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Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis
Numerous genome-wide association studies (GWAS) have been performed to identify susceptibility genes to various human complex diseases. However, in many cases, neither a functional variant nor a disease susceptibility gene have been clarified. Here, we show an efficient approach for identification o...
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| Published in: | Scientific reports 2017-06, Vol.7 (1), p.2904-10, Article 2904 |
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| creator | Hitomi, Yuki Kojima, Kaname Kawashima, Minae Kawai, Yosuke Nishida, Nao Aiba, Yoshihiro Yasunami, Michio Nagasaki, Masao Nakamura, Minoru Tokunaga, Katsushi |
| description | Numerous genome-wide association studies (GWAS) have been performed to identify susceptibility genes to various human complex diseases. However, in many cases, neither a functional variant nor a disease susceptibility gene have been clarified. Here, we show an efficient approach for identification of a functional variant in a primary biliary cholangitis (PBC)-susceptible region, chromosome 17q12-21 (
ORMDL3
-
GSDMB
-
ZPBP2
-
IKZF3
). High-density association mapping was carried out based on SNP imputation analysis by using the whole-genome sequence data from a reference panel of 1,070 Japanese individuals (1KJPN), together with genotype data from our previous GWAS (PBC patients: n = 1,389; healthy controls: n = 1,508). Among 23 single nucleotide polymorphisms (SNPs) with
P
|
| doi_str_mv | 10.1038/s41598-017-03067-3 |
| format | article |
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ORMDL3
-
GSDMB
-
ZPBP2
-
IKZF3
). High-density association mapping was carried out based on SNP imputation analysis by using the whole-genome sequence data from a reference panel of 1,070 Japanese individuals (1KJPN), together with genotype data from our previous GWAS (PBC patients: n = 1,389; healthy controls: n = 1,508). Among 23 single nucleotide polymorphisms (SNPs) with
P
< 1.0 × 10
−8
, rs12946510 was identified as the functional variant that influences gene expression via alteration of Forkhead box protein O1 (FOXO1) binding affinity
in vitro
. Moreover, expression-quantitative trait locus (e-QTL) analyses showed that the PBC susceptibility allele of rs12946510 was significantly associated with lower endogenous expression of
ORMDL3
and
GSDMB
in whole blood and spleen. This study not only identified the functional variant in chr.17q12-21 and its molecular mechanism through which it conferred susceptibility to PBC, but it also illustrated an efficient systematic approach for post-GWAS analysis that is applicable to other complex diseases.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-017-03067-3</identifier><identifier>PMID: 28588209</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>13/109 ; 38/77 ; 45/23 ; 45/43 ; 631/208/248/144 ; 692/4020/1503/1607/1606 ; Alleles ; Base Sequence ; Binding Sites ; Cholangitis ; Chromosome 17 ; Chromosomes, Human, Pair 17 ; Computational Biology - methods ; Databases, Genetic ; Forkhead Box Protein O1 - metabolism ; Forkhead protein ; FOXO1 protein ; Gene Expression ; Gene mapping ; Genes, Reporter ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genetic Variation ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genotype ; Humanities and Social Sciences ; Humans ; Liver Cirrhosis, Biliary - genetics ; Liver Cirrhosis, Biliary - metabolism ; Liver Cirrhosis, Biliary - pathology ; Membrane Proteins - genetics ; Models, Biological ; multidisciplinary ; Mutation ; Neoplasm Proteins - genetics ; Nucleotide Motifs ; Nucleotide sequence ; Polymorphism, Single Nucleotide ; Protein Binding ; Quantitative trait loci ; Science ; Science (multidisciplinary) ; Single-nucleotide polymorphism ; Spleen</subject><ispartof>Scientific reports, 2017-06, Vol.7 (1), p.2904-10, Article 2904</ispartof><rights>The Author(s) 2017</rights><rights>Copyright Nature Publishing Group Jun 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c606t-68e84dc54494ba894a5db77116f2243b5c56fcc960a8faa339b95a433baa8bb73</citedby><cites>FETCH-LOGICAL-c606t-68e84dc54494ba894a5db77116f2243b5c56fcc960a8faa339b95a433baa8bb73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1955526739/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1955526739?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28588209$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hitomi, Yuki</creatorcontrib><creatorcontrib>Kojima, Kaname</creatorcontrib><creatorcontrib>Kawashima, Minae</creatorcontrib><creatorcontrib>Kawai, Yosuke</creatorcontrib><creatorcontrib>Nishida, Nao</creatorcontrib><creatorcontrib>Aiba, Yoshihiro</creatorcontrib><creatorcontrib>Yasunami, Michio</creatorcontrib><creatorcontrib>Nagasaki, Masao</creatorcontrib><creatorcontrib>Nakamura, Minoru</creatorcontrib><creatorcontrib>Tokunaga, Katsushi</creatorcontrib><title>Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Numerous genome-wide association studies (GWAS) have been performed to identify susceptibility genes to various human complex diseases. However, in many cases, neither a functional variant nor a disease susceptibility gene have been clarified. Here, we show an efficient approach for identification of a functional variant in a primary biliary cholangitis (PBC)-susceptible region, chromosome 17q12-21 (
ORMDL3
-
GSDMB
-
ZPBP2
-
IKZF3
). High-density association mapping was carried out based on SNP imputation analysis by using the whole-genome sequence data from a reference panel of 1,070 Japanese individuals (1KJPN), together with genotype data from our previous GWAS (PBC patients: n = 1,389; healthy controls: n = 1,508). Among 23 single nucleotide polymorphisms (SNPs) with
P
< 1.0 × 10
−8
, rs12946510 was identified as the functional variant that influences gene expression via alteration of Forkhead box protein O1 (FOXO1) binding affinity
in vitro
. Moreover, expression-quantitative trait locus (e-QTL) analyses showed that the PBC susceptibility allele of rs12946510 was significantly associated with lower endogenous expression of
ORMDL3
and
GSDMB
in whole blood and spleen. This study not only identified the functional variant in chr.17q12-21 and its molecular mechanism through which it conferred susceptibility to PBC, but it also illustrated an efficient systematic approach for post-GWAS analysis that is applicable to other complex diseases.</description><subject>13/109</subject><subject>38/77</subject><subject>45/23</subject><subject>45/43</subject><subject>631/208/248/144</subject><subject>692/4020/1503/1607/1606</subject><subject>Alleles</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Cholangitis</subject><subject>Chromosome 17</subject><subject>Chromosomes, Human, Pair 17</subject><subject>Computational Biology - methods</subject><subject>Databases, Genetic</subject><subject>Forkhead Box Protein O1 - metabolism</subject><subject>Forkhead protein</subject><subject>FOXO1 protein</subject><subject>Gene Expression</subject><subject>Gene mapping</subject><subject>Genes, Reporter</subject><subject>Genetic Association Studies</subject><subject>Genetic Predisposition to Disease</subject><subject>Genetic Variation</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Liver Cirrhosis, Biliary - genetics</subject><subject>Liver Cirrhosis, Biliary - metabolism</subject><subject>Liver Cirrhosis, Biliary - pathology</subject><subject>Membrane Proteins - genetics</subject><subject>Models, Biological</subject><subject>multidisciplinary</subject><subject>Mutation</subject><subject>Neoplasm Proteins - genetics</subject><subject>Nucleotide Motifs</subject><subject>Nucleotide sequence</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Protein Binding</subject><subject>Quantitative trait loci</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Single-nucleotide polymorphism</subject><subject>Spleen</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNp1kstu1DAUhiMEolXpC7BAltiwCfia2BskaKGMNFUlLmvrxHFmPErsqZ2M4A14bJyZoZoi4Y0v5z_fObb_onhJ8FuCmXyXOBFKlpjUJWa4qkv2pDinmIuSMkqfnqzPisuUNjgPQRUn6nlxRqWQkmJ1XvxetNaPrnMGRhc8Ch0a1xZ1kzfzHnq0g-jAj6iNbuf8Ct19vb1eMgS-RTffrm8_IvtzG21Kc7bzaD0N4JFZxzCEFAaLSH1PaEnJHNxGN0D8hRrXu3k269CDX7nRpRfFsw76ZC-P80Xx4_On71dfyuXdzeLqw7I0Fa7GspJW8tYIzhVvQCoOom3qmpCqo5SzRhhRdcaoCoPsABhTjRLAGWsAZNPU7KJYHLhtgI0-NqQDOL0_CHGlIY7O9FYLbhgnGFPetpzIWhkqTdtloKUKW5NZ7w-s7dQMtjX5JSP0j6CPI96t9SrsMrnCRMkMeHMExHA_2TTqwSVj-_woNkxJE4XrXB8zlaWv_5FuwhTzB80qIQSt6r2KHlQmhpSi7R6aIVjPvtEH3-jsG733jWY56dXpNR5S_rokC9hBkHLIr2w8qf1_7B8-_M4s</recordid><startdate>20170606</startdate><enddate>20170606</enddate><creator>Hitomi, Yuki</creator><creator>Kojima, Kaname</creator><creator>Kawashima, Minae</creator><creator>Kawai, Yosuke</creator><creator>Nishida, Nao</creator><creator>Aiba, Yoshihiro</creator><creator>Yasunami, Michio</creator><creator>Nagasaki, Masao</creator><creator>Nakamura, Minoru</creator><creator>Tokunaga, Katsushi</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><general>Nature Portfolio</general><scope>C6C</scope><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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</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>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20170606</creationdate><title>Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis</title><author>Hitomi, Yuki ; Kojima, Kaname ; Kawashima, Minae ; Kawai, Yosuke ; Nishida, Nao ; Aiba, Yoshihiro ; Yasunami, Michio ; Nagasaki, Masao ; Nakamura, Minoru ; Tokunaga, Katsushi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c606t-68e84dc54494ba894a5db77116f2243b5c56fcc960a8faa339b95a433baa8bb73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>13/109</topic><topic>38/77</topic><topic>45/23</topic><topic>45/43</topic><topic>631/208/248/144</topic><topic>692/4020/1503/1607/1606</topic><topic>Alleles</topic><topic>Base Sequence</topic><topic>Binding Sites</topic><topic>Cholangitis</topic><topic>Chromosome 17</topic><topic>Chromosomes, Human, Pair 17</topic><topic>Computational Biology - methods</topic><topic>Databases, Genetic</topic><topic>Forkhead Box Protein O1 - metabolism</topic><topic>Forkhead protein</topic><topic>FOXO1 protein</topic><topic>Gene Expression</topic><topic>Gene mapping</topic><topic>Genes, Reporter</topic><topic>Genetic Association Studies</topic><topic>Genetic Predisposition to Disease</topic><topic>Genetic Variation</topic><topic>Genome-wide association studies</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Liver Cirrhosis, Biliary - genetics</topic><topic>Liver Cirrhosis, Biliary - metabolism</topic><topic>Liver Cirrhosis, Biliary - pathology</topic><topic>Membrane Proteins - genetics</topic><topic>Models, Biological</topic><topic>multidisciplinary</topic><topic>Mutation</topic><topic>Neoplasm Proteins - genetics</topic><topic>Nucleotide Motifs</topic><topic>Nucleotide sequence</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Protein Binding</topic><topic>Quantitative trait loci</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Single-nucleotide polymorphism</topic><topic>Spleen</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hitomi, Yuki</creatorcontrib><creatorcontrib>Kojima, Kaname</creatorcontrib><creatorcontrib>Kawashima, Minae</creatorcontrib><creatorcontrib>Kawai, Yosuke</creatorcontrib><creatorcontrib>Nishida, Nao</creatorcontrib><creatorcontrib>Aiba, Yoshihiro</creatorcontrib><creatorcontrib>Yasunami, Michio</creatorcontrib><creatorcontrib>Nagasaki, Masao</creatorcontrib><creatorcontrib>Nakamura, Minoru</creatorcontrib><creatorcontrib>Tokunaga, Katsushi</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</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)</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>ProQuest One Community College</collection><collection>ProQuest Central</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>PML(ProQuest Medical Library)</collection><collection>Science Database</collection><collection>Biological Science Database</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 Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hitomi, Yuki</au><au>Kojima, Kaname</au><au>Kawashima, Minae</au><au>Kawai, Yosuke</au><au>Nishida, Nao</au><au>Aiba, Yoshihiro</au><au>Yasunami, Michio</au><au>Nagasaki, Masao</au><au>Nakamura, Minoru</au><au>Tokunaga, Katsushi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2017-06-06</date><risdate>2017</risdate><volume>7</volume><issue>1</issue><spage>2904</spage><epage>10</epage><pages>2904-10</pages><artnum>2904</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Numerous genome-wide association studies (GWAS) have been performed to identify susceptibility genes to various human complex diseases. However, in many cases, neither a functional variant nor a disease susceptibility gene have been clarified. Here, we show an efficient approach for identification of a functional variant in a primary biliary cholangitis (PBC)-susceptible region, chromosome 17q12-21 (
ORMDL3
-
GSDMB
-
ZPBP2
-
IKZF3
). High-density association mapping was carried out based on SNP imputation analysis by using the whole-genome sequence data from a reference panel of 1,070 Japanese individuals (1KJPN), together with genotype data from our previous GWAS (PBC patients: n = 1,389; healthy controls: n = 1,508). Among 23 single nucleotide polymorphisms (SNPs) with
P
< 1.0 × 10
−8
, rs12946510 was identified as the functional variant that influences gene expression via alteration of Forkhead box protein O1 (FOXO1) binding affinity
in vitro
. Moreover, expression-quantitative trait locus (e-QTL) analyses showed that the PBC susceptibility allele of rs12946510 was significantly associated with lower endogenous expression of
ORMDL3
and
GSDMB
in whole blood and spleen. This study not only identified the functional variant in chr.17q12-21 and its molecular mechanism through which it conferred susceptibility to PBC, but it also illustrated an efficient systematic approach for post-GWAS analysis that is applicable to other complex diseases.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>28588209</pmid><doi>10.1038/s41598-017-03067-3</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 13/109 38/77 45/23 45/43 631/208/248/144 692/4020/1503/1607/1606 Alleles Base Sequence Binding Sites Cholangitis Chromosome 17 Chromosomes, Human, Pair 17 Computational Biology - methods Databases, Genetic Forkhead Box Protein O1 - metabolism Forkhead protein FOXO1 protein Gene Expression Gene mapping Genes, Reporter Genetic Association Studies Genetic Predisposition to Disease Genetic Variation Genome-wide association studies Genome-Wide Association Study Genomes Genotype Humanities and Social Sciences Humans Liver Cirrhosis, Biliary - genetics Liver Cirrhosis, Biliary - metabolism Liver Cirrhosis, Biliary - pathology Membrane Proteins - genetics Models, Biological multidisciplinary Mutation Neoplasm Proteins - genetics Nucleotide Motifs Nucleotide sequence Polymorphism, Single Nucleotide Protein Binding Quantitative trait loci Science Science (multidisciplinary) Single-nucleotide polymorphism Spleen |
| title | Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis |
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