Rezultaty
Prior to the enrollment of the first subject, we will submit (i) Final version of study protocol as submitted to regulators/ethics committee(s), (ii) Registration number of clinical study in a WHO-or ICMJE- approved registry (with the possibility to post results), (iii) Approvals (ethics committees and national competent authority if applicable) required for invitation/enrolment of first subject in at least one clinical centre.
Exposure DNAme signaturesA list of CpGs which collectively change as a function of exposure to a specific conditionfactor and which can be used to define an index eg smokingindex will be provided
List of Working Groups and ToR for the WGs - EXPANSE/HEAPA first set of working groups will be made and Term of Reference for the WGs will be specified including the selection of work group leaders coleads and members
Reference architectureDocument describing the reference architecture for Information Commons and technical requirements.
Secure platform and recruitmentRecruitment using secure electronic customer receipts analysis platform commenced Plan to recruit 10000 individuals
Report on secure data platformDocumentation of the secure data platform and its integration into HEAP.
Ageing DNAme signaturesA list of CpGs which collectively change as a function of age eg general age signature stem cell polycombgroup target signature replicative age etc will be provided
Report on databases mappedReport on databases mapped and how they contribute to the proper implementation of the GDPR and national legislation. Databases are mapped according to their legal bases, relevant other GDPR issues and options for 'further use' for research. The dataflows for the research, data protection by design, data security at the various in-between phases, controller-processor agreements and the final database(s) are mapped. The report will include recommendations for possible improvements from a GDPR perspective and include a DPIA on processing of data on the CSC platform.
Handover document to next coordinating team – EXPANSE/HEAPDocument summarising network activities and ongoing activities to facilitate a smooth transition to the next team. This document will include concise reports from working groups.
Report on consumer receipts data and sample-derived dataSpecial report about how data from a consenting cohort providing data from consumer receipts may be used for public health in an ethically and data protection compliant way In that context also a DPIA will be performed
Knowledge and information sharing - Phase IReport from activities implemented and resources developed in order to support data providers within the consortium to effectively upload data to HEAP
Report on implementation for research use casesReport describing implementation and experiences from HEAP research use cases.
Report on consumer dataScientific report on consumer data’s potential as a tool for lifestyle assessment including methodology needed to facilitate evidence-based consumer-friendly lifestyle advice. Report on potential exposure to nutrients, chemicals, and additives as accessed by consumer data, and association to health-related outcomes, or absence of such outcomes.
Integrated personal exposome and metabolomics profileA complete report of personal exposome and metabolomics profile, and how these factors may impact the health of the participant, and potential risk for certain diseases. The report may be integrated with findings from WP8 and WP9 to provide a fuller vision of the health of a particular participant.
An established setting for evaluationAn established setting for evaluation of the extent of exposures to the populations in 2 EU countries with consecutive time-windows (continuous population-based enrolment ongoing for 10 to 35 years) allows access to bio-specimens taken at any calendar year of interest for evaluating impact of naturally occurring and iatrogenic exposures to the population. This deliverable is linked to task 3.2.
Knowledge and information-sharing planReport from the mapping of key topics to be addressed as well as the mapping of target audiences including a plan for the elaboration and implementation of learning and informational resources and events
Data availability confirmationAn explicit confirmation that the data used in the project is publicly available and can be freely used for the purposes of the project. (KI, M6)
Ontology and semantic metadataOntology and semantic metadata for metagenomic profiles and tools for NGS data management
Test the methods and decision support module implemented in Task 6.6 on the Finnish Maternity Cohort and the Swedish Cervical Screening Cohort.
HEAP Data WarehouseComplete configuration of Hopswork for the requirements of HEAP including data management, analysis, and sharing and the integration with IC and analysis providers. We will create a Hopsworks HEAP repo in GitHub.
Demonstrator of integration of wearable sensorsData from the pilot for testing the workflow for data streaming from to data analysis in close collaboration with WP5.
HEAP Knowledge EngineIn collaboration with WP8, WP9, WP3, WP4, implementation and integration of deep learning and the main analysis pipelines provided by the partners. Updating of Hopsworks HEAP repo in GitHub.
Improved wearable PEMsA wearable and durable PEM that enables everyday monitoring of environmental exposure at the personal level and provides data for streaming and real-time monitoring implemented by WP6.
AI based alignment free (agnostic) taxonomic classificationAI based alignment free (agnostic) taxonomic classification algorithm able to classify virus-related sequences in metagenomic sequencing datasets, fully integrated in the bioinformatics workflow from D9.1.
FAIR Toolbox and BYOD workshopsFAIR Toolbox and BYOD workshops - This deliverable provides a Findable, Accessible, Interoperable and Reusable and Bring Your Own Data (BYOD) workshops where HEAP data provider will get a hands-on training (hackathon) and can improve and evaluate the interoperability and FAIRness of their data sets.
Formalise Knowledge in HEAPA continuously expanding, comprehensive, population-level exposure assessment over time based on high-throughput laboratory analyses of the consecutive sample sets. In collaboration with WP6, this data will be formalised to be integrated into the HEAP IC and Data & Feature Warehouse.
Massively parallel Bioinformatics pipelineBioinformatics pipeline, an ecosystem of bioinformatics tools, for complete analysis of metagenomic data generated from human biospecimens using NGS technologies, optimised for Hadoop and HPC ecosystems and, in collaboration with WP6, integrated to be used through the graphical user interface of the HEAP platform.
Exposome and metabolomics analysis pipelinesAnalysis pipelines for both exposome and metabolomics will be streamlined for integration with WP8 and WP9, and implementation with WP6.
Searchable databaseSearchable database with data on all the donors (age, sex) and registry-derived data on all the disease endpoints that have developed in the three cohorts. The software for the database is developed by partner 2 (SSI) and allows integrity-assured, yet flexible searches that will allow easy design of maximally informative research studies based on the biospecimens and data from these cohorts. In Collaboration with WP10, data from the database will be available to the IC.
Bacterial and viral metagenomics.High performance bioinformatics workflow for mining bacterial de novo analysis of viral genomes in metagenomic sequencing datasets genomes in NGS metagenomic sequencing datasets.
Online platform and toolsAn online platform combining informational and educational material, enriched with learning management and newsletter functionalities.
Demonstrator of the data analysis and data sharing on HEAPThis deliverable will provide a test environment for curating, uploading, managing, analysing and sharing data. Partners providing data and analysis pipelines will use the environment to produce the first results from the cohorts. Shareable data and results will available through the Data & Feature Warehouse.
The HEAP website with information on exposome research in general and the project in particular, with sections targeted either to the scientific community or to the general public.
Network website - HEAPWebsite with network activities and links to all individual network websites.
Data Management Plan - This deliverable will provide the governance and HEAP policies regarding the access, management and sharing of all the used and produced data during and after the project is completed. The plan will cover the generation of metadata from the different data sources of the project including all the cohorts, the raw and processed data and the results to be stored, preserved and shared for future exposome research.
Publikacje
Autorzy:
Mahmoud Ismail, Salman Niazi, Gautier Berthou , Mikael Ronström, Seif Haridi, Jim Dowling
Opublikowane w:
Proceedings of the 21st International Middleware Conference Industrial Track, 2020, Strona(/y) 23-30, ISBN 978-1-4503-8201-4
Wydawca:
ACM
Autorzy:
Alexandru A. Ormenisan, Moritz Meister, Fabio Buso, Robin Andersson, Seif Haridi, Jim Dowling
Opublikowane w:
Proceedings of the 2020 USENIX Conference on Operational Machine Learning (OpML ’20), 2020, Strona(/y) 13-15, ISBN 978-1-939133-15-1
Wydawca:
USENIX Association
Autorzy:
Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Opublikowane w:
New Biotechnology, 2023, ISSN 1871-6784
Wydawca:
Elsevier BV
DOI:
10.1016/j.nbt.2023.09.006
Autorzy:
Frederik T. Møller, Thor Grønborg Junker, Kathrine Kold Sørensen, Caroline Eves, Jan Wohlfahrt, Joakim Dillner, Christian Torp-Pedersen, Bartlomiej Wilkowski, Steven Chong, Tune H. Pers, Victor Yakimov, Heimo Müller, Steen Ethelberg & Mads Melbye
Opublikowane w:
Scientific Reports, 2023, ISSN 2045-2322
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41598-023-47534-6
Autorzy:
Heimo Müller, Catarina Lopes-Dias, Petr Holub, Markus Plass, Emilian Jungiwrth, Robert Reihs, Paul R. Torke, Apostolos Malatras, Anouk Berger, Heather Coombs, Joakim Dillner and Roxana Merino-Martinez
Opublikowane w:
New Biotechnology, 2023, ISSN 1871-6784
Wydawca:
Elsevier BV
DOI:
10.1016/j.nbt.2023.06.001
Autorzy:
James E. Barrett; Chiara Herzog; Yoo-Na Kim; Thomas E. Bartlett; Allison Jones; Iona Evans; David Cibula; Michal Zikan; Line Bjørge; Nadia Harbeck; Nicoletta Colombo; Sacha J. Howell; Angelique Flöter Rådestad; Kristina Gemzell-Danielsson; Martin Widschwendter
Opublikowane w:
Genome Biology, Numer 27, 2022, Strona(/y) 52, ISSN 1474-760X
Wydawca:
BMC SpringerNature
DOI:
10.1186/s13059-022-02603-3
Autorzy:
Andreas Holzinger; Heimo Müller
Opublikowane w:
Computer, Numer 28, 2021, Strona(/y) 78-86, ISSN 1558-0814
Wydawca:
IEEE Computer Society
DOI:
10.1109/mc.2021.3092610
Autorzy:
H. Muller, M. Mayrhofer, E. Van Veen and A. Holzinger
Opublikowane w:
Computer, Numer 54, 2021, Strona(/y) 119-123, ISSN 1558-0814
Wydawca:
IEEE Computer Society
DOI:
10.1109/mc.2021.3074263
Autorzy:
Heimo Müller, Andreas Holzinger, Markus Plass, Luka Brcic, Cornelia Stumptner, Kurt Zatloukal
Opublikowane w:
New Biotechnology, Numer 70, 2022, Strona(/y) 67-72, ISSN 1871-6784
Wydawca:
Elsevier BV
DOI:
10.1016/j.nbt.2022.05.002
Autorzy:
Heather Coombs; Tracy Wootton; Joakim Dillner; Heimo Müller; Anouk Berger; Zisis Kozlakidis
Opublikowane w:
Open Research Europe, 2023, ISSN 2732-5121
Wydawca:
EU
DOI:
10.12688/openreseurope.15474.1
Autorzy:
Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M
Opublikowane w:
International Journal of Cancer, 2023, ISSN 0020-7136
Wydawca:
John Wiley & Sons Inc.
DOI:
10.1002/ijc.34477
Autorzy:
Luca Marelli , Marthe Stevens , Tamar Sharon , Ine Van Hoyweghen , Martin Boeckhout , Ilaria Colussi , Alexander Degelsegger-M ́ arquez , Seliem El-Sayed , Klaus Hoeyer , Robin van Kessel , Dorota Krekora Zaj Î ac , Mihaela Matei , Sara Roda , Barbara Prainsack , Irene Schl ̈ under , Mahsa Shabani , Tom Southerington
Opublikowane w:
Health Policy, 2023, ISSN 0168-8510
Wydawca:
Elsevier BV
DOI:
10.1016/j.healthpol.2023.104861
Autorzy:
Evert-Ben Van Veen; Martin Boeckhout; Irene Schlünder; Jan Willem Boiten; Vasco Dias
Opublikowane w:
Open Research Europe, Numer 28, 2022, ISSN 2732-5121
Wydawca:
European Comission
DOI:
10.12688/openreseurope.14825.1
Autorzy:
Ville N. Pimenoff, Penelope Gray, Karolina Louvanto, Tiina Eriksson, Camilla Lagheden, Anna Söderlund-Strand, Joakim Dillner, Matti Lehtinen
Opublikowane w:
Cell Host & Microbes, 2023, ISSN 1931-3128
Wydawca:
Cell Press
DOI:
10.1016/j.chom.2023.10.001
Autorzy:
Jenny Rydén; Mark Clements; Agneta Wikman; Eva Hellström‐Lindberg; Gustaf Edgren; Petter Höglund
Opublikowane w:
Transfusion, 2023, ISSN 2080-1505
Wydawca:
Wiley
DOI:
10.1111/trf.17562
Autorzy:
Andreas Holzinger; Michaela Kargl; Bettina Kipperer; Peter Regitnig; Markus Plass; Heimo Muller
Opublikowane w:
IEEE Access, Numer 27, 2022, Strona(/y) 23732-23747, ISSN 2169-3536
Wydawca:
Institute of Electrical and Electronics Engineers Inc.
DOI:
10.1109/access.2022.3154776
Autorzy:
Markus Plass; Michaela Kargl; Tim‐Rasmus Kiehl; Peter Regitnig; Christian Geißler; Theodore Evans; Norman Zerbe; Rita Carvalho; Andreas Holzinger; Heimo Müller
Opublikowane w:
The Journal of Pathology Clinical Research, Numer 22, 2023, ISSN 2056-4538
Wydawca:
Wiley
DOI:
10.1002/cjp2.322
Autorzy:
Obón-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Díez-Villanueva A, Moratalla-Navarro F, Guinó E, Ibáñez-Sanz G, Rodríguez-Alonso L, Mulet-Margalef N, Mata A, García-Rodríguez A, Duell EJ, Pimenoff VN, Moreno V.
Opublikowane w:
Cancers, 2022, ISSN 2072-6694
Wydawca:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/cancers14174214
Autorzy:
Ainhoa Garcia‐Serrano; Dhananjay Mukhedkar; Emilie Hultin; Ulla Rudsander; Yvonne Wettergren; Agustín Enrique Ure; Joakim Dillner; Laila Sara Arroyo‐Mühr
Opublikowane w:
Cancer Medicine, Numer 17, 2023, ISSN 2045-7634
Wydawca:
Wiley
DOI:
10.1002/cam4.6483
Autorzy:
Attauabi M, Madsen GR, Bendtsen F, Wewer AV, Wilkens R, Ilvemark J, Vladimirova N, Jensen AB, Jensen FK, Hansen SB, Siebner HR, Nielsen YJW, Møller JM, Thomsen HS, Thomsen SF, Ingels HAS, Theede K, Boysen T, Bjerrum JT, Jakobsen C, Dorn-Rasmussen M, Jansson S, Yao Y, Burian EA, Møller FT, Fana V, Wiell C, Terslev L, Østergaard M, Bertl K, Stavropoulos A, Seidelin JB, Burisch J.
Opublikowane w:
BMJ Open, Numer 12(6), 2022, Strona(/y) e055779, ISSN 2044-6055
Wydawca:
BMJ Publishing Group
DOI:
10.1136/bmjopen-2021-055779
Autorzy:
Andreas Holzinger, Katharina Keiblinger, Petr Holub, Kurt Zatloukal, Heimo Müller
Opublikowane w:
New Biotechnology, 2023, ISSN 1871-6784
Wydawca:
Elsevier BV
DOI:
10.1016/j.nbt.2023.02.001
Autorzy:
Agustin Ure; Dhananjay Mukhedkar; Laila Sara Arroyo Mühr
Opublikowane w:
Scientific Reports, Numer 10, 2022, Strona(/y) 13058, ISSN 2045-2322
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41598-022-17318-5
Autorzy:
Merino Martinez, R. (Roxana); Müller, H. (Heimo); Negru, S. (Stefan); Ormenisan, A. (Alex); Arroyo Mühr, L. S. (Laila Sara); Zhang, X. (Xinyue); Trier Møller, F. (Frederik); Clements, M. S. (Mark S.); Kozlakidis, Z. (Zisis); Pimenoff, V. N. (Ville N.); Wilkowski, B. (Bartlomiej); Boeckhout, M. (Martin); Öhman, H. (Hanna); Chong, S. (Steven); Holzinger, A. (Andreas); Lehtinen, M. (Matti); van V
Opublikowane w:
Environmental Epidemiology, Numer 13, 2021, Strona(/y) e182, ISSN 2474-7882
Wydawca:
Wolters Kluwer
DOI:
10.1097/ee9.0000000000000182
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