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
Thessaloniki
Brno
Uppsala
Ulm
U.K.
Paris
Novara
Salamanca
Copenhagen
Amsterdam
ERIC TP53 NETWORK
Bellinzona
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
ERIC TP53 NETWORK STRUCTURE:
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 2017 5) ERIC TP53 web tools: www.ericll.org – 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“
ERIC TP53 NETWORK - ACTIVITIES
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: http://www.ericll.org/pages/networks/tp53network http://shiny.bat.infspire.org/glass/
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)
ERIC Certified Centres - 4 Rounds
19
14 12
9 7
6 6 5
4 3
2 2 2 2 2 2 2 2 1 1 1 1 1 1
107 Centres from 24 countries
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)
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
Round 4 - Participants by Country
14
3 3 2 2 2 2
1 1 1 1 1 1 1 1 1
Number of Participants
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)
Participating Centers:
Methods used
Sanger; 16
HRM +Sanger; 3
Sanger +MLPA; 1
NGS; 6
Sanger; 18
HRM +Sanger; 2
dHPLC +Sanger; 1
Sanger +MLPA; 2
NGS; 14
Round 3
Round 2 Sanger;
23 Sanger+MLPA; 1
NGS; 13
Round 4 - sample selection
2 3 4 5 6 7 8 9 10 11 Sample 2
c.320_331del p.(Y107_R110del); VAF=73%
2 3 4 5 6 7 8 9 10 11 Sample 5
c.541C>T p.R181C; VAF=26% c.817C>T p.R273C; VAF=4,5%
2 3 4 5 6 7 8 9 10 11 Sample 3
c.503A>G p.(H168R); VAF=5%
2 3 4 5 6 7 8 9 10 11 Sample 4
c.734G>A p.(G245D); VAF=50% c.949C>T p.(Q317*); VAF=50%
3 4 5 6 7 8 9 10 11 Sample 1 2
Polymorphism c.108G>A p.P36=; VAF: 50%
Common polymorphism c.215C>G p.Pro72Arg not reported
Round 4 Certification requirements
2 3 4 5 6 7 8 9 10 11 Sample 2
c.320_331del p.(Y107_R110del); VAF=73%
2 3 4 5 6 7 8 9 10 11 Sample 5
c.541C>T p.R181C; VAF=26% c.817C>T p.R273C; VAF=4,5%
2 3 4 5 6 7 8 9 10 11 Sample 3
c.503A>G p.(H168R); VAF=5%
2 3 4 5 6 7 8 9 10 11 Sample 4
c.734G>A p.(G245D); VAF=50% c.949C>T p.(Q317*); VAF=50%
3 4 5 6 7 8 9 10 11 Sample 1 2
Polymorphism c.108G>A p.P36=; VAF: 50%
Wild type
Mutated
Mutated
Mutated
Wild type/Mutated based on detection
sensitivity
Common polymorphism c.215C>G p.Pro72Arg not reported
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
Certification requirements
Interpretation not evaluated…
Results Failed; 2
Passed; 28
Passed - good
laboratory
practice; 7
Did not identify 12nt deletion in sample 2
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 sensitivi ty <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
TP53 Certification – Round 5
Deadline for applications : February 15 2017 Samples to be sent to participants: March 15 2017 Deadline to receive reports: May 15, 2017 Results Available: June 2017 (report at ERIC meeting during EHA)
• Number of participants in each round will be restricted to 40
• Material to be sent: DNA • Certified methods: both Sanger sequencing and NGS,
Not two methods in one round
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.org – Services – TP53 analysis Certification Applications are collected continuously
Acknowledgements
University of Ulm Eugen Tausch
ERIC Office Natalie Sorolla
Martin Fox
Project initiators Sarka Pospisilova
Paolo Ghia Stephan Stilgenbauer Kostas Stamatopoulos
Emili Montserrat
Top Related