Genome-wide approaches in pharmacogenomics: Heritability estimation and pharmacoethnicity as primary challenges

Pharmacogenomics

Volumn 13, Issue 10, 2012, Pages 1101-1104

  Gamazon, Eric R ^a   Perera, Minoli ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

drug; genetics; GWAS; health disparities; heritability; pharmacoethnicity; pharmacogenomics

Indexed keywords

CLOPIDOGREL; CYTOCHROME P450 2C9; IRINOTECAN; WARFARIN;

ALLELE; DRUG RESPONSE; ETHNICITY; GENE CONTROL; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE MAP; HEALTH DISPARITY; HERITABILITY; HUMAN; LOW DRUG DOSE; PHARMACOETHNICITY; PHARMACOGENETICS; PHARMACOGENOMICS; PHENOTYPE; REVIEW; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; THROMBOCYTE AGGREGATION;

BIOMARKERS, PHARMACOLOGICAL; ETHNIC GROUPS; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; PHARMACOGENETICS;

EID: 84865322438     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.12.88     Document Type: Review

References (32)

1. Metzker ML. Sequencing technologies-the next generation. Nat. Rev. Genet. 11(1), 31-46 (2010).
2. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 11(7), 476-486 (2010).
3. Hindorff LA, Sethupathy P, Junkins HA et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106(23), 9362-9367 (2009).
4. Shuldiner AR, O'Connell JR, Bliden KP et al. Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA 302(8), 849-857 (2009).
5. Watters JW, Kraja A, Meucci MA, Province MA, McLeod HL. Genome-wide discovery of loci influencing chemotherapy cytotoxicity. Proc. Natl Acad. Sci. USA 101(32), 11809-11814 (2004). (Pubitemid 39095376)
6. Huang RS, Johnatty SE, Gamazon ER et al. Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients. Clin. Cancer Res. 17(16), 5490-5500 (2011).
7. Mitra AK, Crews KR, Pounds S et al. Genetic variants in cytosolic 5́-nucleotidase II are associated with its expression and cytarabine sensitivity in HapMap cell lines and in patients with acute myeloid leukemia. J. Pharmacol. Exp. Ther. 339(1), 9-23 (2011).
8. 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. 6(4), e1000888 (2010).
9. Gamazon ER, Huang RS, Cox NJ, Dolan ME. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc. Natl Acad. Sci. USA 107(20), 9287-9292 (2010).
10. Nica AC, Montgomery SB, Dimas AS et al. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 6(4), e1000895 (2010).
11. Cheung VG, Conlin LK, Weber TM et al. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet. 33(3), 422-425 (2003). (Pubitemid 36278862)
12. Stranger BE, Nica AC, Forrest MS et al. Population genomics of human gene expression. Nat. Genet. 39(10), 1217-1224 (2007). (Pubitemid 47482691)
13. Huang RS, Duan S, Shukla SJ et al. Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. Am. J. Hum. Genet. 81(3), 427-437 (2007). (Pubitemid 47330203)
14. Gamazon ER, Duan S, Zhang W et al. PACdb: a database for cell-based pharmacogenomics. Pharmacogenet. Genomics 20(4), 269-273 (2010).
15. Dermitzakis ET. Cellular genomics for complex traits. Nat. Rev. Genet. 13(3), 215-220 (2012).
16. Gamazon ER, Skol AD, Perera MA, The limits of genome-wide methods for pharmacogenomic testing. Pharmacogenet. Genomics 22(4), 261-272 (2012).
17. Welsh M, Mangravite L, Medina MW et al. Pharmacogenomic discovery using cell-based models. Pharmacol. Rev. 61(4), 413-429 (2009).
18. Rieder MJ, Reiner AP, Gage BF et al. Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N. Engl. J. Med. 352(22), 2285-2293 (2005). (Pubitemid 40740552)
19. Innocenti F, Undevia SD, Iyer L et al. Genetic variants in the UDP-glucuronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan. J. Clin. Oncol. 22(8), 1382-1388 (2004). (Pubitemid 41103619)
20. Klein TE, Altman RB, Eriksson N et al.; International Warfarin Pharmacogenetics Consortium. Estimation of the warfarin dose with clinical and pharmacogenetic data. N. Engl. J. Med. 360(8), 753-764 (2009).
21. Goldstein DB. Common genetic variation and human traits. N. Engl. J. Med. 360(17), 1696-1698 (2009).
22. Manolio TA, Collins FS, Cox NJ et al. Finding the missing heritability of complex diseases. Nature 461(7265), 747-753 (2009).
23. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol. 8(1), e1000294 (2010).
24. McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE. From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark. Med. 5(6), 795-806 (2011).
25. Purcell SM, Wray NR, Stone JL et al.; International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460(7256), 748-752 (2009).
26. Lee SH, DeCandia TR, Ripke S et al. Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat. Genet. 44(3), 247-250 (2012).
27. Royal CD, Dunston GM. Changing the paradigm from 'race' to human genome variation. Nat. Genet. 36(Suppl. 11), S5-S7 (2004). (Pubitemid 41103830)
28. Sankar P, Cho MK, Condit CM et al. Genetic research and health disparities. JAMA 291(24), 2985-2989 (2004). (Pubitemid 38802688)
29. O'Donnell PH, Dolan ME. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin. Cancer Res. 15(15), 4806-4814 (2009).
30. Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat. Rev. Genet. 11(5), 356-366 (2010).
31. Teo YY, Small KS, Kwiatkowski DP. Methodological challenges of genome-wide association analysis in Africa. Nat. Rev. Genet. 11, 149-160 (2010).
32. Perera MA, Gamazon E, Cavallari LH et al. The missing association: sequencing-based discovery of novel SNPs in VKORC1 and CYP2C9 that affect warfarin dose in African Americans. Clin. Pharmacol. Ther. 89(3), 408-415 (2011).