Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

• 成果类型: Article
• 署名作者: Wilson, Douglas R.; Ibrahim, Joseph G.; Sun, Wei
• 署名单位: University of North Carolina; University of North Carolina Chapel Hill; Fred Hutchinson Cancer Center
• 刊物名称: JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
• ISSN/ISSBN: 0162-1459
• DOI: 10.1080/01621459.2019.1609968
• 发表日期: 2020
• 页码: 79-89
• 关键词: analyses reveal; cancer; genes

摘要

The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g., immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls Type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells. for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.