Patterns of Cis Regulatory Variation in Diverse Human Populations
Publication Date
April 19, 2012
PLOS Genetics
Barbara E. Stranger, Stephen B. Montgomery, Antigone S. Dimas, Leopold Parts, et al
Publisher URL
PubMed Central
Europe PMC
Web of Science
Loading … Spinner

CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Patterns of Cis regulatory variation in diverse human populations", "type"=>"journal", "authors"=>[{"first_name"=>"Barbara E.", "last_name"=>"Stranger", "scopus_author_id"=>"6507901873"}, {"first_name"=>"Stephen B.", "last_name"=>"Montgomery", "scopus_author_id"=>"8708455800"}, {"first_name"=>"Antigone S.", "last_name"=>"Dimas", "scopus_author_id"=>"16506100400"}, {"first_name"=>"Leopold", "last_name"=>"Parts", "scopus_author_id"=>"23486598500"}, {"first_name"=>"Oliver", "last_name"=>"Stegle", "scopus_author_id"=>"24468888900"}, {"first_name"=>"Catherine E.", "last_name"=>"Ingle", "scopus_author_id"=>"15753810100"}, {"first_name"=>"Magda", "last_name"=>"Sekowska", "scopus_author_id"=>"35076528600"}, {"first_name"=>"George Davey", "last_name"=>"Smith", "scopus_author_id"=>"35354080500"}, {"first_name"=>"David", "last_name"=>"Evans", "scopus_author_id"=>"7601571931"}, {"first_name"=>"Maria", "last_name"=>"Gutierrez-Arcelus", "scopus_author_id"=>"23995220200"}, {"first_name"=>"Alkes", "last_name"=>"Price", "scopus_author_id"=>"10044017100"}, {"first_name"=>"Towfique", "last_name"=>"Raj", "scopus_author_id"=>"39561540100"}, {"first_name"=>"James", "last_name"=>"Nisbett", "scopus_author_id"=>"57189157475"}, {"first_name"=>"Alexandra C.", "last_name"=>"Nica", "scopus_author_id"=>"57189985825"}, {"first_name"=>"Claude", "last_name"=>"Beazley", "scopus_author_id"=>"23569388000"}, {"first_name"=>"Richard", "last_name"=>"Durbin", "scopus_author_id"=>"7102868950"}, {"first_name"=>"Panos", "last_name"=>"Deloukas", "scopus_author_id"=>"7003287098"}, {"first_name"=>"Emmanouil T.", "last_name"=>"Dermitzakis", "scopus_author_id"=>"35354477100"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"1553-7404", "scopus"=>"2-s2.0-84860596557", "pmid"=>"22532805", "issn"=>"15537390", "pui"=>"364739017", "doi"=>"10.1371/journal.pgen.1002639", "sgr"=>"84860596557"}, "id"=>"a3c52ac2-0f28-3e23-bac5-dd7ea6f787af", "abstract"=>"The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations", "link"=>"", "reader_count"=>303, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>21, "Student > Doctoral Student"=>9, "Researcher"=>100, "Student > Ph. D. Student"=>109, "Student > Postgraduate"=>6, "Student > Master"=>26, "Other"=>9, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>13, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>21, "Student > Doctoral Student"=>9, "Researcher"=>100, "Student > Ph. D. Student"=>109, "Student > Postgraduate"=>6, "Student > Master"=>26, "Other"=>9, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>13, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>207, "Business, Management and Accounting"=>2, "Computer Science"=>15, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>33, "Nursing and Health Professions"=>1, "Mathematics"=>7, "Medicine and Dentistry"=>25, "Neuroscience"=>2, "Physics and Astronomy"=>3, "Psychology"=>2, "Social Sciences"=>3, "Linguistics"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>25}, "Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Psychology"=>{"Psychology"=>2}, "Mathematics"=>{"Mathematics"=>7}, "Unspecified"=>{"Unspecified"=>1}, "Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>207}, "Computer Science"=>{"Computer Science"=>15}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>33}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>22, "United Kingdom"=>5, "Thailand"=>1, "New Zealand"=>1, "Canada"=>2, "Netherlands"=>2, "Sweden"=>2, "Austria"=>1, "Belgium"=>3, "Norway"=>1, "Denmark"=>2, "Brazil"=>3, "Mexico"=>1, "Italy"=>3, "South Africa"=>1, "France"=>3, "Germany"=>2}, "group_count"=>13}