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The power of allele-specific gene expression analysis for identification of cis-regulatory SNPs
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
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(English)Manuscript (preprint) (Other academic)
Research subject
Molecular Medicine
Identifiers
URN: urn:nbn:se:uu:diva-158485OAI: oai:DiVA.org:uu-158485DiVA: diva2:439658
Available from: 2011-09-08 Created: 2011-09-08 Last updated: 2011-10-04
In thesis
1. Genetic and Genomic Analysis of DNA Sequence Variation
Open this publication in new window or tab >>Genetic and Genomic Analysis of DNA Sequence Variation
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The studies in this thesis describe the application of genotyping and allele specific expression analysis to genetic studies. The role of the gene NPC1 in Triglyceride metabolism was explored in mouse models and in humans on the population level in study I. NPC1 was found to affect hepatic triglyceride metabolism, and to be relevant for controlling serum triglyceride levels in mice and potentially in humans. In study II the utility of the HapMap CEU samples was investigated for tagSNP selection in six European populations. The HapMap CEU was found to be representative for tagSNP selection in all populations while allele frequencies differed significantly in the sample from Kuusamo, Finland. In study III the power of Allele specific expression as a tool for the mapping of cis-regulatory variation was compared to standard eQTL analysis, ASE was found to be the more powerful type of analysis for a similar sample size. Finally ASE mapping was applied to regions reported to harbour long non-coding RNAs and associated SNPs were compared to published trait-associations. This revealed strong cis-regulatory SNPs of long non-coding RNAs with reported trait or disease associations.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2011. 50 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 702
Keyword
SNP, NPC1, association study, allele specific expression, tagSNP, non-coding RNA
National Category
Medical Genetics
Research subject
Molecular Medicine
Identifiers
urn:nbn:se:uu:diva-158486 (URN)978-91-554-8156-8 (ISBN)
Public defence
2011-10-25, Enghoffsalen, Entrance 50, bottom floor, Uppsala University Hospital, Uppsala, 09:15 (English)
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Supervisors
Available from: 2011-10-04 Created: 2011-09-08 Last updated: 2011-11-04

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