Northwestern University

Tue 12:00 PM

BIDS Seminar: Jiping Wang, PhD - Faculty Research (Normalization of Transcript Degradation Improves Accuracy in RNA-seq Analysis)

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When: Tuesday, April 17, 2018
12:00 PM - 1:00 PM  

Where: Arthur Rubloff Building, Lakeview Conference Room (11th Floor), 750 N Lake Shore Dr, Chicago, IL 60611 map it

Audience: Faculty/Staff - Student - Post Docs/Docs - Graduate Students

Contact: Lindsay Varasteh   312.503.1997

Group: Center for Data Science and Informatics (CDSI)

Category: Lectures & Meetings


Abstract: RNA-sequencing (RNA-seq) is a powerful high-throughput tool to profile transcriptional activities in cells. The observed read counts can be biased by various factors such that they do not accurately represent the true relative abundance of mRNA transcript abundance. Normalization is a critical step to ensure unbiased comparison of gene expression between samples or conditions. Here we show that the gene-specific heterogeneity of transcript degradation pattern across samples presents a common and major source of unwanted variation, and it may substantially bias the results in gene expression analysis. Most existing normalization approaches focused on global adjustment of systematic bias are ineffective to correct for this bias. We propose a novel method based on matrix factorization over-approximation that allows quantification of RNA degradation of each gene within each sample. The estimated degradation index scores are used to build a pipeline named DegNorm (stands for degradation normalization) to adjust read count for RNA degradation heterogeneity on a gene-by-gene basis while simultaneously controlling sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of real RNA-seq data and simulated data.

About Biomedical Informatics Data Science (BIDS): These talks include visiting lecturers, presentations on research by BIDS faculty and trainees, as well as presentations about informatics tools and resources to support research.

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