Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

Abstract

Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/ disease-associated haplotypes at TNFAIP3, 9 have at least one variant meeting one or both of these criteria, 5 of which are further supported by genetic fine-mapping. Our work provides a comprehensive strategy to characterize genetic variation at important disease-associated loci, and aids in the effort to identify trait causal genetic variants.

Functional genomics in autoimmune diseases

“…In addition to the generation of deletions, or specific edits, CRISPR/Cas9 can be used to modify chromatin activity (using catalytically inactivate dCas9 fused to chromatin modifiers). A comparison of various methods used for characterizing autoimmune variants was recently published, focused on multiple autoimmune loci found within the 6q23 region ( 56 ). The authors performed a number of observational techniques, assaying chromatin accessibility (using both DNAse I and ATAC) and activity (using H3K27ac), as well as assessing the impact of variants through two MPRAs (differing based on the method of reporter plasmid delivery) and through two CRISPR screens (both activating and repressing chromatin), all in monocyte, B-cell and T-helper cell lines.…”

Genome-wide discovery of SLE genetic risk variant allelic enhancer activity

“…Allelic activity was assessed for each enVar by comparing enhancer activity between each pairs of alleles. We considered a SLE variant allelic if (1) at least one of its alleles is an enAllele; (2) we observed significant genotype-dependent activity using Student’s t -test 19,35 (see Supplemental Note 2, Supplemental Figure 6 ); and (3) the oligos had more than a 25% change between any pair of alleles. Using these criteria, we identified 51 SLE risk variants (11% of enVars, 1.7% of all SLE risk variants) as allelic enVars in GM12878 ( Figure 3A, Supplemental Data Set 11 ).…”

An efficient lentiviral CRISPRi approach to silence genes in primary human monocytes

“…1 While eQTL provides associations, it does not demonstrate causality, which CRISPRi can do by mapping enhancer-promoter connections. 22,23 Hence, this method will enable systematic functional analysis of causal variants that contribute to immune response variation in the human population.…”