ReviewNature protocols2023
Annotating genetic variants to target genes using H-MAGMA.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
What it found
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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
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dissecting Schizophrenia Biology Using Pleiotropy With Cognitive Genomics.Biological psychiatry · 2025Pooled it
- Article
- Article
- Transcriptome-informed brain cartography of polygenic risk and association with brain structure in major psychiatric disorders.Molecular psychiatry · 2026Article
- Functionally informed annotation influences pathway-specific polygenic risk and disease inference in Alzheimer's disease.medRxiv : the preprint server for health sciences · 2026Article
- Genome-wide association study of delay discounting identifies 11 loci and reveals transdiagnostic associations across mental and physical health.Molecular psychiatry · 2026Article
- Multi-omics and molecular testing: A new insight into the genetic mechanisms of sarcopenia and arthritis.Clinical and experimental medicine · 2026Article
- Genetic variants associated with chronic postsurgical pain: evidence from the China Surgery and Anaesthesia Cohort study.British journal of anaesthesia · 2025Observational
- Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025Review
- Genetic risk for neurodegenerative conditions is linked to disease-specific microglial pathways.PLoS genetics · 2025Article
- The X chromosome's influences on the human brain.Science advances · 2025Article
- A multi-ancestry cerebral cortex transcriptome-wide association study identifies genes associated with smoking behaviors.Molecular psychiatry · 2024Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- Schizophrenia genomics: genetic complexity and functional insights.Nature reviews. Neuroscience · 2024Review
- A cross-tissue transcriptome-wide association study identifies new susceptibility genes for frailty.Frontiers in genetics · 2024Article
- The genetic relationships between brain structure and schizophrenia.Nature communications · 2023Article
- Annotating genetic variants to target genes using H-MAGMA.Nature protocols · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
An outstanding goal in modern genomics is to systematically predict the functional outcome of noncoding variation associated with complex traits. To address this, we developed Hi-C-coupled multi-marker analysis of genomic annotation (H-MAGMA), which builds on traditional MAGMA-a gene-based analysis tool that assigns variants to their target genes-by incorporating 3D chromatin configuration in assigning variants to their putative target genes. Applying this approach, we identified key biological pathways implicated in a wide range of brain disorders and showed its utility in complementing other functional genomic resources such as expression quantitative trait loci-based variant annotation. Here, we provide a detailed protocol for generating the H-MAGMA variant-gene annotation file by using chromatin interaction data from the adult human brain. In addition, we provide an example of how H-MAGMA is run by using genome-wide association study summary statistics of Parkinson's disease. Lastly, we generated variant-gene annotation files for 28 tissues and cell types, with the hope of contributing a resource for researchers studying a broad set of complex genetic disorders. H-MAGMA can be performed in <2 h for any cell type in which Hi-C data are available.
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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.