Genetic mapping of pharmacogenetic regulatory variation

Current Pharmaceutical Design

Volumn 15, Issue 32, 2009, Pages 3773-3781

  Raby, Benjamin A ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Complex trait; Gene expression; Genetical genomics; Pharmacogenetics

Indexed keywords

DNA MICROARRAY; DRUG RESPONSE; EXPRESSION QUANTITATIVE TRAIT LOCUS MAPPING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC PREDISPOSITION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HUMAN; PHARMACOGENETICS; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW;

ANIMALS; CHROMOSOME MAPPING; DRUG DELIVERY SYSTEMS; DRUG DESIGN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; PHARMACOGENETICS; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 70449628092     PISSN: 13816128     EISSN: None     Source Type: Journal    
DOI: 10.2174/138161209789649466     Document Type: Review

References (80)

1. Rieder MJ, Reiner AP, Gage BF, Nickerson DA, Eby CS, McLeod HL, et al. Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med 2005; 352: 2285-2293
2. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004; 351: 2817-2826 (Pubitemid 40051905)
3. 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(23): 9362-9367
4. Turner ST, Bailey KR, Fridley BL, Chapman AB, Schwartz GL, Chai HS, et al. Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic. Hypertension 2008; 52: 359-365
5. Liu C, Batliwalla F, Li W, Lee A, Roubenoff R, Beckman E, et al. Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. Mol Med 2008; 14: 575-581
6. Byun E, Caillier SJ, Montalban X, Villoslada P, Fernandez O, Brassat D, et al. Genome-wide pharmacogenomic analysis of the response to interferon beta therapy in multiple sclerosis. Arch Neurol 2008; 65: 337-344
7. Uhl GR, Liu QR, Drgon T, Johnson C, Walther D, Rose JE, et al. Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Arch Gen Psychiatry 2008; 65: 683-693 (Pubitemid 351787239)
8. Potti A, Dressman HK, Bild A, Riedel RF, Chan G, Sayer R, et al. Genomic signatures to guide the use of chemotherapeutics. Nat Med 2006; 12: 1294-1300 (Pubitemid 44706932)
9. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, et al. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci USA 2001; 98: 10787-10792
10. O'Shaughnessy JA. Molecular signatures predict outcomes of breast cancer. N Engl J Med 2006; 355: 615-617 (Pubitemid 44200656)
11. Hakonarson H, Bjornsdottir US, Halapi E, Bradfield J, Zink F, Mouy M, et al. Profiling of genes expressed in peripheral blood mononuclear cells predicts glucocorticoid sensitivity in asthma patients. Proc Natl Acad Sci USA 2005; 102: 14789-14794 (Pubitemid 41457134)
12. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, et al. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci USA 2007; 104: 15858-15863 (Pubitemid 350035389)
13. Fu LM, Shinnick TM. Understanding the action of INH on a highly INH-resistant Mycobacterium tuberculosis strain using. Genechips Tuberculosis (Edinb) 2007; 87: 63-70.
14. Liu TT, Lee RE, Barker KS, Wei L, Homayouni R, Rogers PD. Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans. Antimicrob Agents Chemother 2005; 49: 2226-2236 (Pubitemid 40734449)
15. Assmus B, Urbich C, Aicher A, Hofmann WK, Haendeler J, Rossig L, et al. HMG-CoA reductase inhibitors reduce senescence and increase proliferation of endothelial progenitor cells via regulation of cell cycle regulatory genes. Circ Res 2003; 92: 1049-1055 (Pubitemid 36588505)
16. Morikawa S, Takabe W, Mataki C, Wada Y, Izumi A, Saito Y, et al. Global analysis of RNA expression profile in human vascular cells treated with statins. J Atheroscler Thromb 2004; 11: 62-72.
17. Chon H, Gaillard CA, van der Meijden BB, Dijstelbloem HM, Kraaijenhagen RJ, van Leenen D, et al. Broadly altered gene expression in blood leukocytes in essential hypertension is absent during treatment. Hypertension 2004; 43: 947-951 (Pubitemid 38579896)
18. Jansen RC, Nap JP. Genetical genomics: the added value from segregation. Trends Genet 2001; 17: 388-391
19. Jais PH. How frequent is altered gene expression among susceptibility genes to human complex disorders? Genet Med 2005; 7: 83-96.
20. Hudson TJ. Wanted: regulatory SNPs. Nat Genet 2003; 33: 439-440
21. Helgadottir A, Manolescu A, Thorleifsson G, Gretarsdottir S, Jonsdottir H, Thorsteinsdottir U, et al. The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke. Nat Genet 2004; 36: 233-239 (Pubitemid 38282747)
22. Horikawa Y, Oda N, Cox N, Li X, Orho-Melander M, Hara M, et al. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet 2000; 26: 163-175 (Pubitemid 30764497)
23. Rioux JD, Daly MJ, Silverberg MS, Lindblad K, Steinhart H, Cohen Z, et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 2001; 29: 223-228 (Pubitemid 32952663)
24. Stefansson H, Sigurdsson E, Steinthorsdottir V, Bjornsdottir S, Sigmundsson T, Ghosh S, et al. Neuregulin 1 and susceptibility to schizophrenia. Am J Hum Genet 2002; 71: 877-892
25. Suzuki A, Yamada R, Chang X, Tokuhiro S, Sawada T, Suzuki M, et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet 2003; 34: 395-402. (Pubitemid 36935332)
26. Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, et al. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 2003; 423: 506-511 (Pubitemid 36648570)
27. Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet 2001; 29: 306-309 (Pubitemid 33096456)
28. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet 2003; 33: 177-182 (Pubitemid 36177070)
29. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, Morley M, et al. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 2003; 33: 422-425 (Pubitemid 36278862)
30. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P, et al. Intra- and interspecific variation in primate gene expression patterns. Science 2002; 296: 340-343 (Pubitemid 34303687)
31. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430: 743-747 (Pubitemid 39071339)
32. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003; 422: 297-302. (Pubitemid 36378355)
33. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, et al. Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci USA 2003; 100: 1896-1901 (Pubitemid 36254545)
34. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002; 296: 752-755 (Pubitemid 34442007)
35. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005; 37: 233-242 (Pubitemid 41716250)
36. Monks SA, Leonardson A, Zhu H, Cundiff P, Pietrusiak P, Edwards S, et al. Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 2004; 75: 1094-1105 (Pubitemid 39532076)
37. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet 2005; 37: 225-232
38. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, Burdick JT. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005; 437: 1365-1369 (Pubitemid 41568683)
39. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 2005; 37: 243-253 (Pubitemid 41716251)
40. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005; 37: 710-717 (Pubitemid 41754887)
41. Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science 1996; 273: 1516-1517 (Pubitemid 26301653)
42. Chakravarti A. Information content of the Centre d'Etude du Polymorphisme Humain (CEPH) family structures for linkage studies. Hum Genet 1991; 87: 721-724
43. Dausset J, Cann H, Cohen D, Lathrop M, Lalouel JM, White R. Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome. Genomics 1990; 6: 575-577 (Pubitemid 20168693)
44. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, et al. Population genomics of human gene expression. Nat Genet 2007; 39: 1217-1224 (Pubitemid 47482691)
45. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KC, et al. A genome-wide association study of global gene expression. Nat Genet 2007; 39: 1202-1207 (Pubitemid 47482680)
46. Goring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 2007; 39: 1208-1216 (Pubitemid 47482685)
47. Price AL, Patterson N, Hancks DC, Myers S, Reich D, Cheung VG, et al. Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet 2008; 4: e1000294.
48. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 2008; 4: e1000214.
49. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, et al. Genetics of gene expression and its effect on disease. Nature 2008; 452: 423-428
50. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008; 6; e107. (Pubitemid 351824739)
51. Petretto E, Mangion J, Dickens NJ, Cook SA, Kumaran MK, Lu H, et al. Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet 2006; 2: e172. (Pubitemid 44656536)
52. Hovatta I, Zapala MA, Broide RS, Schadt EE, Libiger O, Schork NJ, et al. DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies. Genome Biol 2007; 8: R25. (Pubitemid 351851031)
53. Mehrabian M, Allayee H, Stockton J, Lum PY, Drake TA, Castellani LW, et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 2005; 37: 1224-1233 (Pubitemid 41568705)
54. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007; 448: 470-473 (Pubitemid 47123521)
55. Galanter J, Choudhry S, Eng C, Nazario S, Rodriguez-Santana JR, Casal J, et al. ORMDL3 gene is associated with asthma in three ethnically diverse populations. Am J Respir Crit Care Med 2008; 177: 1194-1200 (Pubitemid 351860927)
56. Tavendale R, Macgregor DF, Mukhopadhyay S, Palmer CN. A polymorphism controlling ORMDL3 expression is associated with asthma that is poorly controlled by current medications. J Allergy Clin Immunol 2008; 121: 860-863
57. Wu H, Romieu I, Sienra-Monge JJ, Li H, Del Rio-Navarro BE, London SJ. Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma. Allergy 2008.
58. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008; 452: 429-435
59. Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JA, et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet 2006; 2: e222. (Pubitemid 46045193)
60. Smith EN, Kruglyak L. Gene-environment interaction in yeast gene expression. PLoS Biol 2008; 6: e83. (Pubitemid 351649313)
61. Stram DO, Lee JW. Variance components testing in the longitudinal mixed effects model. Biometrics 1994; 50: 1171-1177
62. Zeger SL, Liang KY. Longitudinal data analysis for discrete and continuous outcomes. Biometrics 1986; 42: 121-130
63. Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001; 29: 482-486 (Pubitemid 34326702)
64. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004; 5: 101-113
65. Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003; 301: 102-105 (Pubitemid 36801571)
66. Johnson GL, Dohlman HG, Graves LM. MAPK kinase kinases (MKKKs) as a target class for small-molecule inhibition to modulate signaling networks and gene expression. Curr Opin Chem Biol 2005; 9: 325-331
67. Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, et al. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet 2009.
68. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008; 4: e1000287.
69. Dimos JT, Rodolfa KT, Niakan KK, Weisenthal LM, Mitsumoto H, Chung W, et al. Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science 2008; 321: 1218-1221
70. Park IH, Arora N, Huo H, Maherali N, Ahfeldt T, Shimamura A, et al. Disease-specific induced pluripotent stem cells. Cell 2008; 134: 877-886
71. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 2007; 39: 226-231 (Pubitemid 46184354)
72. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006; 38; 904-909 (Pubitemid 44141658)
73. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008; 24: 408-415
74. Kendziorski C, Wang P. A review of statistical methods for expression quantitative trait loci mapping. Mamm Genome 2006; 17: 509-517 (Pubitemid 43911472)
75. Rosa GJ, de Leon N, Rosa AJ. Review of microarray experimental design strategies for genetical genomics studies. Physiol Genomics 2006; 28: 15-23. (Pubitemid 46702013)
76. Alberts R, Terpstra P, Li Y, Breitling R, Nap JP, Jansen RC. Sequence polymorphisms cause many false cis eQTLs. PLoS ONE 2007; 2: e622. (Pubitemid 351279929)
77. Melzer D, Perry JR, Hernandez D, Corsi AM, Stevens K, Rafferty I, et al. A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet 2008; 4: e1000072. (Pubitemid 351811508)
78. Bansal AT, Barnes MR. Genomics in drug discovery: the best things come to those who wait. Curr Opin Drug Discov Devel 2008; 11(3): 303-311
79. Dieterle F, Marrer E, Suzuki E, Grenet O, Cordier A, Vonderscher J. Monitoring kidney safety in drug development: emerging technologies and their implications. Curr Opin Drug Discov Devel 2008; 11(1): 60-71.
80. O'Sullivan DJ. Genomics can advance the potential for probiotic cultures to improve liver and overall health. Curr Pharm Des 2008; 14(14): 1376-1381