Whole genome sequencing in pharmacogenomics

Frontiers in Pharmacology

Volumn 6, Issue MAR, 2015, Pages

  Katsila, Theodora ^a   Patrinos, George P ^a  

^a UNIVERSITY OF PATRAS   (Greece)

Author keywords

Genome wide association studies; Genotype; Pesonalized medicine; Pharmacogenomics; Pharmacogenomics biomarkers; Whole genome sequencing

Indexed keywords

DRUG;

ARTICLE; GENE FUNCTION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; PHARMACOGENOMICS; PRACTICE GUIDELINE; TREATMENT RESPONSE;

EID: 84926451219     PISSN: None     EISSN: 16639812     Source Type: Journal    
DOI: 10.3389/fphar.2015.00061     Document Type: Article

References (24)

1. Altman, R. B., Whirl-Carrillo, M., and Klein, T. E. (2013). Challenges in the pharmacogenomic annotation of whole genomes. Clin. Pharmacol. Ther. 94, 211-213. doi: 10.1038/clpt.2013.111.
2. Ardlie, K. G., Kruglyak, L., and Seielstad, M. (2002). Patterns of linkage dis-equilibrium in the human genome. Nat. Rev. Genet. 3, 299-309. doi: 10.1038/nrg777.
3. Ashley, E. A., Butte, A. J., and Wheeler, M. T. (2010). Clinical assessment incorporating a personal genome. Lancet 375, 1525-1535. doi: 10.1016/S0140-6736(10)60452-7.
4. Crews, K. R., Hicks, J. K., Pui, C. H., Relling, M. V., and Evans, W. E. (2012). Pharmacogenomics and individualized medicine: translating science into practice. Clin. Pharmacol. Ther. 92, 467-475. doi: 10.1038/clpt.2012.120.
5. Drögemöller, B. I., Wright, G. E. B., Niehaus, D. J. H., Emsley, R. A., and Warnich, L. (2011). Whole-genome resequencingin pharmacogenomics: moving away from past disparities to globally representative applications. Pharmacogenomics 12, 1717-1728. doi: 10.2217/pgs.11.119.
6. Drögemöller, B. I., Wright, G. E., Niehaus, D. J., Emsley, R., and Warnich, L. (2013). Next-generation sequencing of pharmacogenes: a critical analysis focusing on schizophrenia treatment. Pharmacogenet. Genomics 23, 666-674. doi: 10.1097/FPC.0000000000000006.
7. Feero, W. G. (2014). Clinical application of whole-genome sequencing: proceed with care. JAMA 311, 1017-1019. doi: 10.1001/jama.2014.1718.
8. Fragoulakis, V., Mitropoulou, C., Williams, M. S., and Patrinos, G. P. (2015). Economic Evaluation in Genomic Medicine. Amsterdam, Elsevier.
9. Gamazon, E. R., Skol, A. D., and Perera, M. A. (2012). The limits of genome-wide methods for pharmacogenomics testing. Pharmacogenet. Genomics 22, 261-272. doi: 10.1097/FPC.0b013e328350ca5f.
10. Kampourakis, K., Vayena, E., Mitropoulou, C., van Schaik, R. H., Cooper, D. N., Borg, J., et al. (2014). Key challenges for next-generation pharmacogenomics: science and society series on science and drugs. EMBO Rep. 15, 472-476. doi: 10.1002/embr.201438641.
11. Meyerson, M., Gabriel, S., and Getz, G. (2010). Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11, 685-696. doi: 10.1038/nrg2841.
12. Mizzi, C., Peters, B., Mitropoulou, C., Mitropoulos, K., Katsila, T., Agarwal, M. R., et al. (2014). Personalized pharmacogenomics profiling using whole-genome sequencing. Pharmacogenomics 15, 1223-1234. doi: 10.2217/pgs.14.102.
13. Mooney, S. (2014). Progress towards the integration of pharmacogenomics in practice. Hum. Genet. doi: 10.1007/s00439-014-1484-7 [Epub ahead ofprint].
14. Motsinger-Reif, A. A., Jorgenson, E., Relling, M. V., Kroetz, D. L., Weinshil-boum, R., Cox, N. J., et al. (2013). Genome-wide association studies in pharmacogenomics: successes and lessons. Pharmacogenet. Genomics 23, 383-394. doi: 10.1097/FPC.0b013e32833d7b45.
15. Nekrutenko, A., and Taylor, J. (2012). Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat. Rev. Genet. 13, 667-672. doi: 10.1038/nrg3305.
16. Nelson, M. R., Wegmann, D., Ehm, M. G., Kessner, D., St Jean, P., Verzilli, C., et al. (2012). An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people. Science 337, 100-104. doi: 10.1126/science.1217876.
17. Neuraz, A., Chouchana, L., Malamut, G., Le Beller, C., Roche, D., Beaune, P., et al. (2013). Phe-nome-wide association studies on a quantitative trait: application to TPMT enzyme activity and thiopurine therapy in pharmacog-enomics. PLoS Comput. Biol. 9:e1003405. doi: 10.1371/journal.pcbi.1003405.
18. Pavlopoulos, G. A., Oulas, A., Iacucci, E., Sifrim, A., Moreau, Y., Schneider, R., et al. (2013). Unraveling genomic variation from next generation sequencing data. BioData Min. 6, 13-25. doi: 10.1186/1756-0381-6-13.
19. Potamias, G., Lakiotaki, K., Katsila, T., Lee, M. T., Topouzis, S., Cooper, D. N., et al. (2014). Deciphering next-generation pharmacogenomics: an information technology perspective. Open Biol. 4, 140071. doi: 10.1098/rsob.140071.
20. Price, M. J., Carson, A. R., Murray, S. S., Phillips, T., Janel, L., Tisch, R., et al. (2012). First pharmacogenomic analysis using whole exome sequencing to identify novel genetic determinants of clopidogrel response variability: results of the genotype information and functional testing (gift) exome study. J. Am. Coll. Cardiol. 59, E9. doi: 10.1016/S0735-1097(12)60010-2.
21. Rasmussen-Torvik, L. J., Stallings, S. C., Gordon, A. S., Almoguera, B., Basford, M. A., Bielinski, S. J., et al. (2014). Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems. Clin. Pharmacol. Ther. 96, 482-489. doi: 10.1038/clpt.2014.137.
22. Sheridan, C. (2014). Milestone approval lifts Illumina's NGS from research into clinic. Nat. Biotechnol. 32, 111-112. doi: 10.1038/nbt0214-111.
23. Squassina, A., Manchia, M., Manolopoulos, V. G., Artac, M., Lappa-Manakou, C., Karkabouna, S., et al. (2010). Realities and expectations of pharmacogenomics and personalized medicine: impact of translating genetic knowledge into clinical practice. Pharmacogenomics 11, 1149-1167. doi: 10.2217/pgs.10.97.
24. Wang, L., and Weinshilboum, R. M. (2008). Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum. Mol. Genet. 17, R174-R179. doi: 10.1093/hmg/ddn270.