ARTICLES
Hardt M, Kaiser F, Voss T et al
Pre-analytical properties of different respiratory viruses for PCR-based detection:
Comparative analysis of sampling devices and sample stabilization solutions
New Biotechnology Vol 79, March 24, 2024, pp 60-70
Supported by data that was generated during the SPIDIA project, researchers from BBMRI.at partner Med Uni Graz recently published a paper on implications of inter-patient variability in ischemic injury for the pre-analytical phase in research and diagnostics.
Groiss S, Viertler C., Kap M. et al
Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome
New Biotechnology, Vol 79, March 25, 2024, pp 20-29
In their recent publication, researchers from BBMRI.at partner Medical University of Graz evaluated the applicability of ISO and CEN/TS standards for the pre-analytical quality of whole venous blood for circulation cell free DNA (ccfDNA) and for circulating tumor cells (CTC).
Bonstingl L, Skofler C, Ulz C, et al
Clinical application of ISO and CEN/TS standards for liquid biopsies - information everybody wants but nobody wants to pay for (preprint)
Oelmueller U, Safwat N
Liquid biopsies: Brilliant potential but highly workflow dependent
Medical Laboratory Observer, February 20, 2023 - open access
2 SPIDIA4P tissue technology disseminations in conjunction with standardized and pre-analytical workflows for microbiome analysis:
Radani N., Metwaly A, et al
Analysis of Fecal, Salivary, and Tissue Microbiome in Barrett’s Esophagus, Dysplasia, and Esophageal Adenocarcinoma
Gastro Hep Advances 2022;1:755–766 - open access
Barroux M, Horstmann J, et al
Histological evaluation of PAXgene tissue fixation in Barrett’s esophagus and esophageal adenocarcinoma diagnostics
Virchows Archiv (2023) 482:887–898 - open access
Abuja, P.M.; Pabst, D.; Bourgeois, B.; Loibner, M.; Ulz, C.; Kufferath, I.; Fackelmann, U.; Stumptner, C.; Kraemer, R.; Madl, T.; Zatloukal, K.
Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability
Int. J. Mol. Sci. 2023, 24, 8010 - open access
Researchers from BBMRI.at partner Med Uni Graz, who also have contributed the development of pre-analytical quality standards for FFPE tissue for DNA analyses, investigated the effect of residual humidity in paraffin-embedded tissue on RNA and DNA quality.
Stumptner, C; Stadlbauer, V; O'Neil, D; Gessner, A; Hiergeist, A; Zatloukal, K; Abuja, P.M.
The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit?
Nutrients 2022, 14, 1976 - open access
Experts from BBMRI.at took part in the development of the European norm "CEN/TS 17626:2021 Molecular in vitro diagnostic examinations - Specifications for pre-examination processes for human specimen - Isolated microbiome DNA" in the context of the H2020 project SPIDIA4P. Now, several authors from Med Uni Graz together with other microbiome experts, published a paper describing the implications of this diagnostic standard for research and development (R&D)
Shekhovtsov, V.A.; Eder, J.
Metadata Quality for Biobanks. Appl. Sci. 2022, 12, 9578 - open access
Publication by BBMRI.at partner Med Uni Wien / MedUni Wien Biobank
For reproducible research, high-quality samples are essential. However, also high quality data are a prequisite for good research, because the "garbage in – garbage out" paradigm also accounts to data.
In this publication, the BBMRI.at authors list the properties of biobanks that are most important for metadata quality management and provide a set of metadata quality attributes and their metrics in a design science approach.
De Martino E, Medeot C, D´Amico L, Stanta G, Bonin S
Impact of standardization in tissue processing: the performace of different fixatives
New Biotechnology, Vol. 71, Nov. 2022, pages 30-36 - open access
Mueller H, Holzinger A, Plass M, Brcic L, Stumptner C, Zatloukal K
Explainability and causability for artificial intelligence-supported medical image analysis in the context of the European In Vitro Diagnostic Regulation
New Biotechnology, Vol. 70, Sept. 2022, pages 67-72 - open access
Stumtpner C, Stadlbauer V, O´Neil D, Gessner A, Hiergeist A, Zatloukal K, Abuja PM
The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit?
Nutrients 2022 14(9), May 9, 2022
CEN/TS 17626, the European pre-analytical standard for human specimens intended for microbiome DNA analysis, was published in 2021. It is relevant for in vitro diagnostic (IVD) manufacturers and diagnostic laboratories but also for biobanks and regulatory bodies and as it is considered the state of the art.
The authors present in their paper, why standards are needed in biomedical research, what pre-analytical standards can accomplish, and which elements of the pre-analytical workflow they cover.
Hardt M, Foederlein-Hoebenreich E, Freydl S, Kouros A, Loibner M, Zatloukal K
Pre-analytical sample stabilization by different sampling devices for PCR-based COVID-19 diagnostics
New Biotechnology, Vol. 70, September 25, 2022, pages 19-27
In cooperation with SPIDIA4P partners, the EU HORIZON 2020 project NESARSDia at the Medical University Graz has recently led to this scientific publication that stresses the pre-analytical factors including different sample collection devices for SARS-CoV-2 diagnostics.
NESARSDia is a project under the umbrella of the European Research Infrastructure on Highly Pathogenic Agents (ERINHA/ ERINHA Advance)
Read more about NESARSDia and ERINHA here
Editors: Hainaut, P., Vaught, J., Zatloukal, K., Pasterk, M. (Eds.)
Book: "Biobanking of Human Biospecimens - Lessons from 25 Years of Biobanking Experience", 2nd edition
Springer, Sept. 2021
BBMRI.at and SPIDIA4P members contributed to this book which covers multiple significant experiences in developing biobanks
that have served as reference/models in the community.
It also offers a deep insight into major technological and societal challenges in the field of biobank and personalized medicine.
Voss T; Ullius A; Schoenborn M; Oelmueller U
Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets:
A study design proposal
PLOS ONE, July 6, 2021 - open access
Ghini V, Abuja M P, Polasek O, Kozera L, Laiho P, Anton G, Zins M, Klovins J, Metspalu A, Wichmann H E, Gieger C, Luchinat C, Zatloukal K, Turano P
Metabolomic Fingerprints in Large Population Cohorts: Impact of Preanalytical Heterogeneity
Clinical Chemistry, hvab092, 05.07.2021 - open access
P. Fattorini; C. Forzato; D. Tierno; E. De Martino; E. Azzalini; V. Canzonieri; G. Stanta; S. Bonin
A Novel HPLC-Based Method to Investigate on RNA after Fixation
International Journal of Molecular Sciences, October 2020 - open access
Oelmueller, U.
Standardization of generic pre-analytical procedures for in vitro diagnostics for personalized medicine
Editorial - New Biotechnology, Vol 60, January 25, 2021 - open access
Salvianti F.; Gelmini S.; Costanza F.; Mancini I.; Sonnati G.; Simi L.; Pazzagli M.; Pinzani P.
The pre-analytical phase of the liquid biopsy
New Biotechnology, Vol. 55, March 2020
Bonin S.; Stanta G.
Pre-analytics and tumor heterogeneity
New Biotechnology, Vol. 55, March 2020 - open access
Berrino E, Annaratone L, Miglio U, Maldi E, Piccinelli C, Peano E, Balmativola D, Cassoni P, Pisacane A, Sarotto I, Venesio T, Sapino A, Marchiò C
Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer
Frontiers in Oncology, February 19, 2020 - open access
Mueller H, Dagher G, Loibner M, Stumptner C, Kungl P, Zatloukal K
Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management
Current Opinion in Biotechnology, Vol 65, October 2020 - open access
Compton, C., et al
Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine
Arch Pathol Lab Med (2019) 143 (11): 1346–1363, July 2019
Lampignano, R.; Neumann, M. H. D.; Weber, S.; Kloten, V.; Herdean, A.; Voss, T.; Groelz, D.; Babayan, A.; Tibbesma, M.; Schlumpberger, M.; Chemi, F.; Rothwell, D. G.; Wikman, H.; Galizzi, J. P.; Bergheim, I. R.; Russnes, H.; Mussolin, B.; Bonin, S.; Voigt, C.; Musa, H.; Pinzani, P.; Lianidou, E.; Brady, G.; Speicher, M. R.; Pantel, K.; Betsou, F.; Schuuring, E.; Kubista, M.; Ammerlaan, W.; Sprenger-Haussels, M.; Schlange, T.; Heitzer, E.; Innovative Medicines Initiative, C.-I. D. C.
Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of
Standardized (Pre)analytical Work Flows
Clin Chem October 2019
Kofanova O, Bellora C, Garcia Frasquilho S, Antunes L, ... Fay Betsou
Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses
New Biotechnology, Volume 54, January 2020- open access
Riegman PJ, Becker KF, Zatloukal K, Pazzagli M, Schroeder U, Oelmueller U
How standardiation of the pre-analytical phase of both research and diagnostic biomaterials can increase reproducibility of
biomedical research and diagnosis
New Biotechnology, Vol. 53, Nov. 2019
Stumptner C, Pabst D, Loibner M, Viertler C, Zatloukal K
The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry
New Biotechnology, Vol. 52, Sept. 2019
Verderio P, Pizzamiglio S, Ciniselli CM
Methodological and statistical issues in developing an External Quality Assessment scheme in laboratory medicine:
Focus on biomarker research
New Biotechnology, Vol. 52, Sept. 2019
Annaratone L, Marchiò C, Sapino A
Tissues under-vacuum to overcome suboptimal preservation
New Biotechnology, Vol. 52, Sept. 2019- open access
Ghini V., Quaglio D, Luchinat C., Turano P.
NMR for sample quality assessment in metabolomics
open access
New Biotechnology, Vol. 52, Sept. 2019- open access
Dagher G, Becker K.F., Bonin S., Foy C., Gelmini S., Kubista M., Kungl P., Oelmueller U., Parkes H., Pinzani P., Riegman P.H.J., Schroeder U., Stumptner C., Turano P., Sjöback R., Wutte A., Zatloukal K.
Pre-analytical processes in medical diagnostics: New regulatory requirements and standards
New Biotechnology, Vol. 52, Sept. 2019
M.S.Lim, Thomas Beyer, A. Babayan, K. Zatloukal et al
Advancing Biomarker Development Through Convergent Engagement: Summary Report of the 2nd International Danube Symposium on Biomarker Development, Molecular Imaging and Applied Diagnostics
March 14–16, 2018; Vienna, Austria, published May 2019 - open access
Betsou F, Giagnaux A, Ammerlaan W, Norris PJ, Stone M
Biospecimen science for blood for Peripheral Blood Mononuclear Cell (PBMC) functional applications
Curr Pathobiol Rep. 2019;7(2):17-27, May 2019 - open access
Ammerlaan W, Betsou F
Biospecimen science of blood for cfDNA genetic analyses
Curr Pathobiol Rep. 2019; 7(2):9-15, April 2019 - open acces
Stumptner C, Sargsyan K, Kungl P, Zatloukal K
Crucial Role of high quality biosamples in biomarker development
Handbook of Biomarkers and Precision Medicine, 1st edition, April 2019
Takis PG, Ghini V, Tenori L, Turano P, Luchinat C
Uniqueness of the NMR approach to metabolomics
Trends in Analytical Chemistry, November 2018
Groelz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmueller U
Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows—Venous Whole Blood and Plasma
Current Biopathology Reports, 28 Oct. 2018- open access
Taussig MJ, Fonseca C, Trimmer JS
Antibody validation: a view from the mountains
New Biotechnology, Vol 45, 25 Oct. 2018
Groelz D, Viertler CH, Pabst D, Dettmann N, Zatloukal K
Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues
PLOS ONE, September 2018- open access
Lewczuk P, Gaignaux A, Kofanova O, Ermann N, Betsou F, Brandner S, Mroczko B, Blennow B, Strapagiel D, Paciotti S, Vogelgsang J, Roehrl MH, Mendoza S, Kornhuber J, Teunissen CH
Interlaboratory proficiency processing scheme in CSF aliquoting: implementation and assessment based on biomarkers of Alzheimer’s disease
BioMed Central, Alzheimer´s Disease & Therapy, August 2018 - open access
Vignoli A, Ghini V , Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C.
High‐throughput metabolomics by 1D NMR
Angewandte Chemie International Edition, July 2018 - open access
Greytak S, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall A, Wheeler DA, Doddapaneni HV and Moore HM
National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed,
Paraffin-Embedded Tissue
Biopreservation and Biobanking, Vol. 16, No. 4, August 2018
Zatloukal, Stumptner, Kungl, Müller
Biobanks in personalized medicine
Expert Review of Prec Med & Drug Dev, Vol. 3, 2018, Issue 4, April 2018
Doucet M, Becker KF, Björkman J, Bonnet J, Clément B, Daidone MG, Duyckaerts C, Erb G, Haslacher H, Hofman P, Huppertz B, Junot C, Lundeberg J, Metspalu A, Lavitrano M, Litton JE, Moore HM, Morente M, Naimi BY, Oelmueller U, Ollier B, Parodi B, Ruan L, Stanta G, Turano P, Vaught J, Watson P, Wichmann HE, Yuille M, Zaomi M, Zatloukal K, Dagher G.
Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking
Biopreserv Biobank. 2017 Jun;15(3):270-276.
Loibner et al.
Protocol for HER2 FISH Using a Non-cross-linking, Formalin-free Tissue Fixative to Combine Advantages of Cryo-preservation and Formalin Fixation.
J. Vis. Exp. (130), e55885, doi:10.3791/55885 (2017).
Kap M, Smedt F, Oosterhuis W, Winther R, Christensen N, Reischauer B, Viertler Ch, Groelz D, Becker KF, Zatloukal K, Langer R, Slotta-Huspenina J, Koppany B, de Jong B, Oelmuller W, Riegman P
Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents
PLoS One. 2011 Nov 17.
Ciniselli CM, Pizzamiglio S, Malentacchi F, Gelmini S, Pazzagli M, Hartmann CC3, Ibrahim-Gawel H, Verderio P.
Combining qualitative and quantitative imaging evaluation for the assessment of genomic DNA integrity: The SPIDIA experience.
Anal Biochem. 2015 Jun 15
Malentacchi F, Pizzamiglio S, Verderio P, Pazzagli M, Orlando C, Ciniselli CM, Günther K, Gelmini S.
Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): the SPIDIA-DNAplas External Quality Assessment experience.
Clin Chem Lab Med. 2015 Apr 17
Kap M, Lam KH, Ewing-Graham P, Riegman P.
A Reference Image Based Method for Optimization of Clinical Immunohistochemistry.
Histopathology. 2015 Jan 7. doi: 10.1111/his
Kap M.
The Pre-analytical Phase of Pathology Research and Diagnostics (PhD thesis)
Erasmus University Rotterdam. 2014 Dec
Van der Linden A, Blokker BM, Kap M, Weustink AC, Riegman PH, Oosterhuis JW.
Post-mortem tissue biopsies obtained at minimally invasive autopsy: an RNA-quality analysis.
PLoS One. 2014 Dec 22;9(12):e115675
Malentacchi F, Ciniselli CM, Pazzagli M, Verderio P, Barraud L, Hartmann CC5, Pizzamiglio S, Weisbuch S, Wyrich R, Gelmini S.
Influence of pre-analytical procedures on genomic DNA integrity in blood samples: The SPIDIA experience.
Clin Chim Acta. 2014 Dec 6;440:205-10
Malentacchi F, Pazzagli M, Simi L, Orlando C, Wyrich R, Günther K, Verderio P, Pizzamiglio S, Ciniselli CM, Zhang H, Korenková V, Rainen L, Bar T, Kubista M, Gelmini S.
SPIDIA-RNA: Second External Quality Assessment for the Pre-Analytical Phase of Blood Samples Used for RNA Based Analyses.
PLoS One. 2014 Nov 10;9(11):e112293
Zhang H, Korenková V, Sjöback R, Svec D4, Björkman J, Kruhøffer M, Verderio P, Pizzamiglio S, Ciniselli CM, Wyrich R, Oelmueller U, Kubista M, Lindahl T, Lönneborg A, Rian E.
Biomarkers for monitoring pre-analytical quality variation of mRNA in blood samples.
PLoS One. 2014 Nov 4;9(11):e111644
Gündisch S, Slotta-Huspenina J, Verderio P, Ciniselli CM, Pizzamiglio S, Schott C, Drecoll E, Viertler C, Zatloukal K, Kap M, Riegman P, Esposito I, Specht K, Babaryka G, Asslaber M, Bodó K, den Bakker M, den Hollander J, Fend F, Neumann J, Reu S, Perren A, Langer R, Lugli A, Becker I, Richter T, Kayser G, May AM, Carneiro F, Lopes JM, Sobin L, Höfler H, Becker KF.
Evaluation of colon cancer histomorphology: a comparison between formalin and PAXgene tissue fixation by an international ring trial.
Virchows Arch. 2014 Nov;465(5):509-19
Cacciatore S, Hu X, Viertler C, Kap M, Bernhardt GA, Mischinger HJ, Riegman P, Zatloukal K, Luchinat C, Turano P.
Effects of intra- and post-operative ischemia on the metabolic profile of clinical liver tissue specimens monitored by NMR.
J Proteome Res. 2013 Dec 6;12(12):5723-9
Kap M, Arron GI, Loibner M, Hausleitner A, Siaulyte G, Zatloukal K, Murk JL, Riegman P
Inactivation of Influenza A virus, Adenovirus, and Cytomegalovirus with PAXgene tissue fixative and formalin.
Biopreserv Biobank. 2013 Aug;11(4):229-34
Gündisch S, Grundner-Culemann K, Wolff C, Schott C, Reischauer B, Machatti M, Groelz D, Schaab C, Tebbe A, Becker KF
Delayed Times to Tissue Fixation Result in Unpredictable Global Phosphoproteome Changes.
J Proteome Res. 2013 Oct 4;12(10):4424-4434
Kashofer K, Viertler C, Pichler M, Zatloukal K (2013)
Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis.
PLoS ONE 8(7): e70714. doi:10.1371/journal.pone.0070714
Malentacchi F, Pazzagli M, Simi L, Orlando C, Wyrich R, Hartmann CC, Verderio P, Pizzamiglio S, Ciniselli CM, Tichopad A, Kubista M, Gelmini S.
SPIDIA-DNA: An External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses.
Clinica Chimica Acta, 2013 September 23, 424: 274-286
Gündisch S, Schott C, Wolff C, Tran K, Beese C, Viertler C, Zatloukal K, Becker KF.
The PAXgene Tissue System preserves phosphoproteins in human tissue specimens and enables comprehensive protein biomarker research.
PLoS One, 2013 March 29; 10.1371/journal.pone.0060638
Gündisch S, Hauck S, Sarioglu H, Schott C, Viertler C, Kap M, Schuster T, Reischauer B, Rosenberg R, Verhoef C, Mischinger HJ, Riegman P, Zatloukal K, Becker KF.
Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase.
J Proteome Res. 2012 Dec 7; 11(12):5748-62.
Pazzagli M, Malentacchi F, Simi L, Orlando C, Wyrich R, Günther K, Hartmann CC, Verderio P, Pizzamiglio S, Ciniselli CM, Tichopad A, Kubista M, Gelmini S.
SPIDIA-RNA: First external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses.
Methods. 2013 Jan;59(1):20-31.
Groelz D, Sobin L, Branton P, Compton C, Wyrich R, Rainen L.
Non-formalin fixative versus formalin-fixed tissue: A comparison of histology and RNA quality.
Exp Mol Pathol. 2013 Feb;94(1):188-94.
Viertler C, Groelz D, Gündisch S, Kashofer K, Reischauer B, Riegman PH, Winther R, Wyrich R, Becker KF, Oelmüller U, Zatloukal K.
A New Technology for Stabilization of Biomolecules in Tissues for Combined Histological and Molecular Analyses.
J Mol Diagn. 2012 Sep;14(5):458-66.
Verderio P.
Assessing the Clinical Relevance of Oncogenic Pathways in Neoadjuvant Breast Cancer.
J Clin Oncol. 2012 Jun 1;30(16):1912-5.
Günther K, Malentacchi F, Verderio P, Pizzamiglio S, Ciniselli CM, Tichopad A, Kubista M, Wyrich R, Pazzagli M, Gelmini S.
Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis.
Clin Chim Acta. 2012 Apr 11;413(7-8):779-86.
Bertini I, Cacciatore S, Jensen BV, Schou JV, Johansen JS, Kruhøffer M, Luchinat C, Lisbet Nielsen D, Turano P.
Metabolomic NMR fingerprinting to identify and predict survival of patients with metastatic colorectal cancer.
Cancer Res. 2012 Jan 1;72(1):356-64.
Kap M, Smedts F, Oosterhuis W, Winther R, Christensen N, Reischauer B, Viertler C, Groelz D, Becker KF, Zatloukal K, Langer R, Slotta-Huspenina J, Bodo K, de Jong B, Oelmueller U, Riegman P.
Histological assessment of PAXgene tissue fixation and stabilization reagents.
PLoS ONE 6(11): e27704. doi:10.1371/journal.pone.0027704.
Bernini P, Bertini I, Luchinat C, Nincheri P, Staderini S, Turano P.
Standard operating procedures for pre-analytical handling of blood and urine for metabolomic studies and biobanks.
J Biomol NMR. 2011 Apr;49(3-4):231-43.
Ergin B, Meding S, Langer R, Kap M, Viertler C, Schott C, Ferch U, Riegman P, Zatloukal K, Walch A, Becker KF.
Proteomic analysis of PAXgene-fixed tissues.
J Proteome Res. 2010 Oct 1;9(10):5188-96.