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Advancement: Improving isoform sequencing and analysis with long reads

Speaker Name: 
Roger Volden
Speaker Title: 
PhD Student (Advisor: Christopher Vollmers)
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Friday, November 9, 2018 - 9:00am
End Time: 
Friday, November 9, 2018 - 11:00am
Physical Sciences, Room 305
Christopher Vollmers

Abstract:  High-throughput sequencing has revolutionized how transcriptomes are quantified and annotated. While Illumina short-read sequencers can be used to analyze entire transcriptomes down to individual splicing events, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Long-distance information is thus required to complement short-read sequencing to analyze full-length RNA transcript isoforms. While long-read sequencing technologies provide long-distance information, there are issues with Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing technologies that prevent their widespread adoption. PacBio sequencers produce few reads with high accuracy, while ONT sequencers produce more reads with lower accuracy. We introduce and validate a long-read ONT-based sequencing method. Our Rolling Circle Amplification to Concatemeric Consensus (R2C2) method generat! es more accurate reads of full-length RNA transcript isoforms than other long-read sequencing methods. These reads can be used to generate isoform-level transcriptomes for genome annotation and differential expression analysis in bulk or single-cell samples. I will also implement expectation maximization for isoform identification and quantification for long reads. I will use both of the methods I developed to analyze alternative splicing patterns in primates.