Real Time Genomics, Inc. (RTG) has announced a long-term strategic collaboration with the J. Craig Venter Institute (JCVI), aimed at understanding and analyzing the genetic changes that induced pluripotent stem cells may acquire during the process of differentiation.
RTG and JCVI have 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 sciences community. The two organizations hope to define best practices and to create standardized reference datasets for the genome sequencing community.
“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,” said Mark Adams, Scientific Director for the J. Craig Venter Institute.
Adams continued, “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.”
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.
“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 NGS applications,” said Francisco De La Vega, VP of Genome Sciences at Real Time Genomics.
Vega continued, "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.”