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Characterising copy number polymorphisms using next generation sequencing data
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. (Åsa Johansson)
2019 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

We developed a pipeline to identify the copy number polymorphisms (CNPs) in the Northern Swedish population using whole genome sequencing (WGS) data. Two different methodologies were applied to discover CNPs in more than 1,000 individuals. We also studied the association between the identified CNPs with the expression level of 438 plasma proteins collected in the same population.

The identified CNPs were summarized and filtered as a population copy number matrix for 1,021 individuals in 243,987 non-overlapping CNP loci. For the 872 individuals with both WGS and plasma protein biomarkers data, we conducted linear regression analyses with age and sex as covariance. From the analyses, we detected 382 CNP loci, clustered in 30 collapsed copy number variable regions (CNVRs) that were significantly associated with the levels of 17 plasma protein biomarkers (p < 4.68×10-10).

Place, publisher, year, edition, pages
2019. , p. 25
Keywords [en]
structural variations, copy number variations, copy number polymorphisms, next generation sequencing, The Northern Sweden Population Health Study, Genome-wide association study
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:uu:diva-386050OAI: oai:DiVA.org:uu-386050DiVA, id: diva2:1326816
Educational program
Master Programme in Bioinformatics
Presentation
2019-06-12, 10:00 (English)
Supervisors
Examiners
Available from: 2019-06-18 Created: 2019-06-18 Last updated: 2019-06-18Bibliographically approved

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Biology Education CentreDepartment of Immunology, Genetics and Pathology
Bioinformatics (Computational Biology)

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CiteExportLink to record
Permanent link

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Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
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  • de-DE
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Output format
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