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Volume 54 Issue 6, June 2022

Context-specific eQTLs

This figure is a graphical representation of transcriptional changes that occur in human CD4 T cells as they go through activation. The different colored dots depict individual T cells at different stages of activation that are circulating in the blood during an active immune response. Single-cell transcriptional profiling was used to capture how gene expression is regulated by common genetic variants during this crucial process of immune response.

See Soskic et al.

Image: Eddie Cano Gamez and Suzanne Hayes. Cover Design: Valentina Monaco.


  • Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic studies are lacking in diversity and propose several solutions to address this problem.

    • Charles E. Breeze
    • Stephan Beck
    • Nora Franceschini


  • Calls for diversity in genomics have motivated new global research collaborations across institutions with highly imbalanced resources. We describe practical lessons we have learned so far from designing multidisciplinary international research and capacity-building programs that prioritize equity in two intertwined programs — the NeuroGAP-Psychosis research study and GINGER training program — spanning institutions in Ethiopia, Kenya, South Africa, Uganda and the United States.

    • Alicia R. Martin
    • Rocky E. Stroud II
    • Lori B. Chibnik
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News & Views

  • A new study employs CRISPR–Cas9-based base editing for simultaneous mutagenesis of all copies of histone H3 genes in mammals, highlighting the functional importance of H3K27me3 for Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.

    • Alessandro Scacchetti
    • Roberto Bonasio
    News & Views
  • A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes.

    • Guillaume Lettre
    News & Views
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Research Briefings

  • A large-scale single-nucleus chromatin accessibility profiling study in coronary artery samples from patients with coronary artery disease generated a landscape of the regulatory activity during the disease. These data highlight cell type-specific gene programs that can improve the interpretation of human genome-wide association studies findings for cardiovascular diseases.

    Research Briefing
  • A study using single-cell transcriptomics and mapping of expression quantitative trait loci (eQTLs) in a dynamic model of CD4+ T cell activation reveals novel, context-specific eQTLs linked to genes associated with immune diseases such as inflammatory bowel disease.

    Research Briefing
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Technical Reports

  • snipar is a software package for imputing missing parental genotypes and estimating direct genetic effects. Application to UK Biobank data shows that effects estimated by standard genome-wide association study designs have confounding bias for some phenotypes.

    • Alexander I. Young
    • Seyed Moeen Nehzati
    • Augustine Kong
    Technical Report Open Access
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Amendments & Corrections

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