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PMID: 17966091 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Pathway-based approaches for analysis of genomewide association studies.

American journal of human genetics ·Vol. 81 ·No. 6 ·2007-12-00 ·Pages 1278-83

Wang K, Li M, Bucan M

Abstract

Published genomewide association (GWA) studies typically analyze and report single-nucleotide polymorphisms (SNPs) and their neighboring genes with the strongest evidence of association (the "most-significant SNPs/genes" approach), while paying little attention to the rest. Borrowing ideas from microarray data analysis, we demonstrate that pathway-based approaches, which jointly consider multiple contributing factors in the same pathway, might complement the most-significant SNPs/genes approach and provide additional insights into interpretation of GWA data on complex diseases.

MeSH Terms
Algorithms Genes/genetics Genetic Predisposition to Disease Genome-Wide Association Study Humans Models, Genetic Polymorphism, Single Nucleotide/genetics Research Design Signal Transduction
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Wang Kai
Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. kai@mail.med.upenn.edu
Li Mingyao
Bucan Maja
References (26)
26 references, click to expand
  1. Glutamate receptors and Parkinson's disease: opportunities for intervention.
    Drugs Aging. 2003;20(5):377-97 PMID: 12696997
  2. Assessing the probability that a positive report is false: an approach for molecular epidemiology studies.
    J Natl Cancer Inst. 2004 Mar 17;96(6):434-42 PMID: 15026468
  3. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  4. Does O-GlcNAc play a role in neurodegenerative diseases?
    Expert Rev Proteomics. 2005 Apr;2(2):265-75 PMID: 15892570
  5. O-Glycosylation in sprouting neurons in Alzheimer disease, indicating reactive plasticity.
    J Neuropathol Exp Neurol. 2001 May;60(5):441-8 PMID: 11379819
  6. Human genetics: variants in common diseases.
    Nature. 2007 Feb 22;445(7130):828-30 PMID: 17293879
  7. Pathways to the analysis of microarray data.
    Trends Biotechnol. 2005 Aug;23(8):429-35 PMID: 15950303
  8. Ranks of genuine associations in whole-genome scans.
    Genetics. 2005 Oct;171(2):813-23 PMID: 16020784
  9. Overview: ABC transporters and human disease.
    J Bioenerg Biomembr. 2001 Dec;33(6):453-8 PMID: 11804186
  10. Complement factor H polymorphism in age-related macular degeneration.
    Science. 2005 Apr 15;308(5720):385-9 PMID: 15761122
  11. Identifying differentially expressed genes using false discovery rate controlling procedures.
    Bioinformatics. 2003 Feb 12;19(3):368-75 PMID: 12584122
  12. Functional expression and localization of P-glycoprotein in the central nervous system: relevance to the pathogenesis and treatment of neurological disorders.
    Pharm Res. 2004 Aug;21(8):1313-30 PMID: 15359566
  13. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  14. Evaluating and improving power in whole-genome association studies using fixed marker sets.
    Nat Genet. 2006 Jun;38(6):663-7 PMID: 16715096
  15. The future of genetic studies of complex human diseases.
    Science. 1996 Sep 13;273(5281):1516-7 PMID: 8801636
  16. Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data.
    Lancet Neurol. 2006 Nov;5(11):911-6 PMID: 17052657
  17. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
    Nat Genet. 2003 Jul;34(3):267-73 PMID: 12808457
  18. High-resolution whole-genome association study of Parkinson disease.
    Am J Hum Genet. 2005 Nov;77(5):685-93 PMID: 16252231
  19. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  20. A note on exact tests of Hardy-Weinberg equilibrium.
    Am J Hum Genet. 2005 May;76(5):887-93 PMID: 15789306
  21. Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins.
    Nature. 2007 Apr 26;446(7139):1017-22 PMID: 17460662
  22. Using linkage genome scans to improve power of association in genome scans.
    Am J Hum Genet. 2006 Feb;78(2):243-52 PMID: 16400608
  23. Glutamate and Parkinson's disease.
    Mol Neurobiol. 1996 Feb;12(1):73-94 PMID: 8732541
  24. Ensembl 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7 PMID: 17148474
  25. Resampling-based multiple hypothesis testing procedures for genetic case-control association studies.
    Genet Epidemiol. 2006 Sep;30(6):495-507 PMID: 16755536
  26. Sum statistics for the joint detection of multiple disease loci in case-control association studies with SNP markers.
    Genet Epidemiol. 2003 Dec;25(4):350-9 PMID: 14639704
Article Info
Journal
American journal of human genetics
Abbr.
Am J Hum Genet
ISSN
1537-6605
DOI
10.1086/522374
Email
kai@mail.med.upenn.edu
Published
2007-12-00
Pages
1278-83
Language
English
Region
United States
NLM ID
0370475
PMCID
PMC2276352
Subset
IM
Grants
NIMH NIH HHS · R01-MH604687 · United States
External Links
PubMed source DOI: 10.1086/522374 PMC Full Text View journal details
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