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Genomic Applications in Pharmacogenomics

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Genomic Applications in Pathology
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Abstract

Pharmacogenomics is the study of the influence of the effect of genetic variations between individuals on drug efficacy, metabolism, and toxicity. With advances in pharmacogenomics, physicians will be able to prescribe the right drug and at the correct dose based on the genomic profile of their patients, thus maximizing the efficacy while minimizing adverse effects. Genomic principles guide the design, implementation, analysis, and inference from pharmacogenomic studies. Applications of genomic principles in pharmacogenomics hold promise for personalized medicine, novel drug discovery and development, and deeper insights into the biological mechanisms.

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References

  1. http://www.ncbi.nlm.nih.gov/About/primer/pharm.html. Accessed 30 Apr 2013.

  2. Nebert DW. Pharmacogenetics and pharmacogenomics: why is this relevant to the clinical geneticist? Clin Genet. 1999;56(4):247–58.

    Article  PubMed  CAS  Google Scholar 

  3. Roden DM, Wilke RA, Kroemer HK, Stein CM. Pharmacogenomics: the genetics of variable drug responses. Circulation. 2011;123(15):1661–70. doi:10.1161/CIRCULATIONAHA.109.914820.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Snyder LH. Inherited taste deficiency. Science. 1931;74(1910):151–2. doi:10.1126/science.74.1910.151.

    Article  PubMed  CAS  Google Scholar 

  5. Snyder L. Studies in human inheritance. IX, the inheritance of taste deficiency in man. Ohio J Sci. 1932;32(5):436–40.

    Google Scholar 

  6. Mundy C. The human genome project: a historical perspective. Pharmacogenomics. 2001;2(1):37–49. doi:10.1517/14622416.2.1.37.

    Article  PubMed  CAS  Google Scholar 

  7. http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm. Accessed 30 Apr 2013.

  8. http://www.pharmaadme.org/joomla/. Accessed 4 Sept 2013.

  9. Daly AK. Genome-wide association studies in pharmacogenomics. Nat Rev Genet. 2010;11(4):241–6. doi:10.1038/nrg2751.

    Article  PubMed  CAS  Google Scholar 

  10. Daly AK. Using genome-wide association studies to identify genes important in serious adverse drug reactions. Annu Rev Pharmacol Toxicol. 2012;52:21–35. doi:10.1146/annurev-pharmtox-010611-134743.

    Article  PubMed  CAS  Google Scholar 

  11. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95–108. doi:10.1038/nrg1521.

    Article  PubMed  CAS  Google Scholar 

  12. Motsinger-Reif AA, Jorgenson E, Relling MV, Kroetz DL, Weinshilboum R, Cox NJ, Roden DM. Genome-wide association studies in pharmacogenomics: successes and lessons. Pharmacogenet Genomics. 2013;23(8):383–94. doi:10.1097/FPC.0b013e32833d7b45.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  13. Moskvina V, Schmidt KM. On multiple-testing correction in genome-wide association studies. Genet Epidemiol. 2008;32(6):567–73. doi:10.1002/gepi.20331.

    Article  PubMed  Google Scholar 

  14. Wagner MJ. Rare-variant genome-wide association studies: a new frontier in genetic analysis of complex traits. Pharmacogenomics. 2013;14(4):413–24. doi:10.2217/pgs.13.36.

    Article  PubMed  CAS  Google Scholar 

  15. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zollner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science. 2012;337(6090):100–4. doi:10.1126/science.1217876.

    Article  PubMed  CAS  Google Scholar 

  16. Hiratsuka M. In vitro assessment of the allelic variants of cytochrome P450. Drug Metab Pharmacokinet. 2012;27(1):68–84.

    Article  PubMed  CAS  Google Scholar 

  17. McGeachie MJ, Stahl EA, Himes BE, Pendergrass SA, Lima JJ, Irvin CG, Peters SP, Ritchie MD, Plenge RM, Tantisira KG. Polygenic heritability estimates in pharmacogenetics: focus on asthma and related phenotypes. Pharmacogenet Genomics. 2013;23(6):324–8. doi:10.1097/FPC.0b013e3283607acf.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Sadee W. The relevance of “missing heritability” in pharmacogenomics. Clin Pharmacol Ther. 2012;92(4):428–30. doi:10.1038/clpt.2012.116.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  19. Faraday N, Yanek LR, Mathias R, Herrera-Galeano JE, Vaidya D, Moy TF, Fallin MD, Wilson AF, Bray PF, Becker LC, Becker DM. Heritability of platelet responsiveness to aspirin in activation pathways directly and indirectly related to cyclooxygenase-1. Circulation. 2007;115(19):2490–6. doi:10.1161/CIRCULATIONAHA.106.667584.

    Article  PubMed  CAS  Google Scholar 

  20. Shuldiner AR, O’Connell JR, Bliden KP, Gandhi A, Ryan K, Horenstein RB, Damcott CM, Pakyz R, Tantry US, Gibson Q, Pollin TI, Post W, Parsa A, Mitchell BD, Faraday N, Herzog W, Gurbel PA. Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA. 2009;302(8):849–57. doi:10.1001/jama.2009.1232.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Isakov O, Perrone M, Shomron N. Exome sequencing analysis: a guide to disease variant detection. Methods Mol Biol. 2013;1038:137–58. doi:10.1007/978-1-62703-514-9_8.

    Article  PubMed  Google Scholar 

  22. Stitziel NO, Kiezun A, Sunyaev S. Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol. 2011;12(9):227. doi:10.1186/gb-2011-12-9-227.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073–81. doi:10.1038/nprot.2009.86.

    Article  PubMed  CAS  Google Scholar 

  24. Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39(17):e118. doi:10.1093/nar/gkr407.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Stone EA, Sidow A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res. 2005;15(7):978–86. doi:10.1101/gr.3804205.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  26. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003;13(9):2129–41. doi:10.1101/gr.772403.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  27. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9. doi:10.1038/nmeth0410-248.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007;35(11):3823–35. doi:10.1093/nar/gkm238.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  29. Yue P, Moult J. Identification and analysis of deleterious human SNPs. J Mol Biol. 2006;356(5):1263–74. doi:10.1016/j.jmb.2005.12.025.

    Article  PubMed  CAS  Google Scholar 

  30. Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 2013;14 Suppl 3:S3. doi:10.1186/1471-2164-14-S3-S3.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009;25(21):2744–50. doi:10.1093/bioinformatics/btp528.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  32. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7(8):575–6. doi:10.1038/nmeth0810-575.

    Article  PubMed  CAS  Google Scholar 

  33. Morgenthaler S, Thilly WG. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 2007;615(1–2):28–56. doi:10.1016/j.mrfmmm.2006.09.003.

    Article  PubMed  CAS  Google Scholar 

  34. Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008;83(3):311–21. doi:10.1016/j.ajhg.2008.06.024.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  35. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010;86(6):832–8. doi:10.1016/j.ajhg.2010.04.005.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010;6(10):e1000954. doi:10.1371/journal.pcbi.1000954.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Luo L, Boerwinkle E, Xiong M. Association studies for next-generation sequencing. Genome Res. 2011;21(7):1099–108. doi:10.1101/gr.115998.110.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  38. Madsen BE, Browning SR. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009;5(2):e1000384. doi:10.1371/journal.pgen.1000384.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Liu DJ, Leal SM. A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet. 2010;6(10):e1001156. doi:10.1371/journal.pgen.1001156.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Sul JH, Han B, He D, Eskin E. An optimal weighted aggregated association test for identification of rare variants involved in common diseases. Genetics. 2011;188(1):181–8. doi:10.1534/genetics.110.125070.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Yick CY, Zwinderman AH, Kunst PW, Grunberg K, Mauad T, Fluiter K, Bel EH, Lutter R, Baas F, Sterk PJ. Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma. Am J Respir Crit Care Med. 2013;187(10):1076–84. doi:10.1164/rccm.201210-1886OC.

    Article  PubMed  CAS  Google Scholar 

  42. Wiviott SD, Braunwald E, McCabe CH, Montalescot G, Ruzyllo W, Gottlieb S, Neumann FJ, Ardissino D, De Servi S, Murphy SA, Riesmeyer J, Weerakkody G, Gibson CM, Antman EM, Investigators T-T. Prasugrel versus clopidogrel in patients with acute coronary syndromes. N Engl J Med. 2007;357(20):2001–15. doi:10.1056/NEJMoa0706482.

    Article  PubMed  CAS  Google Scholar 

  43. Mega JL, Close SL, Wiviott SD, Shen L, Hockett RD, Brandt JT, Walker JR, Antman EM, Macias W, Braunwald E, Sabatine MS. Cytochrome p-450 polymorphisms and response to clopidogrel. N Engl J Med. 2009;360(4):354–62. doi:10.1056/NEJMoa0809171.

    Article  PubMed  CAS  Google Scholar 

  44. Mega JL, Close SL, Wiviott SD, Shen L, Walker JR, Simon T, Antman EM, Braunwald E, Sabatine MS. Genetic variants in ABCB1 and CYP2C19 and cardiovascular outcomes after treatment with clopidogrel and prasugrel in the TRITON-TIMI 38 trial: a pharmacogenetic analysis. Lancet. 2010;376(9749):1312–9. doi:10.1016/S0140-6736(10)61273-1.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  45. Ramsey LB, Panetta JC, Smith C, Yang W, Fan Y, Winick NJ, Martin PL, Cheng C, Devidas M, Pui CH, Evans WE, Hunger SP, Loh M, Relling MV. Genome-wide study of methotrexate clearance replicates SLCO1B1. Blood. 2013;121(6):898–904. doi:10.1182/blood-2012-08-452839.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  46. Ramnath N, Daignault-Newton S, Dy GK, Muindi JR, Adjei A, Elingrod VL, Kalemkerian GP, Cease KB, Stella PJ, Brenner DE, Troeschel S, Johnson CS, Trump DL. A phase I/II pharmacokinetic and pharmacogenomic study of calcitriol in combination with cisplatin and docetaxel in advanced non-small-cell lung cancer. Cancer Chemother Pharmacol. 2013;71(5):1173–82. doi:10.1007/s00280-013-2109-x.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  47. Anthoney DA, Naik J, Macpherson IR, Crawford D, Hartley JM, Hartley JA, Saito T, Abe M, Jones K, Miwa M, Twelves C, Evans TR. Phase I study of TP300 in patients with advanced solid tumors with pharmacokinetic, pharmacogenetic and pharmacodynamic analyses. BMC Cancer. 2012;12:536. doi:10.1186/1471-2407-12-536.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  48. Hayes DN, Lucas AS, Tanvetyanon T, Krzyzanowska MK, Chung CH, Murphy BA, Gilbert J, Mehra R, Moore DT, Sheikh A, Hoskins J, Hayward MC, Zhao N, O'Connor W, Weck KE, Cohen RB, Cohen EE. Phase II efficacy and pharmacogenomic study of Selumetinib (AZD6244; ARRY-142886) in iodine-131 refractory papillary thyroid carcinoma with or without follicular elements. Clin Cancer Res. 2012;18(7):2056–65. doi:10.1158/1078-0432.CCR-11-0563.

    Article  PubMed  CAS  Google Scholar 

  49. Denny JC. Chapter 13: mining electronic health records in the genomics era. PLoS Comput Biol. 2012;8(12):e1002823. doi:10.1371/journal.pcbi.1002823.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  50. Manolio TA. Collaborative genome-wide association studies of diverse diseases: programs of the NHGRI's office of population genomics. Pharmacogenomics. 2009;10(2):235–41. doi:10.2217/14622416.10.2.235.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Yu IW, Bukaveckas BL. Pharmacogenetic tests in asthma therapy. Clin Lab Med. 2008;28(4):645–65. doi:10.1016/j.cll.2008.05.001.

    Article  PubMed  Google Scholar 

  52. Roberts JD, Wells GA, Le May MR, Labinaz M, Glover C, Froeschl M, Dick A, Marquis JF, O'Brien E, Goncalves S, Druce I, Stewart A, Gollob MH, So DY. Point-of-care genetic testing for personalisation of antiplatelet treatment (RAPID GENE): a prospective, randomised, proof-of-concept trial. Lancet. 2012;379(9827):1705–11. doi:10.1016/S0140-6736(12)60161-5.

    Article  PubMed  CAS  Google Scholar 

  53. Sconce EA, Khan TI, Wynne HA, Avery P, Monkhouse L, King BP, Wood P, Kesteven P, Daly AK, Kamali F. The impact of CYP2C9 and VKORC1 genetic polymorphism and patient characteristics upon warfarin dose requirements: proposal for a new dosing regimen. Blood. 2005;106(7):2329–33. doi:10.1182/blood-2005-03-1108.

    Article  PubMed  CAS  Google Scholar 

  54. Anderson JL, Horne BD, Stevens SM, Woller SC, Samuelson KM, Mansfield JW, Robinson M, Barton S, Brunisholz K, Mower CP, Huntinghouse JA, Rollo JS, Siler D, Bair TL, Knight S, Muhlestein JB, Carlquist JF. A randomized and clinical effectiveness trial comparing two pharmacogenetic algorithms and standard care for individualizing warfarin dosing (CoumaGen-II). Circulation. 2012;125(16):1997–2005. doi:10.1161/CIRCULATIONAHA.111.070920.

    Article  PubMed  CAS  Google Scholar 

  55. Karczewski KJ, Daneshjou R, Altman RB. Chapter 7: pharmacogenomics. PLoS Comput Biol. 2012;8(12):e1002817. doi:10.1371/journal.pcbi.1002817.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  56. Baigent C, Keech A, Kearney PM, Blackwell L, Buck G, Pollicino C, Kirby A, Sourjina T, Peto R, Collins R, Simes R, Cholesterol Treatment Trialists C. Efficacy and safety of cholesterol-lowering treatment: prospective meta-analysis of data from 90,056 participants in 14 randomised trials of statins. Lancet. 2005;366(9493):1267–78. doi:10.1016/S0140-6736(05)67394-1.

    Article  PubMed  CAS  Google Scholar 

  57. Search E, Link E, Parish S, Armitage J, Bowman L, Heath S, Matsuda F, Gut I, Lathrop M, Collins R. SLCO1B1 variants and statin-induced myopathy—a genomewide study. N Engl J Med. 2008;359(8):789–99. doi:10.1056/NEJMoa0801936.

    Article  Google Scholar 

  58. Danik JS, Chasman DI, MacFadyen JG, Nyberg F, Barratt BJ, Ridker PM. Lack of association between SLCO1B1 polymorphisms and clinical myalgia following rosuvastatin therapy. Am Heart J. 2013;165(6):1008–14. doi:10.1016/j.ahj.2013.01.025.

    Article  PubMed  CAS  Google Scholar 

  59. Hicks JK, Swen JJ, Thorn CF, Sangkuhl K, Kharasch ED, Ellingrod VL, Skaar TC, Muller DJ, Gaedigk A, Stingl JC, Clinical Pharmacogenetics Implementation. Clinical pharmacogenetics implementation consortium guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin Pharmacol Ther. 2013;93(5):402–8. doi:10.1038/clpt.2013.2.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  60. Sirskyj D, Diaz-Mitoma F, Golshani A, Kumar A, Azizi A. Innovative bioinformatic approaches for developing peptide-based vaccines against hypervariable viruses. Immunol Cell Biol. 2011;89(1):81–9. doi:10.1038/icb.2010.65.

    Article  PubMed  CAS  Google Scholar 

  61. Thomas C, Moridani M. Interindividual variations in the efficacy and toxicity of vaccines. Toxicology. 2010;278(2):204–10. doi:10.1016/j.tox.2009.10.008.

    Article  PubMed  CAS  Google Scholar 

  62. Russell C, Rahman A, Mohammed AR. Application of genomics, proteomics and metabolomics in drug discovery, development and clinic. Ther Deliv. 2013;4(3):395–413. doi:10.4155/tde.13.4.

    Article  PubMed  CAS  Google Scholar 

  63. Scheffler RJ, Colmer S, Tynan H, Demain AL, Gullo VP. Antimicrobials, drug discovery, and genome mining. Appl Microbiol Biotechnol. 2013;97(3):969–78. doi:10.1007/s00253-012-4609-8.

    Article  PubMed  CAS  Google Scholar 

  64. Liou SY, Stringer F, Hirayama M. The impact of pharmacogenomics research on drug development. Drug Metab Pharmacokinet. 2012;27(1):2–8.

    Article  PubMed  CAS  Google Scholar 

  65. Nebert DW, Dalton TP. The role of cytochrome P450 enzymes in endogenous signalling pathways and environmental carcinogenesis. Nat Rev Cancer. 2006;6(12):947–60. doi:10.1038/nrc2015.

    Article  PubMed  CAS  Google Scholar 

  66. Swen JJ, Huizinga TW, Gelderblom H, de Vries EG, Assendelft WJ, Kirchheiner J, Guchelaar HJ. Translating pharmacogenomics: challenges on the road to the clinic. PLoS Med. 2007;4(8):e209. doi:10.1371/journal.pmed.0040209.

    Article  PubMed  PubMed Central  Google Scholar 

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Qayyum, R. (2015). Genomic Applications in Pharmacogenomics. In: Netto, G., Schrijver, I. (eds) Genomic Applications in Pathology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0727-4_31

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