Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1
Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degre...
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Veröffentlicht in: | Human genetics 1999-11, Vol.105 (5), p.418-423 |
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creator | BAIPING ZHANG HENNEY, A ERIKSSON, P HAMSTEN, A WATKINS, H SHU YE |
description | Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved. |
doi_str_mv | 10.1007/s004390051124 |
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Biological and molecular evolution ; Haplotypes ; Human ; Humans ; Linkage Disequilibrium ; Matrix Metalloproteinase 9 - genetics ; Medicin och hälsovetenskap ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic</subject><ispartof>Human genetics, 1999-11, Vol.105 (5), p.418-423</ispartof><rights>2000 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c471t-606fa1220939209b7100c2312cb8a7adeea31f5710b46b3d061fd8306c7bc7a63</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1196385$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10598806$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:16171536$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>BAIPING ZHANG</creatorcontrib><creatorcontrib>HENNEY, A</creatorcontrib><creatorcontrib>ERIKSSON, P</creatorcontrib><creatorcontrib>HAMSTEN, A</creatorcontrib><creatorcontrib>WATKINS, H</creatorcontrib><creatorcontrib>SHU YE</creatorcontrib><title>Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1</title><title>Human genetics</title><addtitle>Hum Genet</addtitle><description>Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved.</description><subject>3' Untranslated Regions</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Chromosomes, Human, Pair 20 - genetics</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>DNA Primers - genetics</subject><subject>Exons</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Frequency</subject><subject>Genetic Variation</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Haplotypes</subject><subject>Human</subject><subject>Humans</subject><subject>Linkage Disequilibrium</subject><subject>Matrix Metalloproteinase 9 - genetics</subject><subject>Medicin och hälsovetenskap</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Promoter Regions, Genetic</subject><issn>0340-6717</issn><issn>1432-1203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kctv1DAQxi0EokvhyBXlgHrLMuNJ7OSIqj6QKnEp52jiOKohibe2w-O_x6vdsnDgMjMa_b556BPiLcIWAfSHCFBRC1AjyuqZ2GBFskQJ9FxsgCoolUZ9Jl7F-BUA61bWL8UZQt02DaiNuL-xi03OFN85OE7OLwWnIj3YYuYU3M9itomnye-CT9YtHG3ZFpM3aywyah6Cn330sy0kPKLc5tW0xdfixchTtG-O-Vx8ub66v7wt7z7ffLr8eFeaSmMqFaiRUUpoqc2h1_khIwml6RvWPFjLhGOd232lehpA4Tg0BMro3mhWdC7Kw9z4w-7WvtsFN3P41Xl23bH1LVe2U0Ck93zzXz4_OJxET0JUqLGmvfTiIM3c42pj6mYXjZ0mXqxfY6daUrKq8XSTCT7GYMc_WxC6vWPdP45l_t1x8NrPdviLPliUgfdHgKPhaQy8GBdPHLaKmpp-A_yNnHU</recordid><startdate>19991101</startdate><enddate>19991101</enddate><creator>BAIPING ZHANG</creator><creator>HENNEY, A</creator><creator>ERIKSSON, P</creator><creator>HAMSTEN, A</creator><creator>WATKINS, H</creator><creator>SHU YE</creator><general>Springer</general><scope>IQODW</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>7X8</scope><scope>ADTPV</scope><scope>AOWAS</scope></search><sort><creationdate>19991101</creationdate><title>Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1</title><author>BAIPING ZHANG ; HENNEY, A ; ERIKSSON, P ; HAMSTEN, A ; WATKINS, H ; SHU YE</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c471t-606fa1220939209b7100c2312cb8a7adeea31f5710b46b3d061fd8306c7bc7a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><topic>3' Untranslated Regions</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Chromosomes, Human, Pair 20 - genetics</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>DNA Primers - genetics</topic><topic>Exons</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Frequency</topic><topic>Genetic Variation</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Haplotypes</topic><topic>Human</topic><topic>Humans</topic><topic>Linkage Disequilibrium</topic><topic>Matrix Metalloproteinase 9 - genetics</topic><topic>Medicin och hälsovetenskap</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Promoter Regions, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>BAIPING ZHANG</creatorcontrib><creatorcontrib>HENNEY, A</creatorcontrib><creatorcontrib>ERIKSSON, P</creatorcontrib><creatorcontrib>HAMSTEN, A</creatorcontrib><creatorcontrib>WATKINS, H</creatorcontrib><creatorcontrib>SHU YE</creatorcontrib><collection>Pascal-Francis</collection><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</collection><collection>SwePub Articles</collection><jtitle>Human genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>BAIPING ZHANG</au><au>HENNEY, A</au><au>ERIKSSON, P</au><au>HAMSTEN, A</au><au>WATKINS, H</au><au>SHU YE</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1</atitle><jtitle>Human genetics</jtitle><addtitle>Hum Genet</addtitle><date>1999-11-01</date><risdate>1999</risdate><volume>105</volume><issue>5</issue><spage>418</spage><epage>423</epage><pages>418-423</pages><issn>0340-6717</issn><eissn>1432-1203</eissn><coden>HUGEDQ</coden><abstract>Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><cop>New York, NY</cop><pub>Springer</pub><pmid>10598806</pmid><doi>10.1007/s004390051124</doi><tpages>6</tpages></addata></record> |
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subjects | 3' Untranslated Regions Base Sequence Biological and medical sciences Chromosomes, Human, Pair 20 - genetics Classical genetics, quantitative genetics, hybrids DNA Primers - genetics Exons Fundamental and applied biological sciences. Psychology Gene Frequency Genetic Variation Genetics of eukaryotes. Biological and molecular evolution Haplotypes Human Humans Linkage Disequilibrium Matrix Metalloproteinase 9 - genetics Medicin och hälsovetenskap Polymorphism, Single Nucleotide Promoter Regions, Genetic |
title | Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1 |
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