Guest talk by Henrik Edgren (Kallioniemi group, Institute for Molecular Medicine Finland, University of Helsinki) in Exactum C222 on Monday 18th January 2010 at 13:15.
Title: Fusion gene identification using Solexa paired-end RNA sequencing
Abstract:
During the last 4-5 years, fusion genes have been shown to occur frequently in a few types of common epithelial cancers, revealing an unanticipated role for this class of mutations that previously was thought limited to leukemias, lymphomas and sarcomas. This opens the question of whether fusion genes are formed in all kinds of cancers? This is an important question, as this would add an unexpected class of mutations that are involved in formation of epithelial cancers.
In order to study whether fusion genes occur in breast cancer, we have used the massively parallel paired-end mRNA sequencing technology from Solexa. Between 10-25 million 56 base pair long short reads were generated from five different samples and a bioinformatics pipeline was developed to identify fusion genes. So far, we have identified 26 new fusion genes in four breast cancer cell lines, showing they occur frequently in breast cancers, at least when their genomes are highly rearranged.
The presentation will concentrate on the biology of fusion genes, the Solexa RNA-sequencing technique and issues related to the identification of fusion genes from the (relatively noisy in this aspect) short read sequence data.
Welcome!