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The impact of rare variation on gene expression across tissues

Author(s): Li, Xin; Kim, Yungil; Tsang, Emily K; Davis, Joe R; Damani, Farhan N; et al

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dc.contributor.authorLi, Xin-
dc.contributor.authorKim, Yungil-
dc.contributor.authorTsang, Emily K-
dc.contributor.authorDavis, Joe R-
dc.contributor.authorDamani, Farhan N-
dc.contributor.authorChiang, Colby-
dc.contributor.authorHess, Gaelen T-
dc.contributor.authorZappala, Zachary-
dc.contributor.authorStrober, Benjamin J-
dc.contributor.authorScott, Alexandra J-
dc.contributor.authorLi, Amy-
dc.contributor.authorGanna, Andrea-
dc.contributor.authorBassik, Michael C-
dc.contributor.authorMerker, Jason D-
dc.contributor.authorGTEx Consortium-
dc.contributor.authorHall, Ira M-
dc.contributor.authorBattle, Alexis-
dc.contributor.authorMontgomery, Stephen B-
dc.date.accessioned2021-10-08T19:50:13Z-
dc.date.available2021-10-08T19:50:13Z-
dc.date.issued2017en_US
dc.identifier.citationLi, Xin, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna, Michael C. Bassik, Jason D. Merker, GTEx Consortium, Ira M. Hall, Alexis Battle, and Stephen B. Montgomery. "The impact of rare variation on gene expression across tissues." Nature 550, no. 7675 (2017): 239-243. doi:10.1038/nature24267en_US
dc.identifier.issn1476-4687-
dc.identifier.urihttp://arks.princeton.edu/ark:/88435/pr1q55x-
dc.description.abstractRare genetic variants are abundant in humans and are expected to contribute to individual disease risk1,2,3,4. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants1,5. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles1,6,7, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues8,9,10,11, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release12. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.en_US
dc.format.extent239 - 243en_US
dc.language.isoen_USen_US
dc.relation.ispartofNatureen_US
dc.rightsFinal published version. This is an open access article.en_US
dc.titleThe impact of rare variation on gene expression across tissuesen_US
dc.typeJournal Articleen_US
dc.identifier.doi10.1038/nature24267-
pu.type.symplectichttp://www.symplectic.co.uk/publications/atom-terms/1.0/journal-articleen_US

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