IT Infrastructure and Biobank Annotation
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1 Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw) Director: Prof. Dr. R. Jahns IT Infrastructure and Biobank Annotation Michael Neumann
2 BMBF: National biobank-initiative (centralized BMB) & GBN Germany concentrates national biobanks at five different sites Kiel Berlin GBN Aachen Würzburg Heidelberg Transkript 04/2011,
3 ibdw About us 3
4 ibdw - Governance Independent central common facility University Hospital Julius-Maximilians University Steering committee Budgetary and administrative liability University Hospital External Advisory Board ibdw steering committee 1) President of the Julius-Maximilians-Universität Würzburg 2) Dean of the Medical Faculty Würzburg 3) Medical Director of the University Hospital Würzburg 4) Director of the CCCM 5) Speaker of the CHFC Würzburg 6) Speaker of the ICCR (interdiscipl. center for clinical research) 7) Speaker of the RVZ 8) Chair of the Ethics-committee of the Medical Faculty Würzburg 9) Chairs of Hospitals and Institutes directly contributing to the ibdw Decision in case of conflicting interests external advisory board Members (5a) - F. Betsou, Luxembourg - W. Hoffmann, Greifswald - M. Hummel, Berlin - M. Kiehntopf, Jena - P. Kleihues, Zürich Request/proposal Decision ibdw executive board 1) Director ibdw 2) Director Institute of Pathology 3) Head IT (SMI/ clinical Datawarehouse) 4) One deputy leader of each reseach group or deputy director of each Institution/Hospital contributing to the ibdw. Advice: 5) One representative of the legal departments of the University and the University Hospital Würzburg. 6) One representative of the (local) data protection officer Request/proposal Decision Feasibility ibdw management board (IBDW Management Board) 1) Head ibdw liquid biosamples 2) Head ibdw solid/tissue samples 3) Head ibdw IT-section (BBMS) 4) Responsible ibdw QM/QC 5) (CFO ibdw) 4 Scientific merits (IBDW Scientific Advisory Board) internal scientific advisory board 1) One representative of each research group or representative of each Institution/Hospital contributing to the ibdw incl. biometrician. 2) One or two external scientists 3) Advice: Legal departments/ data protection officer ibdw
5 Central service-unit, cooperating centers Phase I CHFC Würzburg Dpt. Internal Med. I/Cardiology: CHFC-BB and Fabry-BB ibdw (liquid BM) Dpt. Urology: Biobank Uro-oncology, BDUW ibdw (solid BM) Dpt. Surgery: Biobank GI-tumours, GSBB CCC Mainfranken RVZ Würzburg Dpt. Pharmacology: ETiCS-BB Dpt. Dermatology: SCIAD-BB ibdw (solid BM) Inst. Pathology: LBB-WÜ 5
6 Central service-unit, National Cohort (assoc.) STAAB-study CHFC Würzburg Dpt. Internal Med. I/Cardiology: CHFC-BB and Fabry-BB ibdw (liquid BM) National Cohort (assoc.): lower-franconian (healthy) volunteers Dpt. Neurology: Neuro-BB Dpt. Urology: Biobank Uro-oncology, BDUW ibdw (solid BM) Dpt. Surgery: Biobank GI-tumours, GSBB CCC Mainfranken RVZ Würzburg Dpt. Pharmacology: ETiCS-BB Dpt. Dermatology: SCIAD-BB Dpt. Orthopedy: MSCC ibdw (solid BM) Inst. Pathology: LBB-WÜ 6
7 Central service-unit, cooperating centers Phase II CHFC Würzburg Dpt. Internal Med. I/Endocrinology: WAT-BB Dpt. Internal Med. I/Nephrology: 4D-BB Dpt. Internal Med. I/Cardiology: CHFC-BB and Fabry-BB ibdw (liquid BM) Dpt. Nucl. Medicine: TC-Biobank Dpt. Neurosurgery: NSBB Dpt. Neurology: Neuro-BB Dpt. Urology: Biobank Uro-oncology, BDUW ibdw (solid BM) Dpt. Surgery: Biobank GI-tumours, GSBB CCC Mainfranken Dpt. Psychiatry: K4P-BB RVZ Würzburg Dpt. Pharmacology: ETiCS-BB Dpt. Dermatology: SCIAD-BB Dpt. Orthopedy: MSCC ibdw (solid BM) Brainbank Center Würzburg: BNE-II BB Inst. Pathology: LBB-WÜ 7
8 IT Infrastructure IT Personell Servicezentrum Medizin Informatik (SMI) Research & Education Dedicated personell for departments / responsibilities Laboratory Services 4.0 FTE ibdw 2.5 FTE FTE Clinical Trials 1.0 FTE Biobank Management Software CentraXX (Kairos GmbH, Bochum) Clinical Annotations CentraXX Pathology??? 8
9 Two different CentraXX Systems 9
10 Timeline Feb 2013 May 2013 Nov 2013 Feb 2014 May 2014 Aug 2014 Nov
11 Development & Users Development Kairos Own development Users trained Tissue 6 MLS (Medical Laboratory Scientist) Liquid 3 MLS (Medical Laboratory Scientist) 11
12 CentraXX Annotation Data 12
13 Annotation Data Concept Core data Pseudonym Gender Year of Birth Ethnicity (according UK-Biobank) Patient's Consent (Date, Type) Liquid Core Data Segment Diagnosis Diagnosis (ICD) Diagnosis Date Diagnosis Type Segment Tissue Sample-ID Timestamp Sample Collection Warm, Cold Ischemia Tumordocumentation (TNM, Gleason,...) Grading Histology Segment Liquid Sample-ID Timestamp Sample Collection Material Volume Segment Laboratory Sample-ID Timestamp Sample Collection Lab-Parameter (NA, K, Ca,...) Segment Clinical Trial XY Sample-ID Timestamp Sample Collection Individual Annotations 13
14 Data Flow 14
15 Query Concept # samples / data Yes / No Query Interface predefined variables / parameters to access segment data user restrictions / permission by roles Query Management Layer predefined queries with static clauses allowing requests for material only implicit clauses ensure k-anonymity, e.g. where result count from distinct individuals > 10 15
16 Query CentraXX 16
17 Query padawan* *patient data warehouse nextgeneration 17
18 Query SAP Medical Research Insight 18
19 Query Summary Some ideas on Query concepts No central data repository (yet) Project PaDaWan Project Medical Research Insight (SAP Innovation Center Potsdam, NCT) i2b2 (?) Access policy will (have to) be developed 19
20 MIABIS Check Samples Sample Collection Participant white Black Mixed Asian Chinese Other 20
21 Pseudonymization 21
22 External Cooperation Bavarian Red Cross (BSD) 22
23 Team ibdw 23
24 Electronic Consent Management (Broad consent) ibdw Consent Statistics as of (n = 208) 4% 4% 92% signed consent rejected handed out 24
25 Consent Status consent status unknown patient's consent not (yet) requested consenting not permitted (< 18 years) consent initially rejected documents have been handed out patient's decision pending consent signed and valid consent duration one / five years Permission to collect ibdw samples consent withdrawn by patient consent period expired 25
26 Integration into Clinical Routine Labels have different layout Sorted by routine / ibdw Routine Lab Generating sample IDs and labels ibdw Clinical Trial 26
27 Automation: Sample Tracking Consequent use of barcode reading and use of touch-screen GUI Routine logistics 27
28 Automation: Sample Tracking Make use of timestamp information Routine logistics Monitor temperatures 28
29 Automation: Sample Reception and Processing Automation even for externals Workflow driven sample processing 29
30 Automation: Sample Storage Direct control of automated freezers 30
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