报告人：Dr. Kinfai Au, University of Iowa
时间：11 月 16 日（星期三）下午 3:30-4:30
地点：邯郸校区逸夫楼 604 会议室
联系人：朱山风 zhusf@fudan.edu.cn
Abstract:
New generation sequencing techniques can provide very informative insights into the transcriptome. However, the currently available transcriptome analysis tools are for Second Generation Sequencing (SGS) short reads and the short read length of which can introduce bias and even errors in downstream analysis. While the recent application of Third Generation Sequencing (TGS) long reads, such as PacBio and Oxford Nanopore Technologies data, to human transcriptome analysis has greatly advanced the field, key bioinformatic analysis platforms are missing. Furthermore, hybrid sequencing (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. Indeed, a handful of existing publications demonstrate the potential power of Hybrid-Seq for genome data analysis. Here I present a series of bioinformatics methods to analyze transcriptome at the gene isoform levels. These methods include 1) IDP to identify and quantify gene isoforms; 2) IDP-fusion to annotate fusion genes and identify fusion gene isoforms; 3) IDP-ASE to phase genotype and quantify allele-specific expression at the gene isoform level;The proof-of-concept applications to breast cancer cells and human embryonic stem cells reveal the isoform-level complexity of fusion gene expression and allele-specific expression, and also discover novel genes involved in pluripotency regulation, novel tumorigenesis-relevant gene fusions and ASE bias of oncogenes and pluripotency markers.
Bio:
Dr. Kin Fai Au is an assistant professor of Internal Medicine and Biostatistics at University of Iowa. He received his B.S. degree in Biological Sciences from Tsinghua University in 2004. In 2009, he received his Ph.D. degree in Structural Biology from Oxford University. From 2007 to 2009, he studied in Prof. Wing H. Wong’s group and received his M.S. 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) 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.
