Update on the ERIC TP53 Network Activities and TP53 Certification Overview and Results of Round 4

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1 Update on the ERIC TP53 Network Activities and TP53 Certification Overview and Results of Round 4 Sarka Pospisilova Jitka Malcikova CEITEC, Masaryk University and University Hospital Brno, Czech Republic ERIC meeting, Mannheim, January 31st, 2017

2 ERIC TP53 NETWORK U.K. Uppsala Copenhagen Amsterdam Paris Ulm Novara Brno Bellinzona Salamanca Thessaloniki

3 ERIC TP53 NETWORK STRUCTURE: Training Centres (11) Sarka Pospisilova, Jitka Malcikova, Brno, Czech Republic Stephan Stilgenbauer, Eugen Tausch, Ulm, Germany Fred Davi', Paris, France Kostas Stamatopoulos, Thessaloniki, Greece Gianluca Gaidano, Novara, Italy Ramon Garcia Sanz, Salamanca, Spain Richard Rosenquist, Uppsala, Sweden and Nordic countries Carsten Niemann, Copenhagen, Denmark Arnon Kater, Amsterdam, Netherlands Davide Rossi, Bellinzona, Switzerland David Gonzalez, Mark Catherwood, Belfast, United Kingdom Certifying Centres Sarka Pospisilova, Jitka Malcikova, Brno, Czech Republic Stephan Stilgenbauer, Eugen Tausch, Ulm, Germany

4 ERIC TP53 NETWORK - ACTIVITIES 1) Organization of regular TP53 certification rounds (twice a year) 2) Organization of 2nd TP53 workshop (autumn 2017, date and venue to be announced) 3) CLL - TP53 mutation database (in collaboration with T. Soussi, in connection with ERIC CLL Database) 4) Update on ERIC Recommendations on TP53 mutation analysis planned for ) ERIC TP53 web tools: Networks TP53 Network a) FAQ on TP53 certification b) Helpdesk (ERIC office + expert in charge) c) Manual for TP53 mutational analysis d) Sanger data analysis software for detection and annotation of low - frequent somatic variants GLASS

GLASS standardized assessment of gene variations from Sanger sequences Pal, [ ], Ghia & Stamatopoulos, Pospisilova & Malcikova, Darzentas also on behalf of the European Research Initiative on CLL

preparation genebank files uploading TP53: validated ERIC s TP53 Analysis Certification samples Assisted detection of: minor variant allele small insertion/deletion Output: standardised table of

5 GLASS standardized assessment of gene variations from Sanger sequences Pal, [ ], Ghia & Stamatopoulos, Pospisilova & Malcikova, Darzentas also on behalf of the European Research Initiative on CLL (ERIC) TP53 Network (paper in revision) GLASS = online bioinformatics tool to discover and report gene variants from Sanger ABI files Available for these genes, more on request: TP53, ATM, NOTCH1 in preparation genebank files uploading TP53: validated ERIC s TP53 Analysis Certification samples Assisted detection of: minor variant allele small insertion/deletion Output: standardised table of variants genomic coordinates proper HGVS (varnomen.hgvs.org) nomenclature (on both DNA and protein, when appl.) dbsnp annotation w link Freely available online - also through ERIC s website:

7 ERIC Certified Centres from all 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)

8 ERIC Certified Centres - 4 Rounds Centres from 24 countries

9 TP53 Certification Update Jitka Malcikova on behalf of ERIC TP53 Certification Centers: Brno, Czech Republic (Sarka Pospisilova, Jitka Malcikova) Ulm, Germany (Stephan Stilgenbauer, Eugen Tausch)

10 TP53 Certification Round 4 University Hospital Brno and CEITEC MU Czech Republic Application deadline: September 15, 2016 Samples Sent to Participants: October 10, 2016 Deadline to Submit Reports: December 15, 2016 Number of Applications: 40 Samples sent: 38 Results delivered: 37 Number of Participating Countries: 17

11 Round 4 - Participants by Country 14 Number of Participants

12 Participating Centers: Belgium AZ Sint-Jan Brugge-Oostende AV (Brugge) Brasil University of Sao Paulo (Sao Paulo) Cyprus Karaiskakio Foundation (Nicosia) Czech Republic Faculty Hospital (Hradec Králové) France (EFSBFC) (Besançon) CHU Nancy Hôpitaux de Brabois (Vandœuvre-lès-Nancy) L'Hôpital Robert Debré - CHU de Reims (Reims) Germany University Hospital Cologne (Cologne) IHO GmbH (Mannheim) Ireland St James s Hospital (Dublin) Israel Tel-Aviv Sourasky Medical Centre (Tel-Aviv) Rambam Medical Centre (Haifa) Italy Azienda Ospedaliero Universitaria Policlinico de Modena (Modena) Poland Medical University of Lublin (Lublin) Portugal Hospital de São João (Porto) The Netherlands Erasmus University Medical Center (Rotterdam). Sanquin Diagnostics (Amsterdam) University Medical Centre Groningen (Groningen) Spain Hospital Clinic de Barcelona (Barcelona) ICO - Hospital Germans Trias i Pujol, IJC (Barcelona) Hospital del Mar (Barcelona) Hospital Universitario de Gran Canaria Dr. Negrín Hospital (Las Palmas de Gran Canaria) Hospital Universitario Central de Asturias (Asturias) Universidad de Navarra - CIMA (Navarra) Complejo Hospitalario de Navarra (Navarra) LABCO (Madrid) H.G.U. Gregorio Marañón (Madrid) Hospital Clínico San Carlos (Madrid) Hospital Universitario Fundació Jiménez Díaz (Madrid) NIM Genetics (Madrid) Hospital La Fé (Valencia) Hospital General Universitario Reino Sofia (Murcia) Sweden Akademiska University Hospital (Uppsala) Karolinska University Hospital (Stockholm) Switzerland University Hospital Basel (Basel) Unilabs (Lausanne) United Kingdom Wessex Regional Genetics Laboratory (Salisbury)

13 Methods used Round 3 NGS; 14 Sanger; 18 NGS; 13 Sanger +MLPA; 2 dhplc +Sanger; 1 HRM +Sanger; 2 Sanger+ MLPA; 1 Sanger; 23 NGS; 6 Round 2 Sanger +MLPA; 1 Sanger; 16 HRM +Sanger; 3

14 Round 4 - sample selection Polymorphism c.108g>a p.p36=; VAF: 50% Sample c.320_331del p.(y107_r110del); VAF=73% Sample c.503a>g p.(h168r); VAF=5% Sample 3 Sample 4 Sample c.734g>a p.(g245d); VAF=50% c.949c>t p.(q317*); VAF=50% c.541c>t p.r181c; VAF=26% c.817c>t p.r273c; VAF=4,5% Common polymorphism c.215c>g p.pro72arg not reported

15 Round 4 Certification requirements Polymorphism c.108g>a p.p36=; VAF: 50% Sample Wild type Sample 2 c.320_331del p.(y107_r110del); VAF=73% Mutated Sample 3 Sample 4 c.503a>g p.(h168r); VAF=5% Wild type/mutated based on detection sensitivity c.734g>a p.(g245d); VAF=50% c.949c>t p.(q317*); VAF=50% Mutated Sample 5 c.541c>t p.r181c; VAF=26% c.817c>t p.r273c; VAF=4,5% Mutated Common polymorphism c.215c>g p.pro72arg not reported

16 Certification requirements Minimal requirements Good laboratory practice requirements Identification of sample 1 as unmutated / TP53 wt Identification of sample 2, 4 and 5 as mutated Correct identification of sample 3 Wild type with detection sensitivity >5%VAF Mutated with detection sensitivity <5% VAF Identification of both mutations in sample 4 Provided lab specific report Covering at least exon 4-9 Covering at least exon 4-10 Correct variant annotation Finished and submitted analysis within 28 days Interpretation not evaluated

17 Results Passed - good laboratory practice; 7 Failed; 2 Did not identify 12nt deletion in sample 2 Passed; 28

Individual feedback Your result Minimal requirements Good laboratory practice requirements Identification of sample 1 as unmutated / TP53 wt

sensitivity <5% VAF Identification of both mutations in sample 4 Provided lab specific report Covering at least exon 4-9 Covering at least exon 4-10

18 Individual feedback Your result Minimal requirements Good laboratory practice requirements Identification of sample 1 as unmutated / TP53 wt Identification of sample 2, 4 and 5 as mutated Correct identification of sample 3 Wild type with detection sensitivity >5%VAF Mutated with detection sensitivity <5% VAF Identification of both mutations in sample 4 Provided lab specific report Covering at least exon 4-9 Covering at least exon 4-10 Correct variant annotation Finished and submitted analysis within 28 days Feedback sent last week Certification valid for 3 years ˣ Centers that failed can re-apply in round 5

19 TP53 Certification Round 5 Deadline for applications : February Samples to be sent to participants: March Deadline to receive reports: May 15, 2017 Results Available: June 2017 (report at ERIC meeting during EHA) Material to be sent: DNA Certified methods: both Sanger sequencing and NGS, Not two methods in one round Number of participants in each round will be restricted to 40

20 TP53 Certification Round 6 Expected deadline for applications : September 15st Centers Certified in the round 1 should re-apply in round 6

TP53 Certification APPLICATION Questionnaire at www.ericll.

21 TP53 Certification APPLICATION Questionnaire at Services TP53 analysis Certification Applications are collected continuously

22 Acknowledgements Project initiators Sarka Pospisilova Paolo Ghia Stephan Stilgenbauer Kostas Stamatopoulos Emili Montserrat University of Ulm Eugen Tausch ERIC Office Natalie Sorolla Martin Fox

ERIC TP53 Network activities and outcomes. Sarka Pospisilova

ERIC TP53 Network activities and outcomes Sarka Pospisilova ERIC TP53 NETWORK 11 Training Centres 3 Certifying Centres Uppsala/Stockholm Belfast Copenhagen Amsterdam Paris Ulm Novara Brno Bellinzona Salamanca