B109-12 Aberrant Splicing Analysis Identifies Association Between CFTR Splicing and Lung Function in COPD

Background Whole genome sequencing allows for the detection of vast numbers of genetic variants, a large proportion of which have not been previously characterized. However, the ability to interpret these findings is dependent on accurate interpretation of variant function. Genetic variants that result in aberrant splicing are of particular interest due to their potential to cause drastically altered RNA isoforms, such as through frameshifts or loss of functionally important domains. Here, we use RNAseq data from lung tissue and blood to identify aberrant splicing events associated with rare genetic variants in subjects with severe chronic obstructive pulmonary disease (COPD). Methods RNA sequencing was performed on whole blood from 3743 subjects in the COPDGene Study lung tissue of 1241 subjects in the Lung Tissue Research Consortium (LTRC). Whole genome sequencing data from all subjects was obtained through the NHLBI TOPMed project. We used leafcutterMD, an algorithm for outlier splicing detection, to identify subjects and splice sites with aberrant splicing. Results In LTRC lung, we identified 515 subjects that had at least one aberrant splicing event. A total of 5,251 splice sites from 1,180 genes had outlier splicing with p < 1x10-10. We found that the number of aberrant splicing events was associated with decreased lung function (p = 3.68x10-5, β=-0.023), and severe COPD of GOLD 3-4 (p = 3.64x10-4, odds ratio=61.7) in LTRC. We prioritized the top outlier splice events in subjects with severe COPD, which led to the identification of a splice site in a subject hereafter known as Proband 1. This is a 64 year old male former smoker with severe COPD and chronic bronchitis. We observed that RNASeq data from the subject showed aberrant splicing of a junction spanning exon 10 of the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) (GRCh38 chr7:117542108-117559464). Specifically, Proband 1 had very little inclusion of exon 10 (7% inclusion), while in control subjects this exon has high inclusion rates (67-90% inclusion). Inclusion of exon 10 has previously been shown to be critical for normal CFTR function. We found exon 10 splicing is associated with a rare variant, rs73715573, which was associated with reduced lung function (FEV1) in both LTRC (p = 0.001) and COPDGene (p = 0.02). Conclusions Using outlier splicing analysis we identified aberrant splicing events associated with decreased lung function and severe COPD, including a splice event in CFTR. This demonstrates the utility of outlier splicing analysis in interpretating rare variants. This abstract is funded by: NIH