1. Copyright © 2008, SAS Institute Inc. All rights reserved. Discovering Meaningful Patterns in Genomics Data with JMP Genomics Jordan Hiller JMP Genomics Application Scientist 2/19/2010

2. Copyright © 2008, SAS Institute Inc. All rights reserved. About SAS SAS founded in 1976 About 10,000 employees worldwide Over $2 billion in revenue SAS provides statistical analysis solutions to pharma, financial and retail businesses, among others Provides robust statistical and data mining algorithms SAS programming language is powerful, but complex

3. Copyright © 2008, SAS Institute Inc. All rights reserved. About JMP We are a division of SAS Founded in 1989 by John Sall, co-founder of SAS Originally Mac only, ported to PC in the 90s Desktop software, highly visual Provides easy-to-use statistical analysis software for non-SAS users

4. Copyright © 2008, SAS Institute Inc. All rights reserved. JMP Genomics SAS on the back-end Using established analytic tools: SAS/STAT, IML, SAS/Genetics Powerful and flexible language for data manipulation and statistical analysis Can handle large genomic datasets with file-based analysis JMP up front Point-and-click interface to SAS analytics Dynamic, interactive visual display of results Best of both worlds Choose from JMP or SAS tools

5. Copyright © 2008, SAS Institute Inc. All rights reserved. Philosophy of JMP Genomics We provide pre-built workflows for biologist users …while retaining statistical flexibility and transparency demanded by analysts We offer many options for exploring and visualizing complex data sets

6. Copyright © 2008, SAS Institute Inc. All rights reserved. JMP Genomics Architecture Run Submits Program to to Local SAS SAS Macros Generate Scripts and Output Tables New in 4.1: Option to Submit Job to SAS Server New in 4.1: JMP Genomics 64 bit Edition

7. Copyright © 2008, SAS Institute Inc. All rights reserved. Highlights of Expression Workflows Import, QC, and analyze large datasets Traditional arrays, summaries from next-gen Simplified workflows, advanced options for statisticians

8. Copyright © 2008, SAS Institute Inc. All rights reserved. Highlights of Genetics Workflows GWAS (up to 1.5M SNPs x 15,000 for 4.0) Adjustments for population structure, relatedness QC to filter markers and samples Association Tests Population Structure Assessment/Correction Linkage Disequilibrium Relationship Matrices Individual and Group

9. Copyright © 2008, SAS Institute Inc. All rights reserved. Highlights of Copy Number Workflows Import, QC, Normalization and ANOVA Support SNP6, Illumina 1M SNP Group vs. Group Individual vs. Group Copy Number Partition ( Faster CBS) ANOVA:

10. Copyright © 2008, SAS Institute Inc. All rights reserved. Support for Next-Gen Data Secondary: Sequence Alignment Primary: Image analysis Base-calling Tertiary: Statistical Analysis of Summarized Data National Center for Genome Resources Mudge et al, PloS One, 2008.

11. Copyright © 2008, SAS Institute Inc. All rights reserved. Check our Code All SAS code and JSL (JMP Scripting Language) code underlying Genomics analytic procedures is accessible Key Benefits Transparency: Examine underlying code to understand procedures Reproducibility: Use workflows to document analysis steps, standardize across data sets Extensibility: Adapt existing code or write your own Flexibility: Using our analytic toolkit, run analyses we didnt think of

12. Copyright © 2008, SAS Institute Inc. All rights reserved. Whats New in JMP Genomics 4.1 Support for miRNA, Tiling Arrays, and imputed SNP data New Population Measures and Relationship Matrix Q-K Mixed Model process to test for SNP association while adjusting for family relatedness and population structure simultaneously Manhattan Plots Improved P-Value Browser visualizes statistical results and genomic information together

13. Copyright © 2008, SAS Institute Inc. All rights reserved. Todays Demonstration Gene Expression Analysis Basic Expression Workflow QC Analysis ANOVA

14. Copyright © 2008, SAS Institute Inc. All rights reserved. Todays Dataset Affymetrix MPRO hourly dataset MPRO cell line stimulated with retinoic acid 5 timepoints: 0, 1, 2, 4, and 8 hours 4 technical replicates at each timepoint Murine U74A arrays

15. Copyright © 2008, SAS Institute Inc. All rights reserved. Thank you Contact Info: Jordan Hiller jordan.hiller@jmp.com 919-531-9809

16. Copyright © 2008, SAS Institute Inc. All rights reserved.