Abstract
Background: We have previously identified that polymorphisms spanning the Urokinase Receptor Gene (PLAUR) are associated with asthma, decline in lung function and receptor levels. However, the variants driving genetic associations are not yet fully defined. Using next generation re-sequencing of the 19q13 region we aimed to identify common and rare variants differentially expressed in severe asthma and controls to bridge this gap in knowledge.
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 (67.5kb region on 19q13). 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. Data were compared to reference genome build 37.1.
Results: Mean coverage was 29x and 817 variants were identified, of which 399 (199 rare) were novel. In total, 12 exon variants were identified, with 2 novel rare variants in exons 1 and 6 predicted to cause functional changes to the uPAR protein sequence. Several variants were unique to cases or controls. On correcting for multiple testing, we identified 5 variants showing different representation in cases/controls. These variants were located upstream of PLAUR, with 4 variants forming a 7bp cluster of variation ∼23kb upstream of the start codon.
Conclusions: Re-sequencing PLAUR has identified novel common and rare variants that may be of relevance to asthma.
- © 2014 ERS