SPIDIA for Personalized Medicine - Standardisation of generic Pre-analytical procedures for In-vitro DIAgnostics for Personalized Medicine

Deliverables

Documents, reports (9)

List of standards available

List of standards available

Definition of the communication campaign and reviewed (M24)

Definition of the communication campaign and reviewed once a year

Summary of the validation studies for demonstrating a reduction of diagnostic mistake

Summary of the validation studies for demonstrating a reduction of diagnostic mistake

List of reference biobanks providing biological resources complying with the standards

List of reference biobanks providing biological resources complying with the standards

Education and training curriculum

Education and training curriculum

Definition of the communication campaign and reviewed (M36)

Definition of the communication campaign and reviewed once a year

Definition of the communication campaign and reviewed (M54)

Definition of the communication campaign and reviewed once a year

Definition of the communication campaign and reviewed (M12)

Definition of the communication campaign and reviewed once a year ( M12, M24, M36, M48)

Statistics, summary of incidents and measures taken published in the public domain (M18)

Statistics, summary of incidents and measures taken published in the public domain and any updated figures will be included in the periodic reports (M36 and M48)

Websites, patent fillings, videos etc. (6)

Newsletter of SPIDIA4P (M24)

Newsletter of SPIDIA4P

Newsletter of SPIDIA4P (M54)

Newsletter of SPIDIA4P

Newsletter of SPIDIA4P (M36)

Newsletter of SPIDIA4P

Final conference agenda

Final conference agenda

Newsletter of SPIDIA4P (M12)

Newsletter of SPIDIA4P (M12, M24, M36, M48)

Sub section for SPIDIA4P established on the SPIDIA website

Sub section for SPIDIA4P established on the SPIDIA website

Publications

Peer reviewed articles (24)

A Novel HPLC-Based Method to Investigate on RNA after Fixation

Author(s): Paolo Fattorini, Cristina Forzato, Domenico Tierno, Eleonora De Martino, Eros Azzalini, Vincenzo Canzonieri, Giorgio Stanta, Serena Bonin
Published in: International Journal of Molecular Sciences, Issue 21/20, 2020, Page(s) 7540, ISSN 1422-0067
DOI: 10.3390/ijms21207540

Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows

Author(s): Rita Lampignano, Martin H.D Neumann, Sabrina Weber, Vera Kloten, Andrei Herdean, Thorsten Voss, Daniel Groelz, Anna Babayan, Marco Tibbesma, Martin Schlumpberger, Francesca Chemi, Dominic G Rothwell, Harriet Wikman, Jean-Pierre Galizzi, Inger Riise Bergheim, Hege Russnes, Benedetta Mussolin, Serena Bonin, Christine Voigt, Hanny Musa, Pamela Pinzani, Evi Lianidou, Ged Brady, Michael R Speicher, Kla
Published in: Clinical Chemistry, Issue 66/1, 2019, Page(s) 149-160, ISSN 0009-9147
DOI: 10.1373/clinchem.2019.306837

Standardization of generic pre-analytical procedures for in vitro diagnostics for personalized medicine

Author(s): Uwe Oelmueller
Published in: New Biotechnology, Issue 60, 2021, Page(s) 1, ISSN 1871-6784
DOI: 10.1016/j.nbt.2020.07.003

Liquid biopsies come of age: towards implementation of circulating tumour DNA

Author(s): Jonathan C. M. Wan, Charles Massie, Javier Garcia-Corbacho, Florent Mouliere, James D. Brenton, Carlos Caldas, Simon Pacey, Richard Baird, Nitzan Rosenfeld
Published in: Nature Reviews Cancer, Issue 17/4, 2017, Page(s) 223-238, ISSN 1474-175X
DOI: 10.1038/nrc.2017.7

Metabolomic Fingerprints in Large Population Cohorts: Impact of Preanalytical Heterogeneity

Author(s): Veronica Ghini, Peter M Abuja, Ozren Polasek, Lukasz Kozera, Päivi Laiho, Gabriele Anton, Marie Zins, Janis Klovins, Andres Metspalu, H -Erich Wichmann, Christian Gieger, Claudio Luchinat, Kurt Zatloukal, Paola Turano
Published in: Clinical Chemistry, 2021, ISSN 0009-9147
DOI: 10.1093/clinchem/hvab092

The pre-analytical phase of the liquid biopsy

Author(s): Francesca Salvianti, Stefania Gelmini, Filomena Costanza, Irene Mancini, Gemma Sonnati, Lisa Simi, Mario Pazzagli, Pamela Pinzani
Published in: New Biotechnology, Issue 55, 2020, Page(s) 19-29, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.09.006

Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling

Author(s): Vincent Plagnol, Samuel Woodhouse, Karen Howarth, Stefanie Lensing, Matt Smith, Michael Epstein, Mikidache Madi, Sarah Smalley, Catherine Leroy, Jonathan Hinton, Frank de Kievit, Esther Musgrave-Brown, Colin Herd, Katherine Baker-Neblett, Will Brennan, Peter Dimitrov, Nathan Campbell, Clive Morris, Nitzan Rosenfeld, James Clark, Davina Gale, Jamie Platt, John Calaway, Greg Jones, Tim Forshew
Published in: PLOS ONE, Issue 13/3, 2018, Page(s) e0193802, ISSN 1932-6203
DOI: 10.1371/journal.pone.0193802

Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues

Author(s): Daniel Groelz, Christian Viertler, Daniela Pabst, Nadine Dettmann, Kurt Zatloukal
Published in: PLOS ONE, Issue 13/9, 2018, Page(s) e0203608, ISSN 1932-6203
DOI: 10.1371/journal.pone.0203608

Biobanks in personalized medicine

Author(s): Kurt Zatloukal, Cornelia Stumptner, Penelope Kungl, Heimo Mueller
Published in: Expert Review of Precision Medicine and Drug Development, Issue 3/4, 2018, Page(s) 265-273, ISSN 2380-8993
DOI: 10.1080/23808993.2018.1493921

High-throughput metabolomics by 1D NMR

Author(s): Alessia Vignoli, Veronica Ghini, Gaia Meoni, Cristina Licari, Panteleimon G. Takis, Leonardo Tenori, Paola Turano, Claudio Luchinat
Published in: Angewandte Chemie International Edition, Issue -, 2018, Page(s) -, ISSN 1433-7851
DOI: 10.1002/anie.201804736

Protocol for HER2 FISH Using a Non-cross-linking, Formalin-free Tissue Fixative to Combine Advantages of Cryo-preservation and Formalin Fixation

Author(s): Martina Loibner, Lisa Oberauner-Wappis, Christian Viertler, Daniel Groelz, Kurt Zatloukal
Published in: Journal of Visualized Experiments, Issue 130, 2017, Page(s) Video article, ISSN 1940-087X
DOI: 10.3791/55885

Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking

Author(s): Marika Doucet, Karl Friedrich Becker, Jens Björkman, Jacques Bonnet, Bruno Clément, Maria-Grazia Daidone, Charles Duyckaerts, Gilles Erb, Helmuth Haslacher, Paul Hofman, Berthold Huppertz, Christophe Junot, Joakim Lundeberg, Andres Metspalu, Marialuisa Lavitrano, Jan-Eric Litton, Helen M. Moore, Manuel Morente, Ben-Youssef Naimi, Uwe Oelmueller, Bill Ollier, Barbara Parodi, Liangliang Ruan, Gior
Published in: Biopreservation and Biobanking, Issue 15/3, 2017, Page(s) 270-276, ISSN 1947-5535
DOI: 10.1089/bio.2016.0053

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

Author(s): M. S. Lim, Thomas Beyer, A. Babayan, M. Bergmann, M. Brehme, A. Buyx, J. Czernin, G. Egger, K. S. J. Elenitoba-Johnson, B. Gückel, A. Jačan, H. Haslacher, R. J. Hicks, L. Kenner, M. Langanke, M. Mitterhauser, B. J. Pichler, H. R. Salih, R. Schibli, S. Schulz, J. Simecek, J. Simon, M. O. Soares, U. Stelzl, W. Wadsak, K. Zatloukal, M. Zeitlinger, M. Hacker
Published in: Molecular Imaging and Biology, Issue 22/1, 2020, Page(s) 47-65, ISSN 1536-1632
DOI: 10.1007/s11307-019-01361-2

NMR for sample quality assessment in metabolomics

Author(s): Veronica Ghini, Deborah Quaglio, Claudio Luchinat, Paola Turano
Published in: New Biotechnology, Issue 52, 2019, Page(s) 25-34, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.04.004

Pre-analytics and tumor heterogeneity

Author(s): Serena Bonin, Giorgio Stanta
Published in: New Biotechnology, Issue 55, 2020, Page(s) 30-35, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.09.007

The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry

Author(s): Cornelia Stumptner, Daniela Pabst, Martina Loibner, Christian Viertler, Kurt Zatloukal
Published in: New Biotechnology, Issue 52, 2019, Page(s) 69-83, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.05.003

Methodological and statistical issues in developing an External Quality Assessment scheme in laboratory medicine: Focus on biomarker research

Author(s): Paolo Verderio, Sara Pizzamiglio, Chiara Maura Ciniselli
Published in: New Biotechnology, Issue 52, 2019, Page(s) 54-59, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.05.001

Pre-analytical processes in medical diagnostics: New regulatory requirements and standards

Author(s): Georges Dagher, Karl-Friedrich Becker, Serena Bonin, Carole Foy, Stefania Gelmini, Mikael Kubista, Penelope Kungl, Uwe Oelmueller, Helen Parkes, Pamela Pinzani, Peter Riegman, Ulrike Schröder, Cornelia Stumptner, Paola Turano, Robert Sjöback, Andrea Wutte, Kurt Zatloukal
Published in: New Biotechnology, Issue 52, 2019, Page(s) 121-125, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.05.002

Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses

Author(s): Olga Kofanova, Camille Bellora, Sonia Garcia Frasquilho, Laurent Antunes, Gael Hamot, Conny Mathay, Kathleen Mommaerts, Arnaud Muller, Brian DeWitt, Fay Betsou
Published in: New Biotechnology, Issue 54, 2020, Page(s) 52-61, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.07.005

Tissues under-vacuum to overcome suboptimal preservation

Author(s): Laura Annaratone, Caterina Marchiò, Anna Sapino
Published in: New Biotechnology, Issue 52, 2019, Page(s) 104-109, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.05.007

How standardization of the pre-analytical phase of both research and diagnostic biomaterials can increase reproducibility of biomedical research and diagnostics

Author(s): P.H.J. Riegman, K.F. Becker, K. Zatloukal, M. Pazzagli, U. Schröder, U. Oelmuller
Published in: New Biotechnology, Issue 53, 2019, Page(s) 35-40, ISSN 1871-6784
DOI: 10.1016/j.nbt.2019.06.007

Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management

Author(s): Heimo Müller, Georges Dagher, Martina Loibner, Cornelia Stumptner, Penelope Kungl, Kurt Zatloukal
Published in: Current Opinion in Biotechnology, Issue 65, 2020, Page(s) 45-51, ISSN 0958-1669
DOI: 10.1016/j.copbio.2019.12.004

Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients

Author(s): Bente Risberg, Dana W.Y. Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James Morris, Vincent Plagnol, Nitzan Rosenfeld, Carlos Caldas, James D. Brenton, Davina Gale
Published in: The Journal of Molecular Diagnostics, Issue 20/6, 2018, Page(s) 883-892, ISSN 1525-1578
DOI: 10.1016/j.jmoldx.2018.07.005

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

Author(s): Enrico Berrino, Laura Annaratone, Umberto Miglio, Elena Maldi, Chiara Piccinelli, Erica Peano, Davide Balmativola, Paola Cassoni, Alberto Pisacane, Ivana Sarotto, Tiziana Venesio, Anna Sapino, Caterina Marchiò
Published in: Frontiers in Oncology, Issue 10, 2020, ISSN 2234-943X
DOI: 10.3389/fonc.2020.00173

Book chapters (1)

Metabolomic Fingerprints in Large Population Cohorts: Impact of Preanalytical Heterogeneity

Author(s): 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
Published in: Oxford ACADEMIE, 2021

Non-peer reviewed articles (4)

Circulating tumor cells and microemboli can differentiate malignant and benign pulmonary lesions

Author(s): Mario Mascalchi, Cristina Maddau, Lapo Sali, Elena Bertelli, Francesca Salvianti, Stefania Zuccherelli, Marzia Matucci, Alessandra Borgheresi, Claudio Raspanti, Monica Lanzetta, Massimo Falchini, Ernesto Mazza, Alessandra Vella, Michaela Luconi, Pamela Pinzani, Mario Pazzagli
Published in: Journal of Cancer, Issue 8/12, 2017, Page(s) 2223-2230, ISSN 1837-9664
DOI: 10.7150/jca.18418

Uniqueness of the NMR approach to metabolomics

Author(s): Panteleimon G. Takis, Veronica Ghini, Leonardo Tenori, Paola Turano, Claudio Luchinat
Published in: TrAC Trends in Analytical Chemistry, 2018, ISSN 0165-9936
DOI: 10.1016/j.trac.2018.10.036

Biospecimen Science of Blood for cfDNA Genetic Analyses

Author(s): Wim Ammerlaan, Fay Betsou
Published in: Current Pathobiology Reports, Issue 7/2, 2019, Page(s) 9-15, ISSN 2167-485X
DOI: 10.1007/s40139-019-00193-7

Antibody validation: a view from the mountains

Author(s): Michael J. Taussig, Cláudia Fonseca, James S. Trimmer
Published in: New Biotechnology, Issue 45, 2018, Page(s) 1-8, ISSN 1871-6784
DOI: 10.1016/j.nbt.2018.08.002

Monographic books (1)

Handbook of Biomarkers and Precision Medicine

Author(s): Stumptner C, Sargsyan K, Kungl P, Zatloukal K
Published in: Handbook of Biomarkers and Precision Medicine, 2019
DOI: 10.1201/9780429202872