19.2.2007 HIIT seminar

HIIT seminars in spring 2007 will be held in hall **B222** of Exactum, on Fridays starting at 10:15 a.m. Coffee available from 10.

Fri Feb 16
Jaakko Hollmén
Modeling DNA copy number amplification patterns in human cancers

Abstract:
DNA copy number amplifications are hallmarks of nearly all advanced tumors. We present the data collection of genome-wide DNA copy number amplification data consisting of data of over 4500 cases of human neoplasms. The data set has been gathered from scientific journal articles covering a period of ten years and is naturally represented as 0-1 data. Firstly, genome-wide profiling of the data is performed with clustering techniques. In addition, independent component analysis (ICA) is applied to yield sparse, genome-wide amplification hot spots. Results and their interpretation will be presented. Secondly, chromosome-specific amplification patterns are learned from data with a mixture of multivariate Bernoulli distributions. Appropriate complexity for the mixture model for each chromosome is selected with a model selection procedure. Results are interpreted and the diagnostic value of the findings is discussed.

The talk is based on the following papers and on-going work:

• S. Myllykangas, J. Himberg, T. Bohling, J. Hollmén, and S. Knuutila. DNA copy number amplification profiling of human neoplasms. Oncogene, 25(55):7324-7332, November 2006. Available at: http://dx.doi.org/10.1038/sj.onc.1209717
• Jarkko Tikka, Jaakko Hollmén, Samuel Myllykangas, Mixture modeling of DNA copy number amplification patterns. 2007, To appear.