Phenome-wide association studies (PheWASs) for functional variants

European Journal of Human Genetics

Volumn 23, Issue 4, 2015, Pages 523-529

  Ye, Zhan ^a   Mayer, John ^a   Ivacic, Lynn ^a   Zhou, Zhiyi ^b   He, Min ^a   Schrodi, Steven J ^a   Page, David ^c   Brilliant, Murray H ^a   Hebbring, Scott J ^a,c  

^a MARSHFIELD CLINIC   (United States)

^b PARKLAND HEALTH AND HOSPITAL SYSTEM   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGE RELATED MACULAR DEGENERATION; AGED; ARTICLE; DISEASE ASSOCIATION; EFFECT SIZE; FEMALE; GENETIC ASSOCIATION; GENETIC PARAMETERS; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; NONSENSE MUTATION; PHENOME WIDE ASSOCIATION STUDY; PHENOTYPE; PLEIOTROPY; PRIORITY JOURNAL; REVERSE GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY; ELECTRONIC HEALTH RECORD; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MACULAR DEGENERATION; PROCEDURES; REPRODUCIBILITY;

ARMS2 PROTEIN, HUMAN; PROTEIN;

DATABASES, GENETIC; ELECTRONIC HEALTH RECORDS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MACULAR DEGENERATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 84924726240     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.123     Document Type: Article

References (30)

1. Hebbring SJ: The challenges, advantages, and future of phenome-wide association studies. Immunology 2013; 141: 157-165.
2. Hindorff LA, MacArthur J, Morales J et al: A catalog of published genome-wide association studies. Available at: www.genome.gov/gwastudies. Accessed 24 July 2013.
3. U.S. Department of Health and Human Services: improving the health, safety, and well-being of America 2008. Available at: http://www.hhs.gov/news/press/2008pres/08/20080815a.html. Accessed 9 September 2013.
4. Denny JC, Ritchie MD, Basford MA et al: PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics 2010; 26: 1205-1210.
5. Denny JC, Bastarache L, Ritchie MD et al: Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol 2013; 31: 1102-1110.
6. Hebbring SJ, Schrodi SJ, Ye Z et al: A PheWAS approach in studying HLA-DRB1∗1501. Genes Immun 2013; 14: 187-191.
7. Pendergrass SA, Brown-Gentry K, Dudek S et al: Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet 2013; 9: e1003087.
8. Liao KP, Kurreeman F, Li G et al: Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis Rheum 2013; 65: 571-581.
9. Kervestin S, Jacobson A: NMD: a multifaceted response to premature translational termination. Nature Rev Mol Cell Biol 2012; 13: 700-712.
10. Chen R, Davydov EV, Sirota M, Butte AJ: Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One 2010; 5: e13574.
11. Stenson PD, Mort M, Ball EV et al: The Human Gene Mutation Database: 2008 updateGenome Med 2009; 1: 13.
12. Abecasis GR, Altshuler D, Auton A et al: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-1073.
13. McCarty CA, Wilke RA, Giampetro PF, Wesbrook SD, Caldwell MD: Marshfield Clinic Personalized Medicine Research Project (PMRP): design, methods and recruitment for a large population-based biobank. Personalized Med 2005; 2: 49-79.
14. McCarty CA, Chisholm RL, Chute CG et al: The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genomics 2011; 4: 13.
15. Turner SD, Berg RL, Linneman JG et al: Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS One 2011; 6: e19586.
16. Thomas GP, Brown MA: Genetics and genomics of ankylosing spondylitis. Immunol Rev 2010; 233: 162-180.
17. Wistuba II, Gazdar AF: Gallbladder cancer: lessons from a rare tumour. Nat Rev Cancer 2004; 4: 695-706.
18. Gudbjartsson DF, Holm H, Gretarsdottir S et al: A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke. Nat Genet 2009; 41: 876-878.
19. Gudbjartsson DF, Arnar DO, Helgadottir A et al: Variants conferring risk of atrial fibrillation on chromosome 4q25. Nature 2007; 448: 353-357.
20. Gretarsdottir S, Thorleifsson G, Manolescu A et al: Risk variants for atrial fibrillation on chromosome 4q25 associate with ischemic stroke. Ann Neurol 2008; 64: 402-409.
21. Dewan A, Liu M, Hartman S et al: HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 2006; 314: 989-992.
22. Yu W, Dong S, Zhao C et al: Cumulative association between age-related macular degeneration and less studied genetic variants in PLEKHA1/ARMS2/HTRA1: a meta and gene-cluster analysis. Mol Biol Rep 2013; 40: 5551-5561.
23. Denny JC, Crawford DC, Ritchie MD et al: Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome-and phenome-wide studies. Am J Hum Genet 2011; 89: 529-542.
24. Ritchie MD, Denny JC, Zuvich RL et al: Genome-and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation 2013; 127: 1377-1385.
25. Shameer K, Denny JC, Ding K et al: A genome-and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Hum Genet 2013; 133: 95-109.
26. s: McKusick-Nathans Institute of Genetic Medicine. Baltimore, MD: Johns Hopkins University, 2013. Available at: https://omim.org/. Accessed 1 September 2013.
27. MacArthur DG, Balasubramanian S, Frankish A et al: A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012; 335: 823-828.
28. Gorden NT, Arts HH, Parisi MA et al: CC2D2A is mutated in Joubert syndrome and interacts with the ciliopathy-associated basal body protein CEP290. Am J Hum Genet 2008; 83: 559-571.
29. Dick DM, Aliev F, Krueger RF et al: Genome-wide association study of conduct disorder symptomatology. Mol Psychiatry 2011; 16: 800-808.
30. Centers for Medicare and Medicaid Services: ICD-10. Baltimore (MD): CMS.gov. 2010. Available at: http://www.cms.gov/Medicare/Coding/ICD10/index.html?redirect=/icd10. Accessed 9 September 2013.