Humans; Europe; Biological Specimen Banks; Cohort Studies; Retrospective Studies; Colorectal Neoplasms/genetics; Colorectal Neoplasms/pathology; Colorectal Neoplasms; Statistics and Probability; Information Systems; Education; Computer Science Applications; Statistics, Probability and Uncertainty; Library and Information Sciences
Abstract :
[en] Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. The Biobanking and Biomolecular Resources European Research Infrastructure (BBMRI-ERIC) established a CRC-Cohort with European coverage contributed by 26 biobanks from 12 countries. This retrospective, multi-center study contains structured and curated clinical data, supporting research on biomarkers for early detection, prognosis, and treatment. A phenotypical/clinical data model has been defined and individual-level data from 10,780 CRC patients have been collected at BBMRI-ERIC in the central data deposition service hosted as part of its services. The participating biobanks host additional data, which can be accessed on request and used to derive additional data. This mechanism has been used to extend the collected data with scans of histopathological slides to support research in artificial intelligence in digital pathology and with whole genome sequencing data to pilot a use case of the upcoming European Health Data Space (EHDS). Here we present the methodology, the quality assurance mechanisms, and the implementation of FAIR and FAIR-Health principles applied to build the CRC-Cohort.
Disciplines :
Oncology
Author, co-author :
Holub, Petr ; BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria. petr.holub@bbmri-eric.eu ; Insitute of Computer Science, Masaryk University, Šumavská 525/33, 60200, Brno, Czech Republic. petr.holub@bbmri-eric.eu
Törnwall, Outi; BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
Garcia Alvarez, Eva ; BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria. eva.garcia-alvarez@bbmri-eric.eu
Proynova, Rumyana; BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
Stampe, Florian; BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
Maqsood, Saher; BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
Ataian, Maxmilian; Institute of Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Schlünder, Irene; BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
Carpén, Olli; University of Helsinki, Helsinki, Finland
Meijer, Gerrit; Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
Nenutil, Rudolf; Masaryk Memorial Cancer Institute, Žlutý kopec 543/7, 60200, Brno, Czech Republic
Gofflot, Stéphanie ; Université de Liège - ULiège > Département des sciences de la santé publique
Mate, Sebastian; Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, Krankenhausstraße 12, 91054, Erlangen, Germany
Prokosch, Hans-Ulrich; Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, Krankenhausstraße 12, 91054, Erlangen, Germany ; Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Wetterkreuz 15, 91058, Erlangen-Tennenlohe, Germany
Romano, Paolo ; IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genova, Italy
Pistillo, Daniela; Center for Biological Resources, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
Hoffmeister, Michael; German Cancer Research Center (DKFZ), Division of Clinical Epidemiology of Early Cancer Detection, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
Brobeil, Alexander; Institute of Pathology, Tissue Bank of the National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
Kugic, Amila ; Biobank Graz, Medical University of Graz, Neue Stiftingtalstraße 2/B/2, 8010, Graz, Austria
Huppertz, Berthold; Medical University of Graz, Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Graz, Austria
Paleari, Valentina; Center for Biological Resources, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
Müller, Heimo ; International Biobanking and Education, Medical University Graz, Neue Stiftingtalstrasse 2, 8010, Graz, Austria
Reihs, Robert ; International Biobanking and Education, Medical University Graz, Neue Stiftingtalstrasse 2, 8010, Graz, Austria
Gemoll, Timo; Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Luebeck and University Hospital Clinic Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
Sjöblom, Tobias ; Uppsala University, Dept Immunology, Genetics and Pathology, Dag Hammarskjöldsväg 20, 75185, Uppsala, Sweden
Kyriacou, Kyriacos; The Cyprus Institute of Neurology and Genetics, Iroon Avenue, Agios Dometios, 2371, Cyprus
Martino, Simona di; Pathology Unit and Biobank IRCCS- Regina Elena National Cancer Institute, via elio chianesi 53, Rome, Italy
Ciliberto, Gennaro; IRCCS National Cancer institute Regina Elena, Via Elio Chianesi 53, 00144, Rome, Italy
Kock-Schoppenhauer, Ann-Kristin; IT Center for Clinical Research, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
Oberländer, Martina; Interdisciplinary Biobank Centre - Lübeck, University of Luebeck and University Hospital Clinic Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
Habermann, Jens K; BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria ; IT Center for Clinical Research, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
Husmann, Gabriele; University Cancer Center Frankfurt, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
Edqvist, Per-Henrik D; Uppsala University, Dept Immunology, Genetics and Pathology, Dag Hammarskjöldsväg 20, 75185, Uppsala, Sweden
Zlobec, Inti; Institute of Tissue Medicine and Pathology, University of Bern, Murtenstrasse 31, CH-3008, Bern, Switzerland
Berger, Martin D; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
Boeckmann, Lars; Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Luebeck and University Hospital Clinic Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany ; Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, Strempelstraße 13, 18057, Rostock, Germany
Vella, Joanna; The Centre for Molecular Medicine and Biobanking, University of Malta, MSD2080, Msida, Malta
Felice, Alex; The Centre for Molecular Medicine and Biobanking, University of Malta, MSD2080, Msida, Malta
Pace, Malcolm; The Centre for Molecular Medicine and Biobanking, University of Malta, MSD2080, Msida, Malta
Fallerini, Chiara; University of Siena, Viale Bracci, 1, 53100, Siena, Italy
Renieri, Alessandra ; University of Siena, Viale Bracci, 1, 53100, Siena, Italy
Hadjisavvas, Andreas; Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology The Cyprus, Iroon Avenue, 2371, Ayios Dometios, Nicosia, Cyprus
Sargsyan, Karine; International Biobanking and Education, Medical University Graz, Neue Stiftingtalstrasse 2, 8010, Graz, Austria ; Department of Medical genetics, Yerevan State Medical University Yerevan, Yerevan, Armenia ; Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Loizidou, Maria A; The Cyprus Institute of Neurology and Genetics, Iroon Avenue, Agios Dometios, 2371, Cyprus
Besse-Hammer, Tatiana; CHU Brugmann, Place A. Van Gehuchten 4, 1020, Bruxelles, Belgium
Vogl, Franziska; Biobank Graz, Medical University of Graz, Neue Stiftingtalstraße 2/B/2, 8010, Graz, Austria
Litton, Jan-Eric; Karolinska Instituet, Stockholm, Sweden
Morgan E et al. Global burden of colorectal cancer in 2020 and 2040: incidence and mortality estimates from globocan Gut 2023 72 338 344 10.1136/gutjnl-2022-327736 36604116
Sawicki T et al. A review of colorectal cancer in terms of epidemiology, risk factors, development, symptoms and diagnosis Cancers 2021 13 2025 1:CAS:528:DC%2BB3MXis1SgsLvP 10.3390/cancers13092025 33922197 8122718
Baxter NN et al. Adjuvant therapy for stage ii colon cancer: Asco guideline update Journal of Clinical Oncology 2022 40 892 910 1:CAS:528:DC%2BB38Xmt1Sntbk%3D 10.1200/JCO.21.02538 34936379
Shaukat A Levin TR Current and future colorectal cancer screening strategies Nature Reviews Gastroenterology & Hepatology 2022 19 521 531 10.1038/s41575-022-00612-y
Bretthauer M Colorectal cancer screening Journal of internal medicine 2011 270 87 98 1:STN:280:DC%2BC3MnnsVykug%3D%3D 10.1111/j.1365-2796.2011.02399.x 21575082
Bailey JR Aggarwal A Imperiale TF Colorectal cancer screening: stool dna and other noninvasive modalities Gut and Liver 2016 10 204 1:CAS:528:DC%2BC1cXmtVSitrs%3D 10.5009/gnl15420 26934885 4780449
Harlé, A. Cell-free dna in the management of colorectal cancer. Tumor Liquid Biopsies 253–261 (2020).
Sepulveda AR et al. Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology Archives of Pathology & Laboratory Medicine 2017 141 625 657 1:CAS:528:DC%2BC1MXlsVClu7o%3D 10.5858/arpa.2016-0554-CP
Tan C Du X KRAS mutation testing in metastatic colorectal cancer World journal of gastroenterology: WJG 2012 18 5171 1:CAS:528:DC%2BC38XhsFajtLjE 23066310 3468848
Lynch HT Snyder CL Shaw TG Heinen CD Hitchins MP Milestones of lynch syndrome: 1895–2015 Nature Reviews Cancer 2015 15 181 194 1:CAS:528:DC%2BC2MXisFCnsr4%3D 10.1038/nrc3878 25673086
Ho C et al. A promising deep learning-assistive algorithm for histopathological screening of colorectal cancer Scientific Reports 2022 12 1 9 2022NatSR.12..2H 10.1038/s41598-022-06264-x
Yu G et al. Accurate recognition of colorectal cancer with semi-supervised deep learning on pathological images Nature communications 2021 12 1 13 2021NatCo.12..1M 10.1038/s41467-021-26643-8
Wulczyn E et al. Interpretable survival prediction for colorectal cancer using deep learning NPJ digital medicine 2021 4 10.1038/s41746-021-00427-2 33875798 8055695 71
Vacante M Borzì AM Basile F Biondi A Biomarkers in colorectal cancer: Current clinical utility and future perspectives World journal of clinical cases 2018 6 869 10.12998/wjcc.v6.i15.869 30568941 6288499
Nguyen LH Goel A Chung DC Pathways of colorectal carcinogenesis Gastroenterology 2020 158 291 302 1:CAS:528:DC%2BB3cXhtVOlsbbN 10.1053/j.gastro.2019.08.059 31622622
Muscholl M Lablans M Wagner TO Ückert F OSSE–open source registry software solution Orphanet journal of rare diseases 2014 9 10.1186/1750-1172-9-S1-O9 4249653 O9
Proynova, R., Ataian, M., Törnwall, O. & Holub, P. Technical documentation for contributing to BBMRI- ERIC CRC-Cohort, https://doi.org/10.5281/zenodo.7514312 (2023).
Mate S et al. Pan-european data harmonization for biobanks in ADOPT BBMRI-ERIC Applied Clinical Informatics 2019 10 679 692 10.1055/s-0039-1695793 31509880 6739205
Siegel RL Miller KD Wagle NS Jemal A Cancer statistics, 2023 CA: A Cancer Journal for Clinicians 2023 73 17 48 10.3322/caac.21763 36633525
WHO report on cancer: setting priorities, investing wisely and providing care for all (World Health Organization, 2020).
Howlader, N. et al. Tech. Rep., National Cancer Institute, Bethesda, MD (2020). Based on November 2019 SEER data submission, posted to the SEER web site.
Nunes L et al. Prognostic genome and transcriptome signatures in colorectal cancers Nature 2024 633 137 146 2024Natur.633.137N 1:CAS:528:DC%2BB2cXhslWksbjN 10.1038/s41586-024-07769-3 39112715 11374687
Cerami E et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data Cancer discovery 2012 2 401 404 10.1158/2159-8290.CD-12-0095 22588877 3956037
Gao J et al. Integrative analysis of complex cancer genomics and clinical profiles using the cbioportal Science signaling 2013 6 pl1 pl1 2013AIPC.1547..1G 10.1126/scisignal.2004088 23550210 4160307
de Bruijn I et al. Analysis and visualization of longitudinal genomic and clinical data from the aacr project genie biopharma collaborative in cbioportal Cancer research 2023 83 3861 3867 10.1158/0008-5472.CAN-23-0816 37668528 10690089
xopat: explainable open pathology analysis tool. In Computer Graphics Forum, vol. 42, 63-73 (Wiley Online Library, 2023).
Atalag, K. et al. openehr—a semantically enabled, vendor-independent health computing platform. University College London, (2016).
Principles of health interoperability: SNOMED CT, HL7 and FHIR (Springer, 2016).
Goode A Gilbert B Harkes J Jukic D Satyanarayanan M Openslide: A vendor-neutral software foundation for digital pathology Journal of pathology informatics 2013 4 27 10.4103/2153-3539.119005 24244884 3815078
Linkert M et al. Metadata matters: access to image data in the real world Journal of Cell Biology 2010 189 777 782 1:CAS:528:DC%2BC3cXnt1GnsrY%3D 10.1083/jcb.201004104 20513764 2878938
Leigh, R. et al. OME files-an open source reference library for the OME-XML metadata model and the OME-TIFF file format. BioRxiv 088740 (2017).
Besson, S. et al. Bringing open data to whole slide imaging. In European Congress on Digital Pathology, 3-10 (Springer, 2019).
Schaaf J et al. OSSE goes FAIR-implementation of the FAIR data principles for an open-source registry for rare diseases Studies in health technology and informatics 2018 253 209 213 30147075
Kadioglu D et al. Samply.MDR - a metadata repository and its application in various research networks Studies in Health Technology and Informatics 2018 253 50 54 10.3233/978-1-61499-896-9-50 30147039
Ihaka R Gentleman R R: a language for data analysis and graphics Journal of computational and graphical statistics 1996 5 299 314 10.1080/10618600.1996.10474713
Senf A et al. Crypt4GH: a file format standard enabling native access to encrypted data Bioinformatics 2021 37 2753 2754 1:CAS:528:DC%2BB3MXisVyqtrrP 10.1093/bioinformatics/btab087 33543751 8522443
