Next Generation DNA Sequencing of Novel Loci in Workers with Diisocyanate Asthma (DA)

Abstract

RATIONALE: Genetic markers of susceptibility for DA are needed to identify exposed workers at highest risk. We have used GWAS and Next Generation Sequencing (NGS) methodologies to identify gene variants associated with specific inhalation challenge confirmed DA. METHODS: Workers with occupational asthma caused by diisocyanates (i.e., HDI, MDI, or TDI) were recruited at occupational health clinics in Canada and Spain. Based on a prior GWAS study, 14 DA associated loci and their flanking regions were selected for sequencing (6,996,180 base pairs). NGS was performed in 91 workers with confirmed DA (cases) and compared to 293 subjects with sequencing data from the 1,000 genomic (1KG) control data set. RESULTS: NGS analysis of DA cases compared to 1KG controls yielded 143 significant SNP associations with DA (Chi-Squared-log 10 P< 3.0) (range 3.006-5.504), of which all but one SNP were located in intronic regions. Transcriptomic analysis was carried out for the top 70 DA associated SNPs using available transcription factor (TF) datasets from relevant lungderived tissues and cell lines, including ChIP-seq datasets for TFs, regulatory histone marks, and DNase-seq (open chromatin). SNPs were ranked based on the number of datasets they overlap and the biologic relevance of the associated SNPs. The top 22 SNPs identified for further study are contained in 7 loci: CDH17 (10), ATF3 (6), FAM71A (2), PITPNC1, TACR1, ZBTB16, LOC101929565. CONCLUSIONS: This study identified DA-associated SNPs linked with transcription binding sites. The possible roles of these variants on gene expression and protein function are under investigation.

Identification of SNPs Potentially Associated with Asthma Using a Di-isocyanate Luciferase Reporter Assay

“…Some studies identified and characterized the interaction between SNPs and inflammatory disease (Kim et al, 2009) (Tokuhiro et al, 2003). (Lummus et al, 2017). Based on the locations of the 23 SNPs, many of them are located near to each other, so we also designed two haplotypes long fragments containing those linked SNPs as two new samples.…”

“…A preliminary study recruited workers with occupational asthma caused by di-isocyanates at occupational health clinics in Canada and Spain. The next-generation sequencing was performed in 91 workers with confirmed DA (cases) and compared to 293 subjects with sequencing data from the 1,000 genomic (1KG) control data set and 143 significant SNPs associated with DA were found (Lummus et al, 2017).…”