SPIDIA Newsletter 02
WHAT IS SPIDIA
SPIDIA is a four-year large-scale integrating project that will work on the missing standardisation and improvement of pre-analytical procedures for in vitro diagnostics. SPIDIA’s research and standardisation activities cover all steps from creation of evidence-based guidelines to creation of tools for the pre-analytical phase to testing and optimisation of these tools through the development of novel assays and biomarkers. The consortium is built by seven public research organisations, eight research companies and an official European standards organisation. SPIDIA’s budget is € 13,000,000 with an EC contribution of € 9,000,000.
WHY WAS SPIDIA INITIATED
In vitro diagnostics have enabled a significant progress in medicine. Further progress is expected by new technologies analysing cellular biomolecule profiles as nucleic acids, proteins, and metabolites. Studies have demonstrated that the profiles of these molecules can change drastically during transport and storage thus making a reliable diagnostic or pharmaceutical research unreliable or even impossible. Therefore further progress is limited due to the lack of guidelines in sample collection, handling, stabilisation and storage of clinical samples and due to still missing new and improved sample technologies. The project SPIDIA aims to close this gap by providing guidelines, quality assurance schemes and innovative pre-analytical tools.
SPIDIA is organised around three activities. Each consists of multiple work packages. The first activity leads to pan-European quality assurance schemes and guidelines for the pre-analytical phase of in vitro diagnostics. Such documents will be based on evidence gathered during ring trials to be performed in order to elucidate problematic steps in pre-analytical procedures. These procedures will have a specific focus on DNA, RNA, protein, and metabolite targets isolated from tissue, tumour, whole blood, serum and plasma samples. In addition, quality assurance biomarker(s) will be discovered to serve as indicators for artificial, post collection changes of clinical and biological samples. Our second activity is dedicated to the discovery and integration of breakthrough technologies that strengthen weak steps and links in the pre-analytical phase of in vitro diagnostics. The results are intended to allow the association of classical and molecular diagnostics. This work includes the discovery of novel stabilisation technologies for tissues, blood, and non-invasive samples, such as swab samples to the integration of multiple pre-analytical steps into an automated workflow. Finally, our third activity focuses on management, ethics and spreading of excellence. This activity aims to perform training to disseminate information about discoveries and guidelines to the clinical, scientific and biobanking communities. It will also ensure ethical sensitivity and compliance.
SPIDIA’S PROJECT PROGRESS
Significant progress can be reported. Members of the SPIDIA Consortium:
- Continued large studies for evaluating the newly developed two step tissue fixation and stabilisation technology (PAXgene® Tissue) at different SPIDIA laboratories with meanwhile more than 3400 human tissue samples of different organs and diseases. The samples were collected and processed according to different protocols representing critical parameters for sample quality in a routine clinical setting (e.g. warm/cold ischemia, fixation times and storage conditions). Furthermore, a dedicated study was initiated to evaluate the impact of ischemia on sample quality and to identify biomarkers for tissue sample quality control.
- Within these studies, continued the evaluation of several parameters for tissues stabilized by the new technology mentioned above: morphology, antigenicity, proteins, metabolites, DNA and miRNA, including downstream applications. Based on data generated, the novel tissue fixation and stabilisation system continued to show very promising results in meanwhile various applications. The first results of this thorough evaluation were published: “Proteomic analysis of PAXgene-fixed tissues”, J Proteome Res. 2010 Oct 1;9(10):5188-96. Two additional manuscripts were submitted for publication.
- Continued to integrate the new tissue stabilisation technology into complete standardised pre-analytical workflows and optimized downstream analyses like immunohistochemistry (IHC), morphology analysis, and molecular analysis. The striking benefit of the new technology is better nucleic acids, especially RNA preservation in tissue samples compared to classical formalin fixation while still allowing morphology and IHC analysis from the same sample. This was found already within the first reporting period, but is now confirmed by a large data pool. It was clearly worked out, that the new technology can be used for both, classical histological as well as molecular analyses from the same tissue samples.
- Finalised a prototypical device for tissue collection, stabilisation, shipment and storage for molecular and pathological applications. The container holds a standard histocassette for use in routine clinical pathology workflows. Meanwhile it was tested by different SPIDIA partners for its usability in routine settings.
- In order to develop evidence-based quality guidelines for the pre-analytical phase of blood samples, performed a ring trial with uniform samples shipped to various European laboratories for analysing pre-analytical variations for DNA analysis from blood and plasma samples. 131 applicants were enrolled in the DNA Blood Ring Trial, 67 applicants joined the DNA Plasma Ring Trial. The studies were supported by the European Federation of Clinical Chemistry and Laboratory Medicine (EFCC, www.efcclm.org). The participants extracted DNA according to their current standard procedures. The isolated DNA samples were returned to SPIDIA laboratories (DNA Blood: 118, DNA Plasma: 62) and were analysed for DNA quantity and quality by spectrophotometric measurements, pulsed field gel electrophoresis, real time PCR and for the presence of interfering substances by special PCR assays. In addition, DNA integrity was determined for the plasma samples by using the Isohelix™ Quality Check Kit and the Agilent® DNA Kit.
- Executed a similar ring trial for the analysis of cellular RNA from blood samples. Uniform blood samples, collected in different blood collection tubes, were shipped to 102 participating laboratories, who isolated cellular RNA and shipped it back to SPIDIA laboratories. The received RNA samples (91) were analysed for quality, quantity, RIN value, by several RT-PCR assays and for the presence of interferences by RT-PCR assays. A report about a pilot ring trial, performed with 10 different participating laboratories in order to test the sample logistics and sample evaluation strategy, was submitted for publication.
- Set up a pilot study for analysing pre-analytical variations for protein analysis from blood and plasma samples. Serum, plasma EDTA and P100 collection tubes were used, and samples were analysed at 0h, 4h and 24h by 2D-DIGE analysis and comparison studies to identify decay markers.
- Discovered first promising collection and stabilisation technologies for non- or less invasive sample types and adapted nucleic acid extraction protocols for up-concentration and enrichment of target molecules from sample material.
- Created a unique, encrypted tissue identification system. This system includes scanners, printers and software to ensure correct and complete transfer of information between different media.
- Developed successfully a unique workflow for the integrated tissue management able to track incoming tissue samples from the first steps to the final stained slide for the pathologist to evaluate. This requires a unique identifier that follows the sample through the entire process, a database where all information is stored and middleware that makes this information available to the user via a user interface.
- Performed studies for testing in routine applications a newly developed fully automated protocol for isolation of total RNA including miRNA from stabilised blood samples at different SPIDIA laboratories in order to compare the performance. In addition, a first protocol was developed for automated setup of RT-PCR with the long term aim to combine the sample preparation and the reaction setup protocol into one standardised pre-analytical workflow.
- Presented SPIDIA results at the AMP (Association of Molecular Pathology) 2010 Annual Meeting, at The 3rd Annual Biospecimen Research Network (BRN) Symposium: “Advancing Cancer Research Through Biospecimen Science”, at the Symposium “The Biobank as an Instrument for Economic Development at CERM, Florence, Italy”, and at the ISBER (International Society for Biological and Environmental Repositories) 2010 Annual Meeting & Exhibits “Diversity in Biobanking: Embracing Differences, Harnessing Commonalities”.
- Published "Standard Operating Procedures for pre-analytical handling of blood and urine for metabolomic studies and biobanks” in the Metabolomics Special Issue of the Journal of Biomolecular NMR.
- Were invited to the Public Hearing on Health-related Research Infrastructures which has taken place on October 26, 2010 at the European Parliament, and reported there about the importance of quality assurance schemes and guidelines for the pre-analytical phase of in vitro diagnostics.
- Presented their results during the “2nd International Workshop on Protein Analysis of Tissues - Current views and clinical perspectives” in Munich, Germany on February 17-18, 2011. This workshop provided an overview of recent developments for protein-based methods of clinical tissues and addressed recent approaches to improve the quality of human biobanks.
- Started a cooperation with the Office of Biorepositories and Biospecimen Research (OBBR), National Cancer Institute (NCI), USA, on Biospecimen Research.
- Were invited to the National Cancer Institute / Office of Biorepositories and Biospecimen Reseach Meeting “Evaluation of Cryopreservation and Chemical Stabilization Techniques in Biospecimen Tissue Storage” held on January 13, 2011 in Bethesda, US. Study results obtained by the new tissue fixation / stabilisation technology PAXgene Tissue were presented.
- Held the CLSI (Clinical and Laboratory Standards Institute) Webinar on March 17, 2011 about „Molecular Diagnostic Testing: Updated Specimen Handling“.
WHERE TO MEET US
SPIDIA Partners will present more information on the SPIDIA project at the
- 2011 BRN Symposium:
4th Annual Biospecimen Research Network (BRN) Symposium
“Advancing Cancer Research Through Biospecimen Science”
by The National Cancer Institute Office of Biorepositories and Biospecimen Research (OBBR)
on March 28-29, 2011
at the CERM Magnetic Resonance Center Florence, Italy The meeting is co-organized by EPISODE, CERM, FiorGen & da Vinci European Biobank and will take place from
April 13, 2010
in Bethesda, Maryland, USA
Speakers from SPIDIA:
- Uwe Oelmüller: EU Project SPIDIA Update - Standardization and Improvement of Generic Preanalytical Tools and Procedures for In Vitro Diagnostics
- Sibylle Guendisch: Investigating the Impact of Preanalytical Variables on Protein Quality of Human Tissue Samples
Posters from SPIDIA:
- Sibylle Guendisch et al.: Investigating the Impact of Preanalytical Variables on Protein Quality of Human Tissue Samples
- Daniel Grölz et al.: PAXgene Tissue: A New Tissue Fixation Technology for Simultaneous Preservation of Morphology and Nucleic Acids
- 2011 ISBER Meeting:
International Society for Biological and Environmental Repositories (ISBER) 2011 Annual Meeting & Exhibits
“Impact and Public Benefits of Biorepositories”
on May 15-18, 2011
in Arlington, Virginia (Washington DC)
Speaker from SPIDIA:
- Marcel Kap: PAXgene Tissue System in Routine Pathology; Increased Biobanking Opportunities of the Pathology Archive
- 2011 IFCC Symposium:
IFCC-WorldLab EuroMedLab Berlin 2011
“Standardization of the Pre-Analytical Phase for Biomarkers”
on May 15-19, 2011
in Berlin, Germany
Speakers from SPIDIA:
- Uwe Oelmüller: EU Project SPIDIA - Standardisation and Improvement of Generic Preanalytical Tools and Procedures for In-vitro Diagnostics
- Kurt Zatloukal: Pre-analytical Aspects of Tissue-based Biomarkers
- Mario Pazzagli: Evidence-based Quality Guidelines for the Pre-analytical Phase of Blood Samples
- 2011 TIDES Conference:
TIDES -OligonucleoTIDE and PepTIDE Research, Technology and Product Development Boston 2011
on May 22-25, 2011
in Boston, Massachusetts, USA
Speaker from SPIDIA:
- Uwe Oelmüller: Standardization and Improvement of Generic Pre-analytical Workflows for Human Samples
within “Applications of Nucleic Acids Technologies for Molecular Diagnostics” as one of three parallel symposia running at this conference
- qPCR Symposium:
“Developments in Real-time PCR – From Preanalytics to Molecular Diagnostics“
by SPIDIA Partner TATAA Biocenter
on June 13-17, 2011
in Prague, Czech Republic
Speakers from SPIDIA:
- Uwe Oelmüller: Generic Pre-analytical Workflows: Challenges and Solutions
- Uwe Oelmüller (within SPIDIA invited speakers course): EU Project SPIDIA - Standardization and Improvement of Generic Pre-analytical Tools and Procedures for Sample Workflows
- Mario Pazzagli: The Pre-analytical Phase for Molecular Methods in Blood Samples
- Christian Viertler: The Impact of Tissue Pre-Analytics on Molecular Analyses
- Peter Riegman: How to Work with Biobanked Samples, the Possibilities and Impossibilities
- Mikael Kubista: Single Cell Expression Profiling
- Ales Tichopad: Errors in qPCR Quantification
- Claudio Orlando: Altered Expression of microRNAs in Human Cancer: The Influence of Genetic and Epigenetic Factors
- Mogens Kruhoffer: Extraction and Profiling of mRNA and miRNA from Blood and Plasma
- 2011 DGP Annual Meeting:
Annual Meeting of the German Society of Pathology (Deutsche Gesellschaft für Pathologie (DGP))
on June 16-19, 2011
in Leipzig, Germany
- ESBB Inaugural Conference:
First conference of the European, Middle Eastern & African Society for Biopreservation & Biobanking
“Identifying the challenges and opportunities for biorepositories in the next five years”
on November 16-19, 2011
in Marseille, France
Trademarks: PAXgene® (PreAnalytiX GmbH); Agilent® (Agilent Corporation); Isohelix™ (Cell Projects Ltd.)
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