ArticlePLoS genetics2022
eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Allele-specific expression in the brain links genetic risk and cortical thinning in psychiatric disorders.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Monoallelic expression characterizes a distinct molecular and clinical group of breast tumors.Research square · 2026Article
- Gravitropic Gene Expression Divergence Associated With Adaptation to Contrasting Environments in an Australian Wildflower.Molecular ecology · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- Ornaments for efficient allele-specific expression estimation with bias correction.American journal of human genetics · 2024Article
- eQTL studies: from bulk tissues to single cells.Journal of genetics and genomics = Yi chuan xue bao · 2023Review
- Learning gene networks under SNP perturbation using SNP and allele-specific expression data.bioRxiv : the preprint server for biology · 2023Article
- Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects.Nature communications · 2023Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data.Nature communications · 2023Article
- eQTL Studies: from Bulk Tissues to Single Cells.ArXiv · 2023Article
- Article
- eQTLs as causal instruments for the reconstruction of hormone linked gene networks.Frontiers in endocrinology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP, a computationally efficient method to estimate permutation p-values, which makes it computationally feasible to perform eQTL mapping with ASE counts for large cohorts. We have applied geoP to map eQTLs in 28 human tissues using the data from the Genotype-Tissue Expression (GTEx) project. We demonstrate that using ASE data not only substantially improve the power to detect eQTLs, but also allow us to quantify individual-specific genetic effects, which can be used to study the variation of eQTL effect sizes with respect to other covariates. We also compared two popular methods for eQTL mapping with ASE: TReCASE and RASQUAL. TReCASE is ten times or more faster than RASQUAL and it provides more robust type I error control.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.