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Copyright © 2008, SAS Institute Inc. All rights reserved. Discovering Meaningful Patterns in Genomics Data with JMP Genomics Jordan Hiller JMP Genomics.

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Presentation on theme: "Copyright © 2008, SAS Institute Inc. All rights reserved. Discovering Meaningful Patterns in Genomics Data with JMP Genomics Jordan Hiller JMP Genomics."— Presentation transcript:

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

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


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