The data management and interpreta`on challenge

From personal genomics to personal diagnos1cs The data management and interpreta.on challenge Program 11:30 – 11:50 Terry Vrijenhoek Personal genomics -­‐ diagnos1c DNA sequencing 11:50 – 12:10 Peter Walgemoed The Dutch Health Hub 12:10 – 12:30 Maud Radstake Responsible Data Management for Personalised Diagnos1cs Personal genomics Diagnos.c DNA sequencing DNA developments 1953 2001 2010 2012 Utrecht DNA sequencing facility Hubrecht
Institute
WKZ
Children’s Hospital
UMC Utrecht
Stratenum
“It is 'me to develop guidelines to harmonise further implementa'on [of NGS into diagnos'cs]” – Work program Health Council “The primary goal of this program is to develop infrastructure, procedures and guidelines for NGS-­‐based personalized diagnos'cs for na'on-­‐
wide implementa'on.” – Grant applica1on CGD CARDIO – pilot project •  10 (9) pa.ents with cardiomyopathy •  DNA and medical reports •  Iden.fy need for policy Four phases; five topics 1.  Intake – samples and medical reports 2.  Sequencing – library prepara.on, enrichment and sequencing procedures 3.  Data analysis – tools and pipelines 4.  Diagnosis – interpreta.on and counseling 5.  Ethical and legal framework – consent, pa.ent rights, data protec.on, liability GENOME EXOME CARDIO GENE SET Detected variants !"#"
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General observa1on The diagnos.c outcomes for the CARDIO pa.ents are generally similar… …despite the differences in sequencing approach, plaQorm and data analysis So, do we need guidelines? Numbers 3,154,971,228 56,217,673,809 2,885,536,685 2,208,479,859 2,155,162 114,938 5,585 937 111 112 ? Bases in human genome assembly Bases in SOLiD run (2 slides paired-­‐end) 18x Bases covered at least once (93.6%) Bases covered at least 10 x (~70%) SNPs Indels Non-­‐synonymous coding variants Splice sites affected Essen.al splice site affected Stop codon introduced Post-­‐CARDIO RESEARCH PROPOSALS FROM COMMUNITY P-­‐o-­‐C CENTRAL DATA INFRASTRUCTURE •  Ini.a.ve from EMC and LUMC in collabora.on with SURF/
DHH •  Exploring opportuni.es for central data infrastructure •  Features to test: •  Data transport •  Access to central storage •  Virtualisa.on •  Authen.ca.on •  Legal aspects TOWARDS RESPONSIBLE DATA MANAGEMENT IN PERSONALISED DIAGNOSTICS •  Collabora.on with Centre for Society and Genomics •  Mee.ng of minds: technology, clinic, ethics, society, legal •  To facilitate a proposal for a (European) program on societal responsible diagnos.c use of large-­‐scale biomedical data •  Kick-­‐off October 1 Thank you Marcel Mannens Ronald Lekanne Dit Deprez Raoul Hennekam Elcke Kranendonk Correne Ploem Wilbert van Workum Kees van der Berg Derek Butler Adalberto Costessi Bas Reichert Marjolein Kriek Johan den Dunnen Ken Kraaijeveld Gijs Santen Claudia Ruivenkamp Nienke van der Stoep Erik Sistermans Bauke Ylstra Remond Fijneman Jannek Weiss Quinten Waisfisz Frans Hogervorst Hans Kris.an Ploos van Amstel Jasper Saris Marjon van Slegtenhorst Wilfred van Ijcken Ingrid van der Laar Marja Wessels Maarten van den Berg Richard Sinke Morris Swertz Peter van Tintelen Jan Jongbloed Birgit Sikkema Marian Verkerk Nine Knoers Wim Dorlijn Winfried van Eijndhoven Rogier Drenth Gijs van Haaoen Edwin Cuppen Maartje Vogel Bert van der Zwaag Ellen van Binsbergen Mariëlle Swinkels Patrick van Zon Marcel Nelen Chris.an Gilissen Joep de Ligt Joris Veltman Helger Ijntema Ilse Feenstra Steven van Hove Ewout Ouwerkerk Bart de Koning Ingrid Kapels Bert Smeets Arthur van der Wijngaard Rick Kamps Suzanne Frints Marco Rijnen Jan Ghyssaert Simone Guenther Maud Radstake Wybo Dondorp Guido de Wert Tonnie Rijkers Colja Laane Graciela Mar.nez