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Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation
Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using...
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Published in: | American journal of human genetics 2009-12, Vol.85 (6), p.775-785 |
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creator | Chen, Jieming Zheng, Houfeng Bei, Jin-Xin Sun, Liangdan Jia, Wei-hua Li, Tao Zhang, Furen Seielstad, Mark Zeng, Yi-Xin Zhang, Xuejun Liu, Jianjun |
description | Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future. |
doi_str_mv | 10.1016/j.ajhg.2009.10.016 |
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Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.</description><identifier>ISSN: 0002-9297</identifier><identifier>EISSN: 1537-6605</identifier><identifier>DOI: 10.1016/j.ajhg.2009.10.016</identifier><identifier>PMID: 19944401</identifier><identifier>CODEN: AJHGAG</identifier><language>eng</language><publisher>Cambridge, MA: Elsevier Inc</publisher><subject>Algorithms ; Asian Continental Ancestry Group ; Biological and medical sciences ; China ; Computer Simulation ; Ethnic Groups ; Fundamental and applied biological sciences. Psychology ; General aspects. Genetic counseling ; Genetic Variation - genetics ; Genetics of eukaryotes. Biological and molecular evolution ; Genetics, Population ; Genome ; Genome-Wide Association Study ; Genomics ; Humans ; Medical genetics ; Medical sciences ; Migration ; Minority & ethnic groups ; Models, Genetic ; Molecular and cellular biology ; Polymorphism, Single Nucleotide ; Population genetics ; Simulation</subject><ispartof>American journal of human genetics, 2009-12, Vol.85 (6), p.775-785</ispartof><rights>2009 The American Society of Human Genetics</rights><rights>2015 INIST-CNRS</rights><rights>Copyright University of Chicago, acting through its Press Dec 11, 2009</rights><rights>2009 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved.. 2009 The American Society of Human Genetics</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c608t-8ec799b057a7faf2e5729e09ce88cb1d62a3042c6a5bfb031e4f8988ae847f353</citedby><cites>FETCH-LOGICAL-c608t-8ec799b057a7faf2e5729e09ce88cb1d62a3042c6a5bfb031e4f8988ae847f353</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790583/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790583/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,733,786,790,891,27957,27958,53827,53829</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22235446$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19944401$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Jieming</creatorcontrib><creatorcontrib>Zheng, Houfeng</creatorcontrib><creatorcontrib>Bei, Jin-Xin</creatorcontrib><creatorcontrib>Sun, Liangdan</creatorcontrib><creatorcontrib>Jia, Wei-hua</creatorcontrib><creatorcontrib>Li, Tao</creatorcontrib><creatorcontrib>Zhang, Furen</creatorcontrib><creatorcontrib>Seielstad, Mark</creatorcontrib><creatorcontrib>Zeng, Yi-Xin</creatorcontrib><creatorcontrib>Zhang, Xuejun</creatorcontrib><creatorcontrib>Liu, Jianjun</creatorcontrib><title>Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation</title><title>American journal of human genetics</title><addtitle>Am J Hum Genet</addtitle><description>Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.</description><subject>Algorithms</subject><subject>Asian Continental Ancestry Group</subject><subject>Biological and medical sciences</subject><subject>China</subject><subject>Computer Simulation</subject><subject>Ethnic Groups</subject><subject>Fundamental and applied biological sciences. 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Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.</abstract><cop>Cambridge, MA</cop><pub>Elsevier Inc</pub><pmid>19944401</pmid><doi>10.1016/j.ajhg.2009.10.016</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Algorithms Asian Continental Ancestry Group Biological and medical sciences China Computer Simulation Ethnic Groups Fundamental and applied biological sciences. Psychology General aspects. Genetic counseling Genetic Variation - genetics Genetics of eukaryotes. Biological and molecular evolution Genetics, Population Genome Genome-Wide Association Study Genomics Humans Medical genetics Medical sciences Migration Minority & ethnic groups Models, Genetic Molecular and cellular biology Polymorphism, Single Nucleotide Population genetics Simulation |
title | Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation |
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