ArticleBioinformatics (Oxford, England)2016
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.
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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
5 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Genetic Influences on Initial Alcohol Sensitivity.Alcoholism, clinical and experimental research · 2018Pooled it
- GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts.Bioinformatics (Oxford, England) · 2024Article
- Increasing the resolution and precision of psychiatric genome-wide association studies by re-imputing summary statistics using a large, diverse reference panel.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2021Review
- JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.Bioinformatics (Oxford, England) · 2018Article
- Integrative Post-Genome-Wide Association Study Analyses Relevant to Psychiatric Disorders: Imputing Transcriptome and Proteome Signals.Complex psychiatryReview
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
motivationTo increase detection power, gene level analysis methods are used to aggregate weak signals. To greatly increase computational efficiency, most methods use as input summary statistics from genome-wide association studies (GWAS). Subsequently, gene statistics are constructed using linkage disequilibrium (LD) patterns from a relevant reference panel. However, all methods, including our own Joint Effect on Phenotype of eQTL/functional single nucleotide polymorphisms (SNPs) associated with a Gene (JEPEG), assume homogeneous panels, e.g. European. However, this renders these tools unsuitable for the analysis of large cosmopolitan cohorts.
resultsWe propose a JEPEG extension, JEPEGMIX, which similar to one of our software tools, Direct Imputation of summary STatistics of unmeasured SNPs from MIXed ethnicity cohorts, is capable of estimating accurate LD patterns for cosmopolitan cohorts. JEPEGMIX uses this accurate LD estimates to (i) impute the summary statistics at unmeasured functional variants and (ii) test for the joint effect of all measured and imputed functional variants which are associated with a gene. We illustrate the performance of our tool by analyzing the GWAS meta-analysis summary statistics from the multi-ethnic Psychiatric Genomics Consortium Schizophrenia stage 2 cohort. This practical application supports the immune system being one of the main drivers of the process leading to schizophrenia. AVAILABILITY AND IMPLEMENTATION: Software, annotation database and examples are available at http://dleelab.github.io/jepegmix/. CONTACT: donghyung.lee@vcuhealth.org SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.
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Registered trials
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