New JMP® Genomics 3.0 features whole-genome SNP analysis, predictive modeling

Desktop software from SAS offers powerful statistical analysis, 3-D graph

CARY, NC  (May 30, 2007)  –  JMP Genomics 3.0 from SAS sets itself apart with new capabilities for predictive modeling and whole-genome SNP analysis. This new software version, which begins shipping to customers today, also features 3-D graphics and the ability to distill vital research findings from huge volumes of data. Its release was announced by SAS, the leader in business intelligence. 

This unique desktop software dynamically links powerful statistical analysis with advanced graphics to provide a complete and comprehensive picture of research results. 

Biologists, chemists and biostatisticians in research organizations around the world use JMP Genomics to uncover meaningful patterns in whole-genome SNP (single nucleotide polymorphism), expression microarray and proteomics data. Since its launch in March 2006, more than 200 users across pharmaceutical, academic, governmental, nonprofit and biotechnology organizations have adopted JMP Genomics. 

Richard P. Beyer, PhD, a Research Scientist in the University of Washington’s School of Public Health, first saw JMP Genomics in action at a conference he attended with Russ Wolfinger, PhD, Director of Scientific Discovery and Genomics for SAS. “I said, ‘Yeah, we’ve got to have that; it’s really cool,’” Beyer recalled. “I’m really happy with it and will continue to use it.” 

Beyer was a beta tester for JMP Genomics 3.0. “One of the great things about JMP Genomics and SAS is that every time I e-mail for help I get an instant reply,” Beyer said. “You get A-plus on customer support.” Beyer said JMP Genomics developers also respond quickly to suggestions for new features. 

Collaborative development is a JMP hallmark. For this version, developers evaluated feedback from users to design new features and enhancements, and also drew on advances in the JMP platform. “JMP Genomics 3.0 takes advantage of beautiful new 3-D JMP graphics, including the 3-D PCA [principal components analysis] plots and markers that users requested,” said Shannon Conners, JMP Genomics Product Manager. 

With advanced graphics also come advanced analytics. JMP Genomics 3.0 users can perform PCA on huge SNP data sets to visually identify sample groupings. This and other enhancements support very large whole-genome association studies and new SNP-SNP and SNP-trait interaction discovery capabilities. Users of JMP Genomics 3.0 can perform whole-genome SNP analysis for at least 4,000 samples with 1 million SNPs each. 

Researchers working to develop biomarker profiles from genomics data will appreciate the wealth of options available in the new version. “We’re quite excited about the enhanced predictive modeling capabilities of JMP Genomics 3.0, including the ability to compare the performance of a broad variety of predictive models with the new Cross-Validation Model Comparison (CVMC) process,” said Wolfinger. Wolfinger and other members of the JMP Genomics team are participating in the Microarray Quality Control Consortium, an FDA-led effort to validate the use of microarray technology for medical diagnosis and treatment. “Our own development team has already put CVMC to work while evaluating predictive models during phase II of the MAQC.” 

Other new features in JMP Genomics 3.0 include:

• Tutorials, which guide users through the import process for all supported data types.
• Estimate Builder, which allows point-and-click creation of estimate statements for use with ANOVA and Mixed Model processes.
• Workflow Builder, which lets users link sets of commonly used analysis settings into reusable workflows.
• UCSC Genome Browser Link, which creates link tables and custom tracks to display JMP Genomics statistical results in genomic context. 

Through its JMP Genomics software, SAS has developed partnerships with leaders in array platform and genomic software development, including Affymetrix, Illumina and Ingenuity Systems. 

Existing JMP Genomics users can request a complimentary upgrade to version 3.0. Prospective users can license JMP Genomics 3.0 or request a free 30-day trial by completing this inquiry form.

* Affymetrix and GeneChip are registered trademarks owned or used by Affymetrix, Inc. GeneChip-compatible is a trademark owned or used by Affymetrix, Inc.

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