Bayesian method to predict individual SNP genotypes from gene expression data

Nature Genetics

Volumn 44, Issue 5, 2012, Pages 603-608

  Schadt, Eric E ^a   Woo, Sangsoon ^b,d   Hao, Ke ^a,c  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c ROSETTA INPHARMATICS   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ACCURACY; ARTICLE; BAYES THEOREM; EXPRESSION QUANTITATIVE TRAIT LOCUS; GENE EXPRESSION; GENOTYPE; HUMAN; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

ADIPOSE TISSUE; BAYES THEOREM; COHORT STUDIES; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENOTYPE; HUMANS; LIVER; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84860329478     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2248     Document Type: Article

References (30)

1. Beer, D.G. et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat. Med. 8, 816-824 (2002).
2. Hoshida, Y. et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N. Engl. J. Med. 359, 1995-2004 (2008).
3. Barrett, T. et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37, D885-D890 (2009).
4. Parkinson, H. et al. ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35, D747-D750 (2007). (Pubitemid 46056303)
5. Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435 (2008). (Pubitemid 351450844)
6. Dimas, A.S. et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325, 1246-1250 (2009).
7. Greenawalt, D.M. et al. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res. 21, 1008-1016 (2011).
8. Schadt, E.E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008).
9. Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302 (2003). (Pubitemid 36378355)
10. Smith, E.N. & Kruglyak, L. Gene-environment interaction in yeast gene expression. PLoS Biol. 6, e83 (2008).
11. Yang, X. et al. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat. Genet. 41, 415-423 (2009).
12. Hertzberg, L. et al. Prediction of chromosomal aneuploidy from gene expression data. Genes Chromosom. Cancer 46, 75-86 (2007). (Pubitemid 44772874)
13. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
14. Hao, K., Chudin, E., Greenawalt, D. & Schadt, E.E. Magnitude of stratification in human populations and impacts on genome wide association studies. PLoS ONE 5, e8695 (2010).
15. Tan, P.K. et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31, 5676-5684 (2003). (Pubitemid 37441938)
16. Baumbusch, L.O. et al. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics 9, 379 (2008).
17. Barnes, M., Freudenberg, J., Thompson, S., Aronow, B. & Pavlidis, P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res. 33, 5914-5923 (2005). (Pubitemid 41742611)
18. Lamb, J.R. et al. Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting. PLoS ONE 6, e20090 (2011).
19. Wang, S.M., Ooi, L.L. & Hui, K.M. Identification and validation of a novel gene signature associated with the recurrence of human hepatocellular carcinoma. Clin. Cancer Res. 13, 6275-6283 (2007). (Pubitemid 350075015)
20. Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423-428 (2008). (Pubitemid 351450845)
21. Heid, I.M. et al. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat. Genet. 42, 949-960 (2010).
22. Lango Allen, H. et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832-838 (2010).
23. Musunuru, K. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714-719 (2010).
24. Speliotes, E.K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet. 42, 937-948 (2010).
25. Teslovich, T.M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707-713 (2010).
26. Yang, X. et al. Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res. 20, 1020-1036 (2010).
27. Zhong, H. et al. Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 6, e1000932 (2010).
28. Zhong, H., Yang, X., Kaplan, L.M., Molony, C. & Schadt, E.E. Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am. J. Hum. Genet. 86, 581-591 (2010).
29. Lanktree, M.B. et al. Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height. Am. J. Hum. Genet. 88, 6-18 (2011).
30. Couzin-Frankel, J. Ethics. DNA returned to tribe, raising questions about consent. Science 328, 558 (2010).