Dissertation/ Thesis
Chinese population analyses based on next-generation sequencing data
| Τίτλος: | Chinese population analyses based on next-generation sequencing data |
|---|---|
| Συγγραφείς: | Ou, Min, 区敏 |
| Στοιχεία εκδότη: | The University of Hong Kong (Pokfulam, Hong Kong) |
| Έτος έκδοσης: | 2025 |
| Συλλογή: | University of Hong Kong: HKU Scholars Hub |
| Θεματικοί όροι: | Human population genetics - China - Data processing, Nucleotide sequence - Data processing |
| Περιγραφή: | Population analysis studies the characteristics of the population to investigate the population diversity and guide clinical management. Researchers make use of the next-generation sequencing technologies to study the populations via genomic variations more efficiently and cost-effectively. Chinese population analysis is limited due to the lack of publicly available samples with variants. This thesis introduces three population analyses based on NGS data generated from Chinese samples with different levels of demographic data. The first analysis studied the variant distribution, population diversity, and variant severity of whole genome sequencing data of 707 high coverage samples in the Chinese Genome Database (CGDB). Disease or drug-related variants that are common in CGDB but rare in other populations were investigated to improve diagnostic accuracy and guide precision medicine. Moreover, to fill the research gap of no pathogenicity score considering the gene region and non-gene region altogether, a genome-wide pathogenicity score (Phred-scaled immutability, Pim) based on 486 healthy Chinese samples in CGDB was developed. Significant associations between the Pim and pathogenic variants, genes, and regulatory features were found. The second analysis investigated the genomic composition of Chinese subgroups based on whole-exome sequencing data of 205 Hong Kong Cantonese (HKG). HKG is the first variant database for the population and available to the public. Unlike CGDB without the geographic location information, HKG samples are all Cantonese from Hong Kong which enables the Chinese subpopulation comparisons. The unique position of HKG among other Chinese was demonstrated via the principal component analysis. The IBD analysis revealed the population mixture and inbreeding level of HKG is the closest to the southern Chinese. The ancestral compositions of HKG, EAS, and SAS gradual change in proportion along the latitude, which aligns with the geological origin. HKG variants that are ClinVar pathogenic or ... |
| Τύπος εγγράφου: | doctoral or postdoctoral thesis |
| Γλώσσα: | English |
| Relation: | HKU Theses Online (HKUTO); 991044897477003414; https://hub.hku.hk/handle/10722/353400 |
| Διαθεσιμότητα: | https://hub.hku.hk/handle/10722/353400 |
| 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. |
| Αριθμός Καταχώρησης: | edsbas.D52A3787 |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://hub.hku.hk/handle/10722/353400# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Header | DbId: edsbas DbLabel: BASE An: edsbas.D52A3787 RelevancyScore: 900 AccessLevel: 3 PubType: Dissertation/ Thesis PubTypeId: dissertation PreciseRelevancyScore: 899.809631347656 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Chinese population analyses based on next-generation sequencing data – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Ou%2C+Min%22">Ou, Min</searchLink><br /><searchLink fieldCode="AR" term="%22区敏%22">区敏</searchLink> – Name: Publisher Label: Publisher Information Group: PubInfo Data: The University of Hong Kong (Pokfulam, Hong Kong) – Name: DatePubCY Label: Publication Year Group: Date Data: 2025 – 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="%22Human+population+genetics+-+China+-+Data+processing%22">Human population genetics - China - Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence+-+Data+processing%22">Nucleotide sequence - Data processing</searchLink> – Name: Abstract Label: Description Group: Ab Data: Population analysis studies the characteristics of the population to investigate the population diversity and guide clinical management. Researchers make use of the next-generation sequencing technologies to study the populations via genomic variations more efficiently and cost-effectively. Chinese population analysis is limited due to the lack of publicly available samples with variants. This thesis introduces three population analyses based on NGS data generated from Chinese samples with different levels of demographic data. The first analysis studied the variant distribution, population diversity, and variant severity of whole genome sequencing data of 707 high coverage samples in the Chinese Genome Database (CGDB). Disease or drug-related variants that are common in CGDB but rare in other populations were investigated to improve diagnostic accuracy and guide precision medicine. Moreover, to fill the research gap of no pathogenicity score considering the gene region and non-gene region altogether, a genome-wide pathogenicity score (Phred-scaled immutability, Pim) based on 486 healthy Chinese samples in CGDB was developed. Significant associations between the Pim and pathogenic variants, genes, and regulatory features were found. The second analysis investigated the genomic composition of Chinese subgroups based on whole-exome sequencing data of 205 Hong Kong Cantonese (HKG). HKG is the first variant database for the population and available to the public. Unlike CGDB without the geographic location information, HKG samples are all Cantonese from Hong Kong which enables the Chinese subpopulation comparisons. The unique position of HKG among other Chinese was demonstrated via the principal component analysis. The IBD analysis revealed the population mixture and inbreeding level of HKG is the closest to the southern Chinese. The ancestral compositions of HKG, EAS, and SAS gradual change in proportion along the latitude, which aligns with the geological origin. HKG variants that are ClinVar pathogenic or ... – 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); 991044897477003414; https://hub.hku.hk/handle/10722/353400 – Name: URL Label: Availability Group: URL Data: https://hub.hku.hk/handle/10722/353400 – 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.D52A3787 |
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| RecordInfo | BibRecord: BibEntity: Languages: – Text: English Subjects: – SubjectFull: Human population genetics - China - Data processing Type: general – SubjectFull: Nucleotide sequence - Data processing Type: general Titles: – TitleFull: Chinese population analyses based on next-generation sequencing data Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Ou, Min – PersonEntity: Name: NameFull: 区敏 IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2025 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
| ResultId | 1 |