be analysed Equal access to targeted therapy to all cancer patients Short time-to-diagnosis Cost-effective High quality and appropriate coverage/depth The Oncologist 2014 Patient s right to know Molecular diagnostics in Pathology for treatment planning using gene-targeted therapy in NL Content: which predictive markers should be tested? platform? Panel-NGS vs WGS or WES Interpretation of the results and reporting treatment advice (molecular tumor board) archiving, exchanging experiences, Organisation of the laboratory (KMBP)

8 8 Molecular results might as well be hieroglyphs ALK, APC, ASXL1, ATM, BAP1, BCR-ABL, BRAF, BRCA1, BRCA2, CEB, CRAF (RAF1), CSF1R, CTLA4,CTNNB1, DDR1, DNMT3A, ERBB1 (EGFR), ERBB2 (HER2), ESR1, FGFR4, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, MAP2K1 (MEK1), MAP2K2 (MEK2), MAPK3 (ERK1), MET, MLL (KMT2A), MPL (TPOR), MYC, MYD88, NOTCH1, NPM1, NRAS, RP1, PDGFRA, PDGFRB, PIK3CA, PML, PTEN, PTPN11, RARA, RB1, RET (MEN2), RUNX1, TET2, TP53, VEGFA, VEGFR1 (FLT1), VEGFR2 (KDR), VEGFR3 (FLT4), VHL, WT1, mtor List of actionable cancer biomarkers, 2015 AD Hieroglyphs on stone tablet, 5000 BC Courtesy of S. Willems, UMCU Courtesy of Mark Bogulski, MD, Genome Health Solutions University of Alabama Comprehensive Cancer Center Research Retreat, Birmingham, AL, October 6, 2014 Standarization of molecular data (NGS) reporting Courtesy of S. Willems, UMCU NVVP/LGA-taakgroep Module NGS : Willems, Tops, Schuuring, van Dijk, Steeghs, Seegers

9 9 Standarisation of reporting enables linkage to other databases New function at Pathology Klinisch Molecular Bioloog in de Pathologie Unique for Netherlands: clinical scientist in molecular pathology (KMBP) Specific 2-year-training program for molecular biologists within the Dutch Society of Pathology (NVVP) KMBP is responsible for all the molecular diagnostic at pathology, for quality control and the molecular interpretation of the results Unique KMB also in Clinical Genetics, Medical Microbiology In NL (2015): 5 KMBP-opleidingsinstituut, 23 KMBP en ~6 KMBPio NVVP/LGA-taakgroep Module NGS : Willems, Tops, Schuuring, van Dijk, Steeghs, Seegers > Molecular diagnostics in Pathology for treatment planning using gene-targeted therapy in NL ( ) Content: Reporting Mutation Analysis data Handling of unexpected, difficult, rare mutations? which predictive markers should be tested? platform? Panel-NGS vs WGS or WES Interpretation of the results and reporting treatment advice (molecular tumor board) archiving, exchanging experiences, Organisation of the laboratory (KMBP) Example: NSCLC with EGFR: c.2281g>a; p.(d761n) Example: NSCLC with PIK3CA: c.3140a>g; p.(h1047r) Example: NSCLC with PIK3CA: c.3140a>g; p.(h1047r) 80% and p(l858r) 35%. Example: AKT3 amplificatie 80%, EGFR amplificatie 50%, KRAS amplificatie 20%, TSC1 A944T mutatie 10%, MDM2 amplificatie 7%, MCL1 amplificatie 3%, TP53 Y234C mutatie 2%, EPHA5 A454N mutaties 1%, MYST3 amplificatie 1% (1) KMBP/pathologist search for information on general treatment advice and interpretation in -report (2) assistance with specific treatment advice via the Molecular Tumor Board Groningen

10 10 Scholing (verplichte cursus van de NVVP voor AIOS-Pathologie) Every Friday from hrs we discuss requests for advice (since Nov 2014) Moleculaire Pathologie in de regio Noord Molecular Tumor Board Groningen (in dutch) Prof dr Ed Schuuring, KMBP Dr Arja ter Elst, KMBP Prof. dr. Anke van den Berg, KMBP Dr Nils t Hart, lungpatholoog Prof dr Wim Timens, lungpatholoog Prof dr Harry Groen, pulmonologist Dr Jeroen Hiltermann, pulmonologist Drs Anthonie van der Wekken, pulmonologist Prof dr Geke Hospers, medisch oncologist This expert forum combines the expertise of clinical molecular biologists in pathology, pathologists, medical oncologists and pulmonologists (in the near future clinical geneticists, genetic counselor, bio-informaticus and cell biologist). Friesland Leeuwarden TREANT Hoogeveen UMCG Groningen Netwerk voor Moleculaire Pathologie SSZOG Winschoten Martini Groningen Isala Zwolle Noordelijk Netwerk voor Moleculaire Pathologie: Afstemming met pathologen en oncologen Zelfde pakket aan MD-testen Vergelijkbare zorg voor elke patient Centrale MD-testen (complexe assays) Lokale testen (voor lage TAT) Kosten-effectiviteit Kwaliteit Regionaal overleg, bijscholing Scholing voor AIOS 2016: UMCG centrale Moleculaire Tumor Board (nov 2014) Lokale boards binnen netwerk Bij-/nascholing pathologen/oncologen

11 11 Pathology: optimizing access to personalized cancer therapy from tissue to therapy ( ) Goal: To introduce a NGS assay to create optimal and equal access to targeted therapies for all cancer patients in the Netherlands > Consensus on a comprehensive adaptive targeted NGS assay (single platform) analysing all genetic aberrations currently required for selection of targeted therapy optimal and most cost-effective approach to molecular predictive tumor analysis short time-to-diagnosis efficient tissue management Thanks for your attention [email protected] > Build a national expert forum and network of regional molecular tumour boards: optimal translation of test results into selection of the most optimal therapeutic approach > Reporting the molecular results of the predictive analysis in a standardized fashion and Integration with pathology diagnosis using the nationwide LGA database Players: >27 pathology-labs, medical oncologists, pulmonologists, NVALT, NVMO, NVVP, LGA Molecular diagnostics for treatment planning using gene-targeted therapy in Molecular diagnostics: same single NGS-platform used in Pathology with only relevant targeted gene-panel: Equal access to targeted therapy to all cancer patients Short time-to-diagnosis, cost-effective, high quality National network for molecular testing at Pathology labs Therapy decisions: in national molecular tumor forum/boards Research: in parallel collect complete molecular tumor profiles using WGS, WES and/or RNAseq (e.g. via CPTC): essential to add this information to targeted-treatment-response databases to improve prediction and identify new targets