Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases
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...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s13073-025-01467-z |
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| author | 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 MitoMDT Diagnostic Network for Genomics and Omics 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 David A. Stroud |
| author_facet | 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 MitoMDT Diagnostic Network for Genomics and Omics 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 David A. Stroud |
| author_sort | Daniella H. Hock |
| collection | DOAJ |
| description | 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. Freely available bioinformatic tools and criteria developed for this study ( https://rdms.app/ ) allow mitochondrial dysfunction to be identified in proteomics data with high confidence. Application of proteomics to undiagnosed individuals led to 6 additional diagnoses, including a mitochondrial phenocopy disorder, highlighting the disease agnostic nature of proteomics. Use of PBMCs as a sample type allowed rapid return of proteomics data supporting pathogenicity of novel variants identified through ultra-rapid genome sequencing in as little as 54 h. Conclusions This study provides a framework to support the integration of a single untargeted proteomics test into routine diagnostic practice for the diagnosis of mitochondrial and potentially other rare genetic disorders in clinically actionable timelines, offering a paradigm shift for the functional validation of genetic variants. |
| format | Article |
| id | doaj-art-8c1ed0db5f6c44d3b1ebcbfaec8f06fe |
| institution | OA Journals |
| issn | 1756-994X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj-art-8c1ed0db5f6c44d3b1ebcbfaec8f06fe2025-08-20T02:03:36ZengBMCGenome Medicine1756-994X2025-05-0117112410.1186/s13073-025-01467-zUntargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseasesDaniella H. Hock0Nikeisha J. Caruana1Liana N. Semcesen2Nicole J. Lake3Luke E. Formosa4Sumudu S. C. Amarasekera5Tegan Stait6Simone Tregoning7Leah E. Frajman8Adam M. Bournazos9David R. L. Robinson10Megan Ball11Boris Reljic12Bryony Ryder13Mathew J. Wallis14Anand Vasudevan15Cara Beck16Heidi Peters17Joy Lee18Natalie B. Tan19Mary-Louise Freckmann20MitoMDT Diagnostic Network for Genomics and OmicsVasiliki Karlaftis21Chantal Attard22Paul Monagle23Amanda Samarasinghe24Rosie Brown25Weimin Bi26Monkol Lek27Robert McFarland28Robert W. Taylor29Michael T. Ryan30Sandra T. Cooper31Zornitza Stark32John Christodoulou33Alison G. Compton34David R. Thorburn35David A. Stroud36Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneDepartment of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneDepartment of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneDepartment of Genetics, Yale School of MedicineDepartment of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash UniversityMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteKids Neuroscience Centre, The Children’s Hospital at WestmeadDepartment of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneMurdoch Children’s Research InstituteDepartment of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbournePaediatric and Adult National Metabolic Service, Te Toka Tumai, Te Whatu Ora Health New ZealandTasmanian Clinical Genetics Service, Tasmanian Health ServiceRoyal Women’s HospitalVictorian Clinical Genetics Services, Murdoch Children’s Research InstituteDepartment of Paediatrics, University of MelbourneVictorian Clinical Genetics Services, Murdoch Children’s Research InstituteMurdoch Children’s Research InstituteDepartment of Clinical Genetics, The Canberra HospitalMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteDepartment of Molecular and Human Genetics, Baylor College of MedicineDepartment of Genetics, Yale School of MedicineMitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle UniversityMitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle UniversityDepartment of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash UniversityKids Neuroscience Centre, The Children’s Hospital at WestmeadMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteMurdoch Children’s Research InstituteDepartment of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneAbstract 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. Freely available bioinformatic tools and criteria developed for this study ( https://rdms.app/ ) allow mitochondrial dysfunction to be identified in proteomics data with high confidence. Application of proteomics to undiagnosed individuals led to 6 additional diagnoses, including a mitochondrial phenocopy disorder, highlighting the disease agnostic nature of proteomics. Use of PBMCs as a sample type allowed rapid return of proteomics data supporting pathogenicity of novel variants identified through ultra-rapid genome sequencing in as little as 54 h. Conclusions This study provides a framework to support the integration of a single untargeted proteomics test into routine diagnostic practice for the diagnosis of mitochondrial and potentially other rare genetic disorders in clinically actionable timelines, offering a paradigm shift for the functional validation of genetic variants.https://doi.org/10.1186/s13073-025-01467-zProteomicsGenetic diagnosticsMendelian diseaseUltra-rapid genome sequencingVariant prioritisation |
| spellingShingle | 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 MitoMDT Diagnostic Network for Genomics and Omics 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 David A. Stroud Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases Genome Medicine Proteomics Genetic diagnostics Mendelian disease Ultra-rapid genome sequencing Variant prioritisation |
| title | Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases |
| title_full | Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases |
| title_fullStr | Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases |
| title_full_unstemmed | Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases |
| title_short | Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases |
| title_sort | untargeted proteomics enables ultra rapid variant prioritisation in mitochondrial and other rare diseases |
| topic | Proteomics Genetic diagnostics Mendelian disease Ultra-rapid genome sequencing Variant prioritisation |
| url | https://doi.org/10.1186/s13073-025-01467-z |
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