Deliverables
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
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.
Complete 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.
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.
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.
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.
Publications
Author(s):
Mahmoud Ismail, Salman Niazi, Gautier Berthou , Mikael Ronström, Seif Haridi, Jim Dowling
Published in:
Proceedings of the 21st International Middleware Conference Industrial Track, 2020, Page(s) 23-30, ISBN 978-1-4503-8201-4
Publisher:
ACM
Author(s):
Alexandru A. Ormenisan, Moritz Meister, Fabio Buso, Robin Andersson, Seif Haridi, Jim Dowling
Published in:
Proceedings of the 2020 USENIX Conference on Operational Machine Learning (OpML ’20), 2020, Page(s) 13-15, ISBN 978-1-939133-15-1
Publisher:
USENIX Association
Author(s):
Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Published in:
New Biotechnology, 2023, ISSN 1871-6784
Publisher:
Elsevier BV
DOI:
10.1016/j.nbt.2023.09.006
Author(s):
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
Published in:
Scientific Reports, 2023, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-023-47534-6
Author(s):
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
Published in:
New Biotechnology, 2023, ISSN 1871-6784
Publisher:
Elsevier BV
DOI:
10.1016/j.nbt.2023.06.001
Author(s):
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
Published in:
Genome Biology, Issue 27, 2022, Page(s) 52, ISSN 1474-760X
Publisher:
BMC SpringerNature
DOI:
10.1186/s13059-022-02603-3
Author(s):
Andreas Holzinger; Heimo Müller
Published in:
Computer, Issue 28, 2021, Page(s) 78-86, ISSN 1558-0814
Publisher:
IEEE Computer Society
DOI:
10.1109/mc.2021.3092610
Author(s):
H. Muller, M. Mayrhofer, E. Van Veen and A. Holzinger
Published in:
Computer, Issue 54, 2021, Page(s) 119-123, ISSN 1558-0814
Publisher:
IEEE Computer Society
DOI:
10.1109/mc.2021.3074263
Author(s):
Heimo Müller, Andreas Holzinger, Markus Plass, Luka Brcic, Cornelia Stumptner, Kurt Zatloukal
Published in:
New Biotechnology, Issue 70, 2022, Page(s) 67-72, ISSN 1871-6784
Publisher:
Elsevier BV
DOI:
10.1016/j.nbt.2022.05.002
Author(s):
Heather Coombs; Tracy Wootton; Joakim Dillner; Heimo Müller; Anouk Berger; Zisis Kozlakidis
Published in:
Open Research Europe, 2023, ISSN 2732-5121
Publisher:
EU
DOI:
10.12688/openreseurope.15474.1
Author(s):
Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M
Published in:
International Journal of Cancer, 2023, ISSN 0020-7136
Publisher:
John Wiley & Sons Inc.
DOI:
10.1002/ijc.34477
Author(s):
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
Published in:
Health Policy, 2023, ISSN 0168-8510
Publisher:
Elsevier BV
DOI:
10.1016/j.healthpol.2023.104861
Author(s):
Evert-Ben Van Veen; Martin Boeckhout; Irene Schlünder; Jan Willem Boiten; Vasco Dias
Published in:
Open Research Europe, Issue 28, 2022, ISSN 2732-5121
Publisher:
European Comission
DOI:
10.12688/openreseurope.14825.1
Author(s):
Ville N. Pimenoff, Penelope Gray, Karolina Louvanto, Tiina Eriksson, Camilla Lagheden, Anna Söderlund-Strand, Joakim Dillner, Matti Lehtinen
Published in:
Cell Host & Microbes, 2023, ISSN 1931-3128
Publisher:
Cell Press
DOI:
10.1016/j.chom.2023.10.001
Author(s):
Jenny Rydén; Mark Clements; Agneta Wikman; Eva Hellström‐Lindberg; Gustaf Edgren; Petter Höglund
Published in:
Transfusion, 2023, ISSN 2080-1505
Publisher:
Wiley
DOI:
10.1111/trf.17562
Author(s):
Andreas Holzinger; Michaela Kargl; Bettina Kipperer; Peter Regitnig; Markus Plass; Heimo Muller
Published in:
IEEE Access, Issue 27, 2022, Page(s) 23732-23747, ISSN 2169-3536
Publisher:
Institute of Electrical and Electronics Engineers Inc.
DOI:
10.1109/access.2022.3154776
Author(s):
Markus Plass; Michaela Kargl; Tim‐Rasmus Kiehl; Peter Regitnig; Christian Geißler; Theodore Evans; Norman Zerbe; Rita Carvalho; Andreas Holzinger; Heimo Müller
Published in:
The Journal of Pathology Clinical Research, Issue 22, 2023, ISSN 2056-4538
Publisher:
Wiley
DOI:
10.1002/cjp2.322
Author(s):
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.
Published in:
Cancers, 2022, ISSN 2072-6694
Publisher:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/cancers14174214
Author(s):
Ainhoa Garcia‐Serrano; Dhananjay Mukhedkar; Emilie Hultin; Ulla Rudsander; Yvonne Wettergren; Agustín Enrique Ure; Joakim Dillner; Laila Sara Arroyo‐Mühr
Published in:
Cancer Medicine, Issue 17, 2023, ISSN 2045-7634
Publisher:
Wiley
DOI:
10.1002/cam4.6483
Author(s):
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.
Published in:
BMJ Open, Issue 12(6), 2022, Page(s) e055779, ISSN 2044-6055
Publisher:
BMJ Publishing Group
DOI:
10.1136/bmjopen-2021-055779
Author(s):
Andreas Holzinger, Katharina Keiblinger, Petr Holub, Kurt Zatloukal, Heimo Müller
Published in:
New Biotechnology, 2023, ISSN 1871-6784
Publisher:
Elsevier BV
DOI:
10.1016/j.nbt.2023.02.001
Author(s):
Agustin Ure; Dhananjay Mukhedkar; Laila Sara Arroyo Mühr
Published in:
Scientific Reports, Issue 10, 2022, Page(s) 13058, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-022-17318-5
Author(s):
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
Published in:
Environmental Epidemiology, Issue 13, 2021, Page(s) e182, ISSN 2474-7882
Publisher:
Wolters Kluwer
DOI:
10.1097/ee9.0000000000000182
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