Design and Analysis of Genomic Studies for Understanding Adaptability of Daphnia to Water Environments
Karen Kafadar, Guilherme V. Rocha, John Colbourne
Statistics, Indiana University; Statistics, Indiana University; Genomic Biology, Indiana University

Daphnia (waterflea) is a premier animal model in ecotoxicological research. Found in most ponds and lakes, they are unusually sensitive to environmental contaminants and hold a central position in aquatic food webs. Its genomic sequence has been empirically annotated, available on a 12-plex microarray. Changes in the environmental contaminants of the pond or lake are reflected readily in the Daphnia genome and can be measured straightforwardly via microarray analyses. The 12-plex tiling array, together with the potential for future tri-labeling (versus the current double-labeling, or two treatments per subarray), present interesting challenges for the design of microarray studies to study the sensitivities of these organisms to various environmental conditions.

We describe the design of a microarray study investigating multiple environmental stresses that uses the concept of paired treatments (“red” versus “red”) as its basis. Using the analysis of paired data via the “red” (Godfrey 1985), we develop a design specifically tailored for data that arise in the form of paired comparisons and particularly well suited when relatively high amounts of data are missing.

Keywords: Experimental design; Square combining table; Microarray studies; Signal detection

Biography: Karen Kafadar is James Rudy Professor of Statistics at Indiana University. Her research focuses on robust methods and statistical methodology for analyzing data in the physical, chemical, engineering, and biological sciences, including randomized cancer screening trials. She received her B.S. and M.S. from Stanford and her Ph.D. from Princeton, and previously held positions at National Institute of Standards & Technology, Hewlett Packard, National Cancer Institute, and University of Colorado. She has served on several committees for the National Academy of Science including Committee on Applied & Theoretical Statistics (Chair, 2007-2009), and on editorial boards for JASA (Review Editor, 1996-98; AE, 2005-2010), CSDA (AE, 1998-2007), Technometrics (Editor, 1999-2001), and Annals of Applied Statistics (Area Editor, since 2010). She is President-Elect of IASC and is an elected Fellow of ISI and ASA.