Re-sequencing of IL33 and IL1RL1 in severe asthma patients identifies novel variation

Background: IL33 (9p24.1) and IL33 receptor ( IL1RL1, 2q12) have been reproducibly identified as asthma susceptibility genes. However, the variants driving genetic associations are not yet fully defined. Using re-sequencing we aimed to i) identify novel common and rare variants and ii) determine if these variants are differentially represented in severe asthma and control subjects. Method: 200 UK severe asthma patients (GINA ≥3) and 200 non-asthma/non-atopic controls were sequenced. Samples were multiplexed, with each group split into 3 pools (n=66, 66 and 68). Target enrichment was carried out using the Agilent SureSelect kit for 9p24.1 (243kb) and 2q12 (470kb) regions. Paired-end sequencing was utilised and 100bp reads for cases and controls were run on the Illumina HiSeq2000™ System. Realignment around insertion deletions, recalibration of quality scores and variant detection were carried out using the GATK and Syzgy software packages. Results: Mean coverage was 46x for 2q12 and 40x for 9p24.1. 4107 and 2475 total variants were identified with 1644 (1231 rare) and 1125 (779 rare) being novel variants, respectively. We identified 14 exon variants in IL1RL1 and 7 in IL33 , of which 11 and 1 were predicted to be functional, respectively. Several variants were unique to cases or controls. On correcting for multiple testing, we identified 3 differentially expressed variants at 2q12 and 9 at 9p24.1. Variants at 9p24.1 were upstream of IL33, within KIAA2026 and in a 50bp cluster. On 2q12, variants were upstream of IL1RL1 , within IL1RL1 and located in the 39UTR. Conclusion: Re-sequencing of IL33 and IL1RL1 loci has identified novel common and rare variants that may be of relevance to asthma.