SynthesisPLoS genetics2016
A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations.
Synthesis in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 4 of them syntheses that pooled it.
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Who cites it
31 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Pathway Analysis of Renal Cell Carcinoma Genome-Wide Association Studies Identifies Novel Associations.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020Pooled it
- Genetic polymorphisms of IL17A associated with Chagas disease: results from a meta-analysis in Latin American populations.Scientific reports · 2020Pooled it
- Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer.Journal of the National Cancer Institute · 2019Pooled it
- Circadian pathway genetic variation and cancer risk: evidence from genome-wide association studies.BMC medicine · 2018Pooled it
- Identification of immune cell type-specific susceptibility genes in multiple cancers using transcriptome-wide association studies.Journal of the National Cancer Institute · 2026Article
- Different diabetes types and pancreatic ductal adenocarcinoma: a Mendelian randomization and pathway/gene-set analysis.Journal of the National Cancer Institute · 2026Article
- A comprehensive framework for trans-ancestry pathway analysis using GWAS summary data from diverse populations.PLoS genetics · 2024Article
- Article
- Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease.World journal of hepatology · 2024Review
- Shared and distinct genetic etiologies for different types of clonal hematopoiesis.Nature communications · 2023Article
- A multivariate genome-wide association study of psycho-cardiometabolic multimorbidity.PLoS genetics · 2023Article
- Integrative analysis of individual-level data and high-dimensional summary statistics.Bioinformatics (Oxford, England) · 2023Article
- Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection.medRxiv : the preprint server for health sciences · 2023Article
- Hepcidin-regulating iron metabolism genes and pancreatic ductal adenocarcinoma: a pathway analysis of genome-wide association studies.The American journal of clinical nutrition · 2021Article
- A powerful subset-based method identifies gene set associations and improves interpretation in UK Biobank.American journal of human genetics · 2021Article
- Identification of genetic variants in mArchives of toxicology · 2021Article
- Genome-Wide Association Study Data Reveal Genetic Susceptibility to Chronic Inflammatory Intestinal Diseases and Pancreatic Ductal Adenocarcinoma Risk.Cancer research · 2020Article
- Article
- Hierarchical structural component model for pathway analysis of common variants.BMC medical genomics · 2020Article
- Understanding Dietary Intervention-Mediated Epigenetic Modifications in Metabolic Diseases.Frontiers in genetics · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs.
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