Abstract 5229: Candidate gene analysis of exome sequencing data in smokers susceptible and resistant to chronic obstructive pulmonary disease
Authors: Liu Yanhong , Cho Michael H , Qiao Dandi , Kheradmand Farrah , Tsavachidis Spiridon , Armstrong Georgina , Scheurer Michael , Wheeler David , Amos Christopher , Silverman Edwin , Spitz Margaret 
Published: July 2016

Background: Chronic obstructive pulmonary disease (COPD) is a major comorbidity for Lung cancer (LC), the presence of COPD conferring a three- to 10-fold increased risk of LC. Therefore, we employed an extreme-phenotype approach, focused on exome sequencing of 109 susceptibility loci identified in recent genome-wide association studies (GWAS) of LC, COPD, lung function and smoking behavior, to search for COPD disease-causing rare germline mutations.

Methods: We selected two extreme categories of smokers from COPDGene: 1) Resistant long-term smokers with normal lung function defined as post-bronchodilator FEV1 ≥ 80% predicted, FEV1/FVC ≥ 0.7, with smoking histories of 15+ pack-years, considered as resistant to the effects of smoking, n = 318; 2) Susceptible smokers with severe COPD defined as GOLD spirometry grades III-IV (post-bronchodilator FEV1 &lt; 50% predicted and FEV1/FVC &lt; 0.7), with smoking histories of 10+ pack-years, n = 309. We performed whole exome sequencing and analyzed rare (minor allele frequency [MAF] &lt; 0.01 in reference exome databases) variants predicted to be functional in the 109 susceptibility loci previously identified by GWAS. We tested our results using two independent series including the Boston Early-Onset pedigrees sequencing study (n = 350) and the Exome Sequencing Project (ESP)-COPDGene study (n = 400).

Results: Our analysis revealed two genes with multiple rare non-synonymous substitution variants significantly associated with COPD risk. We identified six rare variants in 10q23.33 Myoferlin (MYOF: p.Arg572Gln, p.Phe1400Leu, p.Tyr1163His, p.Glu1339Lys, p.Leu1582Pro, and p.Arg1630Gln) occurring in 12 susceptible smokers with severe COPD, and three rare variants in 15q15.2 Transglutaminase 5 (TGM5: p.Thr42Asn, Pro136Leu, and p.Val202Ile) occurring in nine susceptible smokers with severe COPD, compared with none of these variants identified in resistant smokers. MAF of these mutations were very rare (range from 0 to 0.003) in the 1000 Genomes and ESP databases. All of these mutations were predicted to be protein damaging and deleterious by bioinformatics algorithms (SIFT, PolyPhen2, Mutation Taster, etc.). We also observed three suggestive rare mutations, 6p21.32 ZBTB9 p.Leu43Val, 9q34.2 DBH p.Gly482Arg, and 10q23.33 IFIT3 p.Leu390Arg, each of which were present in three susceptible smokers and none in resistant smokers. However, we were not able to validate these abovementioned candidate variants in the two replication datasets. This could due to potential false positive results or difference of exome sequencing depth and coverage of the target regions from different platforms.

Conclusion: Our results demonstrated potentially disruptive COPD risk-conferring MYOF and TGM5 rare germline mutations that are associated with susceptibility to COPD in one population of smokers, but additional replication of these results in larger populations will be required.

Citation Format: Yanhong Liu, Michael H Cho, Dandi Qiao, Farrah Kheradmand, Spiridon Tsavachidis, Georgina Armstrong, Michael Scheurer, David Wheeler, Christopher Amos, Edwin Silverman, Margaret Spitz. Candidate gene analysis of exome sequencing data in smokers susceptible and resistant to chronic obstructive pulmonary disease. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5229.