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Joint Research Seminar (3 Dec 2015)



Joint Research Seminar

Genomics Strategic Research Theme
Centre for Genomic Sciences

Characterization of Fusion Genes
by Hybrid-Seq

Dr Kin Fai Au

Assistant Professor
Internal Medicine and Biostatistics
University of Iowa

3 December 2015 (Thu)
10:30 – 11:30 am

Seminar Room 2, G/F
The Hong Kong Jockey Club Building for Interdisciplinary Research
5 Sassoon Road, Pokfulam, Hong Kong


New generation sequencing techniques can provide very informative insights into the transcriptome, such as expression of gene isoforms and fusion genes. However, the currently available transcriptome analysis tools are for Second Generation Sequencing (SGS) data, the short read length and unreliable alignments of which can introduce bias and even errors in downstream analysis. The recent application of Third Generation Sequencing (TGS) long reads, such as PacBio data, to human transcriptome analysis has greatly advanced the field. Furthermore, Hybrid-Seq, which integrates SGS short read data into the analysis of TGS data, can improve the overall performance and resolution of the output data. Here I present an innovative Hybrid-Seq approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision, higher sensitivity and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.

About the Speaker:

Dr Kin Fai Au is an assistant professor of Internal Medicine and Biostatistics at University of Iowa. He received his BS degree in Biological Sciences from Tsinghua University in 2004. In 2009, he received his PhD degree in Structural Biology from Oxford University. From 2007 to 2009, he studied in Prof Wing H Wong’s group and received his MS degree in Statistics at Stanford University in 2009. Since 2009, he worked as a postdoctoral scholar in the Department of Statistics at Stanford University to expand his research on Second Generation Sequencing (SGS) and Third Generation Sequencing (TGS) Third Generation Sequencing until 2013. Dr Au is interested in methodology development of TGS (especially for PacBio and Oxford Nanopore sequencing). Au lab is working on both hybrid sequencing (SGS + TGS) and TGS-alone methodology research. His research interests include alternative splicing, isoform-specific events, gene fusion and quantitative analysis of transcriptome.



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