Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits
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{"title"=>"Imputation-based analysis of association studies: Candidate regions and quantitative traits", "type"=>"journal", "authors"=>[{"first_name"=>"Bertrand", "last_name"=>"Servin", "scopus_author_id"=>"6505995817"}, {"first_name"=>"Matthew", "last_name"=>"Stephens", "scopus_author_id"=>"7201574987"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "scopus"=>"2-s2.0-34547622688", "pui"=>"47203979", "doi"=>"10.1371/journal.pgen.0030114", "sgr"=>"34547622688", "pmid"=>"17676998", "issn"=>"15537390"}, "id"=>"00cc16f6-cb6d-325b-9458-b246bf2de4bf", "abstract"=>"We introduce a new framework for the analysis of association studies, designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. The idea is to combine knowledge on patterns of correlation among SNPs (e.g., from the International HapMap project or resequencing data in a candidate region of interest) with genotype data at tag SNPs collected on a phenotyped study sample, to estimate (\"impute\") unmeasured genotypes, and then assess association between the phenotype and these estimated genotypes. Compared with standard single-SNP tests, this approach results in increased power to detect association, even in cases in which the causal variant is typed, with the greatest gain occurring when multiple causal variants are present. It also provides more interpretable explanations for observed associations, including assessing, for each SNP, the strength of the evidence that it (rather than another correlated SNP) is causal. Although we focus on association studies with quantitative phenotype and a relatively restricted region (e.g., a candidate gene), the framework is applicable and computationally practical for whole genome association studies. Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html.", "link"=>"http://www.mendeley.com/research/imputationbased-analysis-association-studies-candidate-regions-quantitative-traits", "reader_count"=>332, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>33, "Librarian"=>1, "Student > Doctoral Student"=>10, "Researcher"=>98, "Student > Ph. D. Student"=>106, "Student > Postgraduate"=>9, "Student > Master"=>24, "Other"=>11, "Student > Bachelor"=>14, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>3, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>33, "Librarian"=>1, "Student > Doctoral Student"=>10, "Researcher"=>98, "Student > Ph. D. Student"=>106, "Student > Postgraduate"=>9, "Student > Master"=>24, "Other"=>11, "Student > Bachelor"=>14, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>3, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Agricultural and Biological Sciences"=>188, "Arts and Humanities"=>4, "Veterinary Science and Veterinary Medicine"=>2, "Computer Science"=>24, "Economics, Econometrics and Finance"=>3, "Engineering"=>5, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>21, "Mathematics"=>27, "Medicine and Dentistry"=>40, "Neuroscience"=>2, "Sports and Recreations"=>1, "Physics and Astronomy"=>2, "Psychology"=>1, "Social Sciences"=>2, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>40}, "Social Sciences"=>{"Social Sciences"=>2}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>27}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>4}, "Engineering"=>{"Engineering"=>5}, "Neuroscience"=>{"Neuroscience"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>188}, "Computer Science"=>{"Computer Science"=>24}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>21}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Colombia"=>2, "Hungary"=>1, "United States"=>21, "Uruguay"=>1, "United Kingdom"=>4, "Portugal"=>1, "Switzerland"=>1, "Spain"=>1, "New Zealand"=>3, "Canada"=>1, "Sweden"=>1, "Korea (South)"=>1, "Belgium"=>1, "Norway"=>1, "China"=>1, "Finland"=>1, "Poland"=>1, "Denmark"=>3, "Brazil"=>2, "Italy"=>1, "Germany"=>1, "Ethiopia"=>1}, "group_count"=>19}

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