Appl Clin Inform 2010; 01(04): 419-429
DOI: 10.4338/ACI-2010-05-RA-0034
Research Article
Schattauer GmbH

IT Infrastructure Components for Biobanking

H.U. Prokosch
1   Chair of Medical Informatics, University of Erlangen-Nuremberg, Germany
,
A. Beck
1   Chair of Medical Informatics, University of Erlangen-Nuremberg, Germany
,
T. Ganslandt
1   Chair of Medical Informatics, University of Erlangen-Nuremberg, Germany
,
M. Hummel
2   Dept. of Pathology, Charité – University Hospital Berlin, Germany
,
M. Kiehntopf
3   Dept. of Clinical Chemistry, University of Jena, Germany
,
U. Sax
4   Division of Information Technology, Dept. of Medical Informatics, Univ. Medical Center Göttingen, Germany
,
F. Ückert
5   Dept. of Medical Informatics, University of Münster, Germany
,
S. Semler
6   TMF e.V. Berlin, Germany
› Author Affiliations
Further Information

Correspondence to:

Prof. Dr. Hans-Ulrich Prokosch
Chair of Medical Informatics
University of Erlangen-Nuremberg
Krankenhausstr. 12
91054 Erlangen
Germany

Publication History

received: 29 May 2010

accepted: 26 August 2010

Publication Date:
16 December 2017 (online)

 

Summary

Objective: Within translational research projects in the recent years large biobanks have been established, mostly supported by homegrown, proprietary software solutions. No general requirements for biobanking IT infrastructures have been published yet. This paper presents an exemplary biobanking IT architecture, a requirements specification for a biorepository management tool and exemplary illustrations of three major types of requirements.

Methods: We have pursued a comprehensive literature review for biobanking IT solutions and established an interdisciplinary expert panel for creating the requirements specification. The exemplary illustrations were derived from a requirements analysis within two university hospitals.

Results: The requirements specification comprises a catalog with more than 130 detailed requirements grouped into 3 major categories and 20 subcategories. Special attention is given to multitenancy capabilities in order to support the project-specific definition of varying research and bio-banking contexts, the definition of workflows to track sample processing, sample transportation and sample storage and the automated integration of preanalytic handling and storage robots.

Conclusion: IT support for biobanking projects can be based on a federated architectural framework comprising primary data sources for clinical annotations, a pseudonymization service, a clinical data warehouse with a flexible and user-friendly query interface and a biorepository management system. Flexibility and scalability of all such components are vital since large medical facilities such as university hospitals will have to support biobanking for varying monocentric and multicentric research scenarios and multiple medical clients.


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Conflict of interest

The author(s) declare that they have no competing interests.

  • References

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  • 2 Grant A. et al. Integrating feedback from a clinical data warehouse into practice organisation. Int J Med Inform 2006; 5 (3-4) 232-239.
  • 3 Rubin DL, Desser TS. A data warehouse for integrating radiologic and pathologic data. J Am Coll Radiol 2008; 5 (03) 210-217.
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  • 6 Brandt CA. et al. TrialDB: A web-based Clinical Study Data Management System. AMIA Annu Symp Proc 2003; 794.
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  • 14 Posch MG. et al. The Biomaterialbank of the German Competence Network of Heart Failure (CNHF) is a valuable resource for biomedical and genetic research. Int J Cardiol 2008; 136: 118-111. Doi:10.1016/j.ijcard.2008.03.089.
  • 15 Angelow A. et al. Methods and implementation of a central biosample and data management in a three-centre clinical study. Computer methods and programs in biomedicine 2008; 91: 82-90.
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  • 17 Loft S, Poulsen HE. Cancer risk and oxidative DNA damage in man. J Mol Med 1996; 74: 297-312.
  • 18 Creation and Governance of Human Genetic Research Databases. OECD Publishing. 25 October 2006. ISBN-92-64-02852-8.
  • 19 Yuille M. et al. Biobanking for Europe. Brief Bioinformatics 2007; 9: 14-24.
  • 20 Patel AA. et al. An informatics model for tissue banks –lessons learned from the Cooperative Prostate Cancer Tissue Resource. BMC Cancer 2006; 6: 120.
  • 21 Patel AA. et al. The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience. BMC Cancer 2005; 5: 108.
  • 22 Ölund G, Lindqvist P, Litton JE. BIMS: An information management system for biobanking in the 21st century. IBM Systems Journal 2007; 46: 171-182.
  • 23 Prokosch HU. et al. TMF IT Strategie, Teilprojekt 3: Erstellung eines Anforderungskatalogs zur ITUnterstützung von Biomaterialbanken und Analyse der derzeit in Deutschland verfügbaren ITWerkzeuge zur Unterstützung des Managements von Biomaterialbanken. TMF Abschlussbericht, 18.1.2010.
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  • 28 Rudan I. et al. "10001 Dalmatians:" Croatia launches its national biobank. Croat Med J 2009; 50 (01) 4-6.
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  • 32 Godard B. et al. Data storage and DNA banking for biomedical research: informed consent, confidentiality, quality issues, ownership, return of benefits. A professional perspective. Eur J Hum Genet 2003; 11 (02) S88-S122. Doi: 10.1038/sj.ejhg.5201114.
  • 33 van Veen EB. et al. TuBaFrost 3: regulatory and ethical issues on the exchange of residual tissue for research across Europe. Eur J Cancer 2006; 42: 2914-2923.
  • 34 Sweeney L. k-Anonymity: A Model for Protecting Privacy. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems 2002; 10 (05) 557-570.
  • 35 Sweeney L. Achieving k-Anonymity privacy protection using generalization and suppression. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems 2002; 10 (05) 571-588.
  • 36 Stark K, Eder H, Zatloukal K. Priority-based k-anonymity accomplished by weighted generalisation structures. Computer Sci 2006; LNCS 4081: 394-404.
  • 37 Betsou F. et al. Standard preanalytical coding for biospecimens: Defining the sample PREanalytical Code. Cancer Epidemiol Biomarkers Prev 19 (Suppl. 04) OF1-8.
  • 38 Watson PH. et al. Evolutionary concepts in biobanking –the BC BioLibrary. J Transl Med 2009; 7: 95. doi: 10.1186/1479-5876-7-95.
  • 39 Betsou F. Biobanks in immunoanalysis and specialised biology. Immunoanalyse et Biologie Spécialisée 2006; 21 (06) 327-332.

Correspondence to:

Prof. Dr. Hans-Ulrich Prokosch
Chair of Medical Informatics
University of Erlangen-Nuremberg
Krankenhausstr. 12
91054 Erlangen
Germany

  • References

  • 1 Butte AJ. Translational Bioinformatics: Coming of Age. J Am Med Inform Assoc 2008; 15 (06) 709-714.
  • 2 Grant A. et al. Integrating feedback from a clinical data warehouse into practice organisation. Int J Med Inform 2006; 5 (3-4) 232-239.
  • 3 Rubin DL, Desser TS. A data warehouse for integrating radiologic and pathologic data. J Am Coll Radiol 2008; 5 (03) 210-217.
  • 4 Barrett JS, Koprowski Jr. SP. The epiphany of data warehousing technologies in the pharmaceutical industry. Int J Clin Pharmacol Ther 2002; 40 (03) S3-S13.
  • 5 Dorda W, Gall W, Duftschmid G. Clinical data retrieval: 25 years of temporal query management at the University of Vienna Medical School. Methods Inf Med 2002; 41 (02) 89-97.
  • 6 Brandt CA. et al. TrialDB: A web-based Clinical Study Data Management System. AMIA Annu Symp Proc 2003; 794.
  • 7 Sahoo U, Bhatt A. Electronic data capture (EDC) –a new mantra for clinical trials. Qual Assur 2003; 3-4: 117-121.
  • 8 Cuticchia AJ, Cooley PC, Hall RD, Qin Y. NIDDK data repository: a central collection of clinical trial data. BMC Med Inform Decis Mak 2006; 6: 19.
  • 9 Welker JA. Implementation of electronic data capture systems: barriers and solutions. Contemp Clin Trials 2007; 3: 329-336.
  • 10 Ene-Iordache B. et al. Developing regulatory-compliant electronic case report forms for clinical trials: experience with the demand trial. J Am Med Inform Assoc 2009; 16 (03) 404-408.
  • 11 El Emam K. et al. The use of electronic data capture tools in clinical trials: Web-survey of 259 Canadian trials. J Med Internet Res 2009; 11 (01) e8.
  • 12 Murray E. et al. Methodological Challenges in Online Trials. J Med Internet Res 2009; 11 (01) e9.
  • 13 Stege A, Hummel M. Erfahrungen bei Einrichtung und Betrieb einer Biobank. Pathologe 2008; (Suppl. 02) 29: 214-217.
  • 14 Posch MG. et al. The Biomaterialbank of the German Competence Network of Heart Failure (CNHF) is a valuable resource for biomedical and genetic research. Int J Cardiol 2008; 136: 118-111. Doi:10.1016/j.ijcard.2008.03.089.
  • 15 Angelow A. et al. Methods and implementation of a central biosample and data management in a three-centre clinical study. Computer methods and programs in biomedicine 2008; 91: 82-90.
  • 16 Sung NS. et al. Central challenges facing the national clinical research enterprise. JAMA 2003; 289 (10) 1278-1287.
  • 17 Loft S, Poulsen HE. Cancer risk and oxidative DNA damage in man. J Mol Med 1996; 74: 297-312.
  • 18 Creation and Governance of Human Genetic Research Databases. OECD Publishing. 25 October 2006. ISBN-92-64-02852-8.
  • 19 Yuille M. et al. Biobanking for Europe. Brief Bioinformatics 2007; 9: 14-24.
  • 20 Patel AA. et al. An informatics model for tissue banks –lessons learned from the Cooperative Prostate Cancer Tissue Resource. BMC Cancer 2006; 6: 120.
  • 21 Patel AA. et al. The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience. BMC Cancer 2005; 5: 108.
  • 22 Ölund G, Lindqvist P, Litton JE. BIMS: An information management system for biobanking in the 21st century. IBM Systems Journal 2007; 46: 171-182.
  • 23 Prokosch HU. et al. TMF IT Strategie, Teilprojekt 3: Erstellung eines Anforderungskatalogs zur ITUnterstützung von Biomaterialbanken und Analyse der derzeit in Deutschland verfügbaren ITWerkzeuge zur Unterstützung des Managements von Biomaterialbanken. TMF Abschlussbericht, 18.1.2010.
  • 24 Asslaber M, Zatloukal K. Biobanks: transnational, European and global networks. Brief Funct Genomic Proteomic 2007; 3: 193-201.
  • 25 Yuille M. et al. The UK DNA banking network: a "fair access" biobank. Cell Tissue Bank 2009; 11: 241-251. Doi: 10.1007/s10561-009-9150-3.
  • 26 Asslaber M. et al. The Genome Austria Tissue Bank (GATiB). Pathobiology 2007; 74 (04) 251-258.
  • 27 Viertler C, Zatloukal K. Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology. Pathologe 2008; 29 (02) 210-213.
  • 28 Rudan I. et al. "10001 Dalmatians:" Croatia launches its national biobank. Croat Med J 2009; 50 (01) 4-6.
  • 29 Reng CM, Debold P, Specker CH, Pommerening K. Generische Lösungen zum Datenschutz für die Forschungsnetze in der Medizin. Schriftenreihe des TMF e. V., Band 1, 2006.
  • 30 Becker R, Ihle P, Pommerening K, Harnischmacher U. Ein generisches Datenschutzkonzept für Biomaterialbanken (Version 1.0),. TMF Bericht, April 2006.
  • 31 Pommerening K, Becker R, Sellge E, Semler SC. Datenschutz in Biomaterialbanken. In: Steyer G, Tolxdorff T. [Eds.]. TELEMED 2006: Gesundheitsversorgung im Netz. Tagungsband zur 11. Fortbildungsveranstaltung und Arbeitstagung –Nationales Forum zur Telematik für die Gesundheit. Berlin: Aka GmbH; 2006: 89-99.
  • 32 Godard B. et al. Data storage and DNA banking for biomedical research: informed consent, confidentiality, quality issues, ownership, return of benefits. A professional perspective. Eur J Hum Genet 2003; 11 (02) S88-S122. Doi: 10.1038/sj.ejhg.5201114.
  • 33 van Veen EB. et al. TuBaFrost 3: regulatory and ethical issues on the exchange of residual tissue for research across Europe. Eur J Cancer 2006; 42: 2914-2923.
  • 34 Sweeney L. k-Anonymity: A Model for Protecting Privacy. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems 2002; 10 (05) 557-570.
  • 35 Sweeney L. Achieving k-Anonymity privacy protection using generalization and suppression. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems 2002; 10 (05) 571-588.
  • 36 Stark K, Eder H, Zatloukal K. Priority-based k-anonymity accomplished by weighted generalisation structures. Computer Sci 2006; LNCS 4081: 394-404.
  • 37 Betsou F. et al. Standard preanalytical coding for biospecimens: Defining the sample PREanalytical Code. Cancer Epidemiol Biomarkers Prev 19 (Suppl. 04) OF1-8.
  • 38 Watson PH. et al. Evolutionary concepts in biobanking –the BC BioLibrary. J Transl Med 2009; 7: 95. doi: 10.1186/1479-5876-7-95.
  • 39 Betsou F. Biobanks in immunoanalysis and specialised biology. Immunoanalyse et Biologie Spécialisée 2006; 21 (06) 327-332.