Abstract
Over the past decade, genome-wide association studies have contributed a wealth of knowledge to our understanding of polygenic disorders such as rheumatoid arthritis. As the size of sample cohorts has improved so too have the computational and experimental methods used to robustly define variants associated with disease susceptibility. The challenge now remains to translate these findings into improved understanding of disease aetiology and patient care. Whilst much of the focus of translating the findings of genome-wide association studies has been on global analysis of all variants identified, careful functional study of individual disease susceptibility loci will be required in order to refine our understanding of how individual variants contribute to disease risk. Here, we present the argument behind such an approach and describe some of the novel tools being used to investigate risk loci. This includes the use of chromosomal conformation capture techniques and modifications of the CRISPR-Cas9 system, with several examples of their implementation being described.
Highlights
Rheumatoid arthritis (RA) is a common autoimmune disease with an estimated global prevalence of approximately 25 million [1]
Over the past decade our ability to confidently describe variants associated with susceptibility to rheumatoid arthritis and other polygenic disorders has improved dramatically
This includes the imputation of associations for single nucleotide polymorphism (SNP) not experimentally investigated and the performance of highdensity fine mapping, to refine observed associations
Summary
Rheumatoid arthritis (RA) is a common autoimmune disease with an estimated global prevalence of approximately 25 million [1]. A 12 bp deletion, including the Crohn’s disease SNP, skewed the response of naïve murine T cells to activation Using this combination of genetic data and functional experimentation the authors were able to convincingly demonstrate how disease susceptibility is mediated at this locus. The enrichment of specific gRNAs in the selected population, is assessed by highthroughput sequencing and used as a readout of the gRNAs ability to confer the phenotype of interest This screening technique was used by Simeonov et al in combination with dCas9-VP64 to identify the IL2RA enhancer mentioned earlier [73], with flow cytometry used to isolate cells expressing high levels of IL2RA This approach may be more conducive to the study of multiple disease susceptibility loci in a single experiment; it comes with additional considerations relating to experimental design and challenges when it comes to interpreting the resulting data
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