ERIC TP53 Network activities and outcomes. Sarka Pospisilova

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1 ERIC TP53 Network activities and outcomes Sarka Pospisilova

2 ERIC TP53 NETWORK 11 Training Centres 3 Certifying Centres Uppsala/Stockholm Belfast Copenhagen Amsterdam Paris Ulm Novara Brno Bellinzona Salamanca Thessaloniki

3 ERIC TP53 NETWORK STRUCTURE: Training Centres Stephan Stilgenbauer, Eugen Tausch, Ulm, Germany Sarka Pospisilova, Jitka Malcikova, Brno, Czech Republic Richard Rosenquist, Stockholm, Sweden and Nordic countries Kostas Stamatopoulos, Thessaloniki, Greece Gianluca Gaidano, Novara, Italy Fred Davi', Paris, France Ramon Garcia Sanz, Salamanca, Spain Carsten Niemann, Copenhagen, Denmark Arnon Kater, Amsterdam, Netherlands Davide Rossi, Bellinzona, Switzerland David Gonzalez de Castro, Belfast, U.K. Certifying Centres Stephan Stilgenbauer, Eugen Tausch, Ulm, Germany Sarka Pospisilova, Jitka Malcikova, Sarka Pavlova, Brno, Czech Rep. Richard Rosenquist, Lesley Ann Sutton, Uppsala/Stockholm, Sweden

1) The p53 protein is crucial for regulation of the cell cycle arrest or apoptosis Tumors with p53 dysfunction - bad prognosis and poor treatment response TP53 dysfunction in CLL - del(17p) and/or

4 Why is TP53 dysfunction so important in CLL? Antioncogene TP53 = "the guardian of the genome" Conserves genetic stability by preventing genome mutation TP53 gene is located on the short arm of chromosome 17 (17p13.1) The p53 protein is crucial for regulation of the cell cycle arrest or apoptosis Tumors with p53 dysfunction - bad prognosis and poor treatment response TP53 dysfunction in CLL - del(17p) and/or TP53 mutation The most important independent prognostic marker High risk of progression within 1-2 years Median overall survival 3-5 years Frequency of TP53 aberrations increases with advanced disease stage and therapy Important predictive marker (resistance to FCR, alkylating agents, purine analogues ) Valid also in novel mutation era New therapeutic options (inhibition of BcR signaling, Bcl2 inhibition)

5 Types of TP53 defects in CLL Del(17p) & TP53 mutation del(17p) sole TP53 mutation sole Frequency increases during disease development Related to previous therapy

6 Independent prognostic impact of del(17p) and TP53 mutations Zenz et al. Blood 2008 Dicker et al. Leukemia 2009 Rossi et al. CCR, 2009 Malcikova et al. Blood, 2009 Stengel et al, Leukemia 2017 GCLLSG CLL4 trial (F vs FC) Zenz et al. JCO, 2010 CLL8 trial (FC vs FCR) Stilgenbauer et al. Blood 2014 LRF CLL4 (Clb vs F vs FC) Gonzalez et al. JCO, 2011 Analysis of both del(17p) by FISH and TP53 mutation recommmended!

7 ERIC TP53 NETWORK ACTIVITIES 1) ERIC Recommendations on TP53 mutation analysis Updates 2) Organization of regular Certification rounds for TP53 mutation analysis 3) Organization of workshop ontp53 analysis (Brno 2015, Stresa 2017, ) ERIC TP53 web: Diagnostics a) Manual for TP53 mutational analysis b) TP53 Analysis Template Report Forms c) TP53 Certification Requirements d) Helpdesk (ERIC office + expert in charge) e) Free Software for Sanger Analysis Data GLASS - for detection and annotation of low - frequent somatic variants

8 ERIC Publications on TP53 analysis Comprehensive profiling and analysis of TP53 mutation in CLL TP53 mutation profile in chronic lymphocytic leukemia: evidence for a disease specific profile from a comprehensive analysis of 268 mutations. T Zenz, D Vollmer, M Trbusek, J Smardova, A Benner, T Soussi, H Helfrich, M Heuberger, P Hoth, M Fuge, T Denzel, S Häbe, J Malcikova, P Kuglik, S Truong, N Patten, L Wu, D Oscier, R Ibbotson, A Gardiner, I Tracy, K Lin, A Pettitt, S Pospisilova, J Mayer, M Hallek, H Döhner, S Stilgenbauer, European Research Initiative on CLL (ERIC): Leukemia, ERIC recommendations on TP53 mutation analysis in Chronic Lymphocytic Leukemia. Pospisilova S, Gonzalez D, Malcikova J, Trbusek M, Rossi D, Kater AP, Cymbalista F, Eichhorst B, Hallek M, Döhner H, Hillmen P, van Oers M, Gribben J, Ghia P, Montserrat E, Stilgenbauer S, Zenz T.: Leukemia, Assessment of TP53 functionality in chronic lymphocytic leukaemia by different assays; an ERIC-wide approach. Te Raa GD, Malčiková J, Mraz M, Trbusek M, Le Garff-Tavernier M, Merle-Béral H, Greil R, Merkel O, Pospisilova S, Lin K, Pettitt AR, Stankovic T, van Oers MH, Eldering E, Stilgenbauer S, Zenz T, Kater AP; European Research Initiative on CLL (ERIC): Brit. J. Haematology, Innovation in the prognostication of chronic lymphocytic leukemia: how far beyond TP53 gene analysis can we go? Pospisilova S, Sutton LA, Malcikova J, Tausch E, Rossi D, Montserrat E, Moreno C, Stamatopoulos K, Gaidano G, Rosenquist R, Ghia P; European Research Initiative on CLL (ERIC): Haematologica, 2016.

9 ERIC Recommendations UPDATE 2017 Currently recommended methods: Sanger sequencing with or without prescreening Next generation sequencing Updated Recommendations Detailed recommendations Which material? Which exons? Methods Sanger sequencing, Next Generation sequencing Interpretation and reporting Manual for TP53 mutational analysis

10 ERIC Recommendations for TP53 Mutation Analysis in Chronic Lymphocytic Leukemia Update on Methodological Approaches and Results Interpretation J. Malcikova, E. Tausch, D. Rossi, L. A. Sutton, T. Soussi, T. Zenz, A.P. Kater, C. U. Niemann, D. Gonzalez, F. Davi, M. Gonzalez Diaz, C. Moreno, G. Gaidano, K. Stamatopoulos, R. Rosenquist, S. Stilgenbauer, P. Ghia, S. Pospisilova on behalf of the European Research Initiative on Chronic Lymphocytic Leukemia (ERIC) TP53 network Supplementary files: Report forms for reporting results of TP53 mutation analysis

11 ERIC recommendation Patients Sampling Always when deciding about treatment. Material Procedure Sanger sequencing NGS Interpretation and clinical reporting Type of material Anticoagulant Cells Nucleic acid Covered region Primers and PCR protocol Sequencing Peripheral blood (PB) EDTA or heparin (in case of PB) Mononuclear cells DNA Optimum: exons 2-11 (coding region), Minimum: exons 4-10, Always include splice sites (+/-2 intronic bp) Available in the IARC TP53 database: Both strands (forward + reverse) Notes and alternatives Bone marrow, lymph nodes suitable alternatives if PB lymphocyte count is <10x10 9 /l, e.g. in SLL/CLL. Fresh/frozen tissues are strongly preferred. When PB or BM contains <60-70% of lymphocytes, separation of CD19+ cells or using deep-ngs with low detection limit is recommended. RNA analysis carries a risk of omitting truncating/splice site variants. Variants found in introns at positions +2/-2 impair splicing. Data analysis Use software designed for somatic variant detection Free web-based software available on the ERIC website. Protocol Sequencing Data analysis Variant description Interpretation Polymorphisms and benign variants Limit of detection and clinical reporting Report form Table: Overview of ERIC recommendations for TP53 analysis. Amplicon or capture-based approaches are applicable. DNA input should be calculated with respect to the limit of detection. Testing the integrity of DNA is recommended Minimum of 100 reads per each position. Number of variant reads for reliable variant calling should be at least 10. Use software designed for somatic variant detection. Validated minimal limit of detection should be 10% VAF. Use HGVS nomenclature: Report the cdna and protein level including reference sequence. Check the detected variants using locus-specific database: IARC TP53 database: or TP53 web site: It is preferred not to include common polymorphisms and benign variants in the report to physicians. Report variants detectable by Sanger sequencing and variants present in >10% VAF if tested by NGS. Reporting variants between 5-10% VAF is acceptable only if explicitly stating that the clinical impact of minor subclonal mutations has not been conclusively documented. Template report form is available on the ERIC website. Several ready-to use kits involving TP53 analysis are commercially available. 99% minimum coverage percentage should be reported. Proper bioinformatics approach represents the most challenging part of NGS and no universal tool is currently available. If a rare variant or variant with preserved functionality is detected: 1) Repeat the analysis by starting from PCR to exclude analytical errors. 2) If the variant is confirmed, test the paired germline DNA. Using dbsnp for filtering out polymorphisms and neutral variants is strongly discouraged. There is not enough evidence for making therapeutic decisions based on the detection of mutations present in low variant allele frequency.

12 ERIC Certification on the assessment of TP53 mutations AIMS: For all laboratories performing the TP53 analysis in CLL validation of different techniques on TP53 mutation analysis Support the introduction of TP53 analysis in labs with less experience (to provide assurance of the results quality) Discuss the problematic issues and give individual recommendations Improve analysis harmonization and interaction between centers Provide an official document on the quality control assessment

13 ERIC Certified Centres from 4 rounds ( ) Round 1: 30 Round 2: 16 Round 3: 29 Round 4: 35 (3 centres participated in 2 rounds with different techniques) Total Number of Certified Centers: 107 (total number of applicants 135, 25 failed)

14 ERIC Certified Centres - 4 Rounds 107 Centres from 24 countries

15 ERIC Certification on the assessment of TP53 mutations TP53 Certification Requirements

16 Institution

17 ERIC Certification on the assessment of TP53 mutations ROUND 5 (2017): 23 participating centres from 16 countries

18 Round 5 List of Participating Centres: Austria Medical University of Vienna (Vienna) Hungary Semmelweis University (Budapest) Belgium UZ Leuven (Leuven) Hopital Erasme (Brussels) Italy University of Bari (Bari) Asst Papa Giovanni XXIII (Bergamo) Brasil Instituto Nacional de Cancer-INCA (Rio de Janeiro) Czech Republic University Hospital Brno (Brno) Denmark Odense University Hospital (Odense) Finland Tykslab (Torku) France (EFSBFC) (Besançon) CHU Bordeaux (Pessac) Germany AgenDix GmbH (Dresden) Labor Dr. Wisplinghoff (Cologne) MVZ Dr Eberhard & Partner Dortmund (Dortmund) Poland The Maria Skłodowska Curie Memorial Cancer Centre and Institute of Oncology MCMCC (Warsaw) Sweden Sahlgrenska University Hospital (Goteborg) Spain Hospital La Fé (Valencia) Switzerland Kantonsspital St.Gallen (St Gallen) The Netherlands UMC Utrecht - 2 departments (Utrecht) The United Kingdom John Radcliffe Hospital (Oxford) King s College Hospital London (London) Round 5 Results: Available in Dec 2017 (ASH meeting)

19 ERIC Certification on the assessment of TP53 mutations Round 6 - Expected deadline for applications: December 15, 2017 Centers Certified in the Round 1 should re-apply in Round 6 Material to be sent: DNA Certified methods: both Sanger sequencing and NGS, Not two methods in one round

20 ERIC TP53 Network Activity: Organization of workshops on TP53 analysis 1st ERIC Workshop on TP53 analysis in CLL (Brno, 2015) 131 participants from 23 countries

21 2nd ERIC Workshop on TP53 analysis in CLL (Stresa, 2017) 134 participants (26 invited speakers, chairs, tutors)

22 ERIC TP53 Workshop Stresa Registration Questionnaire Output 3% 1% 19% 19% 58% 94% Sanger only 4% Sanger + MLPA 2% Sanger + Functional Sanger NGS Sanger + NGS FISH 96% 38% Functional

23 ERIC TP53 Survey Includes both clinical and laboratory questions Aim: better understanding of TP53 analysis and treatment implications of TP53 variants in CLL patients in clinical and laboratory practice More information on survey results will be presented in several lectures this afternoon Supported by Gilead

24 N=81 ERIC TP53 Survey

25 N=81 ERIC TP53 Survey - PARTICIPANTS

26 ERIC TP53 Survey - CLINICIANS N=33 N=33

27 N=55 ERIC TP53 Survey - DIAGNOSTICIANS

28 ACKNOWLEDGEMENTS Jitka Malčíková Šárka Pavlová Karla Plevová Karol Pál Boris Tichý Michael Doubek Certifying Centers: Stephan Stilgenbauer Eugen Tausch Richard Rosenquist Lesley Ann Sutton Jitka Malčíková Natalie Sorolla Training Centers Representatives Paolo Ghia Kostas Stamatopoulos Arnon Kater Carol Moreno Emili Montserrat Natalie Sorolla - ERIC office THANK YOU FOR YOUR ATTENTION!

BASIC PROCEDURES SAMPLING, MATERIAL, SANGER SEQUENCING

Technical aspects of TP53 mutation analysis: BASIC PROCEDURES SAMPLING, MATERIAL, SANGER SEQUENCING Sarka Pavlova University Hospital and Masaryk University, Brno, Czech republic TP53 gene in CLL: KEEP