Biobanks. A research infrastructure for the future of nutritional research 1,2 Guadagni F., 1,2 Ferroni P., 1 Spila A., 1 Riondino S., 1,2 Palmirotta R., 1 Valente M.G., 1 Della Morte D., 3 Nanni U., 4 Roselli M. 1 BioBIM (Interinstitutional Multidisciplinary Biobank) San Raffaele Research Center, IRCCS San Raffaele Pisana, Rome; 2 San Raffaele Rome University; 3 Sapienza University of Rome; 3 University of Rome Tor Vergata All these tasks, however, critically depend upon the availability of a large number of standardized specimens at the point that many research activities are seriously invalidated by the heterogeneous quality of the human specimens used. In particular, pre- Repository banks for biological samples are defined as operational units that provide a service for the storage and management of biological material and associated clinical data. These, if properly complemented with dietary assessment of food and nutrient intake, may offer unique opportunities to investigate the relationships between diet, nutritional status, lifestyle and environmental factors and the incidence of several diseases, as in the case of the EPIC study held within the framework of the European network of Biobanks BBMRI. In the BioBIM the possibility to gain exhaustive records on the whole life cycle of biobank stored samples and their quality has been achieved by means of RFID tag technology reporting OLAP data mining Datamart-1 Datamart-2 Datamart-3 external system-1 external system-2 external services quality control & active monitoring of the human specimens used. In particular, pre- analytical variations render the results derived from specimen of different biobanks and, often, within the same biobank, incomparable. Thus, the need to eliminate, as much as possible, all variables arising from specimen collection, preparation or storage, in order to guarantee that the distributed samples meet the required specifications. This would ultimately preserve the accuracy, reproducibility and compara- bility of results among different research groups. means of RFID tag technology and of standard pre-analytical coding system (SPREC code). Moreover, thanks to a Business Intelligence platform and Service Oriented Architectures, the BioBIM is currently involved in a multi- institutional biobanking network of reference within the southern Italy aimed at defining common preanalytical procedures to standardize biospecimen collection and preservation, identifying a set of “key biomarkers” to be used in assessing sample quality and strengthening of the scientific value of biological collections within the network. The BioBIM Project The BioBIM (Interinstitutional Multidisciplinary Biobank, IRCCS San Raffaele Pisana, Rome) is an interinstitutional center that promotes participation of peripheral health structures that do not have biobanking infrastructures. The structural characteristics, organization and management of the BioBIM allows the development of its research potential in a shorter time than a single institution. Moreover, the participation of various centers with diversified health care expertise, determines the multidisciplinary nature of the collection and the ability to create/ develop a network of multicentric and multidisciplinary Institutes. LIS •sample-ID •preanalytical info SPRECbase SPREC encoder LAB DB customization required SPREC-coded information 1 2 3 4 SPREC-codes sample ID SPREC-code 2349087 SER-SST-A-E-N-A-G 2349089 SER-SST-A-E-N-A-F ... ... SPRECware clinical data records Lab-1 data dev1 dev2 dev3 Datawarehouse Lab-2 data devA devB devC external system-A external system-B patient data sample collection Hospitals/ Institutions ETL – data integration We developed a pilot study on a fragment of the life cycle, namely the storage between the end of the preanalytics and the beginning of the analytics, which is usually not traced by automated tools because it typically includes manual handling. Italian network San Camillo - Forlanini Bio.Ca.Re. 5 different disease-based biorepositories have been structured: 1. Cancer diseases 2. Cardiovascular and respiratory diseases 3. Neurodegenerative diseases 4. Developmental disabilities 5. Rare diseases Healthy volunteers are also recruited handling. By adopting RFID devices we identified the possible critical time delays. At 6, 12, 24 and 36 months RFID- tagged specimens cryopreserved at -80°C were successfully read. ROMA National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Diabetes Research Institute University of Miami, Miller School of Medicine, USA International Institute of Anticancer Research, Atene, Grecia San Raffaele Foundation San Raffaele SpA, Catania Stroke Unit, University of Perugia University of Palermo University of Naples Federico II Integrated Biobank of Luxembourg and International Society for Biological and Environmental Repositories (ISBER) Medical Oncology, Department of Systems Medicine, University of Rome “Tor Vergata” Department of Computer, Control, and Management Engineering, Sapienza University of Rome Anti-diabetic Italian network of the Sovereign Order of Malta Department of Surgery, San Camillo Hospital, Roma Department of Surgery, San Giovanni Hospital, Roma Area Vasta Romagna e I.R.S.T. IRCCS San Raffaele Pisana, Rome Italian network ACISMOM San Camillo - Forlanini Hospital, Rome Unità Sanitaria Locale 2 Salerno San Raffaele Cassino Hospital, Rome University of Perugia Stroke Unit BioBIM Bank 1 Bank 2 Bank 3 Bank 4 Bank 5 Healthy donors San Giovanni Addolorata Hospital, Rome Area Vasta Romagna e I.R.S.T.
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Biobanks. A research infrastructure for thefuture of nutritional research
1,2Guadagni F., 1,2Ferroni P., 1Spila A., 1Riondino S., 1,2Palmirotta R., 1Valente M.G.,1Della Morte D., 3Nanni U., 4Roselli M.
1BioBIM (Interinstitutional Multidisciplinary Biobank) San Raffaele Research Center, IRCCS San Raffaele Pisana, Rome;2San Raffaele Rome University; 3Sapienza University of Rome; 3University of Rome Tor Vergata
All these tasks, however, critically depend upon theavailability of a large number of standardizedspecimens at the point that many research activitiesare seriously invalidated by the heterogeneous qualityof the human specimens used. In particular, pre-
Repository banks for biological samples are defined as oper ational units that provide a servicefor the storage and management of biological material and as sociated clinical data. These, ifproperly complemented with dietary assessment of food and n utrient intake, may offer uniqueopportunities to investigate the relationships between di et, nutritional status, lifestyle andenvironmental factors and the incidence of several disease s, as in the case of the EPIC studyheld within the framework of the European network of Biobank s BBMRI.
In the BioBIM the possibility togain exhaustive records onthe whole life cycle of biobankstored samples and theirquality has been achieved bymeans of RFID tag technology
repo
rtin
g
OLA
P
data
min
ing
Datamart -1 Datamart -2 Datamart -3
externalsystem-1
externalsystem-2
exte
rnal
ser
vice
s
quality control& active
monitoring
of the human specimens used. In particular, pre-analytical variations render the results derived fromspecimen of different biobanks and, often, within thesame biobank, incomparable. Thus, the need toeliminate, as much as possible, all variables arisingfrom specimen collection, preparation or storage, inorder to guarantee that the distributed samples meetthe required specifications. This would ultimatelypreserve the accuracy, reproducibility and compara-bility of results among different research groups.
means of RFID tag technologyand of standard pre-analyticalcoding system (SPREC code).Moreover, thanks to aBusiness Intelligence platformand Service OrientedArchitectures, the BioBIM iscurrently involved in a multi-institutional biobankingnetwork of reference withinthe southern Italy aimed atdefining common preanalyticalprocedures to standardizebiospecimen collection andpreservation, identifying a setof “key biomarkers” to be usedin assessing sample qualityand strengthening of thescientific value of biologicalcollections within the network.
The BioBIM ProjectThe BioBIM (Interinstitutional Multidisciplinary Biobank, IRCCSSan Raffaele Pisana, Rome) is an interinstitutional center thatpromotes participation of peripheral health structures that do nothave biobanking infrastructures. The structural characteristics,organization and management of the BioBIM allows thedevelopment of its research potential in a shorter time than asingle institution. Moreover, the participation of various centerswith diversified health care expertise, determines themultidisciplinary nature of the collection and the ability to create/develop a network of multicentric and multidisciplinary Institutes.
LIS
•sample-ID
•preanalytical
info
SPRECbase
SPRECencoder
LAB
DB
customization required
SPREC-coded information
1
2
3
4
SPREC-codes
sample ID SPREC-code
2349087 SER-SST-A-E-N-A-G
2349089 SER-SST-A-E-N-A-F
... ...
SPRECware
clinicaldata
records
Lab-1data
dev1 dev2 dev3
Datawarehouse
Datamart -1 Datamart -2 Datamart -3
Lab-2data
devA devB devC
externalsystem-A
externalsystem-B
patientdata
samplecollection
Hospitals/Institutions
ETL – data integration
We developed a pilot study on afragment of the life cycle, namelythe storage between the end of thepreanalytics and the beginning ofthe analytics, which is usually nottraced by automated tools becauseit typically includes manualhandling.Italian network San Camillo - Forlanini
Bio.Ca.Re.
5 different disease-based biorepositories have been struc tured:1.Cancer diseases2.Cardiovascular and respiratory diseases3.Neurodegenerative diseases4.Developmental disabilities5.Rare diseases
Healthy volunteers are also recruited
handling.
By adopting RFID devices weidentified the possible critical timedelays.
At 6, 12, 24 and 36 months RFID-tagged specimens cryopreservedat -80°C were successfully read.
ROMA
National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
Diabetes Research Institute University of
Miami, Miller School of Medicine, USA
International Institute of Anticancer Research, Atene, Grecia
San Raffaele Foundation
San Raffaele SpA, Catania
Stroke Unit, Universityof Perugia
Universityof Palermo
University of Naples Federico II
Integrated Biobank of Luxembourg and International Society for Biological and Environmental Repositories (ISBER)
Medical Oncology, Department of Systems Medicine, University of Rome “Tor Vergata”
Department of Computer, Control, and Management
Engineering, Sapienza University of Rome
Anti-diabetic Italian network ofthe Sovereign Order of Malta
Department of Surgery, San Camillo Hospital, Roma
Department of Surgery, San Giovanni Hospital, Roma
Area VastaRomagna e I.R.S.T.
IRCCS San Raffaele Pisana, Rome
Italian network ACISMOM
San Camillo - ForlaniniHospital, Rome
Unità Sanitaria Locale 2 Salerno
San Raffaele Cassino Hospital, Rome
University of PerugiaStroke Unit
BioBIM
Bank 1
Bank 2
Bank 3
Bank 4
Bank 5
Healthy
donors
San Giovanni Addolorata Hospital, Rome
Area Vasta Romagna e I.R.S.T.
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