Journal: International Journal of Epidemiology

Article Title: Identifying factors contributing to increased susceptibility to COVID-19 risk: a systematic review of Mendelian randomization studies

doi: 10.1093/ije/dyac076

Figure Lengend Snippet: The characteristics of the included Mendelian randomization studies of factors on COVID-19 outcomes [(A) severity, (B) hospitalization, (C) susceptibility]

Article Snippet: Pairo-Castineira E 2021 , Two-sample , Druggable targets , eQTL of IFNAR2 , IFNAR1 , IL6R , JAK1 , CTSL , IFNGR2 , CSF3 (SD) , A , GenOMICC, COVID-19 HGI R2, 23andMe, UKB , European , European.

Techniques: Expressing, Activity Assay, Reflux, Cannabis, Cell Counting, Marker, Plasmid Preparation, Coagulation

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus

doi: 10.1007/s00122-025-04867-2

Figure Lengend Snippet: A Procedure for graph-based eQTL analysis: long reads are used for SV identification. SVs identified from long reads along with SNPs identified from short reads are used for graph construction. Graphs are used for transcript expression quantification and SV genotyping using a larger collection of short-read samples. B Distribution of eQTLs relative to genomic features highlights a higher proportion of eQTL-SVs in promoter regions compared to genic and downstream regions

Article Snippet: B Distribution of eQTLs relative to genomic features highlights a higher proportion of eQTL-SVs in promoter regions compared to genic and downstream regions Within our datasets, we identified more SNP-eQTLs on the A subgenome compared to the C subgenome, while a higher proportion of SV-eQTLs was found on the C subgenome (Fig S7, Chi-squared test < 0.001).

Techniques: Expressing

Journal: BMC Genomics

Article Title: Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population

doi: 10.1186/s12864-023-09532-w

Figure Lengend Snippet: Properties of GM detected eQTLs. A Violin plot of Fst values for GM detected eQTLs in each tissue compared to GTEx-am. B MAF histogram plots showing allele frequencies of eQTLs in GM and GTEx-am. Among 3,058 GM-detected eQTLs in both tissues, 2,939 were also available in GTEx-am dataset (of which, 2,610 had the same minor allele). MAF comparison across populations revealed no differences ( P = 0.33; M-W test). C Enrichment of GM eQTLs in adipose tissue functional annotations is shown as estimated odds ratios and 95% confidence intervals on the x axis for each annotation category in the y axis. Odds ratios greater than 1 indicate an enrichment of eQTLs in the given functional annotations, while odds ratios less than 1 indicate a depletion. Significant odds ratios are shown as filled circles or squares ( P < 0.05). Cannon et al. (ref 18), Allum et al. (ref 30). D Enrichment of GM eQTLs in GM ATAC-Seq peaks in S (upper panel) and V (bottom panel) tissue

Article Snippet: D Enrichment of GM eQTLs in GM ATAC-Seq peaks in S (upper panel) and V (bottom panel) tissue To characterise the functional impact of GM eQTLs, we tested their overlap with functional annotations in adipose tissue from RoadMap Epigenomics, ENCODE, Remap2 and from ATAC-Seq publications [ , ].

Techniques: Comparison, Functional Assay

Journal: Nature Communications

Article Title: Genetic coupling of enhancer activity and connectivity in gene expression control

doi: 10.1038/s41467-025-55900-3

Figure Lengend Snippet: A Overview of the main data collection steps. Created in BioRender: https://BioRender.com/v74s856 . B Design of the eQTL CHi-C experiment. We designed capture probes targeting DpnII fragments harbouring previously identified lead eQTLs in monocytes. We also included variants in tight LD with the lead eQTLs in regulatory regions, eGene promoters and the promoters of distance-matched ‘non-eGenes’, which were similar distances from the eQTLs as the eGenes but not associated with their expression. Created in BioRender: https://BioRender.com/z90t537 . C Relationship between the number of interacting enhancers and gene expression. Two-sided Spearman’s rank correlation was performed on log 2 (number active enhancers) against log 2 (expression TPM) for 5729 genes in 34 samples. Boxplots show 25th, 50th and 75th percentiles, with upper and lower whiskers to the largest or smallest value no further than 1.5 x the interquartile range from the hinge. Graphic created in BioRender: https://BioRender.com/s35y475 . D Degree of TAD sharing between eQTLs and eGenes or eQTLs and non-eGenes. E Inverse hyperbolic sine (asinh)-transformed median CHiCAGO scores for interactions between eQTLs and eGenes or non-eGenes within the same TAD. The score for the eGene is shown against the median score for all captured control genes, per eQTL, including cases where the score was zero. Examples of eQTLs intersecting ATAC-seq peaks and interacting with the eGenes: PTGER4 ( F ), SGK1 ( G ) and VIM ( H ). ATAC data are presented as −log 10 ( p value) for the consensus dataset (detected by Genrich ). eGenes are highlighted in green. Contact profiles show the number of reads for each other-end fragment contacting the fragment containing the eGene promoter in the consensus dataset. The eQTL-eGene significant contacts were called using the shown consensus CHi-C interactions (CHiCAGO statistical algorithm on consensus data (score ≥ 5), at DpnII -fragment level). Interactions are restricted to those involving the eQTL or a SNP in tight LD and the eGene promoter. Baited regions are shown as a grey highlight. F – H were plotted using the Plotgardener R package . Source data for C – E are available on OSF .

Article Snippet: The GUESS approach replicated the effects of 84% (16/19) of the CHi-C BaseQTL contact eQTLs on the contacts with six respective eGene promoters ( THBS1 , NAAA , SVIL and KCNK13, TFPT and C7orf50 ), either via direct variant overlap ( N = 7) or by overlap with other variants within the considered GUESS window and in tight LD ( r 2 > 0.9) with the lead trimodal QTL ( N = 9).

Techniques: Expressing, Gene Expression, Transformation Assay, Control

Journal: Nature Communications

Article Title: Genetic coupling of enhancer activity and connectivity in gene expression control

doi: 10.1038/s41467-025-55900-3

Figure Lengend Snippet: A Strategy for testing eQTL-eGene contacts. Created in BioRender: https://BioRender.com/l19m785 . B Manhattan plot of BaseQTL results. The y -axis shows the negative logarithm of the probability that the candidate SNP is not a true QTL for promoter contact: approximate posterior probability (approx. post. prob.; see ‘Methods’). The significant contact eQTLs (for which the 99% credible interval does not contain zero) are depicted in red. The contact eQTL with the highest probability of being a true QTL for promoter contact is labelled in loci with multiple significant contact eQTLs. C – E Genomic visualisation of significant contact eQTLs in the THBS1 , NAAA and TFPT loci. The arches, whose heights correspond to the allelic fold change in contact, show the tested contacts between the eQTL and promoter(s) of the eGene (one eQTL-containing DpnII bait fragment is shown in each case). CHi-C read counts at DpnII fragment resolution are shown from the viewpoint of the eGene promoter (yellow signal tracks). ATAC data is presented as −log 10 ( p value) on consensus data (detected by Genrich ). C – E were plotted using the Plotgardener package . CI, confidence interval.

Article Snippet: The GUESS approach replicated the effects of 84% (16/19) of the CHi-C BaseQTL contact eQTLs on the contacts with six respective eGene promoters ( THBS1 , NAAA , SVIL and KCNK13, TFPT and C7orf50 ), either via direct variant overlap ( N = 7) or by overlap with other variants within the considered GUESS window and in tight LD ( r 2 > 0.9) with the lead trimodal QTL ( N = 9).

Techniques:

Journal: Nature Communications

Article Title: Genetic coupling of enhancer activity and connectivity in gene expression control

doi: 10.1038/s41467-025-55900-3

Figure Lengend Snippet: A Strategy for detecting ATAC QTLs with BaseQTL. Created in BioRender: https://BioRender.com/v31q004 . B Shared allelic effects of QTLs on accessibility and promoter contact at 99% credible interval. C Heatmap of cross-trait effects for contact eQTLs. The positive effect allele (either REF or ALT) is shown for CHi-C, and the direction of effects in other traits (whether log allelic fold change or beta) is shown relative to this. We only show effects for features within 5 kb of the contact eQTL, and we accounted for LD ( r 2 ≥ 0.9). The ATAC QTL effects were taken from BaseQTL results within our 34-donor cohort, whereas the remainder of effects (gene expression, H3K27ac and H3K4me1) were curated from outside of our cohort. The eQTL effects were taken from the original monocyte study or from Blueprint. The histone modifications H3K27ac and H3K4me1 were taken from Blueprint WP10 Phase 2. Epigenetic mechanisms within example contact eQTL loci: ( D ) THBS1 , ( E ) NAAA , F KCNK13 . The red regions show upregulated peaks of ATAC, H3K27ac and H3K4me1 associated with the contact eQTL (or SNPs in LD, r 2 ≥ 0.9); the peaks shown in these plots were not restricted to 5 kb from the contact eQTL. ATAC-seq tracks show the pileups for merged homozygous reference (blue) or homozygous alternative (red) donors for one of the contact eQTLs as an approximation of the allele-specific signal across the locus. Black arrows indicate the ATAC-seq peaks and the fold changes associated with the alternative genotype of each contact eQTL in the BaseQTL analysis (see also Supplementary Data ). D – F were plotted using the Plotgardener package . Source data for ( B ) and ( C ) are available on OSF .

Article Snippet: The GUESS approach replicated the effects of 84% (16/19) of the CHi-C BaseQTL contact eQTLs on the contacts with six respective eGene promoters ( THBS1 , NAAA , SVIL and KCNK13, TFPT and C7orf50 ), either via direct variant overlap ( N = 7) or by overlap with other variants within the considered GUESS window and in tight LD ( r 2 > 0.9) with the lead trimodal QTL ( N = 9).

Techniques: Gene Expression