The University of British Columbia
MSc. THESIS DEFENSE
Fong Chun Chan
BSc. Simon Fraser University, 2009
Friday, December 16, 2011 at 9:30 AM
LOCATION: 2nd floor meeting room of BCCRC
Detection of Differentially Expressed Alternative Transcripts using Conventional Microarrays
Abstract: Alternative splicing, alternative promoter usage and alternative 3′ polyadenylation are the main molecular mechanisms which allow for a single gene to give rise to alternative, biologically, distinct mRNA transcripts. Recently, there has been an increasing number of examples linking specific transcripts to a variety of diseases. Prior studies have observed that alternatively expressed transcripts can be detected using conventional gene expression microarrays by identifying inconsistent expression patterns of probesets interrogating the same gene. However, the enormous repository of conventional microarrays has been disregarded as a potential platform for detecting differentially expressed alternative transcripts between two groups of samples.
We have developed a novel algorithm, called DISCO, for detecting differentially expressed alternative transcripts between two groups of samples that is designed to work on conventional microarrays. Using a published dataset with RT-PCR validated results, we demonstrated DISCO’s ability to accurately discriminate between true positive and true negative events. Using an internal cohort of 36 Affymetrix HG-U133 Plus 2.0 microarrays with matched RNA-Seq libraries and an external cohort of 200 Affymetrix HG-U133 Plus 2.0 microarrays of diffuse large B-cell lymphoma samples, dichotomized into the two subtypes activated B-cell like (ABC) and germinal centre B-cell like (GCB), we showed that DISCO has superior performance over an existing method. Gene enrichment analysis performed on the top 165 DISCO candidate genes, from the comparison of ABC vs. GCB, showed an enrichment for the molecular terms relating to “alternative splicing” and “splice variants”. Of note, genes with differentially expressed transcripts between ABC and GCB identified by DISCO included FOXP1 (a previously reported finding), and PHF19, which to our knowledge has not yet been reported.
Using DISCO, conventional microarrays can now be reanalyzed to detect for differentially expressed transcripts which these microarrays were not originally designed for. To our knowledge, this is the first study to assess the concordancy between conventional microarrays and RNA-Seq predictions for differentially expressed transcripts. The concordancy between these two platforms indicate that the extensive repository of conventional microarrays may serve as a powerful supplement, potentially acting as a first line discovery platform, to RNA-Seq data.
Supervisor: Dr. Randy Gascoyne, Pathology & Laboratory Medicine, UBC
Dr. Sohrab Shah, Pathology & Laboratory Medicine, UBC Dr. Wyeth Wasserman, Medical Genetics, UBC
Chair: Dr. Paul Pavlidis, Psychiatry and CHiBi, UBC