Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine.

Journal

NPJ digital medicine
ISSN: 2398-6352
Titre abrégé: NPJ Digit Med
Pays: England
ID NLM: 101731738

Informations de publication

Date de publication:
04 Jul 2022
Historique:
received: 10 11 2021
accepted: 19 05 2022
entrez: 5 7 2022
pubmed: 6 7 2022
medline: 6 7 2022
Statut: epublish

Résumé

In this modern era of precision medicine, molecular signatures identified from advanced omics technologies hold great promise to better guide clinical decisions. However, current approaches are often location-specific due to the inherent differences between platforms and across multiple centres, thus limiting the transferability of molecular signatures. We present Cross-Platform Omics Prediction (CPOP), a penalised regression model that can use omics data to predict patient outcomes in a platform-independent manner and across time and experiments. CPOP improves on the traditional prediction framework of using gene-based features by selecting ratio-based features with similar estimated effect sizes. These components gave CPOP the ability to have a stable performance across datasets of similar biology, minimising the effect of technical noise often generated by omics platforms. We present a comprehensive evaluation using melanoma transcriptomics data to demonstrate its potential to be used as a critical part of a clinical screening framework for precision medicine. Additional assessment of generalisation was demonstrated with ovarian cancer and inflammatory bowel disease studies.

Identifiants

DOI: 10.1038/s41746-022-00618-5 PMID: 35788693 PMC: PMC9253123
pubmed: 35788693
doi: 10.1038/s41746-022-00618-5
pii: 10.1038/s41746-022-00618-5
pmc: PMC9253123
doi:

Types de publication

Journal Article

Langues

eng

Pagination

85

Informations de copyright

© 2022. The Author(s).

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Auteurs

Kevin Y X Wang (KYX)

Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.

Gulietta M Pupo (GM)

The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, 2006, Australia.
Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia.

Varsha Tembe (V)

The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, 2006, Australia.
Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia.

Ellis Patrick (E)

Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.
The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, 2006, Australia.
Laboratory of Data Discovery for Health Limited (D²4H) Science Park, Hong Kong, SAR, China.

Dario Strbenac (D)

Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.

Sarah-Jane Schramm (SJ)

The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, 2006, Australia.
Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia.

John F Thompson (JF)

Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia.
Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia.
Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia.

Richard A Scolyer (RA)

Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia.
Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia.
Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, 2050, Australia.
ORCID: 0000-0002-8991-0013

Samuel Muller (S)

School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.
School of Mathematical and Physical Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
ORCID: 0000-0002-3087-8127

Garth Tarr (G)

School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.
Laboratory of Data Discovery for Health Limited (D²4H) Science Park, Hong Kong, SAR, China.
ORCID: 0000-0002-6605-7478

Graham J Mann (GJ)

The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, 2006, Australia. graham.mann@anu.edu.au.
Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, 2006, Australia. graham.mann@anu.edu.au.
John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia. graham.mann@anu.edu.au.

Jean Y H Yang (JYH)

Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia. jean.yang@sydney.edu.au.
School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia. jean.yang@sydney.edu.au.
Laboratory of Data Discovery for Health Limited (D²4H) Science Park, Hong Kong, SAR, China. jean.yang@sydney.edu.au.
ORCID: 0000-0002-5271-2603

Classifications MeSH