Background/Purpose: Previous genome-wide association studies of granulomatosis with polyangiitis (Wegener’s, GPA) identified common genetic variants associated with susceptibility to GPA.  However, since GPA is a rare disease, we hypothesize that rare genetic variants may be more strongly associated with disease susceptibility.  Therefore, we conducted an exome-sequencing study to identify rare, deleterious exonic variants associated with GPA. 

Methods: Seventy-seven individuals with GPA underwent exome sequencing using the Illumina HiSeq platform and the Nimblegen SeqCap EZ exome enrichment protocol. All cases of GPA were of European descent, c-ANCA/anti-PR3 positive, and fulfilled either the ACR Classification Criteria or the Chapel Hill Consensus Conference definition of GPA. Exome sequencing reads were processed according to the Genome Analysis Toolkit Best Practices for DNA sequencing. Variants were annotated and filtered with ANNOVAR and Variant Tools. Functional effects of the variant were assessed using in silico bioinformatics algorithms and databases of known pathogenic variants. We applied a gene burden test to identify genes that were enriched with deleterious variants in patients with GPA when compared to publicly available data from the 1000 Genomes and the National Institutes of Health-funded Exome Sequencing Projects. Pathway analysis was performed using the Gene Set Enrichment Analysis Molecular Signatures database.

Results: After quality control filtering and bioinformatics analysis, we identified 4,306 exonic, non-synonymous, deleterious variants in the 77 cases of GPA, of which 3,812 were rare (minor allele frequency <1%). After applying gene burden tests, we identified 153 genes not previously associated with GPA that were enriched with deleterious variants in GPA cases compared to controls. These genes fell into the following 3 groups (with overlap): 1) 98 genes were enriched with rare deleterious variants, 2) 35 genes with homozygous rare deleterious variants not present in controls, and 3) 42 genes enriched with common deleterious variants. Genes with the strongest evidence of enrichment for rare, deleterious variants include FOXD4L1, UMODL1, and PNKP.  Pathways over-represented by the 153 genes include the metabolism of lipoproteins and extracellular matrix organization.  Lastly, we found enrichment for 6 variants in 3 genes previously associated with GPA (ITGB2, RXRB, SERPINA1).

Conclusion: Our initial results indicate that exome sequencing can identify novel genetic associations with GPA beyond what has been previously observed in genome-wide association studies.  These associations implicate new biologic pathways that may contribute to the pathogenesis of disease. To our knowledge, this is the first study to utilize next-generation sequencing to assess for genetic variants associated with GPA susceptibility. The results from this study can be used to inform future genomic and translational investigations of this and other systemic vasculitides.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/using-exome-sequencing-to-identify-novel-genetic-associations-with-granulomatosis-with-polyangiitis-susceptibility/