Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants (original) (raw)

References

1. Egger G, Liang G, Aparicio A, Jones PA . Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004; 429: 457–463.
   Article CAS Google Scholar
2. Park PJ . Epigenetics meets next-generation sequencing. Epigenetics 2008; 3: 318–321.
   Article Google Scholar
3. Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 2006; 34: 528–542.
   Article CAS Google Scholar
4. Feinberg AP . Phenotypic plasticity and the epigenetics of human disease. Nature 2007; 447: 433–440.
   Article CAS Google Scholar
5. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY . Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 1999; 23: 185–188.
   Article CAS Google Scholar
6. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL et al. SCAN: SNP and copy number annotation. Bioinformatics 2010; 26: 259–262.
   Article CAS Google Scholar
7. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ . Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010; 6: e1000888.
   Article Google Scholar
8. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I et al. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 2010; 6: e1000895.
   Article Google Scholar
9. Zhang D, Cheng L, Badner JA, Chen C, Chen Q, Luo W et al. Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet 2010; 86: 411–419.
   Article CAS Google Scholar
10. Liu C, Cheng L, Badner JA, Zhang D, Craig DW, Redman M et al. Whole-genome association mapping of gene expression in the human prefrontal cortex. Mol Psychiatry 2010; 15: 779–784.
    Article CAS Google Scholar
11. Smith EN, Bloss CS, Badner JA, Barrett T, Belmonte PL, Berrettini W et al. Genome-wide association study of bipolar disorder in European American and African American individuals. Mol Psychiatry 2009; 14: 755–763.
    Article CAS Google Scholar
12. Smith EN, Koller DL, Panganiban C, Szelinger S, Zhang P, Badner JA et al. Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes. PLoS Genet 2011; 7: e1002134.
    Article CAS Google Scholar
13. Wellcome Trust Case Control Consortium. Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661–678.
14. Kato T, Iwamoto K, Kakiuchi C, Kuratomi G, Okazaki Y . Genetic or epigenetic difference causing discordance between monozygotic twins as a clue to molecular basis of mental disorders. Mol Psychiatry 2005; 10: 622–630.
    Article CAS Google Scholar
15. Petronis A . Epigenetics and bipolar disorder: new opportunities and challenges. Am J Med Genet C Semin Med Genet 2003; 123C: 65–75.
    Article Google Scholar
16. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR . MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010; 34: 816–834.
    Article Google Scholar
17. Li Y, Willer C, Sanna S, Abecasis G . Genotype imputation. Annu Rev Genomics Hum Genet 2009; 10: 387–406.
    Article CAS Google Scholar
18. Johnson WE, Li C, Rabinovic A . Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8: 118–127.
    Article Google Scholar
19. Leek JT, Storey JD . Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 2007; 3: 1724–1735.
    Article CAS Google Scholar
20. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559–575.
    Article CAS Google Scholar
21. Gamazon ER, Nicolae DL, Cox NJ . A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. PLoS Genet 2011; 7: e1001292.
    Article CAS Google Scholar
22. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009; 106: 9362–9367.
    Article CAS Google Scholar
23. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 2011; 12: R10.
    Article CAS Google Scholar
24. Richards AL, Jones L, Moskvina V, Kirov G, Gejman PV, Levinson DF et al. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain. Mol Psychiatry 2011 (e-pub ahead of print).
25. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 2010; 6: e1000952.
    Article Google Scholar
26. Sasaki J, Kofuji S, Itoh R, Momiyama T, Takayama K, Murakami H et al. The PtdIns(3,4)P phosphatase INPP4A is a suppressor of excitotoxic neuronal death. Nature 2010; 465: 497–501.
    Article CAS Google Scholar
27. Rao JS, Harry GJ, Rapoport SI, Kim HW . Increased excitotoxicity and neuroinflammatory markers in postmortem frontal cortex from bipolar disorder patients. Mol Psychiatry 2010; 15: 384–392.
    Article CAS Google Scholar
28. Berridge MJ . The Albert Lasker medical awards. Inositol trisphosphate, calcium, lithium, and cell signaling. JAMA 1989; 262: 1834–1841.
    Article CAS Google Scholar

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Acknowledgements

This work was funded by 5R01MH080425 (to CL), PAAR (Pharmacogenetics of Anti-cancer Agents Research; U01 GM61393), ENDGAMe (ENhancing Development of Genome-wide Association Methods) initiative (U01 HL084715), and the Genotype-Tissue Expression project (GTeX) (R01 MH090937) (to NJC).

Author Contributions

ERG and CL conceived and designed the study. ERG and JAB performed statistical analyses. ERG and NJC provided analysis tools. ERG and CL wrote the manuscript. CL coordinated and supervised the study. LC, CZ, DZ, ESG, JRK, TAG, CMN, RM, PDS, NJS, ENS, CSB, JIN, Jr HJE, TF, DLK, WAS, WC, JR, WB, FJM, TGS, WHB, JBP, PPZ, PBM, MGM, SZ, PZ, DWC, SS, TBB, CL participated in patient diagnosis and sample collection. All authors edited and approved the manuscript.

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Authors and Affiliations

1. Department of Medicine, University of Chicago, Chicago, IL, USA
   E R Gamazon & N J Cox
2. Department of Psychiatry, University of Chicago, Chicago, IL, USA
   J A Badner & E S Gershon
3. Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
   L Cheng, C Zhang, C Chen & C Liu
4. School of Medicine, University of Zhejiang, Hanzhou, Zhejiang, China
   D Zhang
5. Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
   J R Kelsoe, T A Greenwood, C M Nievergelt, R McKinney & P D Shilling
6. Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, CA, USA
   N J Schork, E N Smith & C S Bloss
7. Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
   J I Nurnberger & D L Koller
8. Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
   H J Edenberg & T Foroud
9. Department of Psychiatry, Rush University, Chicago, IL, USA
   W A Scheftner
10. Department of Psychiatry, University of Iowa, Iowa City, IA, USA
    W Coryell
11. Division of Biostatistics, Washington University, St Louis, MO, USA
    J Rice
12. Department of Psychiatry, Howard University, Washington, DC, USA
    W B Lawson, E A Nwulia & M Hipolito
13. Department of Psychiatry, University of California, San Francisco, CA, USA
    W Byerley
14. US Department of Health and Human Services, Genetic Basis of Mood and Anxiety Disorders Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
    F J McMahon & T G Schulze
15. Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
    T G Schulze
16. Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
    W H Berrettini
17. Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA
    J B Potash, P P Zandi & P B Mahon
18. Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
    M G McInnis, S Zöllner & P Zhang
19. Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
    D W Craig & S Szelinger
20. Department of Psychiatry, Portland VA Medical Center, Portland, OR, USA
    T B Barrett

Authors

1. E R Gamazon
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2. J A Badner
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3. L Cheng
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4. C Zhang
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5. D Zhang
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6. N J Cox
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7. E S Gershon
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8. J R Kelsoe
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9. T A Greenwood
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10. C M Nievergelt
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11. C Chen
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12. R McKinney
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13. P D Shilling
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14. N J Schork
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15. E N Smith
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16. C S Bloss
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17. J I Nurnberger
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18. H J Edenberg
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19. T Foroud
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20. D L Koller
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21. W A Scheftner
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22. W Coryell
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23. J Rice
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24. W B Lawson
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25. E A Nwulia
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26. M Hipolito
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27. W Byerley
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28. F J McMahon
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29. T G Schulze
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30. W H Berrettini
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31. J B Potash
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32. P P Zandi
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33. P B Mahon
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34. M G McInnis
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35. S Zöllner
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36. P Zhang
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37. D W Craig
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38. S Szelinger
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39. T B Barrett
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40. C Liu
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Corresponding author

Correspondence toC Liu.

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The authors declare no conflict of interest.

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Gamazon, E., Badner, J., Cheng, L. et al. Enrichment of _cis_-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants.Mol Psychiatry 18, 340–346 (2013). https://doi.org/10.1038/mp.2011.174

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• Received: 30 August 2011
• Revised: 25 October 2011
• Accepted: 28 October 2011
• Published: 03 January 2012
• Issue Date: March 2013
• DOI: https://doi.org/10.1038/mp.2011.174

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