Identification of common genetic variants controlling transcript isoform variation in human whole blood (original) (raw)

References

  1. Hindorff, L.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106, 9362–9367 (2009).
    CAS Google Scholar
  2. Cookson, W., Liang, L., Abecasis, G., Moffatt, M. & Lathrop, M. Mapping complex disease traits with global gene expression. Nat. Rev. Genet. 10, 184–194 (2009).
    Article CAS Google Scholar
  3. Westra, H.J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45, 1238–1243 (2013).
    Article CAS Google Scholar
  4. Li, Q., Lee, J.A. & Black, D.L. Neuronal regulation of alternative pre-mRNA splicing. Nat. Rev. Neurosci. 8, 819–831 (2007).
    Article CAS Google Scholar
  5. Yeo, G., Holste, D., Kreiman, G. & Burge, C.B. Variation in alternative splicing across human tissues. Genome Biol. 5, R74 (2004).
    Article Google Scholar
  6. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).
    Article CAS Google Scholar
  7. Merkin, J., Russell, C., Chen, P. & Burge, C.B. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593–1599 (2012).
    Article CAS Google Scholar
  8. Coulombe-Huntington, J., Lam, K.C., Dias, C. & Majewski, J. Fine-scale variation and genetic determinants of alternative splicing across individuals. PLoS Genet. 5, e1000766 (2009).
    Article Google Scholar
  9. Kwan, T. et al. Heritability of alternative splicing in the human genome. Genome Res. 17, 1210–1218 (2007).
    Article CAS Google Scholar
  10. Faustino, N.A. & Cooper, T.A. Pre-mRNA splicing and human disease. Genes Dev. 17, 419–437 (2003).
    Article CAS Google Scholar
  11. Nissim-Rafinia, M. & Kerem, B. The splicing machinery is a genetic modifier of disease severity. Trends Genet. 21, 480–483 (2005).
    Article CAS Google Scholar
  12. Kwan, T. et al. Genome-wide analysis of transcript isoform variation in humans. Nat. Genet. 40, 225–231 (2008).
    Article CAS Google Scholar
  13. Montgomery, S.B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773–777 (2010).
    Article CAS Google Scholar
  14. Battle, A. et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res. 24, 14–24 (2014).
    Article CAS Google Scholar
  15. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
  16. Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F. & Dietz, H.C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073–1078 (2004).
    Article CAS Google Scholar
  17. Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).
    Article CAS Google Scholar
  18. Hunt, R., Sauna, Z.E., Ambudkar, S.V., Gottesman, M.M. & Kimchi-Sarfaty, C. Silent (synonymous) SNPs: should we care about them? Methods Mol. Biol. 578, 23–39 (2009).
    Article CAS Google Scholar
  19. Carlini, D.B. & Genut, J.E. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J. Mol. Evol. 62, 89–98 (2006).
    Article CAS Google Scholar
  20. Taggart, A.J., DeSimone, A.M., Shih, J.S., Filloux, M.E. & Fairbrother, W.G. Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat. Struct. Mol. Biol. 19, 719–721 (2012).
    Article CAS Google Scholar
  21. Corvelo, A., Hallegger, M., Smith, C.W. & Eyras, E. Genome-wide association between branch point properties and alternative splicing. PLoS Comput. Biol. 6, e1001016 (2010).
    Article Google Scholar
  22. Keene, J.D. & Tenenbaum, S.A. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 9, 1161–1167 (2002).
    Article CAS Google Scholar
  23. Jayaseelan, S., Doyle, F., Currenti, S. & Tenenbaum, S.A. RIP: an mRNA localization technique. Methods Mol. Biol. 714, 407–422 (2011).
    Article CAS Google Scholar
  24. Nicolae, D.L. et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6, e1000888 (2010).
    Article Google Scholar
  25. Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001–D1006 (2014).
    Article CAS Google Scholar
  26. Zhang, X. et al. Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes. Hum. Mol. Genet. 23, 782–795 (2014).
    Article CAS Google Scholar
  27. Graveley, B.R. The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. Trends Genet. 24, 5–7 (2008).
    Article CAS Google Scholar
  28. Nembaware, V., Wolfe, K.H., Bettoni, F., Kelso, J. & Seoighe, C. Allele-specific transcript isoforms in human. FEBS Lett. 577, 233–238 (2004).
    Article CAS Google Scholar
  29. Bondar', T.N. & Kravchenko, N.A. Cyclooxigenase-1 gene polymorphism and aspirin resistance. Tsitol. Genet. 46, 66–72 (2012).
    CAS PubMed Google Scholar
  30. Licis, N., Krivmane, B., Latkovskis, G. & Erglis, A. A common promoter variant of the gene encoding cyclooxygenase-1 (PTGS1) is related to decreased incidence of myocardial infarction in patients with coronary artery disease. Thromb. Res. 127, 600–602 (2011).
    Article CAS Google Scholar
  31. Zhang, X. et al. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics 15, 532 (2014).
    Article Google Scholar
  32. Heinzen, E.L. et al. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol. 6, e1 (2008).
    Article Google Scholar
  33. Zhernakova, D.V. et al. DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts. PLoS Genet. 9, e1003594 (2013).
    Article CAS Google Scholar
  34. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
  35. Dawber, T.R., Kannel, W.B. & Lyell, L.P. An approach to longitudinal studies in a community: the Framingham Study. Ann. NY Acad. Sci. 107, 539–556 (1963).
    Article CAS Google Scholar
  36. Feinleib, M., Kannel, W.B., Garrison, R.J., McNamara, P.M. & Castelli, W.P. The Framingham Offspring Study. Design and preliminary data. Prev. Med. 4, 518–525 (1975).
    Article CAS Google Scholar
  37. Kannel, W.B., Feinleib, M., McNamara, P.M., Garrison, R.J. & Castelli, W.P. An investigation of coronary heart disease in families. The Framingham offspring study. Am. J. Epidemiol. 110, 281–290 (1979).
    Article CAS Google Scholar
  38. Splansky, G.L. et al. The Third Generation Cohort of the National Heart, Lung, and Blood Institute's Framingham Heart Study: design, recruitment, and initial examination. Am. J. Epidemiol. 165, 1328–1335 (2007).
    Article Google Scholar
  39. Irizarry, R.A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249–264 (2003).
    Article Google Scholar
  40. Li, Y., Willer, C.J., Ding, J., Scheet, P. & Abecasis, G.R. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol. 34, 816–834 (2010).
    Article Google Scholar
  41. Lange, K. Mathematical and Statistical Methods for Genetic Analysis (Springer, 2002).
  42. Ramasamy, A. et al. Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. Nucleic Acids Res. 41, e88 (2013).
    Article CAS Google Scholar
  43. Tenenbaum, S.A., Lager, P.J., Carson, C.C. & Keene, J.D. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26, 191–198 (2002).
    Article CAS Google Scholar
  44. Huang, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009).
    Article Google Scholar
  45. Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
    Article CAS Google Scholar

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