AMSI-SSAI Lecturer Tour: Removing Unwanted Variation from high-throughput omic data

Speaker: Terry Speed

Affiliation: Walter and Eliza Hall Institute of Medical Research

Time: Monday 22/09/2014 from 14:00 to 15:00

Venue: Access Grid UWS. Presented from Parramatta (EB.1.32), accessible from Campbelltown (26.1.50) and Penrith (Y239).

Abstract: Over the last few years, many microarray-based gene expression studies involving a large number of samples have been carried out, with the hope of understanding, predicting or discovering factors of interest such as prognosis or the subtypes of a cancer. The same applies to proteomic and metabolomic data, and to other kinds of data. Such large studies are often carried out over several years, and may involve several hospitals or research centers. Unwanted variation (UV) can arise from technical aspects such as batches, different platforms or laboratories, or from biological signals such as heterogeneity in ages or different ethnic groups which are unrelated to the factor of interest in the study. This can easily lead to poor results. Recently, we proposed a general framework to remove UV (called RUV) in microarray data using control genes. It showed good behavior for differential expression analysis (i.e., with a known factor of interest) when applied to several datasets, in particular better performance than state of the art methods such as Combat or SVA. This suggests that controls can indeed be used to estimate and efficiently remove sources of unwanted variation. The methods are illustrated on a variety of kinds of omic datasets.

Biography:

Professor Terry Speed is a Senior Principal Research Scientist and lab head in the Bioinformatics Division of the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia, and an associate of the Department of Mathematics and Statistics at the University of Melbourne. He remains affiliated with the Department of Statistics of the University of California at Berkeley, where he taught for many years. He mentors graduate students and postdocs in statistics and bioinformatics and is co-investigator on genetic, genomic and bioinformatics projects. He serves on a number of scientific advisory boards, including those of Veracyte, Inc, a Bay area diagnostics company, Cancer UK's Cambridge Institute, and the Wellcome Trust Center for Human Genetics in Oxford.

Professor Speed is recognised as one of the world's leaders in the relatively new field of bioinformatics. He has more than 40 years of experience in statistics, specialising in the design and analysis of studies in genetics and genomics. He was awarded the 2002 Pitman Medal (Statistical Society of Australia), the 2003 Moyal Medal (Macquarie University), and was the joint recipient of 2004 Outstanding Applications Paper Award, American Statistical Association. A fellow of the Australian Academy of Sciences, Professor Speed was recently elected as a fellow of the Royal Society of London, and in 2013 he was awarded the Australian Prime Minister's Prize for Science.