Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview

Patricia Žižkovičová; Yuanting Zheng; Bhagwan Yadav; Janneke Weiss; Beatrice Valenti; Tanushree Tunstall; Jarmila Stanková; Leming Shi; Andreas Scherer; Sabrina Saracino; Esperanza Macarena Rodríguez-Serrano; Miren Edurne Ramos-Muñoz; Ileana Quintero; Maija Puhka; Aino Palva; Elin Övernäs; Emanuela Oldoni; Jessica Nordlund; Anni I. Nieminen; Anna Niehues; Kenneth Nazir; Lukáš Najdekr; Pirkko Mattila; Tom Martin; Roberta Maestro; Yaqing Liu; Hanna Lindgren; Peter Bram ´t Hoen; Sari Hannula; Rashi Halder; Marián Hajdúch; Janine Habier; Alain van Gool; Jolein Gloerich; Bishwa Ghimire; Daniela Gasparotto; Maria Laura García Bermejo; Sara Ekberg; Petr Džubák; Kati Donner; Lorena Crespo-Toro; Elisa Conde Moreno; Qiaochu Chen; Davide Baldazzi; Patricia Alonso-Andrés; EATRIS-Plus Multi-omics working group and Stakeholders

doi:10.1007/s43657-024-00170-0

Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview

Patricia Žižkovičová
, Yuanting Zheng
, Bhagwan Yadav
, Janneke Weiss
, Beatrice Valenti
, Tanushree Tunstall
, Jarmila Stanková
, Leming Shi
, Andreas Scherer^*
, Sabrina Saracino
, Esperanza Macarena Rodríguez-Serrano
, Miren Edurne Ramos-Muñoz
, Ileana Quintero
, Maija Puhka
, Aino Palva
, Elin Övernäs
, Emanuela Oldoni
, Jessica Nordlund
, Anni I. Nieminen
, Anna Niehues

Kenneth Nazir, Lukáš Najdekr, Pirkko Mattila, Tom Martin, Roberta Maestro, Yaqing Liu, Hanna Lindgren, Peter Bram ´t Hoen, Sari Hannula, Rashi Halder, Marián Hajdúch, Janine Habier, Alain van Gool, Jolein Gloerich, Bishwa Ghimire, Daniela Gasparotto, Maria Laura García Bermejo, Sara Ekberg, Petr Džubák, Kati Donner, Lorena Crespo-Toro, Elisa Conde Moreno, Qiaochu Chen, Davide Baldazzi, Patricia Alonso-Andrés, EATRIS-Plus Multi-omics working group and Stakeholders

^*Corresponding author for this work

Clinical Research Project Management 2

Research output: Contribution to journal › Review article › peer-review

3 Citations (Scopus)

Abstract

UNLABELLED: Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most critical aspects. Accurate performance and interpretation of omics techniques is based on consensus, harmonization, and standardization of protocols, procedures, data analysis and reference values and materials. EATRIS, the European Infrastructure for Translational Medicine (www.EATRIS.eu), brings together resources and services to support researchers in developing their biomedical discoveries into novel translational tools and interventions for better health outcomes. Here we describe the efforts within the Horizon 2020 EATRIS-Plus project and activities of member facilities of EATRIS towards quality assessment of pre-clinical sample processing, clinical omics data generation, multi-omics data integration, and dissemination of the resources in a Multi-Omics Toolbox, which is the principal deliverable of the EATRIS-Plus project for the consolidation of EATRIS towards translational medicine.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00170-0.

Original language	English
Pages (from-to)	311-325
Number of pages	15
Journal	Phenomics
Volume	5
Issue number	3
DOIs	https://doi.org/10.1007/s43657-024-00170-0
Publication status	Published - Jun 2025

Keywords

European infrastructure for translational medicine
Multi-omics
Multi-omics toolbox
Quality
Reference samples

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Žižkovičová, P., Zheng, Y., Yadav, B., Weiss, J., Valenti, B., Tunstall, T., Stanková, J., Shi, L., Scherer, A., Saracino, S., Rodríguez-Serrano, E. M., Ramos-Muñoz, M. E., Quintero, I., Puhka, M., Palva, A., Övernäs, E., Oldoni, E., Nordlund, J., Nieminen, A. I., ... EATRIS-Plus Multi-omics working group and Stakeholders (2025). Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview. Phenomics, 5(3), 311-325. https://doi.org/10.1007/s43657-024-00170-0

@article{aec723f54a2f45f8be5a1f3a43e0482d,

title = "Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview",

abstract = "UNLABELLED: Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most critical aspects. Accurate performance and interpretation of omics techniques is based on consensus, harmonization, and standardization of protocols, procedures, data analysis and reference values and materials. EATRIS, the European Infrastructure for Translational Medicine (www.EATRIS.eu), brings together resources and services to support researchers in developing their biomedical discoveries into novel translational tools and interventions for better health outcomes. Here we describe the efforts within the Horizon 2020 EATRIS-Plus project and activities of member facilities of EATRIS towards quality assessment of pre-clinical sample processing, clinical omics data generation, multi-omics data integration, and dissemination of the resources in a Multi-Omics Toolbox, which is the principal deliverable of the EATRIS-Plus project for the consolidation of EATRIS towards translational medicine.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00170-0.",

keywords = "European infrastructure for translational medicine, Multi-omics, Multi-omics toolbox, Quality, Reference samples",

author = "Patricia {\v Z}i{\v z}kovi{\v c}ov{\'a} and Yuanting Zheng and Bhagwan Yadav and Janneke Weiss and Beatrice Valenti and Tanushree Tunstall and Jarmila Stankov{\'a} and Leming Shi and Andreas Scherer and Sabrina Saracino and Rodr{\'i}guez-Serrano, \{Esperanza Macarena\} and Ramos-Mu{\~n}oz, \{Miren Edurne\} and Ileana Quintero and Maija Puhka and Aino Palva and Elin {\"O}vern{\"a}s and Emanuela Oldoni and Jessica Nordlund and Nieminen, \{Anni I.\} and Anna Niehues and Kenneth Nazir and Luk{\'a}{\v s} Najdekr and Pirkko Mattila and Tom Martin and Roberta Maestro and Yaqing Liu and Hanna Lindgren and \{´t Hoen\}, \{Peter Bram\} and Sari Hannula and Rashi Halder and Mari{\'a}n Hajd{\'u}ch and Janine Habier and \{van Gool\}, Alain and Jolein Gloerich and Bishwa Ghimire and Daniela Gasparotto and \{Garc{\'i}a Bermejo\}, \{Maria Laura\} and Sara Ekberg and Petr D{\v z}ub{\'a}k and Kati Donner and Lorena Crespo-Toro and \{Conde Moreno\}, Elisa and Qiaochu Chen and Davide Baldazzi and Patricia Alonso-Andr{\'e}s and \{EATRIS-Plus Multi-omics working group and Stakeholders\}",

note = "Funding Open Access funding provided by University of Helsinki (including Helsinki University Central Hospital). The work conducted has received funding from the European Union's Horizon 2020 research and innovation program under project EATRIS-Plus (Grant Agreement No. 871096). Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = jun,

doi = "10.1007/s43657-024-00170-0",

language = "English",

volume = "5",

pages = "311--325",

journal = "Phenomics",

issn = "2730-583X",

publisher = "Springer",

number = "3",

}

Žižkovičová, P, Zheng, Y, Yadav, B, Weiss, J, Valenti, B, Tunstall, T, Stanková, J, Shi, L, Scherer, A, Saracino, S, Rodríguez-Serrano, EM, Ramos-Muñoz, ME, Quintero, I, Puhka, M, Palva, A, Övernäs, E, Oldoni, E, Nordlund, J, Nieminen, AI, Niehues, A, Nazir, K, Najdekr, L, Mattila, P, Martin, T, Maestro, R, Liu, Y, Lindgren, H, ´t Hoen, PB, Hannula, S, Halder, R, Hajdúch, M, Habier, J, van Gool, A, Gloerich, J, Ghimire, B, Gasparotto, D, García Bermejo, ML, Ekberg, S, Džubák, P, Donner, K, Crespo-Toro, L, Conde Moreno, E, Chen, Q, Baldazzi, D, Alonso-Andrés, P & EATRIS-Plus Multi-omics working group and Stakeholders 2025, 'Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview', Phenomics, vol. 5, no. 3, pp. 311-325. https://doi.org/10.1007/s43657-024-00170-0

TY - JOUR

T1 - Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS)

T2 - An Overview

AU - Žižkovičová, Patricia

AU - Zheng, Yuanting

AU - Yadav, Bhagwan

AU - Weiss, Janneke

AU - Valenti, Beatrice

AU - Tunstall, Tanushree

AU - Stanková, Jarmila

AU - Shi, Leming

AU - Scherer, Andreas

AU - Saracino, Sabrina

AU - Rodríguez-Serrano, Esperanza Macarena

AU - Ramos-Muñoz, Miren Edurne

AU - Quintero, Ileana

AU - Puhka, Maija

AU - Palva, Aino

AU - Övernäs, Elin

AU - Oldoni, Emanuela

AU - Nordlund, Jessica

AU - Nieminen, Anni I.

AU - Niehues, Anna

AU - Nazir, Kenneth

AU - Najdekr, Lukáš

AU - Mattila, Pirkko

AU - Martin, Tom

AU - Maestro, Roberta

AU - Liu, Yaqing

AU - Lindgren, Hanna

AU - ´t Hoen, Peter Bram

AU - Hannula, Sari

AU - Halder, Rashi

AU - Hajdúch, Marián

AU - Habier, Janine

AU - van Gool, Alain

AU - Gloerich, Jolein

AU - Ghimire, Bishwa

AU - Gasparotto, Daniela

AU - García Bermejo, Maria Laura

AU - Ekberg, Sara

AU - Džubák, Petr

AU - Donner, Kati

AU - Crespo-Toro, Lorena

AU - Conde Moreno, Elisa

AU - Chen, Qiaochu

AU - Baldazzi, Davide

AU - Alonso-Andrés, Patricia

AU - EATRIS-Plus Multi-omics working group and Stakeholders

N1 - Funding Open Access funding provided by University of Helsinki (including Helsinki University Central Hospital). The work conducted has received funding from the European Union's Horizon 2020 research and innovation program under project EATRIS-Plus (Grant Agreement No. 871096). Publisher Copyright: © The Author(s) 2025.

PY - 2025/6

Y1 - 2025/6

N2 - UNLABELLED: Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most critical aspects. Accurate performance and interpretation of omics techniques is based on consensus, harmonization, and standardization of protocols, procedures, data analysis and reference values and materials. EATRIS, the European Infrastructure for Translational Medicine (www.EATRIS.eu), brings together resources and services to support researchers in developing their biomedical discoveries into novel translational tools and interventions for better health outcomes. Here we describe the efforts within the Horizon 2020 EATRIS-Plus project and activities of member facilities of EATRIS towards quality assessment of pre-clinical sample processing, clinical omics data generation, multi-omics data integration, and dissemination of the resources in a Multi-Omics Toolbox, which is the principal deliverable of the EATRIS-Plus project for the consolidation of EATRIS towards translational medicine.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00170-0.

AB - UNLABELLED: Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most critical aspects. Accurate performance and interpretation of omics techniques is based on consensus, harmonization, and standardization of protocols, procedures, data analysis and reference values and materials. EATRIS, the European Infrastructure for Translational Medicine (www.EATRIS.eu), brings together resources and services to support researchers in developing their biomedical discoveries into novel translational tools and interventions for better health outcomes. Here we describe the efforts within the Horizon 2020 EATRIS-Plus project and activities of member facilities of EATRIS towards quality assessment of pre-clinical sample processing, clinical omics data generation, multi-omics data integration, and dissemination of the resources in a Multi-Omics Toolbox, which is the principal deliverable of the EATRIS-Plus project for the consolidation of EATRIS towards translational medicine.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00170-0.

KW - European infrastructure for translational medicine

KW - Multi-omics

KW - Multi-omics toolbox

KW - Quality

KW - Reference samples

UR - https://www.scopus.com/pages/publications/105002084056

U2 - 10.1007/s43657-024-00170-0

DO - 10.1007/s43657-024-00170-0

M3 - Review article

C2 - 40895321

AN - SCOPUS:105002084056

SN - 2730-583X

VL - 5

SP - 311

EP - 325

JO - Phenomics

JF - Phenomics

IS - 3

ER -

Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview

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Keywords

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