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Activity Number: 83
Type: Invited
Date/Time: Sunday, July 30, 2017 : 8:30 PM to 10:30 PM
Sponsor: Biometrics Section
Abstract #322815
Title: The Association Between Copy Number Aberration, DNA Methylation, and Gene Expression
Author(s): Wei Sun*
Companies: Fred Hutchinson Cancer Research Center
Keywords:
Abstract:

We systematically studied the association between somatic copy number aberration (SCNA), DNA methylation, and gene expression using -omic data from The Cancer Genome Atlas (TCGA) on six cancer types: breast cancer, colon cancer, glioblastoma, leukemia, lower-grade glioma, and prostate cancer. A major challenge for such integrated study is that the association between DNA methylation and gene expression is severely confounded by tumor purity and cell type composition, which are often unobserved and difficult to estimate. To overcome this challenge, we developed a method to remove confounding effects by calculating the principal components that span the space of the latent factors. After decades of study of DNA methylation, there is still debate on a fundamental question: whether alteration of DNA methylation causes gene expression variation or it reacts to gene expression variation. Our new method allows us to reveal an intriguing observation that the association between SCNA and DNA methylation is mediated at least in part by gene expression. This finding suggests that at least part of the variation of DNA methylation is because DNA methylation is a passive mark rather than an acti


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