HLA and SNP haplotype mapping in the Japanese population
The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; how...
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| Veröffentlicht in: | Genes and immunity 2012-10, Vol.13 (7), p.543-548 |
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| description | The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; however, interpretation of the results is complicated because of the strong linkage disequilibrium (LD) among HLA alleles and single-nucleotide polymorphisms (SNPs). In this study, we evaluated the correlation between the HLA alleles of 6 loci (
HLA-A
,
C
,
B
,
DRB1
,
DQB1
and
DPB1
) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (
r
2
⩾0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (
r
2
⩾0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races. |
| doi_str_mv | 10.1038/gene.2012.35 |
| format | Article |
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HLA-A
,
C
,
B
,
DRB1
,
DQB1
and
DPB1
) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (
r
2
⩾0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (
r
2
⩾0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races.</description><identifier>ISSN: 1466-4879</identifier><identifier>EISSN: 1476-5470</identifier><identifier>DOI: 10.1038/gene.2012.35</identifier><identifier>PMID: 22914434</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/208/207 ; 631/208/2489/144 ; 631/208/457 ; 631/208/727/728 ; Alleles ; Antigens ; Asian Continental Ancestry Group - genetics ; Biomedical and Life Sciences ; Biomedicine ; Cancer Research ; Chromosomes ; Disease ; Drb1 protein ; Gene Expression ; Gene mapping ; Genes ; Genetic aspects ; Genomes ; Haplotypes ; Health aspects ; Histocompatibility antigen HLA ; Histocompatibility antigens ; HLA Antigens - genetics ; HLA histocompatibility antigens ; Human Genetics ; Humans ; Immunology ; Japan ; Japanese ; Leukocytes ; Linkage disequilibrium ; Major histocompatibility complex ; original-article ; Physiological aspects ; Polymorphism, Single Nucleotide ; Population studies ; Races ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism</subject><ispartof>Genes and immunity, 2012-10, Vol.13 (7), p.543-548</ispartof><rights>Macmillan Publishers Limited 2012</rights><rights>COPYRIGHT 2012 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Oct 2012</rights><rights>Macmillan Publishers Limited 2012.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c519t-fb8ee3b108a943f45c28d6fcbc32b841643eafdbc07aae4b0b059fd5b38f63df3</citedby><cites>FETCH-LOGICAL-c519t-fb8ee3b108a943f45c28d6fcbc32b841643eafdbc07aae4b0b059fd5b38f63df3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/gene.2012.35$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/gene.2012.35$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22914434$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kitajima, H</creatorcontrib><creatorcontrib>Sonoda, M</creatorcontrib><creatorcontrib>Yamamoto, K</creatorcontrib><title>HLA and SNP haplotype mapping in the Japanese population</title><title>Genes and immunity</title><addtitle>Genes Immun</addtitle><addtitle>Genes Immun</addtitle><description>The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; however, interpretation of the results is complicated because of the strong linkage disequilibrium (LD) among HLA alleles and single-nucleotide polymorphisms (SNPs). In this study, we evaluated the correlation between the HLA alleles of 6 loci (
HLA-A
,
C
,
B
,
DRB1
,
DQB1
and
DPB1
) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (
r
2
⩾0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (
r
2
⩾0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races.</description><subject>631/208/207</subject><subject>631/208/2489/144</subject><subject>631/208/457</subject><subject>631/208/727/728</subject><subject>Alleles</subject><subject>Antigens</subject><subject>Asian Continental Ancestry Group - genetics</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Chromosomes</subject><subject>Disease</subject><subject>Drb1 protein</subject><subject>Gene Expression</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Haplotypes</subject><subject>Health aspects</subject><subject>Histocompatibility antigen HLA</subject><subject>Histocompatibility antigens</subject><subject>HLA Antigens - genetics</subject><subject>HLA histocompatibility antigens</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Immunology</subject><subject>Japan</subject><subject>Japanese</subject><subject>Leukocytes</subject><subject>Linkage disequilibrium</subject><subject>Major histocompatibility complex</subject><subject>original-article</subject><subject>Physiological aspects</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population studies</subject><subject>Races</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><issn>1466-4879</issn><issn>1476-5470</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqN0t1r1TAYB-AiipvTO6-l4I2CPea76eVhODc5qDi9Dkn6putok9i04P77pZz5cWSI5CIhefImL_yK4jlGG4yofNuBhw1BmGwof1AcY1aLirMaPVzXQlRM1s1R8SSla4SwwKJ5XBwR0mDGKDsu5PluW2rflpcfP5dXOg5hvolQjjrG3ndl78v5CsoPOmoPCcoY4jLouQ_-afHI6SHBs7v5pPh29u7r6Xm1-_T-4nS7qyzHzVw5IwGowUjqhlHHuCWyFc4aS4mRDAtGQbvWWFRrDcwgg3jjWm6odIK2jp4Ur_Z14xS-L5BmNfbJwjDkD4UlKYwJJ1RKLv-DYtpIwlCd6cu_6HVYJp8bUUQwXFMsEPqXyrWIJFxy9lt1egDVexfmSdv1abWlSDQ1YfWqNveoPFoYexs8uD7vH1x4fXAhmxl-zJ1eUlIXl18O7Zu9tVNIaQKn4tSPerpRGKk1JWpNiVpToijP_MVdX4sZof2Ff8Yig2oPUj7yHUx_NH5fwVvguMG4</recordid><startdate>20121001</startdate><enddate>20121001</enddate><creator>Kitajima, H</creator><creator>Sonoda, M</creator><creator>Yamamoto, K</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</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>7T5</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</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>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20121001</creationdate><title>HLA and SNP haplotype mapping in the Japanese population</title><author>Kitajima, H ; Sonoda, M ; Yamamoto, K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c519t-fb8ee3b108a943f45c28d6fcbc32b841643eafdbc07aae4b0b059fd5b38f63df3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>631/208/207</topic><topic>631/208/2489/144</topic><topic>631/208/457</topic><topic>631/208/727/728</topic><topic>Alleles</topic><topic>Antigens</topic><topic>Asian Continental Ancestry Group - genetics</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Cancer Research</topic><topic>Chromosomes</topic><topic>Disease</topic><topic>Drb1 protein</topic><topic>Gene Expression</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Haplotypes</topic><topic>Health aspects</topic><topic>Histocompatibility antigen HLA</topic><topic>Histocompatibility antigens</topic><topic>HLA Antigens - genetics</topic><topic>HLA histocompatibility antigens</topic><topic>Human Genetics</topic><topic>Humans</topic><topic>Immunology</topic><topic>Japan</topic><topic>Japanese</topic><topic>Leukocytes</topic><topic>Linkage disequilibrium</topic><topic>Major histocompatibility complex</topic><topic>original-article</topic><topic>Physiological aspects</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population studies</topic><topic>Races</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kitajima, H</creatorcontrib><creatorcontrib>Sonoda, M</creatorcontrib><creatorcontrib>Yamamoto, K</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>Immunology Abstracts</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>ProQuest Pharma Collection</collection><collection>Public Health Database</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 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 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>AIDS and Cancer Research Abstracts</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>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><jtitle>Genes and immunity</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kitajima, H</au><au>Sonoda, M</au><au>Yamamoto, K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>HLA and SNP haplotype mapping in the Japanese population</atitle><jtitle>Genes and immunity</jtitle><stitle>Genes Immun</stitle><addtitle>Genes Immun</addtitle><date>2012-10-01</date><risdate>2012</risdate><volume>13</volume><issue>7</issue><spage>543</spage><epage>548</epage><pages>543-548</pages><issn>1466-4879</issn><eissn>1476-5470</eissn><abstract>The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; however, interpretation of the results is complicated because of the strong linkage disequilibrium (LD) among HLA alleles and single-nucleotide polymorphisms (SNPs). In this study, we evaluated the correlation between the HLA alleles of 6 loci (
HLA-A
,
C
,
B
,
DRB1
,
DQB1
and
DPB1
) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (
r
2
⩾0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (
r
2
⩾0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>22914434</pmid><doi>10.1038/gene.2012.35</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; EZB-FREE-00999 freely available EZB journals; SpringerLink Journals - AutoHoldings |
| subjects | 631/208/207 631/208/2489/144 631/208/457 631/208/727/728 Alleles Antigens Asian Continental Ancestry Group - genetics Biomedical and Life Sciences Biomedicine Cancer Research Chromosomes Disease Drb1 protein Gene Expression Gene mapping Genes Genetic aspects Genomes Haplotypes Health aspects Histocompatibility antigen HLA Histocompatibility antigens HLA Antigens - genetics HLA histocompatibility antigens Human Genetics Humans Immunology Japan Japanese Leukocytes Linkage disequilibrium Major histocompatibility complex original-article Physiological aspects Polymorphism, Single Nucleotide Population studies Races Single nucleotide polymorphisms Single-nucleotide polymorphism |
| title | HLA and SNP haplotype mapping in the Japanese population |
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