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JMP® Genomics Adds users, Partners, Capabilities

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January 2008

Scientists around the world are using JMP Genomics from SAS to explore the very foundations of life, applying its powerful analysis and visualization capabilities to vast data sets common to genomics research. In 2007, its first full year on the market, this comprehensive desktop genomics software gained new customers, established important commercial partnerships and introduced a new release that includes capabilities for advanced DNA analysis.

HOW IT’S USED: JMP Genomics enables researchers to uncover meaningful patterns in their genetics, microarray and proteomics research data:

* North Carolina State University graduate student Youssef Idaghdour used JMP Genomics to show that lifestyle affects human gene expression – and thus disease patterns. Idaghdour’s team collected RNA samples from Bedouin nomads, isolated farmers and city dwellers in his native Morocco.
* Researchers working with a sweeping FDA-sponsored study of DNA microarray technology are using JMP Genomics in their quest to advance personalized medicine. SAS hosted more than 100 members of the MicroArray Quality Consortium for a two-day meeting last May.
* A University of Texas researcher is studying plant genomes to learn why some plants tolerate drought better than others. JMP Genomics’ microarray capabilities let Tom Juenger, PhD, analyze huge SAS data sets and examine “23,000 genes at once instead of one or two at a time.”

SIGNIFICANT ENHANCEMENTS: In June, JMP Genomics introduced version 3.0 , adding capabilities for predictive modeling and whole-genome SNP analysis, as well as 3-D graphics and the ability to distill vital findings from huge data sets. In November, release of JMP Genomics 3.1 introduced copy-number analysis capabilities – the ability to examine the number of copies of a particular gene in an individual’s DNA – with import engines for copy number data from Affymetrix and Illumina, leading microarray manufacturers.

NEW PARTNERSHIPS, LICENSING PLANS: Through JMP Genomics, SAS has partnerships with Affymetrix, Illumina and life sciences solution vendor Ingenuity Systems. New academic pricing and licensing options make JMP Genomics more affordable for classroom use. Campuswide and department licenses were offered for the first time in 2007. Under a campuswide license, JMP Genomics is at work in three NCSU colleges: agriculture and life sciences, natural resources, and veterinary medicine.

WHAT THEY’RE SAYING: “It’s the most flexible and powerful software available, in my opinion, for this type of analysis,” says Susan Dorsey, PhD, University of Maryland, whose research is aimed at finding treatments for chronic pain. “I can upload raw data from a variety of Affymetrix platforms, including gene-level data from microarrays, exon-level data from exon arrays and SNP data from a 500K array.”

WHAT’S NEXT: JMP Genomics 3.2 will be released this spring.
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