Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations
Our previous genome-wide association study (GWAS) identified three independent single nucleotide polymorphisms (SNPs) in human major histocompatibility complex (MHC) region showing association with esophageal squamous cell carcinoma (ESCC). In this study, we increased GWAS sample size on MHC region...
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| creator | Zhang, Peng Li, Xin-Min Zhao, Xue-Ke Song, Xin Yuan, Ling Shen, Fang-Fang Fan, Zong-Min Wang, Li-Dong |
| description | Our previous genome-wide association study (GWAS) identified three independent single nucleotide polymorphisms (SNPs) in human major histocompatibility complex (MHC) region showing association with esophageal squamous cell carcinoma (ESCC). In this study, we increased GWAS sample size on MHC region and performed validation in an independent ESCC cases and normal controls with aim to find additional loci at MHC region showing association with an increased risk to ESCC.
The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip. After quality control, the selected SNPs were replicated by TaqMan genotyping assay on another 2,026 ESCC cases and 2,384 normal controls.
By excluding low quality SNPs in primary GWAS screening, we selected 2,533 SNPs in MHC region for association analysis, and identified 5 SNPs with p |
| doi_str_mv | 10.1371/journal.pone.0177494 |
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The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip. After quality control, the selected SNPs were replicated by TaqMan genotyping assay on another 2,026 ESCC cases and 2,384 normal controls.
By excluding low quality SNPs in primary GWAS screening, we selected 2,533 SNPs in MHC region for association analysis, and identified 5 SNPs with p <10-4. Further validation analysis in an independent case-control cohort confirmed one of the 5 SNPs (rs911178) that showed significant association with ESCC. rs911178 (PGWAS = 6.125E-04, OR = 0.644 and Preplication = 1.406E-22, OR = 0.489) was located at upstream of SCAND3.
The rs911178 (SCAND3 gene) in MHC region is significantly associated with high risk of ESCC. This study not only reveal the potential role of MHC region for the pathogenesis of ESCC, but also provides important clues for the establishment of tools and methods for screening high risk population of ESCC.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0177494</identifier><identifier>PMID: 28493959</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acute lymphoblastic leukemia ; Adenocarcinoma ; Age ; Antigen presentation ; Antigens ; Asian Continental Ancestry Group - genetics ; Beverages ; Biology and Life Sciences ; Carcinogenesis ; Carcinoma, Squamous Cell - genetics ; Cell adhesion ; Children ; China ; Chromosome 6 ; Defensive behavior ; Deoxyribonucleic acid ; Diagnosis ; DNA ; Embryogenesis ; Embryonic growth stage ; Endoscopy ; Esophageal cancer ; Esophageal Neoplasms - genetics ; Esophageal Squamous Cell Carcinoma ; Esophagus ; Female ; Females ; Genes ; Genetic aspects ; Genetic factors ; Genetic Loci ; Genetic testing ; Genetics ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Geographical distribution ; Health care ; Health risks ; Heterozygosity ; Histopathology ; Hospitals ; Humans ; Inventories ; Laboratories ; Leukemia ; Linkage Disequilibrium - genetics ; Loss of heterozygosity ; Lymphatic leukemia ; Major histocompatibility complex ; Major Histocompatibility Complex - genetics ; Male ; Males ; Maternal & child health ; Medical research ; Medicine and Health Sciences ; Middle Aged ; People and Places ; Physiological aspects ; Polymorphism ; Polymorphism, Single Nucleotide - genetics ; Population density ; Population studies ; Precipitation ; Principal components analysis ; Quality control ; Radiation therapy ; Replication ; Reproducibility of Results ; Research and Analysis Methods ; Risk factors ; Squamous cell carcinoma ; Stem cells ; Studies ; Tumors ; Zinc</subject><ispartof>PloS one, 2017-05, Vol.12 (5), p.e0177494-e0177494</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Zhang et al 2017 Zhang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-e072b95df911db7ddb8cbb585e697e3022b75311a3d95c3ea679fdf52fccbfed3</citedby><cites>FETCH-LOGICAL-c692t-e072b95df911db7ddb8cbb585e697e3022b75311a3d95c3ea679fdf52fccbfed3</cites><orcidid>0000-0002-7933-0410</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426749/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426749/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28493959$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Xu, Zongli</contributor><creatorcontrib>Zhang, Peng</creatorcontrib><creatorcontrib>Li, Xin-Min</creatorcontrib><creatorcontrib>Zhao, Xue-Ke</creatorcontrib><creatorcontrib>Song, Xin</creatorcontrib><creatorcontrib>Yuan, Ling</creatorcontrib><creatorcontrib>Shen, Fang-Fang</creatorcontrib><creatorcontrib>Fan, Zong-Min</creatorcontrib><creatorcontrib>Wang, Li-Dong</creatorcontrib><title>Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Our previous genome-wide association study (GWAS) identified three independent single nucleotide polymorphisms (SNPs) in human major histocompatibility complex (MHC) region showing association with esophageal squamous cell carcinoma (ESCC). In this study, we increased GWAS sample size on MHC region and performed validation in an independent ESCC cases and normal controls with aim to find additional loci at MHC region showing association with an increased risk to ESCC.
The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip. After quality control, the selected SNPs were replicated by TaqMan genotyping assay on another 2,026 ESCC cases and 2,384 normal controls.
By excluding low quality SNPs in primary GWAS screening, we selected 2,533 SNPs in MHC region for association analysis, and identified 5 SNPs with p <10-4. Further validation analysis in an independent case-control cohort confirmed one of the 5 SNPs (rs911178) that showed significant association with ESCC. rs911178 (PGWAS = 6.125E-04, OR = 0.644 and Preplication = 1.406E-22, OR = 0.489) was located at upstream of SCAND3.
The rs911178 (SCAND3 gene) in MHC region is significantly associated with high risk of ESCC. This study not only reveal the potential role of MHC region for the pathogenesis of ESCC, but also provides important clues for the establishment of tools and methods for screening high risk population of ESCC.</description><subject>Acute lymphoblastic leukemia</subject><subject>Adenocarcinoma</subject><subject>Age</subject><subject>Antigen presentation</subject><subject>Antigens</subject><subject>Asian Continental Ancestry Group - genetics</subject><subject>Beverages</subject><subject>Biology and Life Sciences</subject><subject>Carcinogenesis</subject><subject>Carcinoma, Squamous Cell - genetics</subject><subject>Cell adhesion</subject><subject>Children</subject><subject>China</subject><subject>Chromosome 6</subject><subject>Defensive behavior</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>Embryogenesis</subject><subject>Embryonic growth stage</subject><subject>Endoscopy</subject><subject>Esophageal cancer</subject><subject>Esophageal Neoplasms - genetics</subject><subject>Esophageal Squamous Cell Carcinoma</subject><subject>Esophagus</subject><subject>Female</subject><subject>Females</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic factors</subject><subject>Genetic Loci</subject><subject>Genetic testing</subject><subject>Genetics</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Geographical distribution</subject><subject>Health care</subject><subject>Health risks</subject><subject>Heterozygosity</subject><subject>Histopathology</subject><subject>Hospitals</subject><subject>Humans</subject><subject>Inventories</subject><subject>Laboratories</subject><subject>Leukemia</subject><subject>Linkage Disequilibrium - genetics</subject><subject>Loss of heterozygosity</subject><subject>Lymphatic leukemia</subject><subject>Major histocompatibility complex</subject><subject>Major Histocompatibility Complex - genetics</subject><subject>Male</subject><subject>Males</subject><subject>Maternal & child health</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Middle Aged</subject><subject>People and Places</subject><subject>Physiological aspects</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Population density</subject><subject>Population studies</subject><subject>Precipitation</subject><subject>Principal components analysis</subject><subject>Quality control</subject><subject>Radiation therapy</subject><subject>Replication</subject><subject>Reproducibility of Results</subject><subject>Research and Analysis Methods</subject><subject>Risk factors</subject><subject>Squamous cell carcinoma</subject><subject>Stem cells</subject><subject>Studies</subject><subject>Tumors</subject><subject>Zinc</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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><sourceid>DOA</sourceid><recordid>eNqNk0tv1DAUhSMEoqXwDxBEQkKwmMGPOI43laoR0JEKlXhtLce5zrjyxKmdVPDv8XTSaoK6QF7Ecr5zbB_fm2UvMVpiyvGHKz-GTrll7ztYIsx5IYpH2TEWlCxKgujjg_lR9izGK4QYrcryaXZEqkJQwcRxJr_6G3B5Cx0MVufO6zHmasi_nK_yAK31XW58yCH6fqNaUC6P16Pa-kRpcC7XKmjb-a3KbZevNraDCHnv-9GpIYnj8-yJUS7Ci-l7kv389PHH6nxxcfl5vTq7WOhSkGEBiJNasMYIjJuaN01d6bpmFYNScKCIkJozirGijWCagiq5MI1hxGhdG2joSfZ679s7H-WUTZS4EhVCnHOUiPWeaLy6kn2wWxX-SK-svF3woZUqpAwcSEIEog3FohK0UBTXTPOmMhWrOKjCsOR1Ou021ltoNHRDUG5mOv_T2Y1s_Y1kBSnTQyWDd5NB8NcjxEFubdwFqjpI2e7OLTBinJGEvvkHffh2E9WqdAHbGZ_21TtTeVYIzGghKpyo5QNUGg1srU6FZGxanwnezwSJGeD30KoxRrn-_u3_2ctfc_btAbtJdTVsonfjbc3MwWIP6uBjDGDuQ8ZI7vrgLg256wM59UGSvTp8oHvRXeHTv2F0A24</recordid><startdate>20170511</startdate><enddate>20170511</enddate><creator>Zhang, Peng</creator><creator>Li, Xin-Min</creator><creator>Zhao, Xue-Ke</creator><creator>Song, Xin</creator><creator>Yuan, Ling</creator><creator>Shen, Fang-Fang</creator><creator>Fan, Zong-Min</creator><creator>Wang, Li-Dong</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</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>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-7933-0410</orcidid></search><sort><creationdate>20170511</creationdate><title>Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations</title><author>Zhang, Peng ; Li, Xin-Min ; Zhao, Xue-Ke ; Song, Xin ; Yuan, Ling ; Shen, Fang-Fang ; Fan, Zong-Min ; Wang, Li-Dong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-e072b95df911db7ddb8cbb585e697e3022b75311a3d95c3ea679fdf52fccbfed3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Acute lymphoblastic leukemia</topic><topic>Adenocarcinoma</topic><topic>Age</topic><topic>Antigen presentation</topic><topic>Antigens</topic><topic>Asian Continental Ancestry Group - genetics</topic><topic>Beverages</topic><topic>Biology and Life Sciences</topic><topic>Carcinogenesis</topic><topic>Carcinoma, Squamous Cell - genetics</topic><topic>Cell adhesion</topic><topic>Children</topic><topic>China</topic><topic>Chromosome 6</topic><topic>Defensive behavior</topic><topic>Deoxyribonucleic acid</topic><topic>Diagnosis</topic><topic>DNA</topic><topic>Embryogenesis</topic><topic>Embryonic growth stage</topic><topic>Endoscopy</topic><topic>Esophageal cancer</topic><topic>Esophageal Neoplasms - genetics</topic><topic>Esophageal Squamous Cell Carcinoma</topic><topic>Esophagus</topic><topic>Female</topic><topic>Females</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic factors</topic><topic>Genetic Loci</topic><topic>Genetic testing</topic><topic>Genetics</topic><topic>Genome-wide association studies</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Geographical distribution</topic><topic>Health care</topic><topic>Health risks</topic><topic>Heterozygosity</topic><topic>Histopathology</topic><topic>Hospitals</topic><topic>Humans</topic><topic>Inventories</topic><topic>Laboratories</topic><topic>Leukemia</topic><topic>Linkage Disequilibrium - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Peng</au><au>Li, Xin-Min</au><au>Zhao, Xue-Ke</au><au>Song, Xin</au><au>Yuan, Ling</au><au>Shen, Fang-Fang</au><au>Fan, Zong-Min</au><au>Wang, Li-Dong</au><au>Xu, Zongli</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-05-11</date><risdate>2017</risdate><volume>12</volume><issue>5</issue><spage>e0177494</spage><epage>e0177494</epage><pages>e0177494-e0177494</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Our previous genome-wide association study (GWAS) identified three independent single nucleotide polymorphisms (SNPs) in human major histocompatibility complex (MHC) region showing association with esophageal squamous cell carcinoma (ESCC). In this study, we increased GWAS sample size on MHC region and performed validation in an independent ESCC cases and normal controls with aim to find additional loci at MHC region showing association with an increased risk to ESCC.
The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip. After quality control, the selected SNPs were replicated by TaqMan genotyping assay on another 2,026 ESCC cases and 2,384 normal controls.
By excluding low quality SNPs in primary GWAS screening, we selected 2,533 SNPs in MHC region for association analysis, and identified 5 SNPs with p <10-4. Further validation analysis in an independent case-control cohort confirmed one of the 5 SNPs (rs911178) that showed significant association with ESCC. rs911178 (PGWAS = 6.125E-04, OR = 0.644 and Preplication = 1.406E-22, OR = 0.489) was located at upstream of SCAND3.
The rs911178 (SCAND3 gene) in MHC region is significantly associated with high risk of ESCC. This study not only reveal the potential role of MHC region for the pathogenesis of ESCC, but also provides important clues for the establishment of tools and methods for screening high risk population of ESCC.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28493959</pmid><doi>10.1371/journal.pone.0177494</doi><tpages>e0177494</tpages><orcidid>https://orcid.org/0000-0002-7933-0410</orcidid><oa>free_for_read</oa></addata></record> |
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| language | eng |
| recordid | cdi_plos_journals_1898007770 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acute lymphoblastic leukemia Adenocarcinoma Age Antigen presentation Antigens Asian Continental Ancestry Group - genetics Beverages Biology and Life Sciences Carcinogenesis Carcinoma, Squamous Cell - genetics Cell adhesion Children China Chromosome 6 Defensive behavior Deoxyribonucleic acid Diagnosis DNA Embryogenesis Embryonic growth stage Endoscopy Esophageal cancer Esophageal Neoplasms - genetics Esophageal Squamous Cell Carcinoma Esophagus Female Females Genes Genetic aspects Genetic factors Genetic Loci Genetic testing Genetics Genome-wide association studies Genome-Wide Association Study Genomes Genomics Geographical distribution Health care Health risks Heterozygosity Histopathology Hospitals Humans Inventories Laboratories Leukemia Linkage Disequilibrium - genetics Loss of heterozygosity Lymphatic leukemia Major histocompatibility complex Major Histocompatibility Complex - genetics Male Males Maternal & child health Medical research Medicine and Health Sciences Middle Aged People and Places Physiological aspects Polymorphism Polymorphism, Single Nucleotide - genetics Population density Population studies Precipitation Principal components analysis Quality control Radiation therapy Replication Reproducibility of Results Research and Analysis Methods Risk factors Squamous cell carcinoma Stem cells Studies Tumors Zinc |
| title | Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T08%3A07%3A23IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Novel%20genetic%20locus%20at%20MHC%20region%20for%20esophageal%20squamous%20cell%20carcinoma%20in%20Chinese%20populations&rft.jtitle=PloS%20one&rft.au=Zhang,%20Peng&rft.date=2017-05-11&rft.volume=12&rft.issue=5&rft.spage=e0177494&rft.epage=e0177494&rft.pages=e0177494-e0177494&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0177494&rft_dat=%3Cgale_plos_%3EA491534981%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1898007770&rft_id=info:pmid/28493959&rft_galeid=A491534981&rft_doaj_id=oai_doaj_org_article_22903d3198934a31b5c7d8f8587ea4f5&rfr_iscdi=true |