Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions
Publication Date
June 14, 2017
Journal
PLOS Genetics
Authors
Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, et al
Volume
13
Issue
6
Pages
e1006812
DOI
https://dx.plos.org/10.1371/journal.pgen.1006812
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1006812
Scopus
85021826142
Mendeley
http://www.mendeley.com/research/ranking-characterization-established-bmi-lipid-associated-loci-candidates-geneenvironment-interactio
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Mendeley | Further Information

{"title"=>"Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions", "type"=>"journal", "authors"=>[{"first_name"=>"Dmitry", "last_name"=>"Shungin", "scopus_author_id"=>"36448539200"}, {"first_name"=>"Wei Q.", "last_name"=>"Deng", "scopus_author_id"=>"54383048500"}, {"first_name"=>"Tibor V.", "last_name"=>"Varga", "scopus_author_id"=>"8114807200"}, {"first_name"=>"Jian'an", "last_name"=>"Luan", "scopus_author_id"=>"7005172964"}, {"first_name"=>"Evelin", "last_name"=>"Mihailov", "scopus_author_id"=>"57191987814"}, {"first_name"=>"Andres", "last_name"=>"Metspalu", "scopus_author_id"=>"57201282705"}, {"first_name"=>"Andrew P.", "last_name"=>"Morris", "scopus_author_id"=>"7403404824"}, {"first_name"=>"Nita G.", "last_name"=>"Forouhi", "scopus_author_id"=>"6603478414"}, {"first_name"=>"Cecilia", "last_name"=>"Lindgren", "scopus_author_id"=>"7005443464"}, {"first_name"=>"Patrik K.E.", "last_name"=>"Magnusson", "scopus_author_id"=>"24756281600"}, {"first_name"=>"Nancy L.", "last_name"=>"Pedersen", "scopus_author_id"=>"7202300001"}, {"first_name"=>"Göran", "last_name"=>"Hallmans", "scopus_author_id"=>"7006749585"}, {"first_name"=>"Audrey Y.", "last_name"=>"Chu", "scopus_author_id"=>"56386796100"}, {"first_name"=>"Anne E.", "last_name"=>"Justice", "scopus_author_id"=>"55637906400"}, {"first_name"=>"Mariaelisa", "last_name"=>"Graff", "scopus_author_id"=>"8637792200"}, {"first_name"=>"Thomas W.", "last_name"=>"Winkler", "scopus_author_id"=>"36645396400"}, {"first_name"=>"Lynda M.", "last_name"=>"Rose", "scopus_author_id"=>"35604277600"}, {"first_name"=>"Claudia", "last_name"=>"Langenberg", "scopus_author_id"=>"9938997700"}, {"first_name"=>"L. Adrienne", "last_name"=>"Cupples", "scopus_author_id"=>"7007090535"}, {"first_name"=>"Paul M.", "last_name"=>"Ridker", "scopus_author_id"=>"36039269800"}, {"first_name"=>"Nicholas J.", "last_name"=>"Wareham", "scopus_author_id"=>"7006224498"}, {"first_name"=>"Ken K.", "last_name"=>"Ong", "scopus_author_id"=>"57193274074"}, {"first_name"=>"Ruth J.F.", "last_name"=>"Loos", "scopus_author_id"=>"7006771047"}, {"first_name"=>"Daniel I.", "last_name"=>"Chasman", "scopus_author_id"=>"6701612213"}, {"first_name"=>"Erik", "last_name"=>"Ingelsson", "scopus_author_id"=>"57198767135"}, {"first_name"=>"Tuomas O.", "last_name"=>"Kilpeläinen", "scopus_author_id"=>"34067667400"}, {"first_name"=>"Robert A.", "last_name"=>"Scott", "scopus_author_id"=>"56489197300"}, {"first_name"=>"Reedik", "last_name"=>"Mägi", "scopus_author_id"=>"57201126534"}, {"first_name"=>"Guillaume", "last_name"=>"Paré", "scopus_author_id"=>"56506758500"}, {"first_name"=>"Paul W.", "last_name"=>"Franks", "scopus_author_id"=>"7101842109"}], "year"=>2017, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537404", "doi"=>"10.1371/journal.pgen.1006812", "sgr"=>"85021826142", "scopus"=>"2-s2.0-85021826142", "isbn"=>"1111111111", "pmid"=>"28614350", "pui"=>"617190910"}, "id"=>"1e06dbb9-9736-3e18-92c5-98c2b30b3bcb", "abstract"=>"Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G×E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G×E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman’s ρ = 0.401 for triglycerides, and ρ = 0.236 for BMI) compared to all SNPs. When Pv and Pm were compared for all pruned SNPs, only BMI was statistically significant (Spearman’s ρ = 0.010). Overall, SNPs with established marginal effects were overrepresented in the nominally significant part of the Pv distribution (Pbinomial <0.05). SNPs from the top 1% of the Pm distribution for BMI had more significant Pv values (PMann–Whitney = 1.46×10−5), and the odds ratio of SNPs with nominally significant (<0.05) Pm and Pv was 1.33 (95% CI: 1.12, 1.57) for BMI. Moreover, BMI SNPs with nominally significant G×E interaction P-values (Pint<0.05) were enriched with nominally significant Pv values (Pbinomial = 8.63×10−9 and 8.52×10−7 for SNP × smoking and SNP × physical activity, respectively). We conclude that some loci with strong marginal effects may be good candidates for G×E, and variance-based prioritization can be used to identify them.", "link"=>"http://www.mendeley.com/research/ranking-characterization-established-bmi-lipid-associated-loci-candidates-geneenvironment-interactio", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>4, "Student > Master"=>4, "Student > Bachelor"=>5, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>4, "Student > Master"=>4, "Student > Bachelor"=>5, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>6, "Nursing and Health Professions"=>3, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>3, "Philosophy"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Psychology"=>1, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Philosophy"=>{"Philosophy"=>1}}, "group_count"=>0}

Scopus | Further Information

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