Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases
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(Published version)
Date
2025
Authors
Hock, D.H.
Caruana, N.J.
Semcesen, L.N.
Lake, N.J.
Formosa, L.E.
Amarasekera, S.S.C.
Stait, T.
Tregoning, S.
Frajman, L.E.
Bournazos, A.M.
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Journal article
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Genome Medicine, 2025; 17(1):58-1-58-24
Statement of Responsibility
Daniella H. Hock, Nikeisha J. Caruana, Liana N. Semcesen, Nicole J. Lake, Luke E. Formosa, Sumudu S. C. Amarasekera, Tegan Stait, Simone Tregoning, Leah E. Frajman, Adam M. Bournazos, David R. L. Robinson, Megan Ball, Boris Reljic, Bryony Ryder, Mathew J. Wallis, Anand Vasudevan, Cara Beck, Heidi Peters, Joy Lee, Natalie B. Tan, Mary-Louise Freckmann, Vasiliki Karlaftis, Chantal Attard, Paul Monagle, Amanda Samarasinghe, Rosie Brown, Weimin Bi, Monkol Lek, Robert McFarland, Robert W. Taylor, Michael T. Ryan, Sandra T. Cooper, Zornitza Stark, John Christodoulou, Alison G. Compton, David R. Thorburn and David A. Stroud
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Abstract
Background Only half of individuals with suspected rare diseases receive a genetic diagnosis following genomic testing. A genetic diagnosis allows access to appropriate care, restores reproductive confidence and reduces the number of potentially unnecessary interventions. A major barrier is the lack of disease agnostic functional tests suitable for implementation in routine diagnostics that can provide evidence supporting pathogenicity of novel variants, especially those refractory to RNA sequencing. Methods Focusing on mitochondrial disease, we describe an untargeted mass-spectrometry based proteomics pipeline that can quantify proteins encoded by > 50% of Mendelian disease genes and > 80% of known mitochondrial disease genes in clinically relevant sample types, including peripheral blood mononuclear cells (PBMCs). In total we profiled > 90 individuals including undiagnosed individuals suspected of mitochondrial disease and a supporting cohort of disease controls harbouring pathogenic variants in nuclear and mitochondrial genes. Proteomics data were benchmarked against pathology accredited respiratory chain enzymology to assess the performance of proteomics as a functional test. Proteomics testing was subsequently applied to individuals with suspected mitochondrial disease, including a critically ill infant with a view toward rapid interpretation of variants identified in ultra-rapid genome sequencing. Results Proteomics testing provided evidence to support variant pathogenicity in 83% of individuals in a cohort with confirmed mitochondrial disease, outperforming clinical respiratory chain enzymology.
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© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.