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Real Time Genomics, J. Craig Venter Institute announce collaborations
05-01-2013
by Kelsey Kaustinen  |  Email the author
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SAN FRANCISCO BAY AREA, Calif.Real Time Genomics, Inc. (RTG) and the J. Craig Venter Institute (JCVI), a not-for-profit genomic research institute that focuses on research in structural, functional and comparative analysis of genomes and gene products, have established a long-term strategic collaboration. Under the terms of their agreement, the two organizations will seek to understand and analyze the genetic changes that induced pluripotent stem cells might undergo in the process of differentiating. No financial details for the collaboration were disclosed.  
 
RTG and the JCVI also announced a collaboration for the discovery and validation of highly accurate human variant information through the use of the Venter human reference diploid genome and associated orthogonal information. The resulting information will be made available to the life-sciences community through public databases. It is the partners' hope that they will be able to define best practices and create standardized reference datasets for genome sequencers.  
 
"The stem cell collaboration with JCVI is an exciting opportunity to move our technology into new areas, as cell lineage progression studies are becoming important in a wide range of [next-generation sequencing] applications," Francisco De La Vega, vice president of Genome Sciences at Real Time Genomics, commented in a statement. "At the same time, a problem in clinical applications of sequencing is the difficulty knowing whether sequencing data and results meet a specific accuracy criteria. 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."
 
JCVI will utilize RTG's platform and work directly with RTG scientists for the identification of SNPs, indels, structural variants and de novo mutations in data from both collaborations. RTG's platform offers variant accuracy in family studies for both germline and de novo variants, and works with most platforms. Their platform, the company notes, combines a "Bayesian calling framework that delivers variants from [high-throughput sequencing] data by simultaneously considering all samples in a pedigree, incorporating a Mendelian segregation model and leveraging shared haplotypes in the family members." RTG calls Bayesian statistics "the modern approach for variant calling of [high-throughput sequencing] data, integrating sequencing error models with prior knowledge about allele frequencies and population statistics."  
 
"There is considerable interest in understanding the nature of de novo mutations that are acquired during reprogramming and differentiation of iPSCs. These mutations might affect how iPSCs behave as disease models and could limit the therapeutic use of these cells, but there are many pitfalls in analyzing sequence data to locate and interpret these rare mutations," Mark Adams, scientific director for the J. Craig Venter Institute, said in a press release. "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. RTG is an ideal partner for these projects because of their ability to rapidly analyze data from multiple sequencing platforms with improved accuracy of the resulting variant catalog. We are excited to be working with them on these two important collaborations."
 
Code: E05011301

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