Dissertation/ Thesis
Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics
| Τίτλος: | Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics |
|---|---|
| Συγγραφείς: | Naidoo, Lorensha |
| Συνεισφορές: | Patterton, Hugh-George, Vaudel, Marc, Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. |
| Στοιχεία εκδότη: | Stellenbosch University |
| Έτος έκδοσης: | 2025 |
| Συλλογή: | Stellenbosch University: SUNScholar Research Repository |
| Θεματικοί όροι: | Diabetes in children -- Genetic aspects, Proteomics -- Data processing, Proteins -- Analysis, Peptides -- Analysis, Spectrum analysis -- Data processing, Machine learning -- Computer simulation, Bayesian statistical decision theory -- Computer simulation, UCTD |
| Περιγραφή: | Thesis (MSc)--Stellenbosch University, 2025. ; Naidoo, L. 2025. Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/fa2ce23c-42d1-4183-b3ba-b969d378e482 ; ENGLISH ABSTRACT: Monogenic diabetes is a rare form of paediatric diabetes caused by a pathogenic variant occurring in a single gene associated with insulin production from pancreatic β-cells, resulting in hyperglycaemic complications. Maturity-onset diabetes of the young (MODY) is a subtype of monogenic diabetes, accounting for 2 – 5% of diabetic cases. Patient classification has revealed undiagnosed symptomatic cohorts speculated to result from unknown genetic variants. Identifying these variants is essential for advancing precision medicine and providing specialised medical care. Proteogenomics allows for the identification of alternative forms of proteins resulting from genomic variation. Protein samples are processed using mass spectrometry to obtain peptide sequences that are then annotated to a sequence database using search engines, e.g. SEQUEST and X!Tandem. Peptide-spectrum matches (PSMs) with varying confidence scores are produced; however, there is no clear distinction between correct and incorrect PSMs. Additionally, distinguishing variant PSMs from canonical PSMs remains challenging due to their low frequency and sequence similarity. The target-decoy approach (TDA) is a common method for classifying correct and incorrect PSMs and is used in existing PSM processing tools, such as Percolator. Target sequences are peptide sequences from proteomic databases, while decoy sequences are artificially generated to serve as a null model for error rate estimation. To the knowledge of this work, the TDA has not been implemented towards improving the discrimination performance of variant PSMs. To this end, this study conducts an exploratory analysis to improve the classification of ... |
| Τύπος εγγράφου: | thesis |
| Περιγραφή αρχείου: | xiv, 143 pages : illustrations; application/pdf |
| Γλώσσα: | unknown |
| Relation: | https://scholar.sun.ac.za/handle/10019.1/134730 |
| Διαθεσιμότητα: | https://scholar.sun.ac.za/handle/10019.1/134730 |
| Rights: | Stellenbosch University |
| Αριθμός Καταχώρησης: | edsbas.CDF890BC |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://scholar.sun.ac.za/handle/10019.1/134730# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Items | – Name: Title Label: Title Group: Ti Data: Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Naidoo%2C+Lorensha%22">Naidoo, Lorensha</searchLink> – Name: Author Label: Contributors Group: Au Data: Patterton, Hugh-George<br />Vaudel, Marc<br />Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. – Name: Publisher Label: Publisher Information Group: PubInfo Data: Stellenbosch University – Name: DatePubCY Label: Publication Year Group: Date Data: 2025 – Name: Subset Label: Collection Group: HoldingsInfo Data: Stellenbosch University: SUNScholar Research Repository – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Diabetes+in+children+--+Genetic+aspects%22">Diabetes in children -- Genetic aspects</searchLink><br /><searchLink fieldCode="DE" term="%22Proteomics+--+Data+processing%22">Proteomics -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Proteins+--+Analysis%22">Proteins -- Analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Peptides+--+Analysis%22">Peptides -- Analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Spectrum+analysis+--+Data+processing%22">Spectrum analysis -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Machine+learning+--+Computer+simulation%22">Machine learning -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Bayesian+statistical+decision+theory+--+Computer+simulation%22">Bayesian statistical decision theory -- Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22UCTD%22">UCTD</searchLink> – Name: Abstract Label: Description Group: Ab Data: Thesis (MSc)--Stellenbosch University, 2025. ; Naidoo, L. 2025. Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/fa2ce23c-42d1-4183-b3ba-b969d378e482 ; ENGLISH ABSTRACT: Monogenic diabetes is a rare form of paediatric diabetes caused by a pathogenic variant occurring in a single gene associated with insulin production from pancreatic β-cells, resulting in hyperglycaemic complications. Maturity-onset diabetes of the young (MODY) is a subtype of monogenic diabetes, accounting for 2 – 5% of diabetic cases. Patient classification has revealed undiagnosed symptomatic cohorts speculated to result from unknown genetic variants. Identifying these variants is essential for advancing precision medicine and providing specialised medical care. Proteogenomics allows for the identification of alternative forms of proteins resulting from genomic variation. Protein samples are processed using mass spectrometry to obtain peptide sequences that are then annotated to a sequence database using search engines, e.g. SEQUEST and X!Tandem. Peptide-spectrum matches (PSMs) with varying confidence scores are produced; however, there is no clear distinction between correct and incorrect PSMs. Additionally, distinguishing variant PSMs from canonical PSMs remains challenging due to their low frequency and sequence similarity. The target-decoy approach (TDA) is a common method for classifying correct and incorrect PSMs and is used in existing PSM processing tools, such as Percolator. Target sequences are peptide sequences from proteomic databases, while decoy sequences are artificially generated to serve as a null model for error rate estimation. To the knowledge of this work, the TDA has not been implemented towards improving the discrimination performance of variant PSMs. To this end, this study conducts an exploratory analysis to improve the classification of ... – Name: TypeDocument Label: Document Type Group: TypDoc Data: thesis – Name: Format Label: File Description Group: SrcInfo Data: xiv, 143 pages : illustrations; application/pdf – Name: Language Label: Language Group: Lang Data: unknown – Name: NoteTitleSource Label: Relation Group: SrcInfo Data: https://scholar.sun.ac.za/handle/10019.1/134730 – Name: URL Label: Availability Group: URL Data: https://scholar.sun.ac.za/handle/10019.1/134730 – Name: Copyright Label: Rights Group: Cpyrght Data: Stellenbosch University – Name: AN Label: Accession Number Group: ID Data: edsbas.CDF890BC |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=edsbas&AN=edsbas.CDF890BC |
| RecordInfo | BibRecord: BibEntity: Languages: – Text: unknown Subjects: – SubjectFull: Diabetes in children -- Genetic aspects Type: general – SubjectFull: Proteomics -- Data processing Type: general – SubjectFull: Proteins -- Analysis Type: general – SubjectFull: Peptides -- Analysis Type: general – SubjectFull: Spectrum analysis -- Data processing Type: general – SubjectFull: Machine learning -- Computer simulation Type: general – SubjectFull: Bayesian statistical decision theory -- Computer simulation Type: general – SubjectFull: UCTD Type: general Titles: – TitleFull: Assessing the discoverability of variant proteins causing rare forms of paediatric diabetes using proteogenomics Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Naidoo, Lorensha – PersonEntity: Name: NameFull: Patterton, Hugh-George – PersonEntity: Name: NameFull: Vaudel, Marc – PersonEntity: Name: NameFull: Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2025 Identifiers: – Type: issn-locals Value: edsbas |
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