GATES: a rapid and powerful gene-based association test using extended Simes procedure.
paper
Cited
Public
Unavailable
- Authors
- Li, Miao-Xin; Gui, Hong-Sheng; Kwan, Johnny S H; Sham, Pak C
- Year
- 2011
- Journal
- American journal of human genetics
- PMID
- 21397060
- DOI
- 10.1016/j.ajhg.2011.01.019
- PMCID
- PMC3059433
The gene has been proposed as an attractive unit of analysis for association studies, but a simple yet valid, powerful, and sufficiently fast method of evaluating the statistical significance of all genes in large, genome-wide datasets has been lacking. Here we propose the use of an extended Simes test that integrates functional information and association evidence to combine the p values of the single nucleotide polymorphisms within a gene to obtain an overall p value for the association of the entire gene. Our computer simulations demonstrate that this test is more powerful than the SNP-based test, offers effective control of the type 1 error rate regardless of gene size and linkage-disequilibrium pattern among markers, and does not need permutation or simulation to evaluate empirical significance. Its statistical power in simulated data is at least comparable, and often superior, to that of several alternative gene-based tests. When applied to real genome-wide association study (GWAS) datasets on Crohn disease, the test detected more significant genes than SNP-based tests and alternative gene-based tests. The proposed test, implemented in an open-source package, has the potential to identify additional novel disease-susceptibility genes for complex diseases from large GWAS datasets.
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| Missense Variant in MAPK Inactivator PTPN5 Is Associated with Decreased Severity of Post-Burn Hypertrophic Scarring. | Sood RF et al. | β | 2016 | β |
| Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle. | Zhang W et al. | β | 2016 | β |
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| Novel genetic loci underlying human intracranial volume identified through genome-wide association. | Adams HH et al. | β | 2016 | β |
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| The CHRM3 gene is implicated in abnormal thalamo-orbital frontal cortex functional connectivity in first-episode treatment-naive patients with schizophrenia. | Wang Q et al. | β | 2016 | β |
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| GWAS of longitudinal amyloid accumulation on 18F-florbetapir PET in Alzheimer's disease implicates microglial activation gene IL1RAP. | Ramanan VK et al. | β | 2015 | β |
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