Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations
Abstract Background Inherited Metabolic Disorders (IMDs) are rare diseases where one impaired protein leads to a cascade of changes in the adjacent chemical conversions. IMDs often present with non-specific symptoms, a lack of a clear genotype–phenotype correlation, and de novo mutations, complicati...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | Orphanet Journal of Rare Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13023-023-02683-9 |
| _version_ | 1797836319090540544 |
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| author | Denise N. Slenter Irene M. G. M. Hemel Chris T. Evelo Jörgen Bierau Egon L. Willighagen Laura K. M. Steinbusch |
| author_facet | Denise N. Slenter Irene M. G. M. Hemel Chris T. Evelo Jörgen Bierau Egon L. Willighagen Laura K. M. Steinbusch |
| author_sort | Denise N. Slenter |
| collection | DOAJ |
| description | Abstract Background Inherited Metabolic Disorders (IMDs) are rare diseases where one impaired protein leads to a cascade of changes in the adjacent chemical conversions. IMDs often present with non-specific symptoms, a lack of a clear genotype–phenotype correlation, and de novo mutations, complicating diagnosis. Furthermore, products of one metabolic conversion can be the substrate of another pathway obscuring biomarker identification and causing overlapping biomarkers for different disorders. Visualization of the connections between metabolic biomarkers and the enzymes involved might aid in the diagnostic process. The goal of this study was to provide a proof-of-concept framework for integrating knowledge of metabolic interactions with real-life patient data before scaling up this approach. This framework was tested on two groups of well-studied and related metabolic pathways (the urea cycle and pyrimidine de-novo synthesis). The lessons learned from our approach will help to scale up the framework and support the diagnosis of other less-understood IMDs. Methods Our framework integrates literature and expert knowledge into machine-readable pathway models, including relevant urine biomarkers and their interactions. The clinical data of 16 previously diagnosed patients with various pyrimidine and urea cycle disorders were visualized on the top 3 relevant pathways. Two expert laboratory scientists evaluated the resulting visualizations to derive a diagnosis. Results The proof-of-concept platform resulted in varying numbers of relevant biomarkers (five to 48), pathways, and pathway interactions for each patient. The two experts reached the same conclusions for all samples with our proposed framework as with the current metabolic diagnostic pipeline. For nine patient samples, the diagnosis was made without knowledge about clinical symptoms or sex. For the remaining seven cases, four interpretations pointed in the direction of a subset of disorders, while three cases were found to be undiagnosable with the available data. Diagnosing these patients would require additional testing besides biochemical analysis. Conclusion The presented framework shows how metabolic interaction knowledge can be integrated with clinical data in one visualization, which can be relevant for future analysis of difficult patient cases and untargeted metabolomics data. Several challenges were identified during the development of this framework, which should be resolved before this approach can be scaled up and implemented to support the diagnosis of other (less understood) IMDs. The framework could be extended with other OMICS data (e.g. genomics, transcriptomics), and phenotypic data, as well as linked to other knowledge captured as Linked Open Data. |
| first_indexed | 2024-04-09T15:06:54Z |
| format | Article |
| id | doaj.art-eb617e46433e4367a0defedd4be2509e |
| institution | Directory Open Access Journal |
| issn | 1750-1172 |
| language | English |
| last_indexed | 2024-04-09T15:06:54Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Orphanet Journal of Rare Diseases |
| spelling | doaj.art-eb617e46433e4367a0defedd4be2509e2023-04-30T11:28:05ZengBMCOrphanet Journal of Rare Diseases1750-11722023-04-0118111610.1186/s13023-023-02683-9Extending inherited metabolic disorder diagnostics with biomarker interaction visualizationsDenise N. Slenter0Irene M. G. M. Hemel1Chris T. Evelo2Jörgen Bierau3Egon L. Willighagen4Laura K. M. Steinbusch5Department of Bioinformatics (BiGCaT), NUTRIM, Maastricht UniversityDepartment of Bioinformatics (BiGCaT), NUTRIM, Maastricht UniversityDepartment of Bioinformatics (BiGCaT), NUTRIM, Maastricht UniversityDepartment of Clinical Genetics, Maastricht University Medical CenterDepartment of Bioinformatics (BiGCaT), NUTRIM, Maastricht UniversityDepartment of Clinical Genetics, Maastricht University Medical CenterAbstract Background Inherited Metabolic Disorders (IMDs) are rare diseases where one impaired protein leads to a cascade of changes in the adjacent chemical conversions. IMDs often present with non-specific symptoms, a lack of a clear genotype–phenotype correlation, and de novo mutations, complicating diagnosis. Furthermore, products of one metabolic conversion can be the substrate of another pathway obscuring biomarker identification and causing overlapping biomarkers for different disorders. Visualization of the connections between metabolic biomarkers and the enzymes involved might aid in the diagnostic process. The goal of this study was to provide a proof-of-concept framework for integrating knowledge of metabolic interactions with real-life patient data before scaling up this approach. This framework was tested on two groups of well-studied and related metabolic pathways (the urea cycle and pyrimidine de-novo synthesis). The lessons learned from our approach will help to scale up the framework and support the diagnosis of other less-understood IMDs. Methods Our framework integrates literature and expert knowledge into machine-readable pathway models, including relevant urine biomarkers and their interactions. The clinical data of 16 previously diagnosed patients with various pyrimidine and urea cycle disorders were visualized on the top 3 relevant pathways. Two expert laboratory scientists evaluated the resulting visualizations to derive a diagnosis. Results The proof-of-concept platform resulted in varying numbers of relevant biomarkers (five to 48), pathways, and pathway interactions for each patient. The two experts reached the same conclusions for all samples with our proposed framework as with the current metabolic diagnostic pipeline. For nine patient samples, the diagnosis was made without knowledge about clinical symptoms or sex. For the remaining seven cases, four interpretations pointed in the direction of a subset of disorders, while three cases were found to be undiagnosable with the available data. Diagnosing these patients would require additional testing besides biochemical analysis. Conclusion The presented framework shows how metabolic interaction knowledge can be integrated with clinical data in one visualization, which can be relevant for future analysis of difficult patient cases and untargeted metabolomics data. Several challenges were identified during the development of this framework, which should be resolved before this approach can be scaled up and implemented to support the diagnosis of other (less understood) IMDs. The framework could be extended with other OMICS data (e.g. genomics, transcriptomics), and phenotypic data, as well as linked to other knowledge captured as Linked Open Data.https://doi.org/10.1186/s13023-023-02683-9Clinical metabolic biomarkersPurine and pyrimidine metabolismUrea cycleSemantic web technologiesNetwork data analysisSystems biology |
| spellingShingle | Denise N. Slenter Irene M. G. M. Hemel Chris T. Evelo Jörgen Bierau Egon L. Willighagen Laura K. M. Steinbusch Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations Orphanet Journal of Rare Diseases Clinical metabolic biomarkers Purine and pyrimidine metabolism Urea cycle Semantic web technologies Network data analysis Systems biology |
| title | Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| title_full | Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| title_fullStr | Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| title_full_unstemmed | Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| title_short | Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| title_sort | extending inherited metabolic disorder diagnostics with biomarker interaction visualizations |
| topic | Clinical metabolic biomarkers Purine and pyrimidine metabolism Urea cycle Semantic web technologies Network data analysis Systems biology |
| url | https://doi.org/10.1186/s13023-023-02683-9 |
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