Back to Search
Start Over
Gene- and pathway-based association tests for multiple traits with GWAS summary statistics
- Source :
- Bioinformatics. 33:64-71
- Publication Year :
- 2016
- Publisher :
- Oxford University Press (OUP), 2016.
-
Abstract
- Summary To identify novel genetic variants associated with complex traits and to shed new insights on underlying biology, in addition to the most popular single SNP-single trait association analysis, it would be useful to explore multiple correlated (intermediate) traits at the gene- or pathway-level by mining existing single GWAS or meta-analyzed GWAS data. For this purpose, we present an adaptive gene-based test and a pathway-based test for association analysis of multiple traits with GWAS summary statistics. The proposed tests are adaptive at both the SNP- and trait-levels; that is, they account for possibly varying association patterns (e.g. signal sparsity levels) across SNPs and traits, thus maintaining high power across a wide range of situations. Furthermore, the proposed methods are general: they can be applied to mixed types of traits, and to Z-statistics or P-values as summary statistics obtained from either a single GWAS or a meta-analysis of multiple GWAS. Our numerical studies with simulated and real data demonstrated the promising performance of the proposed methods. Availability and Implementation The methods are implemented in R package aSPU, freely and publicly available at: https://cran.r-project.org/web/packages/aSPU/. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- 0301 basic medicine
Statistics and Probability
Association test
Genome-wide association study
Single-nucleotide polymorphism
Computational biology
Biostatistics
Biology
computer.software_genre
Polymorphism, Single Nucleotide
Biochemistry
03 medical and health sciences
0302 clinical medicine
SNP
Molecular Biology
Gene
030304 developmental biology
Genetic association
0303 health sciences
Genetic Variation
Multiple traits
Original Papers
Summary statistics
Computer Science Applications
Computational Mathematics
030104 developmental biology
Genes
Computational Theory and Mathematics
Data mining
computer
030217 neurology & neurosurgery
Metabolic Networks and Pathways
Software
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 33
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....fc4f033d556c728c78e9f6e131bf081f