rs35675666

Genome-wide association studies typically identify hundreds to thousands of loci, many of which harbor multiple independent peaks, each parsimoniously assumed to be due to the activity of a single causal variant. Fine-mapping of such variants has become a priority and since most associations are located within regulatory regions, it is also assumed that they colocalize with regulatory variants that influence the expression of nearby genes. Here we examine these assumptions by using a moderate throughput expression CROPseq protocol in which Cas9 nuclease is used to induce small insertions and deletions across the credible set of SNPs that may account for expression quantitative trait loci (eQTL) for genes associated with inflammatory bowel disease (IBD). Of the 4,384 SNPs targeted in 88 loci (an average of 50 per locus), 439 were significant and further examined for validation. From these, 98 significantly altered target gene expression in HL-60 myeloid cell line, 74 in induced macrophages from these HL-60 cells, and 78 in induced neutrophils for a total of 201 validated effects (46%), 43 of which were observed in at least two of the cell types. Considering the observed sensitivity and specificity of the controls, we estimate that there are at least 150 true positives per cell type, an average of almost 2.4 for each of the 64 eQTL for which putative causal variants have been fine-mapped. This implies that haplotype effects are likely to explain many of the associations. We also demonstrate that the same approach can be used to investigate the activity of very rare variants in regulatory regions for 89 genes, providing a rapid strategy for establishing clinical relevance of non-coding mutations.

2025 · Emily Greenwood, Mingming Cao, Ciaran M. Lee, Anh Thu Liu, Buhle Moyo, Gang Bao, Greg Gibson

Low DJ-1 protein level caused by DJ-1 gene mutation leads to autosomal recessive Parkinson’s disease (PD) due to impaired antioxidative activity. In sporadic PD patients, although mutations were rarely found, lower DJ-1 protein level was also reported. Dysregulation of DJ-1 gene expression might contribute to low DJ-1 protein level. Since the promoter is the most important element to initiate gene expression, whether polymorphisms in the DJ-1 promoter result in the dysregulation of gene expression, thus leading to low protein level and causing PD, is worth exploring. The DJ-1 promoter region was sequenced in a Chinese cohort to evaluate possible links between DJ-1 promoter polymorphisms, PD risk and clinical phenotypes. Dual-luciferase reporter assay was conducted to evaluate the influence of promoter polymorphisms on DJ-1 transcriptional activity. Related information in an existing genome-wide association studies (GWAS) database were looked up, meta-analysis of the present study and other previous reports was conducted, and expression quantitative trait loci (eQTL) analysis was performed to further explore the association. Three single nucleotide polymorphisms (SNPs) (rs17523802, rs226249, and rs35675666) and one 18 bp deletion (rs200968609) were observed in our cohort. However, there was no significant association between the four detected genetic variations and the risk of PD either in allelic or genotype model, in single-point analysis or haplotype analysis. This was supported by the meta-analysis of this study and previous reports as well as that of GWAS database PDGene. Dual luciferase reporter assay suggested these promoter polymorphisms had no influence on DJ-1 transcriptive activity, which is consistent with the eQTL analysis results using the data from GTEx database. Thus, DJ-1 promoter polymorphisms may play little role in the dysregulation of DJ-1 expression and PD susceptibility in sporadic PD.

2019 · L He, S Lin, H Pan, R Shen, M Wang, Z Liu, S Sun, Y Tan, Y Wang, S Chen, J Ding

The inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are immune-mediated disorders resulting in chronic, relapsing inflammation of the gastrointestinal tract. The complex nature of IBD supports the notion that its origin is likely multifactorial, constituting both genes and environmental factors. It has been hypothesized that environmental factors and maladaptive immune responses to gastrointestinal flora generate a dysregulated inflammatory cascade creating mucosal injury in genetically susceptible individuals. Over the last decade, considerable interest and research has focused on the genetic aspect of IBD. The identification of linkage between Crohn disease and the pericentromeric region of chromosome 16 (IBD1) by Hugot in 1996 spawned a series of genome scans and linkage analyses in search of susceptibility and phenotypic modifier genes (Nature 379:821–3, 1996). In 2001, the discovery that specific polymorphisms in the CARD15/NOD2 gene at the IBD1 locus were associated with Crohn disease engendered a new era of genotype–phenotype investigations (Nature 411:599–603, 2001; Nature 411:603–6, 2001). The advent of genome-wide association studies has resulted in the successful identification of new, well-replicated disease associations. The heterogeneity of IBD phenotypes suggests that it is a polygenic disorder in which susceptibility loci act in epistasis with other disease-modifying genes and the environment to produce disease. Understanding genetic associations of IBD can provide patients and their families with useful information that may help them cope with the disease. Furthermore, as our knowledge of genotype–phenotype associations grows, it is anticipated that genotyping at the onset of disease may enable physicians to predict disease course and tailor medical therapies specific for each patient.

2013 · Zhi Wei, Steven N. Baldassano, Hakon Hakonarson

Genome-wide association studies (GWAS) have provided a large set of genetic loci influencing the risk for many common diseases. Association studies typically analyze one specific trait in single populations in an isolated fashion without taking into account the potential phenotypic and genetic correlation between traits. However, GWA data can be efficiently used to identify overlapping loci with analogous or contrasting effects on different diseases. Here, we describe a new approach to systematically prioritize and interpret available GWA data. We focus on the analysis of joint and disjoint genetic determinants across diseases. Using network analysis, we show that variant-based approaches are superior to locus-based analyses. In addition, we provide a prioritization of disease loci based on network properties and discuss the roles of hub loci across several diseases. We demonstrate that, in general, agonistic associations appear to reflect current disease classifications, and present the potential use of effect sizes in refining and revising these agonistic signals. We further identify potential branching points in disease etiologies based on antagonistic variants and describe plausible small-scale models of the underlying molecular switches. The observation that a surprisingly high fraction (>15%) of the SNPs considered in our study are associated both agonistically and antagonistically with related as well as unrelated disorders indicates that the molecular mechanisms influencing causes and progress of human diseases are in part interrelated. Genetic overlaps between two diseases also suggest the importance of the affected entities in the specific pathogenic pathways and should be investigated further.

2012 · Matthias Arnold, Mara L. Hartsperger, Hansjörg Baurecht, Elke Rodriguez, Benedikt Wachinger, Andre Franke, Michael Kabesch, Juliane Winkelmann, Arne Pfeufer, Marcel Romanos, Thomas Illig, Hans‐Werner Mewes, Volker Stümpflen, Stephan Weidinger