#5 · Metabolomics
GWAS associations are integrated into genomic and phenotype prediction frameworks
The dominant thread is the use of GWAS-derived information as an input to prediction and prioritization rather than as an end point. GAPIT v4 embeds GWAS results into GBLUP genomic prediction, with BLINK-based GWAS input raising accuracy by over 20% relative to GBLUP alone on a real trait. An exploratory EFGPP framework applies a reproducible pipeline combining genetic, clinical and metabolomic inputs to migraine prediction in UK Biobank, with a best AUC of 0.688. A preprint on the human pleiotropic map of GWAS associations argues that genetic support raises clinical success rates for drug targets, positioning GWAS as central to therapeutic research. ShadowVIMP contributes a permutation-based random forest variable selection method with multiple-testing control that preserves variable correlation structure. The new element across these items is the coupling of association evidence with predictive modeling and explicit error control. The strength of the individual claims varies, and the items are not uniformly comparable.
Published papers
Tandem repeat variation shapes immune cell type-specific gene expression.
Multiomic meta-analysis of 1.7M tandem repeats in 5.4M immune cells maps TR effects on cell-type expression and chromatin.
Rare and common genetic variants shape single-cell immune gene expression.
TenK10K phase 1 maps common and rare variant effects on immune gene expression across 28 cell types in 5M+ single cells.
Genetic variants shape single-cell chromatin accessibility and disease risk.
scATAC-seq of 3.5M PBMCs from 1,042 donors maps caQTLs; a graph neural network links peaks to genes using QTL layers.
VarNexus: an integrative database for interpreting disease-associated regulatory variants through multimodal predictions and functional evidence.
Genome-wide association studies (GWAS) have identified numerous loci associated with complex diseases and traits, yet the functional interpretation of non-codin
scMRdb: a comprehensive resource for cell-type-resolved Mendelian randomization of complex traits.
scMRdb is a web resource harmonizing 5206 GWAS summary statistics with 585 sc-eQTL datasets for cell-type-resolved Mendelian randomization, with Steiger and…
MetabHub: an integrative platform for plasma nuclear magnetic resonance metabolomics using mediation analysis, disease prediction, and risk stratification.
Web resource mining UK Biobank plasma NMR metabolomics for mediation pathways, disease prediction and risk stratification.
MetabDB: an integrated resource for human metabolic measures, disease associations, and genetic evidence.
MetabDB integrates 16 public metabolomics studies into a searchable resource linking metabolic measures, QTLs, GWAS traits, diseases, and genetic evidence.
Preprints
A Pipeline for Predicting Variant Associations with Complex Disorders via Functional Annotations
Introduces a scalable, reproducible pipeline that builds CADD-annotated, class-balanced variant datasets from GWAS summary statistics for complex disorders…
Genetic control and tissue specificity of transcriptomic rhythmicity
Genotype-by-rhythm cosinor framework on GTEx v10 finds 167 circadian eQTLs across 28 tissues; PheWAS links traits.
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