JMP® Genomics, NCGR Partnership to Foster Development of Next-Gen Sequencing Tools
News Nov 07, 2008
A new strategic partnership between SAS and the National Center for Genome Resources (NCGR) will strengthen ongoing collaboration between JMP and NCGR for the co-development of software tools for next-generation sequencing data analysis. The partnership was announced by SAS. JMP is a business unit of SAS.
NCGR is a nonprofit research institute dedicated to improving human health and nutrition through next-gen sequencing, bioinformatics analysis and development of bioinformatics tools. The institute has developed more than a dozen software tools and databases to analyze and store a multitude of biological data types.
In addition, NCGR researchers use JMP® Genomics in scientific research projects ranging from the study of changes in the brains of schizophrenia sufferers to soybean research aimed at finding genetic differences linked to important agronomic traits.
“We have been pleased to see NCGR’s JMP Genomics users apply standard JMP Genomics tools to summarized sequence data sets, and provide us valuable suggestions for enhancements that will shape the software’s capabilities in future versions,” said Russ Wolfinger, Director of Scientific Discovery and Genomics at SAS.
“As a customer, NCGR has worked with the JMP Genomics team to achieve groundbreaking endeavors in this exciting and rapidly changing area of scientific research,” said Faye Schilkey, Associate Director of NCGR’s New Mexico Genome Sequencing Center. “We’ve created an in-house pipeline for aligning and summarizing sequencing data, and JMP Genomics plays a vital role for our scientists, letting us work more quickly and efficiently to explore that data.”
The New Mexico center houses six Illumina Genome Analyzer II sequencers, in addition to other sequence technology platforms, and provides sequencing services to NCGR and external clients. Raw sequence reads are analyzed and filtered by NCGR’s internally developed Alpheus® software system to extract the significant findings.
Alpheus users who also license JMP Genomics can then export their data for further exploration. “The remarkable visualization features of JMP Genomics give us immediate insight into our research findings,” Schilkey said. “Important differences just pop right out.”
“We are very pleased to expand our relationship with NCGR into a partnership with their services group,” said Shannon Conners, JMP Genomics Product Manager. Schilkey was a featured speaker at a successful seminar series in California co-sponsored by JMP Genomics and partner Ingenuity Systems.
In addition to NCGR, Illumina and Ingenuity Systems, JMP Genomics also has partnerships through SAS with InforSense and Affymetrix.
In a new study in cells, University of Illinois researchers have adapted CRISPR gene-editing technology to cause the cell’s internal machinery to skip over a small portion of a gene when transcribing it into a template for protein building. This gives researchers a way not only to eliminate a mutated gene sequence, but to influence how the gene is expressed and regulated.
Researchers published today a detailed description of the complete genome of bread wheat, the world's most widely-cultivated crop. This work will pave the way for the production of wheat varieties better adapted to climate challenges, with higher yields, enhanced nutritional quality and improved sustainability.