Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease caused by the disturbance of genetic and environmental factors. Single-nucleotide polymorphisms (SNPs) play a vital role in the genetic dissection of complex diseases. In-depth analysis of SNP-related information could recognize disease-associated biomarkers and further uncover the genetic mechanism of complex diseases. Risk-related variants might act on the disease by affecting gene expression and gene function. Through integrating SNP disease association study and expression quantitative trait loci (eQTL) analysis, as well as functional enrichment of containing known causal genes, four risk SNPs and four corresponding susceptibility genes were identified utilizing next-generation sequencing (NGS) data of COPD. Of the four risk SNPs, one could be found in the SNPedia database that stored disease-related SNPs and has been linked to a disease in the literature. Four genes showed significant differences from the perspective of normal/disease or variant/nonvariant samples, as well as the high performance of sample classification. It is speculated that the four susceptibility genes could be used as biomarkers of COPD. Furthermore, three of our susceptibility genes have been confirmed in the literature to be associated with COPD. Among them, two genes had an impact on the significance of expression correlation of known causal genes they interact with, respectively. Overall, this research may present novel insights into the diagnosis and pathogenesis of COPD and susceptibility gene identification of other complex diseases.
Highlights
Chronic obstructive pulmonary disease (COPD) is an inflammatory disease of the respiratory system, which is one of the most important causes of death in most countries [1]
Based on RNA-seq data for COPD, we proposed a strategy for identifying disease risk SNPs and susceptibility genes
In this study, based on the high-throughput sequencing data of COPD, we proposed an integrated strategy to identify risk SNPs and susceptibility genes from the perspectives of expression-related SNPs and SNP association
Summary
Chronic obstructive pulmonary disease (COPD) is an inflammatory disease of the respiratory system, which is one of the most important causes of death in most countries [1]. Real-time polymerase chain reaction (real-time PCR) and other methods, Li et al unraveled that the upstream functional SNP rs12654778 of the ADRB2 gene affected the expression of ADRB2 in COPD [7]. These studies were performed for an individual or some specific known genes or SNPs. In hereditary complex diseases, SNP disease-associated test method can detect the potential genetic association between genetic variation on the genome and specific diseases or traits and has emerged as an effective way to facilitate COPD
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