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Senior Scientist, Cato Research, Ltd. It is increasingly apparent that the scientific advances of the last decade are not quickly converted into innovative pharmaceutical products. This trend applies to the field of oncology too, and happens despite continuous increases in the funding available for medical research in the field. This session will attempt a comparative review of regulatory experience, current tools procedures, and future plans for facilitating the development of oncology products in the US and EU regulatory regions.

M31 Filtering and normalization of cDNA microarray data A tutorial W. Kusnierczyk1 1 Dept. of Information and Computer Science, Norwegian University of Science and Technology Since the invention of cDNA microarray technology, different statistical properties of the microarray gene expression data were studied. Some of the most important questions in the analysis of microarray experiments are how to remove noisy and low quality data, and how to compensate for errors coming from different sources. Here we describe a set of procedures used to filter spots with respect to their size and relative intensity. We also show how to implement different normalization techniques, including tip- and intensity dependent methods with locally weighted regression curves. The procedures are explained with a real-life example data of microarray experiments from our laboratories. M32 A comparison of BAC- and cDNA-arrays for the detection of copy number alterations in human breast tumors L.O. Baumbusch1, O.-C. Lingjrde2, K. Liestl2, I. Glad3, J.R. Pollack4, T. Srlie1 , K. Chin5, J.W. Gray5 and A.-L. Brresen-Dale1 1 Dept. of Genetics, The Norwegian Radium Hospital, Oslo, Norway; 2Dept. of Informatics, University of Oslo, N; 3 Dept. of Mathematics, University of Oslo, N; 4 Dept. of Pathology and Howard Hughes Medical Inst., Stanford University School of Medicine, USA; 5 UCSF Cancer Center, University of California, San Francisco, USA. The fundamental defects in many human cancers are DNA copy number aberrations in the genome. Detection of copy number abnormalities provides a possibility to associate genomic alterations with expression of tumor suppressor genes and oncogenes. Conventional Comparative Genomic Hybridization CGH ; was developed for the genome-wide analysis of deletions, gains and amplifications on the cytogenetic map. Microarray Comparative Genomic Hybridization array CGH ; provides the possibility of more precise high-resolution mapping of candidate genes to genomic positions. In a first attempt to compare data from different types of array methods, samples from 8 breast tumors were analyzed using classical CGH and array CGH with either 2338 BAC Bacterial Artificial Chromosomes ; clones arrays Snijders et al. 2001 ; or cDNA clones from 6691 mapped human genes. The 2338 BAC clones were selected to be roughly equally spaced on the genomic sequence. The measurement resolution differs between the two array CGH methods. Microarray gene expression data for the same eight tumors were obtained, using the same 6691 cDNAs as in the cDNA-array CGH Pollack et al. 2002 ; . Besides functionality, availability and practicality of the methods, the choice between BACand cDNA-arrays is more fundamental than just an academic controversy. There has been a lack of robust methods to test the resulting discrepancies and similarities of the two applied techniques. We propose a statistical method for comparing the results and resolutions of the two array methods in respect to their ability to detect copy number anomalies. We investigate in detail how BACarrays and cDNA-arrays compare in amplification or deletion sites over single chromosomes and the complete genome. It is in our intention that the illustrated method might be applicable to further microarray applications. Pollack, J.R. et al. PNAS 99, 12963-68 2002 ; . Snijders, A.M. et al. Nature Genet. 29, 263-64 2001 and cerivastatin.