ArticleGenetic epidemiology2010
Pathway-based analysis for genome-wide association studies using supervised principal components.
Article in Genetic epidemiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed.
- Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.Genetic epidemiology · 2012Trial
- A review of post-GWAS studies in schizophrenia.Translational psychiatry · 2025Review
- Integrated Systems Analysis Deciphers Transcriptome and Glycoproteome Links in Alzheimer's Disease.bioRxiv : the preprint server for biology · 2024Article
- Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation.Science advances · 2023Article
- Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions.Molecular biology and evolution · 2021Article
- PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data.Proteomics · 2020Article
- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
- Article
- Post genome-wide association analysis: dissecting computational pathway/network-based approaches.Briefings in bioinformatics · 2019Review
- Article
- The Molecular Revolution in Cutaneous Biology: The Era of Genome-Wide Association Studies and Statistical, Big Data, and Computational Topics.The Journal of investigative dermatology · 2017Review
- Gene-based genome-wide association study identified 19p13.3 for lean body mass.Scientific reports · 2017Article
- How far from the SNP may the causative genes be?Nucleic acids research · 2016Article
- A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies.PloS one · 2016Article
- Gene set analysis: A step-by-step guide.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2015Review
- A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants.American journal of human genetics · 2015Article
- Comparison of dimension reduction-based logistic regression models for case-control genome-wide association study: principal components analysis vs. partial least squares.Journal of biomedical research · 2015Article
- A Bayesian approach to identify genes and gene-level SNP aggregates in a genetic analysis of cancer data.Statistics and its interface · 2015Article
- Pathway-based analysis tools for complex diseases: a review.Genomics, proteomics & bioinformatics · 2014Review
- Functional and genomic context in pathway analysis of GWAS data.Trends in genetics : TIG · 2014Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Many complex diseases are influenced by genetic variations in multiple genes, each with only a small marginal effect on disease susceptibility. Pathway analysis, which identifies biological pathways associated with disease outcome, has become increasingly popular for genome-wide association studies (GWAS). In addition to combining weak signals from a number of SNPs in the same pathway, results from pathway analysis also shed light on the biological processes underlying disease. We propose a new pathway-based analysis method for GWAS, the supervised principal component analysis (SPCA) model. In the proposed SPCA model, a selected subset of SNPs most associated with disease outcome is used to estimate the latent variable for a pathway. The estimated latent variable for each pathway is an optimal linear combination of a selected subset of SNPs; therefore, the proposed SPCA model provides the ability to borrow strength across the SNPs in a pathway. In addition to identifying pathways associated with disease outcome, SPCA also carries out additional within-category selection to identify the most important SNPs within each gene set. The proposed model operates in a well-established statistical framework and can handle design information such as covariate adjustment and matching information in GWAS. We compare the proposed method with currently available methods using data with realistic linkage disequilibrium structures, and we illustrate the SPCA method using the Wellcome Trust Case-Control Consortium Crohn Disease (CD) data set.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.