Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Gerasimova, Anna ^a   Chavez, Lukas ^a   Li, Bin ^a   Seumois, Gregory ^a   Greenbaum, Jason ^a   Rao, Anjana ^a   Vijayanand, Pandurangan ^a   Peters, Bjoern ^a  

^a LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; HISTONE H3; HISTONE H3 LYSINE 27; HISTONE H3 LYSINE 4; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; ASTHMA; BIOACCUMULATION; CD4+ T LYMPHOCYTE; CELL ASSAY; CELL TYPE; CONTROLLED STUDY; DISEASE ASSOCIATION; ENHANCER REGION; EPIGENETICS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HISTONE METHYLATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MOLECULAR DYNAMICS; PREDICTION; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

ASTHMA; ENHANCER ELEMENTS, GENETIC; EPIGENOMICS; GENETIC LINKAGE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84873876753     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054359     Document Type: Article

References (55)

1. Granada M, Wilk JB, Tuzova M, Strachan DP, Weidinger S, et al. (2012) A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study. J Allergy Clin Immunol 129: 840-845 e821.
2. Mondul AM, Yu K, Wheeler W, Zhang H, Weinstein SJ, et al. (2011) Genome-wide association study of circulating retinol levels. Hum Mol Genet 20: 4724-4731.
3. Hirota T, Takahashi A, Kubo M, Tsunoda T, Tomita K, et al. (2011) Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population. Nat Genet 43: 893-896.
4. Noguchi E, Sakamoto H, Hirota T, Ochiai K, Imoto Y, et al. (2011) Genome-wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations. PLoS Genet 7: e1002170.
5. Ege MJ, Strachan DP, Cookson WO, Moffatt MF, Gut I, et al. (2011) Gene-environment interaction for childhood asthma and exposure to farming in Central Europe. J Allergy Clin Immunol 127: 138-144, 144 e131-134.
6. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, et al. (2010) A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 363: 1211-1221.
7. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, et al. (2007) Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448: 470-473.
8. Himes BE, Hunninghake GM, Baurley JW, Rafaels NM, Sleiman P, et al. (2009) Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Am J Hum Genet 84: 581-593.
9. Li X, Howard TD, Zheng SL, Haselkorn T, Peters SP, et al. (2010) Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. J Allergy Clin Immunol 125: 328-335 e311.
10. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, et al. (2011) Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet 43: 887-892.
11. Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, et al. (2010) Variants of DENND1B associated with asthma in children. N Engl J Med 362: 36-44.
12. Castro-Giner F, Bustamante M, Ramon Gonzalez J, Kogevinas M, Jarvis D, et al. (2009) A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). BMC Med Genet 10: 128.
13. Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, et al. (2009) Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. PLoS Genet 5: e1000623.
14. Weidinger S, Gieger C, Rodriguez E, Baurecht H, Mempel M, et al. (2008) Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus. PLoS Genet 4: e1000166.
15. Ober C, Tan Z, Sun Y, Possick JD, Pan L, et al. (2008) Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function. N Engl J Med 358: 1682-1691.
16. Miller EK, Dumitrescu L, Cupp C, Dorris S, Taylor S, et al. (2011) Atopy history and the genomics of wheezing after influenza vaccination in children 6-59 months of age. Vaccine 29: 3431-3437.
17. Kim JH, Park BL, Cheong HS, Bae JS, Park JS, et al. (2010) Genome-wide and follow-up studies identify CEP68 gene variants associated with risk of aspirin-intolerant asthma. PLoS One 5: e13818.
18. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
19. The International HapMap Consortium, (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
20. Li Y, Willer C, Sanna S, Abecasis G, (2009) Genotype imputation. Annu Rev Genomics Hum Genet 10: 387-406.
21. Michel S, Liang L, Depner M, Klopp N, Ruether A, et al. (2010) Unifying candidate gene and GWAS Approaches in Asthma. PLoS One 5: e13894.
22. Visscher PM, Brown MA, McCarthy MI, Yang J, (2012) Five years of GWAS discovery. Am J Hum Genet 90: 7-24.
23. Jaenisch R, Bird A, (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33Suppl: 245-254.
24. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
25. Talbert PB, Henikoff S, (2010) Histone variants-ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11: 264-275.
26. Pekowska A, Benoukraf T, Ferrier P, Spicuglia S, (2010) A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res 20: 1493-1502.
27. Zentner GE, Tesar PJ, Scacheri PC, (2011) Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21: 1273-1283.
28. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
29. Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, et al. (2010) Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res 20: 428-433.
30. Ward LD, Kellis M, (2012) HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 40: D930-934.
31. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
32. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
33. Yu W, Yesupriya A, Wulf A, Hindorff LA, Dowling N, et al. (2011) GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies. Eur J Hum Genet 19: 1095-1099.
34. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-496.
35. Karolchik D, Hinrichs AS, Kent WJ (2009) The UCSC Genome Browser. Curr Protoc Bioinformatics Chapter 1: Unit1 4.
36. Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
37. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
38. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 107: 21931-21936.
39. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28: 1045-1048.
40. Milosavljevic A, (2011) Emerging patterns of epigenomic variation. Trends Genet 27: 242-250.
41. Ansel KM, Djuretic I, Tanasa B, Rao A, (2006) Regulation of Th2 differentiation and Il4 locus accessibility. Annu Rev Immunol 24: 607-656.
42. Pham TH, Benner C, Lichtinger M, Schwarzfischer L, Hu Y, et al. (2012) Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. Blood 119: e161-171.
43. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337: 1190-1195.
44. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res 22: 1760-1774.
45. Chanock S, (2012) Toward mapping the biology of the genome. Genome Res 22: 1612-1615.
46. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M, (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22: 1748-1759.
47. Farrell JJ, Sherva RM, Chen ZY, Luo HY, Chu BF, et al. (2011) A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression. Blood 117: 4935-4945.
48. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
49. Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD, (2011) ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol 12: R67.
50. Hon G, Ren B, Wang W, (2008) ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201.
51. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
52. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
53. de Hoon MJ, Imoto S, Nolan J, Miyano S, (2004) Open source clustering software. Bioinformatics 20: 1453-1454.
54. Saldanha AJ, (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
55. The ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.