Dissertation/ Thesis
Statistical analysis of parent-of-origin effects on the X chromosome and DNA methylation on age prediction
| Title: | Statistical analysis of parent-of-origin effects on the X chromosome and DNA methylation on age prediction |
|---|---|
| Authors: | Lau, Pui Yin, 劉沛彥 |
| Contributors: | Fung, TWK |
| Publisher Information: | The University of Hong Kong (Pokfulam, Hong Kong) |
| Publication Year: | 2019 |
| Collection: | University of Hong Kong: HKU Scholars Hub |
| Subject Terms: | X chromosome, DNA - Methylation - Statistical methods |
| Description: | Parent-of-origin effects, which describe an occurrence where the expression of a gene depends on its parental origin, are an important phenomenon in epigenetics. Statistical methods for detecting parent-of-origin effects on autosomes have been investigated for 20 years, but the development of statistical methods for detecting parent-of-origin effects on the X chromosome is relatively new. In the literature, a class of Q-XPAT-type tests are the only tests for the parent-of-origin effects for quantitative traits on the X chromosome. In this thesis, two simple and powerful classes of tests are proposed to detect parent-of-origin effects for quantitative trait values on X chromosome. The proposed tests can accommodate complete and incomplete nuclear families with any number of daughters. The simulation study shows that our proposed tests produce empirical type I error rates that close to their respective nominal levels, as well as powers that are larger than the Q-XPAT-type tests. The proposed tests are applied to a real data set on Turner's syndrome, and the proposed tests give a more significant finding than the Q-C-XPAT. In forensic investigation, retrieving biological information from DNA evidence is a promising field of interest. One of the applications is on the estimation of the age of the donor based on DNA methylation. A large number of studies focused on age prediction using the 450K Human Methylation Beadchip. Various marker selection methods and prediction models have been considered. However, there is a lack of research evaluating different high-dimensional variable selection methods of CpG sites with various statistical and machine learning models for age prediction. The aim of this study is to evaluate five variable selection methods (forward selection, LASSO, elastic net, SCAD and ISIS) combined with a classical statistical model and machine learning models based on the mean absolute deviation (MAD) and the root-mean-square error (RMSE). Publicly available 450K data set containing 991 whole blood ... |
| Document Type: | doctoral or postdoctoral thesis |
| Language: | English |
| Relation: | HKU Theses Online (HKUTO); 991044158738403414; https://hub.hku.hk/handle/10722/286594 |
| Availability: | https://hub.hku.hk/handle/10722/286594 |
| Rights: | The author retains all proprietary rights, (such as patent rights) and the right to use in future works. ; This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. |
| Accession Number: | edsbas.655C5C6 |
| Database: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://hub.hku.hk/handle/10722/286594# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Header | DbId: edsbas DbLabel: BASE An: edsbas.655C5C6 RelevancyScore: 805 AccessLevel: 3 PubType: Dissertation/ Thesis PubTypeId: dissertation PreciseRelevancyScore: 805.215454101563 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Statistical analysis of parent-of-origin effects on the X chromosome and DNA methylation on age prediction – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Lau%2C+Pui+Yin%22">Lau, Pui Yin</searchLink><br /><searchLink fieldCode="AR" term="%22劉沛彥%22">劉沛彥</searchLink> – Name: Author Label: Contributors Group: Au Data: Fung, TWK – Name: Publisher Label: Publisher Information Group: PubInfo Data: The University of Hong Kong (Pokfulam, Hong Kong) – Name: DatePubCY Label: Publication Year Group: Date Data: 2019 – Name: Subset Label: Collection Group: HoldingsInfo Data: University of Hong Kong: HKU Scholars Hub – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22X+chromosome%22">X chromosome</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+-+Methylation+-+Statistical+methods%22">DNA - Methylation - Statistical methods</searchLink> – Name: Abstract Label: Description Group: Ab Data: Parent-of-origin effects, which describe an occurrence where the expression of a gene depends on its parental origin, are an important phenomenon in epigenetics. Statistical methods for detecting parent-of-origin effects on autosomes have been investigated for 20 years, but the development of statistical methods for detecting parent-of-origin effects on the X chromosome is relatively new. In the literature, a class of Q-XPAT-type tests are the only tests for the parent-of-origin effects for quantitative traits on the X chromosome. In this thesis, two simple and powerful classes of tests are proposed to detect parent-of-origin effects for quantitative trait values on X chromosome. The proposed tests can accommodate complete and incomplete nuclear families with any number of daughters. The simulation study shows that our proposed tests produce empirical type I error rates that close to their respective nominal levels, as well as powers that are larger than the Q-XPAT-type tests. The proposed tests are applied to a real data set on Turner's syndrome, and the proposed tests give a more significant finding than the Q-C-XPAT. In forensic investigation, retrieving biological information from DNA evidence is a promising field of interest. One of the applications is on the estimation of the age of the donor based on DNA methylation. A large number of studies focused on age prediction using the 450K Human Methylation Beadchip. Various marker selection methods and prediction models have been considered. However, there is a lack of research evaluating different high-dimensional variable selection methods of CpG sites with various statistical and machine learning models for age prediction. The aim of this study is to evaluate five variable selection methods (forward selection, LASSO, elastic net, SCAD and ISIS) combined with a classical statistical model and machine learning models based on the mean absolute deviation (MAD) and the root-mean-square error (RMSE). Publicly available 450K data set containing 991 whole blood ... – Name: TypeDocument Label: Document Type Group: TypDoc Data: doctoral or postdoctoral thesis – Name: Language Label: Language Group: Lang Data: English – Name: NoteTitleSource Label: Relation Group: SrcInfo Data: HKU Theses Online (HKUTO); 991044158738403414; https://hub.hku.hk/handle/10722/286594 – Name: URL Label: Availability Group: URL Data: https://hub.hku.hk/handle/10722/286594 – Name: Copyright Label: Rights Group: Cpyrght Data: The author retains all proprietary rights, (such as patent rights) and the right to use in future works. ; This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. – Name: AN Label: Accession Number Group: ID Data: edsbas.655C5C6 |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=edsbas&AN=edsbas.655C5C6 |
| RecordInfo | BibRecord: BibEntity: Languages: – Text: English Subjects: – SubjectFull: X chromosome Type: general – SubjectFull: DNA - Methylation - Statistical methods Type: general Titles: – TitleFull: Statistical analysis of parent-of-origin effects on the X chromosome and DNA methylation on age prediction Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Lau, Pui Yin – PersonEntity: Name: NameFull: 劉沛彥 – PersonEntity: Name: NameFull: Fung, TWK IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2019 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
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