Imputing Gene Expression in Uncollected Tissues Within and beyond GTEx

American Journal of Human Genetics

Volumn 98, Issue 4, 2016, Pages 697-708

  Wang, Jiebiao ^a   Gamazon, Eric R ^b,c   Pierce, Brandon L ^a   Stranger, Barbara E ^a,d   Im, Hae Kyung ^a   Gibbons, Robert D ^a   Cox, Nancy J ^b   Nicolae, Dan L ^a   Chen, Lin S ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

eQTL; GTEx; multi tissue imputation; tissue tissue expression level correlation; transcriptome

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENOTYPE; GENOTYPE TISSUE EXPRESSION; HERITABILITY; HUMAN; HUMAN TISSUE; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RANDOM FOREST; TISSUE SPECIFICITY; GENE EXPRESSION REGULATION; PILOT STUDY; REPRODUCIBILITY;

TRANSCRIPTOME;

GENE EXPRESSION REGULATION; GENOTYPE; HUMANS; PHENOTYPE; PILOT PROJECTS; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME;

EID: 84962081673     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.02.020     Document Type: Article

References (41)

1. E.E. Schadt, S. Woo, and K. Hao Bayesian method to predict individual SNP genotypes from gene expression data Nat. Genet. 44 2012 603 608
2. R.B. Brem, G. Yvert, R. Clinton, and L. Kruglyak Genetic dissection of transcriptional regulation in budding yeast Science 296 2002 752 755
3. M.V. Rockman, and L. Kruglyak Genetics of global gene expression Nat. Rev. Genet. 7 2006 862 872
4. T. Flutre, X. Wen, J. Pritchard, and M. Stephens A statistical framework for joint eQTL analysis in multiple tissues PLoS Genet. 9 2013 e1003486
5. J.M. Torres, E.R. Gamazon, E.J. Parra, J.E. Below, A. Valladares-Salgado, N. Wacher, M. Cruz, C.L. Hanis, and N.J. Cox Cross-tissue and tissue-specific eQTLs: partitioning the heritability of a complex trait Am. J. Hum. Genet. 95 2014 521 534
6. Li, G., Shabalin, A.A., Rusyn, I., Wright, F.A., and Nobel, A.B. (2016). An empirical Bayes approach for multiple tissue eQTL analysis. arXiv, arXiv:1311.2948, http://arxiv.org/abs/1311.2948.
7. T. Raj, K. Rothamel, S. Mostafavi, C. Ye, M.N. Lee, J.M. Replogle, T. Feng, M. Lee, N. Asinovski, I. Frohlich, and et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes Science 344 2014 519 523
8. F.S. Collins, and H. Varmus A new initiative on precision medicine N. Engl. J. Med. 372 2015 793 795
9. GTEx Consortium (The Genotype-Tissue Expression (GTEx) project Nat. Genet. 45 2013 580 585
10. J.C. Keen, and H.M. Moore The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine J. Pers. Med. 5 2015 22 29
11. GTEx Consortium The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans Science 348 2015 648 660
12. N.M. Laird, and J.H. Ware Random-effects models for longitudinal data Biometrics 38 1982 963 974
13. M. Celton, A. Malpertuy, G. Lelandais, and A.G. de Brevern Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments BMC Genomics 11 2010 15
14. A.W.-C. Liew, N.-F. Law, and H. Yan Missing value imputation for gene expression data: computational techniques to recover missing data from available information Brief. Bioinform. 12 2011 498 513
15. Y. Donner, T. Feng, C. Benoist, and D. Koller Imputing gene expression from selectively reduced probe sets Nat. Methods 9 2012 1120 1125
16. D.J. Stekhoven, and P. Bühlmann MissForest - non-parametric missing value imputation for mixed-type data Bioinformatics 28 2012 112 118
17. O. Troyanskaya, M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, and R.B. Altman Missing value estimation methods for DNA microarrays Bioinformatics 17 2001 520 525
18. G.N. Brock, J.R. Shaffer, R.E. Blakesley, M.J. Lotz, and G.C. Tseng Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes BMC Bioinformatics 9 2008 12
19. S.G. Liao, Y. Lin, D.D. Kang, D. Chandra, J. Bon, N. Kaminski, F.C. Sciurba, and G.C. Tseng Missing value imputation in high-dimensional phenomic data: imputable or not, and how? BMC Bioinformatics 15 2014 346
20. E.R. Gamazon, H.E. Wheeler, K.P. Shah, S.V. Mozaffari, K. Aquino-Michaels, R.J. Carroll, A.E. Eyler, J.C. Denny, D.L. Nicolae, N.J. Cox, H.K. Im GTEx Consortium A gene-based association method for mapping traits using reference transcriptome data Nat. Genet. 47 2015 1091 1098
21. J.W. Tukey One degree of freedom for non-additivity Biometrics 5 1949 232 242
22. N. Chatterjee, Z. Kalaylioglu, R. Moslehi, U. Peters, and S. Wacholder Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions Am. J. Hum. Genet. 79 2006 1002 1016
23. L. Breiman, J.H. Friedman, R.A. Olshen, and C.J. Stone Classification and Regression Trees 1984 Chapman and Hall/CRC
24. J. Friedman A recursive partitioning decision rule for nonparametric classification IEEE Trans. Comput. 4 1977 404 408
25. R.J. Sela, and J.S. Simonoff RE-EM trees: a data mining approach for longitudinal and clustered data Mach. Learn. 86 2012 169 207
26. L. Breiman Random forests Mach. Learn. 45 2001 5 32
27. A. Liaw, and M. Wiener Classification and regression by randomForest 2002 R news 18 22 https://www.r-project.org/doc/Rnews/Rnews-2002-3.pdf
28. A.S. Dimas, A.C. Nica, S.B. Montgomery, B.E. Stranger, T. Raj, A. Buil, T. Giger, T. Lappalainen, M. Gutierrez-Arcelus, M.I. McCarthy, E.T. Dermitzakis MuTHER Consortium Sex-biased genetic effects on gene regulation in humans Genome Res. 22 2012 2368 2375
29. R. Tibshirani Regression shrinkage and selection via the Lasso J. R. Statist. Soc. B 58 1996 267 288
30. J. Stephan, O. Stegle, and A. Beyer A random forest approach to capture genetic effects in the presence of population structure Nat. Commun. 6 2015 7432
31. B.L. Pierce, L. Tong, L.S. Chen, R. Rahaman, M. Argos, F. Jasmine, S. Roy, R. Paul-Brutus, H.-J. Westra, L. Franke, and et al. Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians PLoS Genet. 10 2014 e1004818
32. B.E. Stranger, S.B. Montgomery, A.S. Dimas, L. Parts, O. Stegle, C.E. Ingle, M. Sekowska, G.D. Smith, D. Evans, M. Gutierrez-Arcelus, and et al. Patterns of cis regulatory variation in diverse human populations PLoS Genet. 8 2012 e1002639
33. A.A. Shabalin Matrix eQTL: ultra fast eQTL analysis via large matrix operations Bioinformatics 28 2012 1353 1358
34. S.A. Stouffer, E.A. Suchman, L.C. Devinney, S.A. Star, and R.M. Williams Jr. The American Soldier: Adjustment during Army Life, Studies in Social Psychology in World War II Vol. 1 1949 Princeton University Press
35. S.C. Elbein, E.R. Gamazon, S.K. Das, N. Rasouli, P.A. Kern, and N.J. Cox Genetic risk factors for type 2 diabetes: a trans-regulatory genetic architecture? Am. J. Hum. Genet. 91 2012 466 477
36. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A.R. Ferreira, D. Bender, J. Maller, P. Sklar, P.I.W. de Bakker, M.J. Daly, and P.C. Sham PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575
37. S. Van Buuren, and K. Groothuis-Oudshoorn Multivariate Imputation by Chained Equations J. Stat. Softw. 45 2011 1 67
38. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550
39. E. Grundberg, K.S. Small, A.K. Hedman, A.C. Nica, A. Buil, S. Keildson, J.T. Bell, T.-P. Yang, E. Meduri, A. Barrett, et al. Multiple Tissue Human Expression Resource (MuTHER) Consortium Mapping cis- and trans-regulatory effects across multiple tissues in twins Nat. Genet. 44 2012 1084 1089
40. F.A. Wright, P.F. Sullivan, A.I. Brooks, F. Zou, W. Sun, K. Xia, V. Madar, R. Jansen, W. Chung, Y.-H. Zhou, and et al. Heritability and genomics of gene expression in peripheral blood Nat. Genet. 46 2014 430 437
41. A. Chhibber, C.E. French, S.W. Yee, E.R. Gamazon, E. Theusch, X. Qin, A. Webb, A.C. Papp, A. Wang, C.Q. Simmons, and et al. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines Pharmacogenomics J. 2016 10.1038/tpj.2015.93 Published online February 9, 2016