ARTICLES

 

Articles generated by SPIDIA and SPIDIA4P project partners:

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 sequecning analyses
New Biotechnology, Volume 54, January 2020- open access

www.sciencedirect.com

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

www.sciencedirect.com

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

www.sciencedirect.com

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

www.sciencedirect.com

Annaratone L, Marchiò C, Sapino A
Tissues under-vacuum to overcome suboptimal preservation
New Biotechnology, Vol. 52, Sept. 2019- open access

www.sciencedirect.com

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

www.sciencedirect.com

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

www.sciencedirect.com

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

SPRINGER.COM

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

www.taylorfrancis.com

Takis PG, Ghini V, Tenori L, Turano P, Luchinat C
Uniqueness of the NMR approach to metabolomics
Trends in Analytical Chemistry, November 2018

TrAC Trends in Analytical Chemistry.com

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

springer.com

Taussig MJ, Fonseca C, Trimmer JS
Antibody validation: a view from the mountains
New Biotechnology, Vol 45, 25 Oct. 2018

sciencedirect.com

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

www.journals.plos.org

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

www.alzres.biomedcentral.com

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

onlinelibrary.wiley.com

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

liebertpub.com

Zatloukal, Stumptner, Kungl, Müller
Biobanks in personalized medicine
Expert Review of Prec Med & Drug Dev, Vol. 3, 2018, Issue 4, April 2018

tandfonline.com

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.

www.liebertpub.com

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).

www.ncbi.nlm.nih.gov

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.

www.journals.plos.org

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

Kap M.
The Pre-analytical Phase of Pathology Research and Diagnostics (PhD thesis)
Erasmus University Rotterdam. 2014 Dec

www.repub.eur.nl

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov

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

www.ncbi.nlm.nih.gov


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.

www.ncbi.nlm.nih.gov

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.

www.ncbi.nlm.nih.gov

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.
 

www.ncbi.nlm.nih.gov

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.

www.ncbi.nlm.nih.gov

Verderio P.
Assessing the Clinical Relevance of Oncogenic Pathways in Neoadjuvant Breast Cancer.
J Clin Oncol. 2012 Jun 1;30(16):1912-5.

www.ncbi.nlm.nih.gov

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.

www.ncbi.nlm.nih.gov

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.
 

www.ncbi.nlm.nih.gov

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.

www.journals.plos.org

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.

www.ncbi.nlm.nih.gov

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.

www.ncbi.nlm.nih.gov