ArticleBioinformatics (Oxford, England)2015
DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 2 of them syntheses that pooled it.
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Who cites it
18 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-Analysis of Associations Between Hypothalamic-Pituitary-Adrenal Axis Genes and Risk of Posttraumatic Stress Disorder.Journal of traumatic stress · 2020Pooled it
- Japanese GWAS identifies variants for bust-size, dysmenorrhea, and menstrual fever that are eQTLs for relevant protein-coding or long non-coding RNAs.Scientific reports · 2018Pooled it
- Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations.Scientific reports · 2018Trial
- PRED-LD: efficient imputation of GWAS summary statistics.BMC bioinformatics · 2025Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- 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
- ZMIX: estimating ancestry proportions using GWAS association Z-scores.Bioinformatics advances · 2024Article
- KOMPUTE: imputing summary statistics of missing phenotypes in high-throughput model organism data.Bioinformatics advances · 2023Article
- 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
- TWAS pathway method greatly enhances the number of leads for uncovering the molecular underpinnings of psychiatric disorders.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2020Article
- Overcoming the challenges of imputation of rare variants in a Taiwanese cohort.Translational cancer research · 2020Article
- Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts.Bioinformatics (Oxford, England) · 2018Article
- Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region.Scientific reports · 2018Article
- Dissecting the genetics of complex traits using summary association statistics.Nature reviews. Genetics · 2017Review
- Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.BioData mining · 2017Article
- A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans.Bioinformatics (Oxford, England) · 2016Article
- Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation.PLoS genetics · 2016Article
- JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationTo increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts.
resultsTo decrease computational and access requirements for the analysis of cosmopolitan cohorts, we propose DISTMIX, which extends DIST capabilities to the analysis of mixed ethnicity cohorts. The method uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistics at measured SNPs and estimated/user-specified ethnic proportions. Simulations show that the proposed method adequately controls the Type I error rates. The 1000 Genomes panel imputation of summary statistics from the ethnically diverse Psychiatric Genetic Consortium Schizophrenia Phase 2 suggests that, when compared to genotype imputation methods, DISTMIX offers comparable imputation accuracy for only a fraction of computational resources. AVAILABILITY AND IMPLEMENTATION: DISTMIX software, its reference population data, and usage examples are publicly available at http://code.google.com/p/distmix. CONTACT: dlee4@vcu.edu SUPPLEMENTARY INFORMATION: Supplementary Data are available at Bioinformatics online.
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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.