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Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population
: The genetic predisposition to ankylosing spondylitis (AS) has been most widely studied in cohorts with European ancestry. However, within Europe, disease prevalence is higher in Sweden. Given this, we aimed to characterize known AS susceptibility variants in a homogeneous Swedish data set, assessi...
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| Published in: | Scandinavian journal of rheumatology 2022, Vol.51 (1), p.21-24 |
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| Main Authors: | , , , , , , , |
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| container_title | Scandinavian journal of rheumatology |
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| creator | Mathioudaki, A Nordin, J Kastbom, A Söderkvist, P Eriksson, P Cedergren, J Lindblad-Toh, K Meadows, Jrs |
| description | : The genetic predisposition to ankylosing spondylitis (AS) has been most widely studied in cohorts with European ancestry. However, within Europe, disease prevalence is higher in Sweden. Given this, we aimed to characterize known AS susceptibility variants in a homogeneous Swedish data set, assessing reproducibility and direction of effect.
: The power to detect association within an existing Swedish targeted sequencing study (381 controls; 310 AS cases) was examined, and a set of published associations (n = 151) was intersected with available genotypes. Association to disease was calculated using logistic regression accounting for population structure, and
status was determined with direct polymerase chain reaction genotyping.
: The cases were found to be 92.3%
positive, with the data set showing ≥ 80% predictive power to replicate associations, with odds ratios ≥ 1.6 over a range of allele frequencies (0.1-0.7). Thirty-four markers, representing 23 gene loci, were available for investigation. The replicated variants tagged
and
loci (p |
| doi_str_mv | 10.1080/03009742.2021.1916202 |
| format | article |
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: The power to detect association within an existing Swedish targeted sequencing study (381 controls; 310 AS cases) was examined, and a set of published associations (n = 151) was intersected with available genotypes. Association to disease was calculated using logistic regression accounting for population structure, and
status was determined with direct polymerase chain reaction genotyping.
: The cases were found to be 92.3%
positive, with the data set showing ≥ 80% predictive power to replicate associations, with odds ratios ≥ 1.6 over a range of allele frequencies (0.1-0.7). Thirty-four markers, representing 23 gene loci, were available for investigation. The replicated variants tagged
and
loci (p < 1.47 × 10
), with variable direction of effect noted for gene loci
and
.
: The Swedish data set successfully replicated both major histocompatibility complex (MHC) and non-MHC loci, and revealed a different replication pattern compared to discovery data sets. This was possibly due to population demographics, including
frequency and measured comorbidities.</description><identifier>ISSN: 0300-9742</identifier><identifier>ISSN: 1502-7732</identifier><identifier>EISSN: 1502-7732</identifier><identifier>DOI: 10.1080/03009742.2021.1916202</identifier><identifier>PMID: 34169791</identifier><language>eng</language><publisher>England</publisher><subject>Gene Frequency ; Genetic Predisposition to Disease ; HLA-B27 Antigen - genetics ; Humans ; Reproducibility of Results ; Spondylitis, Ankylosing - epidemiology ; Spondylitis, Ankylosing - genetics ; Sweden - epidemiology</subject><ispartof>Scandinavian journal of rheumatology, 2022, Vol.51 (1), p.21-24</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c431t-c9cb044d824554a8c59a7c014ad7b9aff510900ecee5ae292902df797af6aeff3</citedby><cites>FETCH-LOGICAL-c431t-c9cb044d824554a8c59a7c014ad7b9aff510900ecee5ae292902df797af6aeff3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,4024,27923,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34169791$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-180093$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-468590$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Mathioudaki, A</creatorcontrib><creatorcontrib>Nordin, J</creatorcontrib><creatorcontrib>Kastbom, A</creatorcontrib><creatorcontrib>Söderkvist, P</creatorcontrib><creatorcontrib>Eriksson, P</creatorcontrib><creatorcontrib>Cedergren, J</creatorcontrib><creatorcontrib>Lindblad-Toh, K</creatorcontrib><creatorcontrib>Meadows, Jrs</creatorcontrib><title>Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population</title><title>Scandinavian journal of rheumatology</title><addtitle>Scand J Rheumatol</addtitle><description>: The genetic predisposition to ankylosing spondylitis (AS) has been most widely studied in cohorts with European ancestry. However, within Europe, disease prevalence is higher in Sweden. Given this, we aimed to characterize known AS susceptibility variants in a homogeneous Swedish data set, assessing reproducibility and direction of effect.
: The power to detect association within an existing Swedish targeted sequencing study (381 controls; 310 AS cases) was examined, and a set of published associations (n = 151) was intersected with available genotypes. Association to disease was calculated using logistic regression accounting for population structure, and
status was determined with direct polymerase chain reaction genotyping.
: The cases were found to be 92.3%
positive, with the data set showing ≥ 80% predictive power to replicate associations, with odds ratios ≥ 1.6 over a range of allele frequencies (0.1-0.7). Thirty-four markers, representing 23 gene loci, were available for investigation. The replicated variants tagged
and
loci (p < 1.47 × 10
), with variable direction of effect noted for gene loci
and
.
: The Swedish data set successfully replicated both major histocompatibility complex (MHC) and non-MHC loci, and revealed a different replication pattern compared to discovery data sets. This was possibly due to population demographics, including
frequency and measured comorbidities.</description><subject>Gene Frequency</subject><subject>Genetic Predisposition to Disease</subject><subject>HLA-B27 Antigen - genetics</subject><subject>Humans</subject><subject>Reproducibility of Results</subject><subject>Spondylitis, Ankylosing - epidemiology</subject><subject>Spondylitis, Ankylosing - genetics</subject><subject>Sweden - epidemiology</subject><issn>0300-9742</issn><issn>1502-7732</issn><issn>1502-7732</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNqFkU1vEzEQhi0EomnhJ4B85MCGsdfOro9RCxSpEgc-rpbjHRdTx17Wa6L8e7xK2isnj-Rn3hnNQ8gbBmsGPXyAFkB1gq85cLZmim1q8YysmATedF3Ln5PVwjQLdEEuc_4NAEJ16iW5aAXb1IqtCG5DwIDUTfinYLRHmke081T2NDn6ENMhUhMfjiFlH-_rZ4rDMfjZZ2pyTtabGQf610zexDlTX2n67YCDz7_omMYSzOxTfEVeOBMyvj6_V-THp4_fr2-bu6-fv1xv7xorWjY3VtkdCDH0XEgpTG-lMp0FJszQ7ZRxTjJQAGgRpUGuuAI-uE51xm0MOtdekfen3HzAsez0OPm9mY46Ga9v_M-tTtO9LkWLTS8VVLz5Px580ayvx24r_-7Ej1Oq18qz3vtsMQQTMZWsuax7K9H3S7Q8oXZKOU_onsIZ6EWgfhSoF4H6LLD2vT2PKLs9Dk9dj8baf3AVmOE</recordid><startdate>2022</startdate><enddate>2022</enddate><creator>Mathioudaki, A</creator><creator>Nordin, J</creator><creator>Kastbom, A</creator><creator>Söderkvist, P</creator><creator>Eriksson, P</creator><creator>Cedergren, J</creator><creator>Lindblad-Toh, K</creator><creator>Meadows, Jrs</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>ABXSW</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D8T</scope><scope>DG8</scope><scope>ZZAVC</scope><scope>ACNBI</scope><scope>DF2</scope></search><sort><creationdate>2022</creationdate><title>Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population</title><author>Mathioudaki, A ; Nordin, J ; Kastbom, A ; Söderkvist, P ; Eriksson, P ; Cedergren, J ; Lindblad-Toh, K ; Meadows, Jrs</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c431t-c9cb044d824554a8c59a7c014ad7b9aff510900ecee5ae292902df797af6aeff3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Gene Frequency</topic><topic>Genetic Predisposition to Disease</topic><topic>HLA-B27 Antigen - genetics</topic><topic>Humans</topic><topic>Reproducibility of Results</topic><topic>Spondylitis, Ankylosing - epidemiology</topic><topic>Spondylitis, Ankylosing - genetics</topic><topic>Sweden - epidemiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mathioudaki, A</creatorcontrib><creatorcontrib>Nordin, J</creatorcontrib><creatorcontrib>Kastbom, A</creatorcontrib><creatorcontrib>Söderkvist, P</creatorcontrib><creatorcontrib>Eriksson, P</creatorcontrib><creatorcontrib>Cedergren, J</creatorcontrib><creatorcontrib>Lindblad-Toh, K</creatorcontrib><creatorcontrib>Meadows, Jrs</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>SWEPUB Linköpings universitet full text</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SWEPUB Linköpings universitet</collection><collection>SwePub Articles full text</collection><collection>SWEPUB Uppsala universitet full text</collection><collection>SWEPUB Uppsala universitet</collection><jtitle>Scandinavian journal of rheumatology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mathioudaki, A</au><au>Nordin, J</au><au>Kastbom, A</au><au>Söderkvist, P</au><au>Eriksson, P</au><au>Cedergren, J</au><au>Lindblad-Toh, K</au><au>Meadows, Jrs</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population</atitle><jtitle>Scandinavian journal of rheumatology</jtitle><addtitle>Scand J Rheumatol</addtitle><date>2022</date><risdate>2022</risdate><volume>51</volume><issue>1</issue><spage>21</spage><epage>24</epage><pages>21-24</pages><issn>0300-9742</issn><issn>1502-7732</issn><eissn>1502-7732</eissn><abstract>: The genetic predisposition to ankylosing spondylitis (AS) has been most widely studied in cohorts with European ancestry. However, within Europe, disease prevalence is higher in Sweden. Given this, we aimed to characterize known AS susceptibility variants in a homogeneous Swedish data set, assessing reproducibility and direction of effect.
: The power to detect association within an existing Swedish targeted sequencing study (381 controls; 310 AS cases) was examined, and a set of published associations (n = 151) was intersected with available genotypes. Association to disease was calculated using logistic regression accounting for population structure, and
status was determined with direct polymerase chain reaction genotyping.
: The cases were found to be 92.3%
positive, with the data set showing ≥ 80% predictive power to replicate associations, with odds ratios ≥ 1.6 over a range of allele frequencies (0.1-0.7). Thirty-four markers, representing 23 gene loci, were available for investigation. The replicated variants tagged
and
loci (p < 1.47 × 10
), with variable direction of effect noted for gene loci
and
.
: The Swedish data set successfully replicated both major histocompatibility complex (MHC) and non-MHC loci, and revealed a different replication pattern compared to discovery data sets. This was possibly due to population demographics, including
frequency and measured comorbidities.</abstract><cop>England</cop><pmid>34169791</pmid><doi>10.1080/03009742.2021.1916202</doi><tpages>4</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Scandinavian journal of rheumatology, 2022, Vol.51 (1), p.21-24 |
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| language | eng |
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| source | Taylor and Francis:Jisc Collections:Taylor and Francis Read and Publish Agreement 2024-2025:Medical Collection (Reading list) |
| subjects | Gene Frequency Genetic Predisposition to Disease HLA-B27 Antigen - genetics Humans Reproducibility of Results Spondylitis, Ankylosing - epidemiology Spondylitis, Ankylosing - genetics Sweden - epidemiology |
| title | Allele frequency spectrum of known ankylosing spondylitis associated variants in a Swedish population |
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