Common deletion polymorphisms in the human genome
The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating del...
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| Veröffentlicht in: | Nature genetics 2006-01, Vol.38 (1), p.86-92 |
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| creator | McCarroll, Steven A Hadnott, Tracy N Perry, George H Sabeti, Pardis C Zody, Michael C Barrett, Jeffrey C Dallaire, Stephanie Gabriel, Stacey B Lee, Charles Daly, Mark J Altshuler, David M The International HapMap Consortium |
| description | The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies. |
| doi_str_mv | 10.1038/ng1696 |
| format | Article |
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We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/ng1696</identifier><identifier>PMID: 16468122</identifier><identifier>CODEN: NGENEC</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>Agriculture ; Animal Genetics and Genomics ; Biological and medical sciences ; Biomedical and Life Sciences ; Biomedicine ; Cancer Research ; Chromosome aberrations ; Continental Population Groups - genetics ; Databases, Genetic ; Exons ; Fundamental and applied biological sciences. Psychology ; Gene Function ; Gene mutations ; Genetic polymorphisms ; Genetic Techniques ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Human ; Homozygote ; Human Genetics ; Human genome ; Humans ; In Situ Hybridization, Fluorescence ; letter ; Linkage Disequilibrium ; Medical genetics ; Medical sciences ; Models, Genetic ; Mutation ; Olfaction ; Physiological aspects ; Polymerase Chain Reaction - methods ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Deletion ; Steroids</subject><ispartof>Nature genetics, 2006-01, Vol.38 (1), p.86-92</ispartof><rights>Springer Nature America, Inc. 2006</rights><rights>2006 INIST-CNRS</rights><rights>COPYRIGHT 2006 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Jan 2006</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c598t-d2575c0faee36d19e46b1bf63bbb7ee2c9b467bc523a7cce43ef5356805a28513</citedby><cites>FETCH-LOGICAL-c598t-d2575c0faee36d19e46b1bf63bbb7ee2c9b467bc523a7cce43ef5356805a28513</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/ng1696$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/ng1696$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17660232$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16468122$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>McCarroll, Steven A</creatorcontrib><creatorcontrib>Hadnott, Tracy N</creatorcontrib><creatorcontrib>Perry, George H</creatorcontrib><creatorcontrib>Sabeti, Pardis C</creatorcontrib><creatorcontrib>Zody, Michael C</creatorcontrib><creatorcontrib>Barrett, Jeffrey C</creatorcontrib><creatorcontrib>Dallaire, Stephanie</creatorcontrib><creatorcontrib>Gabriel, Stacey B</creatorcontrib><creatorcontrib>Lee, Charles</creatorcontrib><creatorcontrib>Daly, Mark J</creatorcontrib><creatorcontrib>Altshuler, David M</creatorcontrib><creatorcontrib>The International HapMap Consortium</creatorcontrib><creatorcontrib>International HapMap Consortium</creatorcontrib><title>Common deletion polymorphisms in the human genome</title><title>Nature genetics</title><addtitle>Nat Genet</addtitle><addtitle>Nat Genet</addtitle><description>The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies.</description><subject>Agriculture</subject><subject>Animal Genetics and Genomics</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Chromosome aberrations</subject><subject>Continental Population Groups - genetics</subject><subject>Databases, Genetic</subject><subject>Exons</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Function</subject><subject>Gene mutations</subject><subject>Genetic polymorphisms</subject><subject>Genetic Techniques</subject><subject>Genetics of eukaryotes. 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Academic</collection><jtitle>Nature genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>McCarroll, Steven A</au><au>Hadnott, Tracy N</au><au>Perry, George H</au><au>Sabeti, Pardis C</au><au>Zody, Michael C</au><au>Barrett, Jeffrey C</au><au>Dallaire, Stephanie</au><au>Gabriel, Stacey B</au><au>Lee, Charles</au><au>Daly, Mark J</au><au>Altshuler, David M</au><au>The International HapMap Consortium</au><aucorp>International HapMap Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Common deletion polymorphisms in the human genome</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2006-01-01</date><risdate>2006</risdate><volume>38</volume><issue>1</issue><spage>86</spage><epage>92</epage><pages>86-92</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><coden>NGENEC</coden><abstract>The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome. We identified 541 deletion variants (94% novel) ranging from 1 kb to 745 kb in size; 278 of these variants were observed in multiple, unrelated individuals, 120 in the homozygous state. The coding exons of ten expressed genes were found to be commonly deleted, including multiple genes with roles in sex steroid metabolism, olfaction and drug response. These common deletion polymorphisms typically represent ancestral mutations that are in linkage disequilibrium with nearby SNPs, meaning that their association to disease can often be evaluated in the course of SNP-based whole-genome association studies.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>16468122</pmid><doi>10.1038/ng1696</doi><tpages>7</tpages></addata></record> |
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| subjects | Agriculture Animal Genetics and Genomics Biological and medical sciences Biomedical and Life Sciences Biomedicine Cancer Research Chromosome aberrations Continental Population Groups - genetics Databases, Genetic Exons Fundamental and applied biological sciences. Psychology Gene Function Gene mutations Genetic polymorphisms Genetic Techniques Genetics of eukaryotes. Biological and molecular evolution Genome, Human Homozygote Human Genetics Human genome Humans In Situ Hybridization, Fluorescence letter Linkage Disequilibrium Medical genetics Medical sciences Models, Genetic Mutation Olfaction Physiological aspects Polymerase Chain Reaction - methods Polymorphism, Genetic Polymorphism, Single Nucleotide Sequence Deletion Steroids |
| title | Common deletion polymorphisms in the human genome |
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