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WASP: allele-specific software for robust molecular quantitative trait locus discovery

https://doi.org/10.1038/nmeth.3582
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/gepi.21846openalex-snapshot
Comparing Computational Methods for Identification of Allele‐Specific Expression based on Next Generation Sequencing Data
inferredcites →https://doi.org/10.1038/msb.2011.54openalex-snapshot
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
inferredcites →https://doi.org/10.1038/nature08872openalex-snapshot
Understanding mechanisms underlying human gene expression variation with RNA sequencing
inferredcites →https://doi.org/10.1038/nature08903openalex-snapshot
Transcriptome genetics using second generation sequencing in a Caucasian population
inferredcites →https://doi.org/10.1038/nature10808openalex-snapshot
DNase I sensitivity QTLs are a major determinant of human expression variation
inferredcites →https://doi.org/10.1038/nature12531openalex-snapshot
Transcriptome and genome sequencing uncovers functional variation in humans
inferredcites →https://doi.org/10.1038/nbt.2450openalex-snapshot
Differential analysis of gene regulation at transcript resolution with RNA-seq
inferredcites →https://doi.org/10.1038/nmeth.1528openalex-snapshot
Analysis and design of RNA sequencing experiments for identifying isoform regulation
inferredcites →https://doi.org/10.1038/nmeth.2251openalex-snapshot
Streaming fragment assignment for real-time analysis of sequencing experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp579openalex-snapshot
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu802openalex-snapshot
QuASAR: quantitative allele-specific analysis of reads
inferredcites →https://doi.org/10.1093/nar/gks001openalex-snapshot
Summarizing and correcting the GC content bias in high-throughput sequencing
inferredcites →https://doi.org/10.1101/gr.119784.110openalex-snapshot
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
inferredcites →https://doi.org/10.1111/j.1541-0420.2011.01654.xopenalex-snapshot
A Statistical Framework for eQTL Mapping Using RNA‐seq Data
inferredcites →https://doi.org/10.1126/science.1242429openalex-snapshot
Identification of Genetic Variants That Affect Histone Modifications in Human Cells
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
inferredcites →https://doi.org/10.1186/gb-2011-12-2-r13openalex-snapshot
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
inferredcites →https://doi.org/10.1186/s13059-014-0467-2openalex-snapshot
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and function in human neurons
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Promoter shape varies across populations and affects promoter evolution and expression noise
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Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression
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Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
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Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age
inferred← citeshttps://doi.org/10.1038/s41467-020-14404-yopenalex-snapshot
Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations
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Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture
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Chromatin information content landscapes inform transcription factor and DNA interactions
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A scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction
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Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
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Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease
inferred← citeshttps://doi.org/10.1038/s41467-021-23544-8openalex-snapshot
Replicate sequencing libraries are important for quantification of allelic imbalance
inferred← citeshttps://doi.org/10.1038/s41467-021-24824-zopenalex-snapshot
Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization
inferred← citeshttps://doi.org/10.1038/s41467-022-32972-zopenalex-snapshot
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
inferred← citeshttps://doi.org/10.1038/s41467-022-35389-wopenalex-snapshot
CRISPR-based targeted haplotype-resolved assembly of a megabase region
inferred← citeshttps://doi.org/10.1038/s41467-023-35833-5openalex-snapshot
Epigenomic charting and functional annotation of risk loci in renal cell carcinoma
inferred← citeshttps://doi.org/10.1038/s41467-023-40616-zopenalex-snapshot
A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus
inferred← citeshttps://doi.org/10.1038/s41467-024-44710-8openalex-snapshot
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data
inferred← citeshttps://doi.org/10.1038/s41467-024-44935-7openalex-snapshot
Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle
inferred← citeshttps://doi.org/10.1038/s41467-024-45133-1openalex-snapshot
The dynamic genetic determinants of increased transcriptional divergence in spermatids
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Complex regulatory networks influence pluripotent cell state transitions in human iPSCs
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Author Correction: Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle
inferred← citeshttps://doi.org/10.1038/s41467-024-49923-5openalex-snapshot
Multi-omic characterization of allele-specific regulatory variation in hybrid pigs
inferred← citeshttps://doi.org/10.1038/s41467-024-53449-1openalex-snapshot
Population variability in X-chromosome inactivation across 10 mammalian species
inferred← citeshttps://doi.org/10.1038/s41467-024-54110-7openalex-snapshot
A landscape of X-inactivation during human T cell development
inferred← citeshttps://doi.org/10.1038/s41467-024-54448-yopenalex-snapshot
A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping
inferred← citeshttps://doi.org/10.1038/s41467-024-55513-2openalex-snapshot
Statistical framework for calling allelic imbalance in high-throughput sequencing data
inferred← citeshttps://doi.org/10.1038/s41467-025-55900-3openalex-snapshot
Genetic coupling of enhancer activity and connectivity in gene expression control
inferred← citeshttps://doi.org/10.1038/s41467-025-61669-2openalex-snapshot
Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk
inferred← citeshttps://doi.org/10.1038/s41467-025-61870-3openalex-snapshot
Comprehensive resolution and classification of the Epstein Barr virus transcriptome
inferred← citeshttps://doi.org/10.1038/s41467-025-62884-7openalex-snapshot
Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone production
inferred← citeshttps://doi.org/10.1038/s41467-026-68428-xopenalex-snapshot
Dynamic allele usage of X-linked genes ameliorates neurodevelopmental disease phenotypes in brain organoids
inferred← citeshttps://doi.org/10.1038/s41467-026-70419-xopenalex-snapshot
Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits
inferred← citeshttps://doi.org/10.1038/s41467-026-72392-xopenalex-snapshot
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
inferred← citeshttps://doi.org/10.1038/s41556-022-00996-8openalex-snapshot
The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A
inferred← citeshttps://doi.org/10.1038/s41586-021-03211-0openalex-snapshot
Systematic analysis of binding of transcription factors to noncoding variants
inferred← citeshttps://doi.org/10.1038/s41586-021-03343-3openalex-snapshot
Primate cell fusion disentangles gene regulatory divergence in neurodevelopment
inferred← citeshttps://doi.org/10.1038/s41586-021-03577-1openalex-snapshot
Enhancer release and retargeting activates disease-susceptibility genes
inferred← citeshttps://doi.org/10.1038/s41586-025-09486-xopenalex-snapshot
PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia
inferred← citeshttps://doi.org/10.1038/s41586-026-10798-9openalex-snapshot
An expanded codebook of human transcription factor DNA-binding specificity
inferred← citeshttps://doi.org/10.1038/s41586-026-11053-xopenalex-snapshot
The gene-regulatory evolution of the human skeleton
inferred← citeshttps://doi.org/10.1038/s41586-026-11078-2openalex-snapshot
Population-scale immune multiome atlas reveals regulatory disease mechanisms
inferred← citeshttps://doi.org/10.1038/s41588-017-0004-9openalex-snapshot
Annotation-free quantification of RNA splicing using LeafCutter
inferred← citeshttps://doi.org/10.1038/s41588-018-0092-1openalex-snapshot
Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights
inferred← citeshttps://doi.org/10.1038/s41588-018-0173-1openalex-snapshot
Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells
inferred← citeshttps://doi.org/10.1038/s41588-018-0195-8openalex-snapshot
Integrative detection and analysis of structural variation in cancer genomes
inferred← citeshttps://doi.org/10.1038/s41588-018-0238-1openalex-snapshot
Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility
inferred← citeshttps://doi.org/10.1038/s41588-019-0455-2openalex-snapshot
High-throughput identification of human SNPs affecting regulatory element activity
inferred← citeshttps://doi.org/10.1038/s41588-019-0499-3openalex-snapshot
Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits
inferred← citeshttps://doi.org/10.1038/s41588-019-0505-9openalex-snapshot
Landscape of stimulation-responsive chromatin across diverse human immune cells
inferred← citeshttps://doi.org/10.1038/s41588-020-0579-4openalex-snapshot
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci
inferred← citeshttps://doi.org/10.1038/s41588-020-0644-zopenalex-snapshot
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability
inferred← citeshttps://doi.org/10.1038/s41588-021-00804-3openalex-snapshot
Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution
inferred← citeshttps://doi.org/10.1038/s41588-021-00823-0openalex-snapshot
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk
inferred← citeshttps://doi.org/10.1038/s41588-021-00863-6openalex-snapshot
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains
inferred← citeshttps://doi.org/10.1038/s41588-021-00955-3openalex-snapshot
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
inferred← citeshttps://doi.org/10.1038/s41588-022-01075-2openalex-snapshot
Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms
inferred← citeshttps://doi.org/10.1038/s41588-022-01149-1openalex-snapshot
Genetics of the human microglia regulome refines Alzheimer’s disease risk loci
inferred← citeshttps://doi.org/10.1038/s41588-022-01154-4openalex-snapshot
Genetic control of RNA splicing and its distinct role in complex trait variation
inferred← citeshttps://doi.org/10.1038/s41588-022-01168-yopenalex-snapshot
Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation
inferred← citeshttps://doi.org/10.1038/s41588-023-01397-9openalex-snapshot
Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes
inferred← citeshttps://doi.org/10.1038/s41588-023-01506-8openalex-snapshot
Functional characterization of Alzheimer’s disease genetic variants in microglia
inferred← citeshttps://doi.org/10.1038/s41588-024-01682-1openalex-snapshot
Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
inferred← citeshttps://doi.org/10.1038/s41588-024-01776-wopenalex-snapshot
Genotype × environment interactions in gene regulation and complex traits
inferred← citeshttps://doi.org/10.1038/s41588-024-01872-xopenalex-snapshot
Global impact of unproductive splicing on human gene expression
inferred← citeshttps://doi.org/10.1038/s41588-024-01904-6openalex-snapshot
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function
inferred← citeshttps://doi.org/10.1038/s41588-025-02249-4openalex-snapshot
Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression
inferred← citeshttps://doi.org/10.1038/s41591-019-0579-zopenalex-snapshot
Genome-wide germline correlates of the epigenetic landscape of prostate cancer
inferred← citeshttps://doi.org/10.1038/s41591-024-03040-4openalex-snapshot
Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment
inferred← citeshttps://doi.org/10.1038/s41592-022-01731-9openalex-snapshot
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
inferred← citeshttps://doi.org/10.1038/s41593-021-00858-wopenalex-snapshot
Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation
inferred← citeshttps://doi.org/10.1038/s41593-024-01773-6openalex-snapshot
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
inferred← citeshttps://doi.org/10.1038/s41593-025-02020-2openalex-snapshot
Alzheimer’s disease transcriptional landscape in ex vivo human microglia
inferred← citeshttps://doi.org/10.1038/s41593-025-02081-3openalex-snapshot
The neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development
inferred← citeshttps://doi.org/10.1038/s41593-025-02112-zopenalex-snapshot
Multi-region m6A epitranscriptome profiling of the human brain reveals spatial and temporal variation and enrichment of disease-associated loci
inferred← citeshttps://doi.org/10.1038/s41594-019-0187-0openalex-snapshot
Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase
inferred← citeshttps://doi.org/10.1038/s41594-025-01655-wopenalex-snapshot
Interactions between the genome and the nuclear lamina are multivalent and cooperative
inferred← citeshttps://doi.org/10.1038/s41598-017-06516-1openalex-snapshot
Novel risk genes for systemic lupus erythematosus predicted by random forest classification
inferred← citeshttps://doi.org/10.1038/s41598-017-16550-8openalex-snapshot
Rare non-coding variants are associated with plasma lipid traits in a founder population
inferred← citeshttps://doi.org/10.1038/s41598-019-42815-5openalex-snapshot
Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method
inferred← citeshttps://doi.org/10.1038/s41598-024-73743-8openalex-snapshot
Characterizing the allele-specific gene expression landscape in high hyperdiploid acute lymphoblastic leukemia with BASE
inferred← citeshttps://doi.org/10.1038/s41598-025-96248-4openalex-snapshot
Active regulatory elements recruit cohesin to establish cell specific chromatin domains
inferred← citeshttps://doi.org/10.1038/s42003-018-0267-4openalex-snapshot
Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree
inferred← citeshttps://doi.org/10.1038/s42003-022-04344-2openalex-snapshot
Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines
inferred← citeshttps://doi.org/10.1038/s42003-024-06050-7openalex-snapshot
Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits
inferred← citeshttps://doi.org/10.1038/s42003-026-09596-wopenalex-snapshot
Molecular QTL are enriched for structural variants in a cattle long-read cohort
inferred← citeshttps://doi.org/10.1038/s43586-022-00188-6openalex-snapshot
Molecular quantitative trait loci
inferred← citeshttps://doi.org/10.1038/s43588-021-00087-yopenalex-snapshot
Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL
inferred← citeshttps://doi.org/10.1038/s44161-025-00714-1openalex-snapshot
Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression
inferred← citeshttps://doi.org/10.1038/srep46203openalex-snapshot
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
inferred← citeshttps://doi.org/10.1055/s-0044-1787948openalex-snapshot
Differential Expression Analyses on Aortic Tissue reveal Novel Genes and Pathways Associated with Abdominal Aortic Aneurysm Onset and Progression
inferred← citeshttps://doi.org/10.1073/pnas.1621192114openalex-snapshot
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes
inferred← citeshttps://doi.org/10.1073/pnas.1810568115openalex-snapshot
Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics
inferred← citeshttps://doi.org/10.1073/pnas.2006474118openalex-snapshot
Parental bias in expression and interaction of genes in the equine placenta
inferred← citeshttps://doi.org/10.1073/pnas.2206612120openalex-snapshot
Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits
inferred← citeshttps://doi.org/10.1073/pnas.2214614120openalex-snapshot
Environmentally robust cis -regulatory changes underlie rapid climatic adaptation
inferred← citeshttps://doi.org/10.1073/pnas.2322924121openalex-snapshot
Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington’s disease
inferred← citeshttps://doi.org/10.1089/thy.2016.0009openalex-snapshot
Demonstration of Autosomal Monoallelic Expression in Thyroid Tissue Assessed by Whole-Exome and Bulk RNA Sequencing
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