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Making sense of mutations
June 2013
by Ilene Schneider  |  Email the author


SAN FRANCISCOŚReal Time Genomics Inc. (RTG), a genome analytics company, and the J. Craig Venter Institute (JCVI), a not-for-profit genomic research institute, have established a long-term strategic collaboration to understand and analyze the genetic changes that induced pluripotent stem cells (iPSCs) may acquire during the process of differentiation.   
RTG and JCVI also announced a collaboration to discover and validate highly accurate human variant information using the Venter human reference diploid genome and associated orthogonal information.  
The teams will deposit this information into the public databases for use by the life- science community. The two organizations hope to define best practices and to create standardized reference datasets for the genome sequencing community.  
RTG, which offers software tools and applications for the extraction of unique value from genomes, applies the combination of its patented core technology and computational expertise in algorithms to solve problems in next-generation genomic analysis. JCVI, a world leader in genomic research, was formed in October 2006 through the merger of several affiliated and legacy organizations: The Institute for Genomic Research and the Center for the Advancement of Genomics, the J. Craig Venter Science Foundation, the Joint Technology Center and the Institute for Biological Energy Alternatives.  
According to Mark Adams, scientific director of JCVI, there is considerable interest in understanding the nature of de-novo mutations that are acquired during reprogramming and differentiation of iPSCs. While these mutations might affect how iPSCs behave as disease models and could limit the therapeutic use of these cells, there are "many pitfalls in analyzing sequence data to locate and interpret these rare mutations."  
Adams adds, "Since sequencing and publishing the Venter reference human genome in 2007, we have built a significant dataset around this genome and want to help others leverage the information to improve their own research. "  
JVI has "worked with Francisco De la Vega of RTG for some time on analysis of the HuRef genome sequence," according to Adams. He says HuRef is "unique among human genome assemblies for having extensive data from multiple sequencing platforms including Sanger, Illumina, SOLiD and CGI. The high-quality genome and now phased haplotypes from Ewen Kirkness's recent paper ( make it by far the best characterized human genome." Adams describeds it as "an excellent reference for evaluating the quality of new sequencing approaches and analysis methods" and says RTG plans to continue to improve the HuRef sequence and demonstrate its value as a reference standard for comparing analytical methods.
"This should also highlight the power of RTG's software," he notes.  
According to Adams, JCVI will also work with RTG on analysis of data from a series of cell lines derived from the HuRef individual by iPS cell reprogramming.   
"The accuracy of the HuRef sequencing means that discerning novel SNVs acquired during reprogramming and differentiation is enhanced," he explains. "RTG has new methods of joint SNV detection across related samples and is an ideal partner for these projects because of the ability to rapidly analyze data from multiple sequencing platforms with improved accuracy of the resulting variant catalog."
As part of the collaboration, JCVI will be using the RTG platform and working directly with RTG scientists to identify SNPs, indels, structural variants and de-novo mutations in data from both projects. The RTG platform will be seamlessly integrated into JCVI's existing pipeline infrastructure.
De La Vega, who is vice president of genome sciences at RTG, describes the stem cell collaboration with JCVI as "an exciting opportunity to move our technology into new areas as cell lineage progression studies are becoming important in a wide range of NGS applications." He says that a problem in clinical applications of sequencing is "the difficulty knowing whether sequencing data and results meet specific accuracy criteria."
De La Vega adds, "RTG and the broader community are working to collectively settle on a set of validated datasets to improve research. Because JCVI has considerable orthogonal information related to the Venter reference genome, including Sanger long-read sequence data, data from multiple next-generation sequencing platforms, and even RNAseq data and full phasing information, there is an opportunity to contribute a standard back to the community to improve the sensitivity and specificity of human disease applications using NGS.  
"We hope that these interactions will be completed in the next several months and lead to further interactions with RTG," Adams concludes.

Real Time Genomics and Knome team up to speed genome analysis
SAN FRANCISCOŚReal Time Genomics Inc. (RTG) also announced last month that it will work with Knome Inc. to integrate the RTG Variant platform into every shipment of the knoSYS100 interpretation system. The agreement enables customers to easily purchase the RTG analytics engine as an upgrade to the system.
According to the companies, the product will combine two world-class commercial platforms to deliver end-to-end genome analytics and interpretation with superior accuracy and speed. Financial terms of the agreement were not disclosed.  
"In the past year, demand for genome interpretation has surged as translational researchers and clinicians adopt sequencing for human disease discovery and diagnosis," said Wolfgang Daum, CEO of Knome, in a statement. "Concomitant with that demand is the need for accurate and easy-to-use industrial grade analysis that meets expectations of clinical accuracy. The RTG platform is both incredibly fast and truly differentiating to customers doing family studies, and we are excited to add such a powerful platform to the knoSYS ecosystem."  
The partnership simplifies the purchasing process by allowing knoSYS customers to purchase the RTG platform directly from Knome sales representatives.
"The Knome system is a perfect complementary channel to further expand our commercial effort to bring the RTG platform to market," says Steve Lombardi, CEO of RTG. "Knome has built a recognizable brand around human clinical genome interpretation, and by delivering the RTG platform within their system, both companies are simplifying genomics to help customers understand human disease and guide clinical actions."
Code: E061324



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