GWAS and transcriptional analysis prioritize ITPR1 and CNTN4 for a serum uric acid 3p26 QTL in Mexican Americans
The variation in serum uric acid concentrations is under significant genetic influence. Elevated SUA concentrations have been linked to increased risk for gout, kidney stones, chronic kidney disease, and cardiovascular disease whereas reduced serum uric acid concentrations have been linked to multip...
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creator | Chittoor, Geetha Kent, Jr, Jack W Almeida, Marcio Puppala, Sobha Farook, Vidya S Cole, Shelley A Haack, Karin Göring, Harald H H MacCluer, Jean W Curran, Joanne E Carless, Melanie A Johnson, Matthew P Moses, Eric K Almasy, Laura Mahaney, Michael C Lehman, Donna M Duggirala, Ravindranath Comuzzie, Anthony G Blangero, John Voruganti, Venkata Saroja |
description | The variation in serum uric acid concentrations is under significant genetic influence. Elevated SUA concentrations have been linked to increased risk for gout, kidney stones, chronic kidney disease, and cardiovascular disease whereas reduced serum uric acid concentrations have been linked to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Previously, we identified a novel locus on chromosome 3p26 affecting serum uric acid concentrations in Mexican Americans from San Antonio Family Heart Study. As a follow up, we examined genome-wide single nucleotide polymorphism data in an extended cohort of 1281 Mexican Americans from multigenerational families of the San Antonio Family Heart Study and the San Antonio Family Diabetes/Gallbladder Study. We used a linear regression-based joint linkage/association test under an additive model of allelic effect, while accounting for non-independence among family members via a kinship variance component.
Univariate genetic analysis indicated serum uric acid concentrations to be significant heritable (h (2) = 0.50 ± 0.05, p < 4 × 10(-35)), and linkage analysis of serum uric acid concentrations confirmed our previous finding of a novel locus on 3p26 (LOD = 4.9, p < 1 × 10(-5)) in the extended sample. Additionally, we observed strong association of serum uric acid concentrations with variants in following candidate genes in the 3p26 region; inositol 1,4,5-trisphosphate receptor, type 1 (ITPR1), contactin 4 (CNTN4), decapping mRNA 1A (DCP1A); transglutaminase 4 (TGM4) and rho guanine nucleotide exchange factor (GEF) 26 (ARHGEF26) [p < 3 × 10(-7); minor allele frequencies ranged between 0.003 and 0.42] and evidence of cis-regulation for ITPR1 transcripts.
Our results confirm the importance of the chromosome 3p26 locus and genetic variants in this region in the regulation of serum uric acid concentrations. |
doi_str_mv | 10.1186/s12864-016-2594-5 |
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Univariate genetic analysis indicated serum uric acid concentrations to be significant heritable (h (2) = 0.50 ± 0.05, p < 4 × 10(-35)), and linkage analysis of serum uric acid concentrations confirmed our previous finding of a novel locus on 3p26 (LOD = 4.9, p < 1 × 10(-5)) in the extended sample. Additionally, we observed strong association of serum uric acid concentrations with variants in following candidate genes in the 3p26 region; inositol 1,4,5-trisphosphate receptor, type 1 (ITPR1), contactin 4 (CNTN4), decapping mRNA 1A (DCP1A); transglutaminase 4 (TGM4) and rho guanine nucleotide exchange factor (GEF) 26 (ARHGEF26) [p < 3 × 10(-7); minor allele frequencies ranged between 0.003 and 0.42] and evidence of cis-regulation for ITPR1 transcripts.
Our results confirm the importance of the chromosome 3p26 locus and genetic variants in this region in the regulation of serum uric acid concentrations.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-016-2594-5</identifier><identifier>PMID: 27039371</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adult ; Chromosomes, Human, Pair 3 ; Contactins - genetics ; Female ; Genetic aspects ; Genetic Linkage ; Genome-Wide Association Study ; Genomics ; Humans ; Inositol 1,4,5-Trisphosphate Receptors - genetics ; Male ; Mexican Americans ; Mexican Americans - genetics ; Middle Aged ; Physiological aspects ; Polymorphism, Single Nucleotide ; Quantitative genetics ; Quantitative Trait Loci ; Uric acid ; Uric Acid - blood</subject><ispartof>BMC genomics, 2016-04, Vol.17 (261), p.276-276, Article 276</ispartof><rights>COPYRIGHT 2016 BioMed Central Ltd.</rights><rights>Copyright BioMed Central 2016</rights><rights>Chittoor et al. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-5d7af9f212ac21196edc3b59f155f6c6b77226d38b3b5a2e30ad3c772bebfcae3</citedby><cites>FETCH-LOGICAL-c528t-5d7af9f212ac21196edc3b59f155f6c6b77226d38b3b5a2e30ad3c772bebfcae3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818944/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818944/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27039371$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chittoor, Geetha</creatorcontrib><creatorcontrib>Kent, Jr, Jack W</creatorcontrib><creatorcontrib>Almeida, Marcio</creatorcontrib><creatorcontrib>Puppala, Sobha</creatorcontrib><creatorcontrib>Farook, Vidya S</creatorcontrib><creatorcontrib>Cole, Shelley A</creatorcontrib><creatorcontrib>Haack, Karin</creatorcontrib><creatorcontrib>Göring, Harald H H</creatorcontrib><creatorcontrib>MacCluer, Jean W</creatorcontrib><creatorcontrib>Curran, Joanne E</creatorcontrib><creatorcontrib>Carless, Melanie A</creatorcontrib><creatorcontrib>Johnson, Matthew P</creatorcontrib><creatorcontrib>Moses, Eric K</creatorcontrib><creatorcontrib>Almasy, Laura</creatorcontrib><creatorcontrib>Mahaney, Michael C</creatorcontrib><creatorcontrib>Lehman, Donna M</creatorcontrib><creatorcontrib>Duggirala, Ravindranath</creatorcontrib><creatorcontrib>Comuzzie, Anthony G</creatorcontrib><creatorcontrib>Blangero, John</creatorcontrib><creatorcontrib>Voruganti, Venkata Saroja</creatorcontrib><title>GWAS and transcriptional analysis prioritize ITPR1 and CNTN4 for a serum uric acid 3p26 QTL in Mexican Americans</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>The variation in serum uric acid concentrations is under significant genetic influence. Elevated SUA concentrations have been linked to increased risk for gout, kidney stones, chronic kidney disease, and cardiovascular disease whereas reduced serum uric acid concentrations have been linked to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Previously, we identified a novel locus on chromosome 3p26 affecting serum uric acid concentrations in Mexican Americans from San Antonio Family Heart Study. As a follow up, we examined genome-wide single nucleotide polymorphism data in an extended cohort of 1281 Mexican Americans from multigenerational families of the San Antonio Family Heart Study and the San Antonio Family Diabetes/Gallbladder Study. We used a linear regression-based joint linkage/association test under an additive model of allelic effect, while accounting for non-independence among family members via a kinship variance component.
Univariate genetic analysis indicated serum uric acid concentrations to be significant heritable (h (2) = 0.50 ± 0.05, p < 4 × 10(-35)), and linkage analysis of serum uric acid concentrations confirmed our previous finding of a novel locus on 3p26 (LOD = 4.9, p < 1 × 10(-5)) in the extended sample. Additionally, we observed strong association of serum uric acid concentrations with variants in following candidate genes in the 3p26 region; inositol 1,4,5-trisphosphate receptor, type 1 (ITPR1), contactin 4 (CNTN4), decapping mRNA 1A (DCP1A); transglutaminase 4 (TGM4) and rho guanine nucleotide exchange factor (GEF) 26 (ARHGEF26) [p < 3 × 10(-7); minor allele frequencies ranged between 0.003 and 0.42] and evidence of cis-regulation for ITPR1 transcripts.
Our results confirm the importance of the chromosome 3p26 locus and genetic variants in this region in the regulation of serum uric acid concentrations.</description><subject>Adult</subject><subject>Chromosomes, Human, Pair 3</subject><subject>Contactins - genetics</subject><subject>Female</subject><subject>Genetic aspects</subject><subject>Genetic Linkage</subject><subject>Genome-Wide Association Study</subject><subject>Genomics</subject><subject>Humans</subject><subject>Inositol 1,4,5-Trisphosphate Receptors - genetics</subject><subject>Male</subject><subject>Mexican Americans</subject><subject>Mexican Americans - genetics</subject><subject>Middle Aged</subject><subject>Physiological aspects</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative genetics</subject><subject>Quantitative Trait Loci</subject><subject>Uric acid</subject><subject>Uric Acid - blood</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNptkktv1DAUhSMEog_4AWyQJTZ0kZLrZ7JBGo2gjDQUaAextBzHGVwldmonqOXX4zCldBDywlfX3znWvTpZ9gKKU4CSv4mAS07zAniOWUVz9ig7BCogx8Dp4wf1QXYU41VRgCgxe5odYFGQigg4zIazb4tLpFyDxqBc1MEOo_VOdamnuttoIxqC9cGO9qdBq83nC_hNL8835xS1PiCFoglTj6ZgNVLaNogMmKMvmzWyDn00N1Yrhxa9CXMRn2VPWtVF8_zuPs6-vn-3WX7I15_OVsvFOtcMl2POGqHaqsWAlcYAFTeNJjWrWmCs5ZrXQmDMG1LWqauwIYVqiE7N2tStVoYcZ293vsNU90lsXBqwk2mYXoVb6ZWV-y_Ofpdb_0PSEsqK0mTw-s4g-OvJxFH2NmrTdcoZP0UJQpSiYJiLhL76B73yU0j7m6lKsIoUvPpLbVVnpHWtT__q2VQuKC0JB4Zn6vQ_VDqN6a32zrQ29fcEJ3uCxIzmZtyqKUa5urzYZ2HH6uBjDKa93wcUco6U3EVKpkjJOVKSJc3Lh4u8V_zJEPkFPNXEVQ</recordid><startdate>20160402</startdate><enddate>20160402</enddate><creator>Chittoor, Geetha</creator><creator>Kent, Jr, Jack W</creator><creator>Almeida, Marcio</creator><creator>Puppala, Sobha</creator><creator>Farook, Vidya S</creator><creator>Cole, Shelley A</creator><creator>Haack, Karin</creator><creator>Göring, Harald H H</creator><creator>MacCluer, Jean W</creator><creator>Curran, Joanne E</creator><creator>Carless, Melanie A</creator><creator>Johnson, Matthew P</creator><creator>Moses, Eric K</creator><creator>Almasy, Laura</creator><creator>Mahaney, Michael C</creator><creator>Lehman, Donna M</creator><creator>Duggirala, Ravindranath</creator><creator>Comuzzie, Anthony G</creator><creator>Blangero, John</creator><creator>Voruganti, Venkata Saroja</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><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>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160402</creationdate><title>GWAS and transcriptional analysis prioritize ITPR1 and CNTN4 for a serum uric acid 3p26 QTL in Mexican Americans</title><author>Chittoor, Geetha ; Kent, Jr, Jack W ; Almeida, Marcio ; Puppala, Sobha ; Farook, Vidya S ; Cole, Shelley A ; Haack, Karin ; Göring, Harald H H ; MacCluer, Jean W ; Curran, Joanne E ; Carless, Melanie A ; Johnson, Matthew P ; Moses, Eric K ; Almasy, Laura ; Mahaney, Michael C ; Lehman, Donna M ; Duggirala, Ravindranath ; Comuzzie, Anthony G ; Blangero, John ; Voruganti, Venkata Saroja</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-5d7af9f212ac21196edc3b59f155f6c6b77226d38b3b5a2e30ad3c772bebfcae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Adult</topic><topic>Chromosomes, Human, Pair 3</topic><topic>Contactins - genetics</topic><topic>Female</topic><topic>Genetic aspects</topic><topic>Genetic Linkage</topic><topic>Genome-Wide Association Study</topic><topic>Genomics</topic><topic>Humans</topic><topic>Inositol 1,4,5-Trisphosphate Receptors - genetics</topic><topic>Male</topic><topic>Mexican Americans</topic><topic>Mexican Americans - genetics</topic><topic>Middle Aged</topic><topic>Physiological aspects</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Quantitative genetics</topic><topic>Quantitative Trait Loci</topic><topic>Uric acid</topic><topic>Uric Acid - blood</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chittoor, Geetha</creatorcontrib><creatorcontrib>Kent, Jr, Jack W</creatorcontrib><creatorcontrib>Almeida, Marcio</creatorcontrib><creatorcontrib>Puppala, Sobha</creatorcontrib><creatorcontrib>Farook, Vidya S</creatorcontrib><creatorcontrib>Cole, Shelley A</creatorcontrib><creatorcontrib>Haack, Karin</creatorcontrib><creatorcontrib>Göring, Harald H H</creatorcontrib><creatorcontrib>MacCluer, Jean W</creatorcontrib><creatorcontrib>Curran, Joanne E</creatorcontrib><creatorcontrib>Carless, Melanie A</creatorcontrib><creatorcontrib>Johnson, Matthew P</creatorcontrib><creatorcontrib>Moses, Eric K</creatorcontrib><creatorcontrib>Almasy, Laura</creatorcontrib><creatorcontrib>Mahaney, Michael C</creatorcontrib><creatorcontrib>Lehman, Donna M</creatorcontrib><creatorcontrib>Duggirala, Ravindranath</creatorcontrib><creatorcontrib>Comuzzie, Anthony G</creatorcontrib><creatorcontrib>Blangero, John</creatorcontrib><creatorcontrib>Voruganti, Venkata Saroja</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chittoor, Geetha</au><au>Kent, Jr, Jack W</au><au>Almeida, Marcio</au><au>Puppala, Sobha</au><au>Farook, Vidya S</au><au>Cole, Shelley A</au><au>Haack, Karin</au><au>Göring, Harald H H</au><au>MacCluer, Jean W</au><au>Curran, Joanne E</au><au>Carless, Melanie A</au><au>Johnson, Matthew P</au><au>Moses, Eric K</au><au>Almasy, Laura</au><au>Mahaney, Michael C</au><au>Lehman, Donna M</au><au>Duggirala, Ravindranath</au><au>Comuzzie, Anthony G</au><au>Blangero, John</au><au>Voruganti, Venkata Saroja</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>GWAS and transcriptional analysis prioritize ITPR1 and CNTN4 for a serum uric acid 3p26 QTL in Mexican Americans</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2016-04-02</date><risdate>2016</risdate><volume>17</volume><issue>261</issue><spage>276</spage><epage>276</epage><pages>276-276</pages><artnum>276</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>The variation in serum uric acid concentrations is under significant genetic influence. Elevated SUA concentrations have been linked to increased risk for gout, kidney stones, chronic kidney disease, and cardiovascular disease whereas reduced serum uric acid concentrations have been linked to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Previously, we identified a novel locus on chromosome 3p26 affecting serum uric acid concentrations in Mexican Americans from San Antonio Family Heart Study. As a follow up, we examined genome-wide single nucleotide polymorphism data in an extended cohort of 1281 Mexican Americans from multigenerational families of the San Antonio Family Heart Study and the San Antonio Family Diabetes/Gallbladder Study. We used a linear regression-based joint linkage/association test under an additive model of allelic effect, while accounting for non-independence among family members via a kinship variance component.
Univariate genetic analysis indicated serum uric acid concentrations to be significant heritable (h (2) = 0.50 ± 0.05, p < 4 × 10(-35)), and linkage analysis of serum uric acid concentrations confirmed our previous finding of a novel locus on 3p26 (LOD = 4.9, p < 1 × 10(-5)) in the extended sample. Additionally, we observed strong association of serum uric acid concentrations with variants in following candidate genes in the 3p26 region; inositol 1,4,5-trisphosphate receptor, type 1 (ITPR1), contactin 4 (CNTN4), decapping mRNA 1A (DCP1A); transglutaminase 4 (TGM4) and rho guanine nucleotide exchange factor (GEF) 26 (ARHGEF26) [p < 3 × 10(-7); minor allele frequencies ranged between 0.003 and 0.42] and evidence of cis-regulation for ITPR1 transcripts.
Our results confirm the importance of the chromosome 3p26 locus and genetic variants in this region in the regulation of serum uric acid concentrations.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>27039371</pmid><doi>10.1186/s12864-016-2594-5</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; DOAJ Directory of Open Access Journals; SpringerLink Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Springer Nature OA Free Journals |
subjects | Adult Chromosomes, Human, Pair 3 Contactins - genetics Female Genetic aspects Genetic Linkage Genome-Wide Association Study Genomics Humans Inositol 1,4,5-Trisphosphate Receptors - genetics Male Mexican Americans Mexican Americans - genetics Middle Aged Physiological aspects Polymorphism, Single Nucleotide Quantitative genetics Quantitative Trait Loci Uric acid Uric Acid - blood |
title | GWAS and transcriptional analysis prioritize ITPR1 and CNTN4 for a serum uric acid 3p26 QTL in Mexican Americans |
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