ArticlePLoS computational biology2016
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 202 papers, 17 of them syntheses that pooled it.
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Who cites it
202 citing papers in PubMed, 17 syntheses or guidelines pooled it.
- Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis.Nature communications · 2023Pooled it
- Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease.Diabetologia · 2022Pooled it
- Potential Pleiotropic Genes and Shared Biological Pathways in Epilepsy and Depression Based on GWAS Summary Statistics.Computational intelligence and neuroscience · 2022Pooled it
- Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology.Nature genetics · 2021Pooled it
- Pooled it
- Genetic factors affect the susceptibility to bacterial infections in diabetes.Scientific reports · 2021Pooled it
- Genome-wide association study on coronary artery disease in type 1 diabetes suggests beta-defensin 127 as a risk locus.Cardiovascular research · 2021Pooled it
- Common variants in SOX-2 and congenital cataract genes contribute to age-related nuclear cataract.Communications biology · 2020Pooled it
- A large-scale genome-wide association study meta-analysis of cannabis use disorder.The lancet. Psychiatry · 2020Pooled it
- A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.Frontiers in genetics · 2020Pooled it
- Genome-wide association study identifies 14 previously unreported susceptibility loci for adolescent idiopathic scoliosis in Japanese.Nature communications · 2019Pooled it
- Genome-wide association analysis of self-reported daytime sleepiness identifies 42 loci that suggest biological subtypes.Nature communications · 2019Pooled it
- A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis.Nature communications · 2019Pooled it
- Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.Nature genetics · 2019Pooled it
- Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use.Nature genetics · 2019Pooled it
- Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus.Arthritis research & therapy · 2018Pooled it
- A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations.PLoS genetics · 2016Pooled it
- Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain.Neurogenetics · 2020Trial
- Identification of comprehensive genetic factors, pathways, and shared genetic architecture of putamen volume in adolescent cohort.Translational psychiatry · 2026Article
- Integration of genetic evidence to identify approved drug targets.Genome medicine · 2026Article
142 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries.
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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.