Keynote Topics: 1. Human genome annotations: emergence of non-coding transcripts

1. Affymetrix User’s Group Meeting Boston, MA May 2005 • Keynote Topics: • 1. Human genome annotations: emergence of non-coding transcripts • -tiling arrays: study gene regulation (complement expression arrays), • explore genome functions including: DNA methylation, origins of replication, mapping sites of TF binding • 2. mRNA transcript variation across ‘druggable’ genome: novel targets from exon array data • - exon arrays: study alternative splicing, explore transcript based pathways vs gene based pathways • 3. Enabling microarrays for routine clinical use • personalized medicine • -example = SNP chips (mapping & linkage analysis) • -10K, 100K & 500K SNP chips • - Serono Identifies 80 genes involved in MS using 100K SNPs

2. Data Analysis Track: • 1. Microarray Expts: Conceptual view & Practical Considerations • - Experiment design-begin w/end in mind, focus on questions seeking to be addressed & have specific goals (i.e. transcriptional changes vs cluster analysis) • - Replicates: biological vs technical, no need for technical replicates if sample preparation, etc is done consistently, # of biological replicates depends on focus of experiment, pooling – suppresses changes • - data analysis: 1) look at the data statistically 2) look at the data biologically • 2. Plier algorithm: higher differential sensitivity for low expressors • - signal detection algorithm • - normalization • - background correction (PM-MM) • 3. Statistical tools & data visualization • - RMA = robust multi-chip average • T-test (ANOVA) – compare signal across biological replicates • software

3. Software • Affy Array Assist Lite (Stratagene) • – download for free off Affymetrix website (www.affymetrix.com) • Poster • Effects of RNA Degradation on Gene Expression Analysis of Human Post-mortem Tissues • – Jerry Lee, Dept of Molecular Medicine, Neurocrine Biosciences, Inc., San Diego, CA • Summary: RNA from Human Brain (and other tissues) & RNA from Rat duodenum was used to address how RNA quality affects gene expression data generated using Affy chips • – Conclusion: Degraded RNA gave comparable signal to “good quality” RNA

4. Effects of Exercise on Gene Expression in Bone & Brain Tissues from different strains and sexes of mice Updates: 1. Exercise Program (sufficient to produce significant changes in skeletal system) -mice ~6 months old (growth should have stopped) -mice randomly selected to exercise -10 degree incline (treadmill design) -exercise during dark cycle (when mice naturally more active) -30 min/day, 5 days/wk, 6 wks total 2. Experimental Considerations a. RNA quality b. # of replicates/pooling c. chip array type? ($175 price difference) 1. 430A 2.0 - $350/chip, 14,000 genes 2. 430 2.0 - $525/chip, 39,000 transcripts