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A computational framework for complex disease stratification from multiple large-scale datasets

A computational framework for complex disease stratification from multiple large-scale datasets
A computational framework for complex disease stratification from multiple large-scale datasets

Background: Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states.

Methods: The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification.

Results: We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. 

Conclusions: This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine.

'Omics data, Molecular signatures, Stratification, Systems medicine
1752-0509
1-23
De Meulder, Bertrand
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Lefaudeux, Diane
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Sun, Kai
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Pandis, Ioannis
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Auffray, Charles
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Gibeon, David
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Hoda, Uruj
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Kuo, Scott
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Burg, Dominic
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Dennison, Patrick
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Nicholas, Ben
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Schofield, James P.R.
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Skipp, Paul J.
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Staykova, Doroteya
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Tariq, Kamran
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Ward, Jonathan
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Wilson, Susan J.
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Barber, Clair
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Hewitt, Lorraine
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Howarth, Peter
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Roberts, Graham
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Gove, Kerry
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the U-BIOPRED Study Group and the eTRIKS Consortium
De Meulder, Bertrand
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Lefaudeux, Diane
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Bansal, Aruna T.
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Mazein, Alexander
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Chaiboonchoe, Amphun
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Ahmed, Hassan
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Balaur, Irina
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Saqi, Mansoor
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Pellet, Johann
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Lemonnier, Nathanaël
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Sun, Kai
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Pandis, Ioannis
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Yang, Xian
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Batuwitage, Manohara
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Kretsos, Kosmas
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van Eyll, Jonathan
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Dodson, Paul
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Larminie, Christopher
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Postle, Anthony
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Corfield, Julie
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Chung, Kian Fan
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Adcock, Ian M.
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Guo, Yi Ke
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Sterk, Peter J.
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Manta, Alexander
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Rowe, Anthony
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Baribaud, Frédéric
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Auffray, Charles
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Gibeon, David
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Burg, Dominic
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Dennison, Patrick
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Nicholas, Ben
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Schofield, James P.R.
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Skipp, Paul J.
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Staykova, Doroteya
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Tariq, Kamran
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Ward, Jonathan
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Wilson, Susan J.
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Barber, Clair
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Hewitt, Lorraine
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Howarth, Peter
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Roberts, Graham
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Gove, Kerry
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De Meulder, Bertrand, Lefaudeux, Diane, Bansal, Aruna T., Mazein, Alexander, Chaiboonchoe, Amphun, Ahmed, Hassan, Balaur, Irina, Saqi, Mansoor, Pellet, Johann, Ballereau, Stéphane, Lemonnier, Nathanaël, Sun, Kai, Pandis, Ioannis, Yang, Xian, Batuwitage, Manohara, Kretsos, Kosmas, van Eyll, Jonathan, Bedding, Alun, Davison, Timothy, Dodson, Paul, Larminie, Christopher, Postle, Anthony, Corfield, Julie, Djukanovic, Ratko, Chung, Kian Fan, Adcock, Ian M., Guo, Yi Ke, Sterk, Peter J., Manta, Alexander, Rowe, Anthony, Baribaud, Frédéric, Auffray, Charles, Gibeon, David, Hoda, Uruj, Kuo, Scott, Brandsma, Joost, Burg, Dominic, Dennison, Patrick, Nicholas, Ben, Schofield, James P.R., Skipp, Paul J., Staykova, Doroteya, Tariq, Kamran, Ward, Jonathan, Wilson, Susan J., Barber, Clair, Hewitt, Lorraine, Howarth, Peter, Roberts, Graham and Gove, Kerry , the U-BIOPRED Study Group and the eTRIKS Consortium (2018) A computational framework for complex disease stratification from multiple large-scale datasets. BMC Systems Biology, 12 (60), 1-23, [60]. (doi:10.1186/s12918-018-0556-z).

Record type: Article

Abstract

Background: Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states.

Methods: The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification.

Results: We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. 

Conclusions: This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine.

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Accepted/In Press date: 21 February 2018
e-pub ahead of print date: 29 May 2018
Published date: 2018
Keywords: 'Omics data, Molecular signatures, Stratification, Systems medicine

Identifiers

Local EPrints ID: 421511
URI: http://eprints.soton.ac.uk/id/eprint/421511
ISSN: 1752-0509
PURE UUID: 4c29eaed-6fd3-4645-8cf0-74c9f923e55d
ORCID for Anthony Postle: ORCID iD orcid.org/0000-0001-7361-0756
ORCID for Ratko Djukanovic: ORCID iD orcid.org/0000-0001-6039-5612
ORCID for Ben Nicholas: ORCID iD orcid.org/0000-0003-1467-9643
ORCID for Paul J. Skipp: ORCID iD orcid.org/0000-0002-2995-2959
ORCID for Jonathan Ward: ORCID iD orcid.org/0000-0002-9278-0002
ORCID for Susan J. Wilson: ORCID iD orcid.org/0000-0003-1305-8271
ORCID for Clair Barber: ORCID iD orcid.org/0000-0001-5335-5129
ORCID for Graham Roberts: ORCID iD orcid.org/0000-0003-2252-1248

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Date deposited: 14 Jun 2018 16:30
Last modified: 16 Mar 2024 03:44

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Contributors

Author: Bertrand De Meulder
Author: Diane Lefaudeux
Author: Aruna T. Bansal
Author: Alexander Mazein
Author: Amphun Chaiboonchoe
Author: Hassan Ahmed
Author: Irina Balaur
Author: Mansoor Saqi
Author: Johann Pellet
Author: Stéphane Ballereau
Author: Nathanaël Lemonnier
Author: Kai Sun
Author: Ioannis Pandis
Author: Xian Yang
Author: Manohara Batuwitage
Author: Kosmas Kretsos
Author: Jonathan van Eyll
Author: Alun Bedding
Author: Timothy Davison
Author: Paul Dodson
Author: Christopher Larminie
Author: Anthony Postle ORCID iD
Author: Julie Corfield
Author: Kian Fan Chung
Author: Ian M. Adcock
Author: Yi Ke Guo
Author: Peter J. Sterk
Author: Alexander Manta
Author: Anthony Rowe
Author: Frédéric Baribaud
Author: Charles Auffray
Author: David Gibeon
Author: Uruj Hoda
Author: Scott Kuo
Author: Joost Brandsma
Author: Dominic Burg
Author: Patrick Dennison
Author: Ben Nicholas ORCID iD
Author: James P.R. Schofield
Author: Paul J. Skipp ORCID iD
Author: Doroteya Staykova
Author: Kamran Tariq
Author: Jonathan Ward ORCID iD
Author: Susan J. Wilson ORCID iD
Author: Clair Barber ORCID iD
Author: Lorraine Hewitt
Author: Peter Howarth
Author: Graham Roberts ORCID iD
Author: Kerry Gove
Corporate Author: the U-BIOPRED Study Group and the eTRIKS Consortium

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