Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations
Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used...
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| creator | Li, Jian Yang, Tielin Wang, Liang Yan, Han Zhang, Yinping Guo, Yan Pan, Feng Zhang, Zhixin Peng, Yumei Zhou, Qi He, Lina Zhu, Xuezhen Deng, Hongyi Levy, Shawn Papasian, Christopher J Drees, Betty M Hamilton, James J Recker, Robert R Cheng, Jing Deng, Hong-Wen |
| description | Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R) Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p |
| doi_str_mv | 10.1371/journal.pone.0007958 |
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In the present study, we used the Affymetrix GeneChip(R) Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0007958</identifier><identifier>PMID: 19956714</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adult ; Aged ; Algorithms ; Arrays ; Asian Continental Ancestry Group ; Bioinformatics ; Cancer ; Chromosome Mapping ; Copy number ; Deoxyribonucleic acid ; Differentiation ; DNA ; Education ; Engineering ; Esophagus ; Ethnic Groups ; European Continental Ancestry Group ; Female ; Gene Dosage ; Gene expression ; Gene mapping ; Genetic Variation ; Genetics and Genomics/Genetics of Disease ; Genetics and Genomics/Genomics ; Genetics and Genomics/Population Genetics ; Genome, Human ; Genomes ; Genomics ; Genotype & phenotype ; Humans ; Laboratories ; Life sciences ; Male ; Medicine ; Middle Aged ; Minority & ethnic groups ; Oligonucleotide Array Sequence Analysis ; Population ; Retailing ; Studies ; Variation ; X Chromosomes</subject><ispartof>PloS one, 2009-11, Vol.4 (11), p.e7958-e7958</ispartof><rights>COPYRIGHT 2009 Public Library of Science</rights><rights>2009 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (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>Li et al. 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c793t-ed2cd04fea4f17ac47e092f14d0700b3dab99cc7591f0d587e7d40aa38da13be3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776354/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776354/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19956714$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Jian</creatorcontrib><creatorcontrib>Yang, Tielin</creatorcontrib><creatorcontrib>Wang, Liang</creatorcontrib><creatorcontrib>Yan, Han</creatorcontrib><creatorcontrib>Zhang, Yinping</creatorcontrib><creatorcontrib>Guo, Yan</creatorcontrib><creatorcontrib>Pan, Feng</creatorcontrib><creatorcontrib>Zhang, Zhixin</creatorcontrib><creatorcontrib>Peng, Yumei</creatorcontrib><creatorcontrib>Zhou, Qi</creatorcontrib><creatorcontrib>He, Lina</creatorcontrib><creatorcontrib>Zhu, Xuezhen</creatorcontrib><creatorcontrib>Deng, Hongyi</creatorcontrib><creatorcontrib>Levy, Shawn</creatorcontrib><creatorcontrib>Papasian, Christopher J</creatorcontrib><creatorcontrib>Drees, Betty M</creatorcontrib><creatorcontrib>Hamilton, James J</creatorcontrib><creatorcontrib>Recker, Robert R</creatorcontrib><creatorcontrib>Cheng, Jing</creatorcontrib><creatorcontrib>Deng, Hong-Wen</creatorcontrib><title>Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R) Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.</description><subject>Adult</subject><subject>Aged</subject><subject>Algorithms</subject><subject>Arrays</subject><subject>Asian Continental Ancestry Group</subject><subject>Bioinformatics</subject><subject>Cancer</subject><subject>Chromosome Mapping</subject><subject>Copy number</subject><subject>Deoxyribonucleic acid</subject><subject>Differentiation</subject><subject>DNA</subject><subject>Education</subject><subject>Engineering</subject><subject>Esophagus</subject><subject>Ethnic Groups</subject><subject>European Continental Ancestry Group</subject><subject>Female</subject><subject>Gene Dosage</subject><subject>Gene expression</subject><subject>Gene mapping</subject><subject>Genetic Variation</subject><subject>Genetics and Genomics/Genetics of Disease</subject><subject>Genetics and Genomics/Genomics</subject><subject>Genetics and Genomics/Population Genetics</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Humans</subject><subject>Laboratories</subject><subject>Life sciences</subject><subject>Male</subject><subject>Medicine</subject><subject>Middle Aged</subject><subject>Minority & ethnic groups</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Population</subject><subject>Retailing</subject><subject>Studies</subject><subject>Variation</subject><subject>X 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In the present study, we used the Affymetrix GeneChip(R) Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>19956714</pmid><doi>10.1371/journal.pone.0007958</doi><tpages>e7958</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2009-11, Vol.4 (11), p.e7958-e7958 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1292228311 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Adult Aged Algorithms Arrays Asian Continental Ancestry Group Bioinformatics Cancer Chromosome Mapping Copy number Deoxyribonucleic acid Differentiation DNA Education Engineering Esophagus Ethnic Groups European Continental Ancestry Group Female Gene Dosage Gene expression Gene mapping Genetic Variation Genetics and Genomics/Genetics of Disease Genetics and Genomics/Genomics Genetics and Genomics/Population Genetics Genome, Human Genomes Genomics Genotype & phenotype Humans Laboratories Life sciences Male Medicine Middle Aged Minority & ethnic groups Oligonucleotide Array Sequence Analysis Population Retailing Studies Variation X Chromosomes |
| title | Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T04%3A52%3A56IST&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=Whole%20genome%20distribution%20and%20ethnic%20differentiation%20of%20copy%20number%20variation%20in%20Caucasian%20and%20Asian%20populations&rft.jtitle=PloS%20one&rft.au=Li,%20Jian&rft.date=2009-11-23&rft.volume=4&rft.issue=11&rft.spage=e7958&rft.epage=e7958&rft.pages=e7958-e7958&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0007958&rft_dat=%3Cgale_plos_%3EA472797626%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=1292228311&rft_id=info:pmid/19956714&rft_galeid=A472797626&rft_doaj_id=oai_doaj_org_article_24783bf6a9014d52bd01bf6ba040bbfc&rfr_iscdi=true |