Characterising copy number polymorphisms using next generation sequencing data
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...
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Uppsala universitet, Institutionen för biologisk grundutbildning
2019
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ftuppsalauniv:oai:DiVA.org:uu-386050 2023-05-15T17:44:37+02:00 Characterising copy number polymorphisms using next generation sequencing data Li, Zhiwei 2019 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050 eng eng Uppsala universitet, Institutionen för biologisk grundutbildning Uppsala universitet, Institutionen för immunologi, genetik och patologi http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050 info:eu-repo/semantics/openAccess structural variations copy number variations copy number polymorphisms next generation sequencing The Northern Sweden Population Health Study Genome-wide association study Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) Student thesis info:eu-repo/semantics/bachelorThesis text 2019 ftuppsalauniv 2023-02-23T21:50:03Z 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). Bachelor Thesis Northern Sweden Uppsala University: Publications (DiVA) |
institution |
Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
structural variations copy number variations copy number polymorphisms next generation sequencing The Northern Sweden Population Health Study Genome-wide association study Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) |
spellingShingle |
structural variations copy number variations copy number polymorphisms next generation sequencing The Northern Sweden Population Health Study Genome-wide association study Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) Li, Zhiwei Characterising copy number polymorphisms using next generation sequencing data |
topic_facet |
structural variations copy number variations copy number polymorphisms next generation sequencing The Northern Sweden Population Health Study Genome-wide association study Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) |
description |
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). |
format |
Bachelor Thesis |
author |
Li, Zhiwei |
author_facet |
Li, Zhiwei |
author_sort |
Li, Zhiwei |
title |
Characterising copy number polymorphisms using next generation sequencing data |
title_short |
Characterising copy number polymorphisms using next generation sequencing data |
title_full |
Characterising copy number polymorphisms using next generation sequencing data |
title_fullStr |
Characterising copy number polymorphisms using next generation sequencing data |
title_full_unstemmed |
Characterising copy number polymorphisms using next generation sequencing data |
title_sort |
characterising copy number polymorphisms using next generation sequencing data |
publisher |
Uppsala universitet, Institutionen för biologisk grundutbildning |
publishDate |
2019 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050 |
genre |
Northern Sweden |
genre_facet |
Northern Sweden |
op_relation |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050 |
op_rights |
info:eu-repo/semantics/openAccess |
_version_ |
1766146870167470080 |