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Non-negative matrix factorisation of Raman spectra finds common patterns relating to neuromuscular disease across differing equipment configurations, preclinical models and human tissue

Lookup NU author(s): Professor Grainne Gorman, Professor Robert Taylor



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


© 2022 The Authors. Journal of Raman Spectroscopy published by John Wiley & Sons Ltd. Raman spectroscopy shows promise as a biomarker for complex nerve and muscle (neuromuscular) diseases. To maximise its potential, several challenges remain. These include the sensitivity to different instrument configurations, translation across preclinical/human tissues and the development of multivariate analytics that can derive interpretable spectral outputs for disease identification. Nonnegative matrix factorisation (NMF) can extract features from high-dimensional data sets and the nonnegative constraint results in physically realistic outputs. In this study, we have undertaken NMF on Raman spectra of muscle obtained from different clinical and preclinical settings. First, we obtained and combined Raman spectra from human patients with mitochondrial disease and healthy volunteers, using both a commercial microscope and in-house fibre optic probe. NMF was applied across all data, and spectral patterns common to both equipment configurations were identified. Linear discriminant models utilising these patterns were able to accurately classify disease states (accuracy 70.2–84.5%). Next, we applied NMF to spectra obtained from the mdx mouse model of a Duchenne muscular dystrophy and patients with dystrophic muscle conditions. Spectral fingerprints common to mouse/human were obtained and able to accurately identify disease (accuracy 79.5–98.8%). We conclude that NMF can be used to analyse Raman data across different equipment configurations and the preclinical/clinical divide. Thus, the application of NMF decomposition methods could enhance the potential of Raman spectroscopy for the study of fatal neuromuscular diseases.

Publication metadata

Author(s): Alix JJP, Plesia M, Schooling CN, Dudgeon AP, Kendall CA, Kadirkamanathan V, McDermott CJ, Gorman GS, Taylor RW, Mead RJ, Shaw PJ, Day JC

Publication type: Article

Publication status: Published

Journal: Journal of Raman Spectroscopy

Year: 2022

Volume: 54

Issue: 3

Pages: 258-268

Print publication date: 01/03/2023

Online publication date: 01/12/2022

Acceptance date: 02/11/2022

Date deposited: 12/01/2023

ISSN (print): 0377-0486

ISSN (electronic): 1097-4555

Publisher: John Wiley and Sons Ltd


DOI: 10.1002/jrs.6480


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Funder referenceFunder name
203105/ Z/16/Z
Alzheimer Society
Brains for Dementia Research (BDR)
Lily Foundation
Medical Research Council
Newcastle Mitochondrial Research Biobank
MR/S005021/1Medical Research Council (MRC)
NIHR Oxford Biomedical Research Centre
NIHR Sheffield Clinical Research Facility
Oxford Brain Bank
NIHR Newcastle Biomedical Research Centre
Pathological Society