The University of Southampton
University of Southampton Institutional Repository

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
2eb16e68-bc1a-4e71-bc76-a6ebcb079cbd
Lefaudeux, Diane
924a38e0-ace4-4344-a2a4-33e41df1805d
Bansal, Aruna T.
35fbf858-fffc-474a-b176-28ed5a20b9c8
Mazein, Alexander
3e806700-fc8c-447b-b596-f523a749d1a3
Chaiboonchoe, Amphun
fc6a8f65-c3ee-466a-9737-97b3ee0a9aac
Ahmed, Hassan
a1311d26-0cea-4df9-aff2-59a105386be9
Balaur, Irina
015be093-789a-4a66-bfc0-9495f5a61d92
Saqi, Mansoor
4a352118-cf4d-4d1d-be81-cb80846f47cd
Pellet, Johann
73b54a9e-e3cd-42ef-9e3d-9a18ed88c375
Ballereau, Stéphane
1ffd03d3-b367-4dcb-ae7a-72647c4d0288
Lemonnier, Nathanaël
1be4a050-9397-4f2d-99c2-c0b59cb60fe6
Sun, Kai
e551cc88-5a54-447b-b682-d36b96303b64
Pandis, Ioannis
78007b43-3aea-4198-80f6-741a9afaf380
Yang, Xian
4558883a-3219-41b8-b128-db265b69fd3f
Batuwitage, Manohara
6eea7c15-f528-4e2e-a5b9-65d297a739dc
Kretsos, Kosmas
0d986f2e-537c-4243-b091-7d785227b27c
van Eyll, Jonathan
a95ee4ea-41d5-4a71-98a4-f67f17633780
Bedding, Alun
18dcda83-65f3-4c30-97d0-759c040c7a29
Davison, Timothy
8d54ff2a-fdcd-466a-8326-8295f317d9b2
Dodson, Paul
bee85da7-0af4-4715-a1f7-39b7c04f6174
Larminie, Christopher
bb257265-3fb0-485d-8dd4-62c8a5cac289
Postle, Anthony
0fa17988-b4a0-4cdc-819a-9ae15c5dad66
Corfield, Julie
3709614a-7bb0-4657-8eec-6f40a32fda7e
Djukanovic, Ratko
d9a45ee7-6a80-4d84-a0ed-10962660a98d
Chung, Kian Fan
dc062fa0-b6c4-4b03-a0c2-917904e0ea2a
Adcock, Ian M.
427153bc-3b8b-4066-aa4e-5bc41a6c36dd
Guo, Yi Ke
450dd28e-5f7b-4a4a-899e-feeac1338330
Sterk, Peter J.
94936306-c360-4b90-bf54-ca9e8d231bfb
Manta, Alexander
2e91eac1-1d67-44ab-b3c1-0b47fa95bf93
Rowe, Anthony
a5ba3c09-8a84-4856-8ec6-0031f980dd94
Baribaud, Frédéric
ec0ccfc5-4106-46cc-ba0e-709bc2241fba
Auffray, Charles
16fdf8f6-e7bc-4559-b6b6-d425160867c6
Gibeon, David
f9fc2674-c951-466e-aa3e-caba5631babb
Hoda, Uruj
979a6de0-269b-4d8f-a1e9-58b42c81a774
Kuo, Scott
312f151d-6214-4883-a3a6-62bd386dca14
Brandsma, Joost
b4c553dc-9444-466a-b352-25fd8fa25ee7
Burg, Dominic
a51bc2a5-54d3-40ee-ac66-4ca0bc4d9d1d
Dennison, Patrick
30c232e3-c218-4dd8-979f-061ac70513d5
Nicholas, Ben
785c44fb-6536-4189-803b-4545425e9385
Schofield, James P.R.
529d3c88-857e-4431-93c2-e76577377ba7
Skipp, Paul J.
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5
Staykova, Doroteya
9fd281a1-3ba1-4cbb-9dc6-0d500c37ef6a
Tariq, Kamran
0dac2aed-ca47-4dfe-92f5-bc65a3a7ec27
Ward, Jonathan
a8107b98-069d-4263-bd70-d29d79f07edc
Wilson, Susan J.
21c6875d-6870-441b-ae7a-603562a646b8
Barber, Clair
ff31b460-34c3-466c-90e4-f70b3e954c82
Hewitt, Lorraine
c4086add-4028-4002-b418-8766a1be0610
Howarth, Peter
ff19c8c4-86b0-4a88-8f76-b3d87f142a21
Roberts, Graham
ea00db4e-84e7-4b39-8273-9b71dbd7e2f3
Gove, Kerry
8f043bbb-080d-49b3-9ee5-046f3a636ee0
the U-BIOPRED Study Group and the eTRIKS Consortium
De Meulder, Bertrand
2eb16e68-bc1a-4e71-bc76-a6ebcb079cbd
Lefaudeux, Diane
924a38e0-ace4-4344-a2a4-33e41df1805d
Bansal, Aruna T.
35fbf858-fffc-474a-b176-28ed5a20b9c8
Mazein, Alexander
3e806700-fc8c-447b-b596-f523a749d1a3
Chaiboonchoe, Amphun
fc6a8f65-c3ee-466a-9737-97b3ee0a9aac
Ahmed, Hassan
a1311d26-0cea-4df9-aff2-59a105386be9
Balaur, Irina
015be093-789a-4a66-bfc0-9495f5a61d92
Saqi, Mansoor
4a352118-cf4d-4d1d-be81-cb80846f47cd
Pellet, Johann
73b54a9e-e3cd-42ef-9e3d-9a18ed88c375
Ballereau, Stéphane
1ffd03d3-b367-4dcb-ae7a-72647c4d0288
Lemonnier, Nathanaël
1be4a050-9397-4f2d-99c2-c0b59cb60fe6
Sun, Kai
e551cc88-5a54-447b-b682-d36b96303b64
Pandis, Ioannis
78007b43-3aea-4198-80f6-741a9afaf380
Yang, Xian
4558883a-3219-41b8-b128-db265b69fd3f
Batuwitage, Manohara
6eea7c15-f528-4e2e-a5b9-65d297a739dc
Kretsos, Kosmas
0d986f2e-537c-4243-b091-7d785227b27c
van Eyll, Jonathan
a95ee4ea-41d5-4a71-98a4-f67f17633780
Bedding, Alun
18dcda83-65f3-4c30-97d0-759c040c7a29
Davison, Timothy
8d54ff2a-fdcd-466a-8326-8295f317d9b2
Dodson, Paul
bee85da7-0af4-4715-a1f7-39b7c04f6174
Larminie, Christopher
bb257265-3fb0-485d-8dd4-62c8a5cac289
Postle, Anthony
0fa17988-b4a0-4cdc-819a-9ae15c5dad66
Corfield, Julie
3709614a-7bb0-4657-8eec-6f40a32fda7e
Djukanovic, Ratko
d9a45ee7-6a80-4d84-a0ed-10962660a98d
Chung, Kian Fan
dc062fa0-b6c4-4b03-a0c2-917904e0ea2a
Adcock, Ian M.
427153bc-3b8b-4066-aa4e-5bc41a6c36dd
Guo, Yi Ke
450dd28e-5f7b-4a4a-899e-feeac1338330
Sterk, Peter J.
94936306-c360-4b90-bf54-ca9e8d231bfb
Manta, Alexander
2e91eac1-1d67-44ab-b3c1-0b47fa95bf93
Rowe, Anthony
a5ba3c09-8a84-4856-8ec6-0031f980dd94
Baribaud, Frédéric
ec0ccfc5-4106-46cc-ba0e-709bc2241fba
Auffray, Charles
16fdf8f6-e7bc-4559-b6b6-d425160867c6
Gibeon, David
f9fc2674-c951-466e-aa3e-caba5631babb
Hoda, Uruj
979a6de0-269b-4d8f-a1e9-58b42c81a774
Kuo, Scott
312f151d-6214-4883-a3a6-62bd386dca14
Brandsma, Joost
b4c553dc-9444-466a-b352-25fd8fa25ee7
Burg, Dominic
a51bc2a5-54d3-40ee-ac66-4ca0bc4d9d1d
Dennison, Patrick
30c232e3-c218-4dd8-979f-061ac70513d5
Nicholas, Ben
785c44fb-6536-4189-803b-4545425e9385
Schofield, James P.R.
529d3c88-857e-4431-93c2-e76577377ba7
Skipp, Paul J.
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5
Staykova, Doroteya
9fd281a1-3ba1-4cbb-9dc6-0d500c37ef6a
Tariq, Kamran
0dac2aed-ca47-4dfe-92f5-bc65a3a7ec27
Ward, Jonathan
a8107b98-069d-4263-bd70-d29d79f07edc
Wilson, Susan J.
21c6875d-6870-441b-ae7a-603562a646b8
Barber, Clair
ff31b460-34c3-466c-90e4-f70b3e954c82
Hewitt, Lorraine
c4086add-4028-4002-b418-8766a1be0610
Howarth, Peter
ff19c8c4-86b0-4a88-8f76-b3d87f142a21
Roberts, Graham
ea00db4e-84e7-4b39-8273-9b71dbd7e2f3
Gove, Kerry
8f043bbb-080d-49b3-9ee5-046f3a636ee0

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. (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.

Text
document-1 - Version of Record
Available under License Creative Commons Attribution.
Download (1MB)

More information

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: https://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 Paul J. Skipp: ORCID iD orcid.org/0000-0002-2995-2959
ORCID for Clair Barber: ORCID iD orcid.org/0000-0001-5335-5129

Catalogue record

Date deposited: 14 Jun 2018 16:30
Last modified: 14 Mar 2019 01:57

Export record

Altmetrics

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
Author: James P.R. Schofield
Author: Paul J. Skipp ORCID iD
Author: Doroteya Staykova
Author: Kamran Tariq
Author: Jonathan Ward
Author: Susan J. Wilson
Author: Clair Barber ORCID iD
Author: Lorraine Hewitt
Author: Peter Howarth
Author: Graham Roberts
Author: Kerry Gove

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of https://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×